diff --git a/Framework/PythonInterface/plugins/algorithms/GSASIIRefineFitPeaks.py b/Framework/PythonInterface/plugins/algorithms/GSASIIRefineFitPeaks.py
index 4bf52120e8fd7c36082ea84f286e1825fd52861c..d7b86221146e43e69cbd279f367ae3a2f97b6238 100644
--- a/Framework/PythonInterface/plugins/algorithms/GSASIIRefineFitPeaks.py
+++ b/Framework/PythonInterface/plugins/algorithms/GSASIIRefineFitPeaks.py
@@ -470,6 +470,8 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
@return a tuple with: 1) a tuple with the Rwp and GoF values (weighted profile
R-factor, goodness of fit), 2) the parameters dictionary
"""
+ import GSASIIpwd
+
(limits, peaks_list, background_def) = fit_inputs
(inst_parm1, inst_parm2) = gs2_rd.pwdparms['Instrument Parameters']
# peaks: ['pos','int','alp','bet','sig','gam'] / with the refine flag each
@@ -538,6 +540,8 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
# algorithm finishes and is destroyed!
# This seems to destroy/close safely
import wx
+ import GSASII
+
self._gsas2_app = wx.App()
gs2 = GSASII.GSASII(None)
@@ -700,7 +704,7 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
usedRanIdList=['noGUI'], Start=False)
if err_msg:
raise RuntimeError("There was a problem while importing the phase information file ({0}. "
- "Error details: {1}".format(phase_filename, errm_msg))
+ "Error details: {1}".format(phase_filename, err_msg))
phase_reader = phase_readers_list[0]
GSASIIphsGUI.SetupGeneralWithoutGUI(gs2, phase_reader.Phase)
@@ -744,7 +748,9 @@ class GSASIIRefineFitPeaks(PythonAlgorithm):
@param phase_data :: from GSAS-II, the first entry in 'Phases'
"""
+ import GSASII
import GSASIIspc
+
SGData = phase_data['General']['SGData']
use_list = phase_data['Histograms']
NShkl = len(GSASIIspc.MustrainNames(SGData))
diff --git a/Framework/PythonInterface/plugins/algorithms/RefLReduction.py b/Framework/PythonInterface/plugins/algorithms/RefLReduction.py
index 5da86fd3a5bbc0b31f0a38f1d395e233bdabc6b3..f3779d9528b4347793eea11ebfe04822258c0c3b 100644
--- a/Framework/PythonInterface/plugins/algorithms/RefLReduction.py
+++ b/Framework/PythonInterface/plugins/algorithms/RefLReduction.py
@@ -181,14 +181,6 @@ class RefLReduction(PythonAlgorithm):
is_nexus_detector_rotated_flag = wks_utility.isNexusTakeAfterRefDate(ws_event_data.getRun().getProperty('run_start').value)
print('-> is NeXus taken with new detector geometry: ' + str(is_nexus_detector_rotated_flag))
- #dimension of the detector (256 by 304 pixels)
- if is_nexus_detector_rotated_flag:
- maxX = 256
- maxY = 304
- else:
- maxX = 304
- maxY = 256
-
## retrieve general informations
# calculate the central pixel (using weighted average)
print('-> retrieving general informations')
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/TransmissionUtils.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/TransmissionUtils.py
index ae543a541616c1167211ac1502365103b7e308f5..666057fedeffefd5400e51c5f236a09a8bf23434 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/TransmissionUtils.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/TransmissionUtils.py
@@ -302,12 +302,6 @@ def subtract_dark_current(self, workspace, property_manager):
use_sample_dc = self.getProperty("UseSampleDarkCurrent").value
dark_current_data = self.getPropertyValue("DarkCurrentFilename")
property_manager_name = self.getProperty("ReductionProperties").value
- # Get instrument to use with FileFinder
- #instrument = ''
- #if property_manager.existsProperty("InstrumentName"):
- # instrument = property_manager.getProperty("InstrumentName").value
-
- dark_current_property = "DefaultDarkCurrentAlgorithm"
def _dark(ws, dark_current_property, dark_current_file=None):
if property_manager.existsProperty(dark_current_property):
diff --git a/Testing/SystemTests/tests/analysis/EQSANSBeamCenterAPIv2.py b/Testing/SystemTests/tests/analysis/EQSANSBeamCenterAPIv2.py
index 1b412bdc0637fe6398dbe8094bacb18d9edef369..982b6cc5471c45d1d564126578e22c816034f32b 100644
--- a/Testing/SystemTests/tests/analysis/EQSANSBeamCenterAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/EQSANSBeamCenterAPIv2.py
@@ -1,9 +1,11 @@
#pylint: disable=no-init,attribute-defined-outside-init
import stresstesting
from mantid.simpleapi import *
-from reduction_workflow.instruments.sans.sns_command_interface import *
from mantid.api import *
+from reduction_workflow.instruments.sans.sns_command_interface import *
+from reduction_workflow.instruments.sans.hfir_command_interface import DirectBeamCenter, NoSolidAngle, SetTransmission
+
import os
diff --git a/Testing/SystemTests/tests/analysis/EQSANSDarkCurrentAPIv2.py b/Testing/SystemTests/tests/analysis/EQSANSDarkCurrentAPIv2.py
index 59851d70863a350ec17e560b5ea5c49f9c0c0f0b..4385450b9ca03f1edf2c288c95b2956e272aaee1 100644
--- a/Testing/SystemTests/tests/analysis/EQSANSDarkCurrentAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/EQSANSDarkCurrentAPIv2.py
@@ -2,6 +2,7 @@
import stresstesting
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.sns_command_interface import *
+from reduction_workflow.instruments.sans.hfir_command_interface import DarkCurrent,SetTransmission
from mantid.api import *
import os
diff --git a/Testing/SystemTests/tests/analysis/EQSANSEffAPIv2.py b/Testing/SystemTests/tests/analysis/EQSANSEffAPIv2.py
index 5baca714eb34699552cc164f231c6e19d15bfadd..9435a56ca14cccd4e62fbba1720f730ce546d419 100644
--- a/Testing/SystemTests/tests/analysis/EQSANSEffAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/EQSANSEffAPIv2.py
@@ -2,6 +2,7 @@
import stresstesting
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.sns_command_interface import *
+from reduction_workflow.instruments.sans.hfir_command_interface import SensitivityCorrection, SetTransmission
from mantid.api import FileFinder
import os
diff --git a/Testing/SystemTests/tests/analysis/EQSANSFlatTestAPIv2.py b/Testing/SystemTests/tests/analysis/EQSANSFlatTestAPIv2.py
index defe5ed58801cf96c9c603354689547452397c4e..987dbfc82ed514451a7d0404f878d5e1b4ea44d7 100644
--- a/Testing/SystemTests/tests/analysis/EQSANSFlatTestAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/EQSANSFlatTestAPIv2.py
@@ -2,6 +2,7 @@
import stresstesting
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.sns_command_interface import *
+from reduction_workflow.instruments.sans.hfir_command_interface import *
FILE_LOCATION = "/SNS/EQSANS/IPTS-5636/data/"
diff --git a/Testing/SystemTests/tests/analysis/EQSANSIQOutputAPIv2.py b/Testing/SystemTests/tests/analysis/EQSANSIQOutputAPIv2.py
index 06e12aca27d2494c8d9674c0ddc70f18cbd595a0..ab569c401bd75b9ace1dfb3699fbd10a7c879218 100644
--- a/Testing/SystemTests/tests/analysis/EQSANSIQOutputAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/EQSANSIQOutputAPIv2.py
@@ -4,6 +4,7 @@ import math
import os
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.sns_command_interface import *
+from reduction_workflow.instruments.sans.hfir_command_interface import *
from mantid.api import *
diff --git a/Testing/SystemTests/tests/analysis/EQSANSProcessedEffAPIv2.py b/Testing/SystemTests/tests/analysis/EQSANSProcessedEffAPIv2.py
index bb2bc5f7b3b1bad72903d3e9d7d3dda722225df4..5c58f593d89b9772174f23eee7ea19f59991e068 100644
--- a/Testing/SystemTests/tests/analysis/EQSANSProcessedEffAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/EQSANSProcessedEffAPIv2.py
@@ -2,6 +2,7 @@
import stresstesting
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.sns_command_interface import *
+from reduction_workflow.instruments.sans.hfir_command_interface import SensitivityCorrection, SetTransmission
from mantid.api import FileFinder
import os
diff --git a/Testing/SystemTests/tests/analysis/EQSANSSolidAPIv2.py b/Testing/SystemTests/tests/analysis/EQSANSSolidAPIv2.py
index 125b40c3046f3adda65c380db7ca9ee6745be8e8..f518d2ca37e720e53c41bd7aa91b52a0ff41df5f 100644
--- a/Testing/SystemTests/tests/analysis/EQSANSSolidAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/EQSANSSolidAPIv2.py
@@ -2,6 +2,7 @@
import stresstesting
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.sns_command_interface import *
+from reduction_workflow.instruments.sans.hfir_command_interface import *
from mantid.api import *
import os
diff --git a/Testing/SystemTests/tests/analysis/EQSANSTransAPIv2.py b/Testing/SystemTests/tests/analysis/EQSANSTransAPIv2.py
index 29e3ebba3aaa63b6b8958bc1083126bb0c2c2ffb..4746a5cb6252f80dbb3f44b64b17242e73e6eede 100644
--- a/Testing/SystemTests/tests/analysis/EQSANSTransAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/EQSANSTransAPIv2.py
@@ -2,6 +2,7 @@
import stresstesting
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.sns_command_interface import *
+from reduction_workflow.instruments.sans.hfir_command_interface import *
from mantid.api import *
import os
diff --git a/Testing/SystemTests/tests/analysis/HFIRBackgroundAPIv2.py b/Testing/SystemTests/tests/analysis/HFIRBackgroundAPIv2.py
index 9d70413b3d4d3aac3d1ebf338b19cdfd8acf9018..925598081392de11638c79fa55e48d96ec2c22c2 100644
--- a/Testing/SystemTests/tests/analysis/HFIRBackgroundAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/HFIRBackgroundAPIv2.py
@@ -3,6 +3,7 @@ import stresstesting
from mantid.api import FileFinder
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.hfir_command_interface import *
+from reduction_workflow.command_interface import AppendDataFile, Reduce1D
import os
diff --git a/Testing/SystemTests/tests/analysis/HFIREffAPIv2.py b/Testing/SystemTests/tests/analysis/HFIREffAPIv2.py
index 804419f7bc2ff105704f3bd8f0c77dbdcf0a09ff..507ee341ae3c94375d353db26292912414e00945 100644
--- a/Testing/SystemTests/tests/analysis/HFIREffAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/HFIREffAPIv2.py
@@ -3,6 +3,7 @@ import stresstesting
from mantid.api import FileFinder
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.hfir_command_interface import *
+from reduction_workflow.command_interface import AppendDataFile, Reduce1D
import os
diff --git a/Testing/SystemTests/tests/analysis/HFIRReductionAPIv2.py b/Testing/SystemTests/tests/analysis/HFIRReductionAPIv2.py
index d0ab5a1d523f1f31d3bed108232209d3b0b6026e..6a2f37cbcec421aee254eebb406e57bf31df90c3 100644
--- a/Testing/SystemTests/tests/analysis/HFIRReductionAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/HFIRReductionAPIv2.py
@@ -3,6 +3,7 @@ import stresstesting
from mantid.api import FileFinder
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.hfir_command_interface import *
+from reduction_workflow.command_interface import AppendDataFile, Reduce
import os
diff --git a/Testing/SystemTests/tests/analysis/HFIRTestsAPIv2.py b/Testing/SystemTests/tests/analysis/HFIRTestsAPIv2.py
index 66c3cc4dca7840daa25b28cb231b1430ea568e93..43d23b90f658696e83aec63f8c543f9ac778ec75 100644
--- a/Testing/SystemTests/tests/analysis/HFIRTestsAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/HFIRTestsAPIv2.py
@@ -17,6 +17,7 @@ import stresstesting
from mantid.api import *
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.hfir_command_interface import *
+from reduction_workflow.command_interface import AppendDataFile, Reduce, Reduce1D
# Set directory containing the test data, relative to the Mantid release
diff --git a/Testing/SystemTests/tests/analysis/HFIRTransAPIv2.py b/Testing/SystemTests/tests/analysis/HFIRTransAPIv2.py
index 7c53a24adf8c92c0999fe2f8cb9461aa29391e33..1fe141c924c7fca709450b5483807aa06c95fd4f 100644
--- a/Testing/SystemTests/tests/analysis/HFIRTransAPIv2.py
+++ b/Testing/SystemTests/tests/analysis/HFIRTransAPIv2.py
@@ -3,6 +3,7 @@ import stresstesting
from mantid.api import FileFinder
from mantid.simpleapi import *
from reduction_workflow.instruments.sans.hfir_command_interface import *
+from reduction_workflow.command_interface import AppendDataFile, Reduce1D
import os
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_All.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_All.py
index 9054bd94ec97217b7ceab4e5330602e19dffd887..cda7cc19a66fe3c5bd9b00d922264f7caefe6b92 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_All.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_All.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
"""
Tube Calibration Demonstration for MAPS instrument.
@@ -52,21 +52,21 @@ Calibration technique: Finding tubes not well calibrated
"""
-from mantid.simpleapi import *
+import mantid.simpleapi as mantid
import tube
import numpy
def loadingStep(filename):
filename = str(filename)
- rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
- rangeUpper = 10000 #
+ rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
+ rangeUpper = 10000 #
# Get calibration raw file and integrate it
- rawCalibInstWS = Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
- print "Integrating Workspace"
- CalibInstWS = Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
- DeleteWorkspace(rawCalibInstWS)
- print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+ rawCalibInstWS = mantid.Load(filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
+ print("Integrating Workspace")
+ CalibInstWS = mantid.Integration(rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper)
+ mantid.DeleteWorkspace(rawCalibInstWS)
+ print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
return CalibInstWS
@@ -89,12 +89,12 @@ def minimalInput(filename):
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
- knownPos, funcFactor = [-0.50,-0.16,-0.00, 0.16, 0.50 ],[2,1,1,1,2]
+ knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# == Get the calibration and put results into calibration table ==
calibrationTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor)
# == Apply the Calibation ==
- ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+ mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
def provideTheExpectedValue(filename):
@@ -111,7 +111,7 @@ def provideTheExpectedValue(filename):
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
- knownPos, funcFactor = [-0.50,-0.16,-0.00, 0.16, 0.50 ],[2,1,1,1,2]
+ knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
@@ -122,7 +122,7 @@ def provideTheExpectedValue(filename):
calibrationTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
fitPar=fitPar)
# == Apply the Calibation ==
- ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+ mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
def changeMarginAndExpectedValue(filename):
@@ -153,7 +153,7 @@ def changeMarginAndExpectedValue(filename):
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
- knownPos, funcFactor = [-0.50,-0.16,-0.00, 0.16, 0.50 ],[2,1,1,1,2]
+ knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
@@ -161,10 +161,10 @@ def changeMarginAndExpectedValue(filename):
fitPar.setAutomatic(True)
# == Get the calibration and put results into calibration table ==
- calibrationTable, peakTable= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
- fitPar=fitPar, plotTube=[1,10,100], outputPeak=True, margin=10)
+ calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
+ fitPar=fitPar, plotTube=[1, 10, 100], outputPeak=True, margin=10)
# == Apply the Calibation ==
- ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+ mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
tube.savePeak(peakTable, 'TubeDemoMaps01.txt')
@@ -202,7 +202,7 @@ def improvingCalibrationSingleTube(filename):
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
- knownPos, funcFactor = [-0.50,-0.16,-0.00, 0.16, 0.50 ],[2,1,1,1,2]
+ knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
@@ -210,10 +210,11 @@ def improvingCalibrationSingleTube(filename):
fitPar.setAutomatic(True)
# == Get the calibration and put results into calibration table ==
- calibrationTable, peakTable= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
- fitPar=fitPar, outputPeak=True, plotTube=[18,19,20], rangeList=[18,19,20])
+ calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
+ fitPar=fitPar, outputPeak=True, plotTube=[18, 19, 20],
+ rangeList=[18, 19, 20])
- ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+ mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
# reload to reset the calibration applied
CalibInstWS = loadingStep(filename)
@@ -221,16 +222,17 @@ def improvingCalibrationSingleTube(filename):
# as 14.9788, -0.303511, 9.74828
# let's change the peak from -0.303511 to 8.14
- #to override the peaks definition, we use the overridePeaks
+ # to override the peaks definition, we use the overridePeaks
overridePeaks = {19: [8.14, 80.9771, 123.221, 164.993, 245.717]}
# == Get the calibration and put results into calibration table ==
# we will not plot anymore, because it will not plot the overrided peaks
- calibrationTable, peakTable= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
- fitPar=fitPar, outputPeak=True, rangeList=[18,19,20], overridePeaks=overridePeaks)
+ calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
+ fitPar=fitPar, outputPeak=True, rangeList=[18, 19, 20],
+ overridePeaks=overridePeaks)
- ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
- #check using the InstrumentView and you will see that it is better than before
+ mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
+ # check using the InstrumentView and you will see that it is better than before
def improvingCalibrationOfListOfTubes(filename):
@@ -255,7 +257,7 @@ def improvingCalibrationOfListOfTubes(filename):
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
- knownPos, funcFactor = [-0.50,-0.16,-0.00, 0.16, 0.50 ],[2,1,1,1,2]
+ knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
@@ -263,28 +265,28 @@ def improvingCalibrationOfListOfTubes(filename):
fitPar.setAutomatic(True)
# == Get the calibration and put results into calibration table ==
- #calibrationTable, peakTable= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
+ # calibrationTable, peakTable= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
# fitPar=fitPar, outputPeak=True, plotTube=not_good, rangeList=not_good)
- #CalibInstWS = loadingStep(filename)
+ # CalibInstWS = loadingStep(filename)
# it is defined as the mean values around the neighbours
- define_peaks = {19:[10, 80.9771, 123.221, 164.993, 245.717], # the first one was bad
- 37: [6.36, 80.9347, 122.941, 165.104, 248.32], # the first one was bad
- 71: [8.62752, 85.074, 124.919, 164.116, 246.82 ], # the last one was bad - check if we can inprove
- 75: [14.4285, 90.087, 128.987, 167.047, 242.62], # the last one was bad - check if we can inprove
- 181: [11.726, 94.0496, 137.816, 180, 255], # the third peak was lost
- 186:[11.9382, 71.5203, 107, 147.727, 239.041], #lost the second peak
- 234: [4.84, 82.7824, 123.125, 163.945, 241.877], # the first one was bad
- 235: [4.84, 80.0077, 121.002, 161.098, 238.502], # the first one was bad
- 245: [9.88089, 93.0593, 136.911, 179.5, 255], # the third peak was bad
- 273: [18.3711, 105.5, 145.5, 181.6, 243.252], # lost first and third peaks
- 345: [4.6084, 87.0351, 128.125, 169.923, 245.3] # the last one was bad
+ define_peaks = {19: [10, 80.9771, 123.221, 164.993, 245.717], # the first one was bad
+ 37: [6.36, 80.9347, 122.941, 165.104, 248.32], # the first one was bad
+ 71: [8.62752, 85.074, 124.919, 164.116, 246.82], # the last one was bad - check if we can inprove
+ 75: [14.4285, 90.087, 128.987, 167.047, 242.62], # the last one was bad - check if we can inprove
+ 181: [11.726, 94.0496, 137.816, 180, 255], # the third peak was lost
+ 186: [11.9382, 71.5203, 107, 147.727, 239.041], # lost the second peak
+ 234: [4.84, 82.7824, 123.125, 163.945, 241.877], # the first one was bad
+ 235: [4.84, 80.0077, 121.002, 161.098, 238.502], # the first one was bad
+ 245: [9.88089, 93.0593, 136.911, 179.5, 255], # the third peak was bad
+ 273: [18.3711, 105.5, 145.5, 181.6, 243.252], # lost first and third peaks
+ 345: [4.6084, 87.0351, 128.125, 169.923, 245.3] # the last one was bad
}
- calibrationTable, peakTable= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
- fitPar=fitPar, outputPeak=True, overridePeaks=define_peaks)
+ calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
+ fitPar=fitPar, outputPeak=True, overridePeaks=define_peaks)
- ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+ mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
def calibrateB2Window(filename):
@@ -305,14 +307,14 @@ def calibrateB2Window(filename):
"""
from tube_calib_fit_params import TubeCalibFitParams
# b2 with 2 peaks range
- b2_range = range(196,212) + range(222,233)
+ b2_range = list(range(196, 212)) + list(range(222, 233))
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
- knownPos, funcFactor = [-0.50,-0.16, 0.16, 0.50 ],[2,1,1,2]
+ knownPos, funcFactor = [-0.50, -0.16, 0.16, 0.50], [2, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 161.0, 252.0]
@@ -320,10 +322,11 @@ def calibrateB2Window(filename):
fitPar.setAutomatic(True)
# == Get the calibration and put results into calibration table ==
- calibrationTable, peakTable= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
- fitPar=fitPar, outputPeak=True, plotTube=[b2_range[0], b2_range[-1]], rangeList=b2_range)
+ calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
+ fitPar=fitPar, outputPeak=True, plotTube=[b2_range[0], b2_range[-1]],
+ rangeList=b2_range)
- ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+ mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
def findThoseTubesThatNeedSpecialCareForCalibration(filename):
@@ -354,7 +357,7 @@ def findThoseTubesThatNeedSpecialCareForCalibration(filename):
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
- knownPos, funcFactor = [-0.50,-0.16,-0.00, 0.16, 0.50 ],[2,1,1,1,2]
+ knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
@@ -362,50 +365,50 @@ def findThoseTubesThatNeedSpecialCareForCalibration(filename):
fitPar.setAutomatic(True)
# == Get the calibration and put results into calibration table ==
- calibrationTable, peakTable= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
- fitPar=fitPar, outputPeak=True)
+ calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
+ fitPar=fitPar, outputPeak=True)
# == now, lets investigate the peaks
- #parsing the peakTable to produce a numpy array with dimension (number_of_tubes x number_of_peaks)
- print 'parsing the peak table'
+ # parsing the peakTable to produce a numpy array with dimension (number_of_tubes x number_of_peaks)
+ print('parsing the peak table')
n = len(peakTable)
- peaksId = n*['']
- data = numpy.zeros((n,5))
+ peaksId = n * ['']
+ data = numpy.zeros((n, 5))
line = 0
for row in peakTable:
- data_row = [row['Peak%d'%(i)] for i in [1,2,3,4,5]]
- data[line,:] = data_row
+ data_row = [row['Peak%d' % (i)] for i in [1, 2, 3, 4, 5]]
+ data[line, :] = data_row
peaksId[line] = row['TubeId']
- line+=1
+ line += 1
# data now has all the peaks positions for each tube
# the mean value is the expected value for the peak position for each tube
- expected_peak_pos = numpy.mean(data,axis=0)
- #calculate how far from the expected position each peak position is
- distance_from_expected = numpy.abs(data - expected_peak_pos)
+ expected_peak_pos = numpy.mean(data, axis=0)
+ # calculate how far from the expected position each peak position is
+ distance_from_expected = numpy.abs(data - expected_peak_pos)
- print 'Creating the Peaks Workspace that shows the distance from the expected value for all peaks for each tube'
+ print('Creating the Peaks Workspace that shows the distance from the expected value for all peaks for each tube')
# Let's see these peaks:
- CreateWorkspace(range(n),distance_from_expected,NSpec=5,OutputWorkspace='Peaks')
+ mantid.CreateWorkspace(list(range(n)), distance_from_expected, NSpec=5, OutputWorkspace='Peaks')
# plot all the 5 peaks for Peaks Workspace. You will see that most of the tubes differ
# at most 12 pixels from the expected values.
- #so let's investigate those that differ more than 12
+ # so let's investigate those that differ more than 12
# return an array with the indexes for the first axis which is the tube indentification
check = numpy.where(distance_from_expected > 12)[0]
- #remove repeated values
- #select only those tubes inside the problematic_tubes
+ # remove repeated values
+ # select only those tubes inside the problematic_tubes
problematic_tubes = list(set(check))
- print 'Tubes whose distance is far from the expected value: ', problematic_tubes
+ print('Tubes whose distance is far from the expected value: ', problematic_tubes)
- print 'Calibrating again only these tubes'
- #let's confir that our suspect works
+ print('Calibrating again only these tubes')
+ # let's confir that our suspect works
CalibInstWS = loadingStep(filename)
tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
- fitPar=fitPar, rangeList= problematic_tubes, plotTube=problematic_tubes)
+ fitPar=fitPar, rangeList=problematic_tubes, plotTube=problematic_tubes)
# plot the FittedTube agains TubePlot for each detector and you will see that there were problems on those tubes.
@@ -430,16 +433,16 @@ def completeCalibration(filename):
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
- knownPos, funcFactor = [-0.50,-0.16,-0.00, 0.16, 0.50 ],[2,1,1,1,2]
+ knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
fitPar = TubeCalibFitParams(expectedPositions)
fitPar.setAutomatic(True)
- #execute the improvingCalibrationOfListOfTubes excluding the range of b2 window
+ # execute the improvingCalibrationOfListOfTubes excluding the range of b2 window
# correct the definition of the peaks for the folowing indexes
- #define_peaks = {19:[10, 80.9771, 123.221, 164.993, 245.717], # the first one was bad
+ # define_peaks = {19:[10, 80.9771, 123.221, 164.993, 245.717], # the first one was bad
# 37: [6.36, 80.9347, 122.941, 165.104, 248.32], # the first one was bad
# 71: [8.62752, 85.074, 124.919, 164.116, 246.82 ], # the last one was bad - check if we can inprove
# 75: [14.4285, 90.087, 128.987, 167.047, 242.62], # the last one was bad - check if we can inprove
@@ -450,34 +453,35 @@ def completeCalibration(filename):
# 245: [9.88089, 93.0593, 136.911, 179.5, 255], # the third peak was bad
# 273: [18.3711, 105.5, 145.5, 181.6, 243.252],# lost first and third peaks
# 345: [4.6084, 87.0351, 128.125, 169.923, 245.3]} # the last one was bad
- define_peaks = {19:[10, 80.9771, 123.221, 164.993, 245.717],
+ define_peaks = {19: [10, 80.9771, 123.221, 164.993, 245.717],
37: [6.36, 80.9347, 122.941, 165.104, 248.32],
- 71: [8.62752, 85.074, 124.919, 164.116, 246.82 ],
+ 71: [8.62752, 85.074, 124.919, 164.116, 246.82],
75: [14.4285, 90.087, 128.987, 167.047, 242.62],
- 181: [11.726, 94.0496, 137.816, 180, 255],
- 186:[11.9382, 71.5203, 107, 147.727, 239.041],
+ 181: [11.726, 94.0496, 137.816, 180, 255],
+ 186: [11.9382, 71.5203, 107, 147.727, 239.041],
234: [4.84, 82.7824, 123.125, 163.945, 241.877],
235: [4.84, 80.0077, 121.002, 161.098, 238.502],
245: [9.88089, 93.0593, 136.911, 179.5, 255],
273: [18.3711, 105.5, 145.5, 181.6, 243.252],
345: [4.6084, 87.0351, 128.125, 169.923, 245.3]}
- b2_window = range(196,212) + range(222,233)
+ b2_window = list(range(196, 212)) + list(range(222, 233))
- complete_range = range(648)
+ complete_range = list(range(648))
# this data can not be used to calibrate the E1 window, so, let's remove it.
- e1_window = range(560,577)
+ e1_window = list(range(560, 577))
aux = numpy.setdiff1d(complete_range, b2_window)
# the group that have 3 stripts are all the tubes except the b2 window and e window.
range_3_strips = numpy.setdiff1d(aux, e1_window)
- calibrationTable, peak3Table= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
- fitPar=fitPar, outputPeak=True, overridePeaks=define_peaks, rangeList=range_3_strips)
+ calibrationTable, peak3Table = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
+ fitPar=fitPar, outputPeak=True, overridePeaks=define_peaks,
+ rangeList=range_3_strips)
# now calibrate the b2_window REMOVE SECOND PEAK
# define the known positions and function factor (edge, peak, peak, edge)
- knownPos, funcFactor = [-0.50,-0.16, 0.16, 0.50 ],[2,1,1,2]
+ knownPos, funcFactor = [-0.50, -0.16, 0.16, 0.50], [2, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 161.0, 252.0]
@@ -486,31 +490,31 @@ def completeCalibration(filename):
# apply the calibration for the b2_window 2 strips values
calibrationTable, peak2Table = tube.calibrate(CalibInstWS, CalibratedComponent,
- knownPos, #these parameters now have only 4 points
+ knownPos, # these parameters now have only 4 points
funcFactor,
fitPar=fitPar,
outputPeak=True,
- calibTable = calibrationTable, # it will append to the calibTable
- rangeList = b2_window)
+ calibTable=calibrationTable, # it will append to the calibTable
+ rangeList=b2_window)
- ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+ mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
# == Save workspace ==
- #SaveNexusProcessed( CalibInstWS, path+'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
- #print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
+ # SaveNexusProcessed( CalibInstWS, path+'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
+ # print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
####
## Uncomment one of the following lines to execute one of the examples
#####
-filename = 'MAP14919.raw' #found at \\isis\inst$\NDXMAPS\Instrument\data\cycle_09_5
+filename = 'MAP14919.raw' # found at \\isis\inst$\NDXMAPS\Instrument\data\cycle_09_5
if __name__ == "__main__":
filename = 'MAP14919.raw'
- #minimalInput(filename)
- #provideTheExpectedValue(filename)
- #changeMarginAndExpectedValue(filename)
- #improvingCalibrationSingleTube(filename)
- #improvingCalibrationOfListOfTubes(filename)
- #calibrateB2Window(filename)
+ # minimalInput(filename)
+ # provideTheExpectedValue(filename)
+ # changeMarginAndExpectedValue(filename)
+ # improvingCalibrationSingleTube(filename)
+ # improvingCalibrationOfListOfTubes(filename)
+ # calibrateB2Window(filename)
completeCalibration(filename)
- #findThoseTubesThatNeedSpecialCareForCalibration(filename)
+ # findThoseTubesThatNeedSpecialCareForCalibration(filename)
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_B1.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_B1.py
index b049ea959d1d815ab3f5ac87c5ae392bbc423a8c..37a02fa1e3e6d709f086607a7f1f19f4b86e3873 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_B1.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_B1.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
#
# TUBE CALIBRATION DEMONSTRATION PROGRAM FOR MAPS - Execute this
#
@@ -7,56 +7,56 @@
#
import tube
from tube_calib_fit_params import TubeCalibFitParams
+import mantid.simpleapi as mantid
+
# == Set parameters for calibration ==
-filename = 'MAP14919.raw' # Calibration run ( found in \\isis\inst$\NDXMAPS\Instrument\data\cycle_09_5 )
-rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
-rangeUpper = 10000 #
+filename = 'MAP14919.raw' # Calibration run ( found in \\isis\inst$\NDXMAPS\Instrument\data\cycle_09_5 )
+rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
+rangeUpper = 10000 #
# Set initial parameters for peak finding
-ExpectedHeight = -1000.0 # Expected Height of Gaussian Peaks (initial value of fit parameter)
-ExpectedWidth = 8.0 # Expected width of Gaussian peaks in pixels (initial value of fit parameter)
+ExpectedHeight = -1000.0 # Expected Height of Gaussian Peaks (initial value of fit parameter)
+ExpectedWidth = 8.0 # Expected width of Gaussian peaks in pixels (initial value of fit parameter)
ExpectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
# Expected positions of the edges and Gaussian peaks in pixels (initial values of fit parameters)
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent = 'B1_window' # Calibrate B1 window
-
# Get calibration raw file and integrate it
-rawCalibInstWS = Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
-print "Integrating Workspace"
-CalibInstWS = Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
-DeleteWorkspace(rawCalibInstWS)
-print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+rawCalibInstWS = mantid.Load(filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
+print("Integrating Workspace")
+CalibInstWS = mantid.Integration(rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper)
+mantid.DeleteWorkspace(rawCalibInstWS)
+print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
# == Create Objects needed for calibration ==
# The positions of the shadows and ends here are an intelligent guess.
# First array gives positions in Metres and second array gives type 1=Gaussian peak 2=edge.
# See http://www.mantidproject.org/IdealTube for details.
-knownPos = [-0.50,-0.165,-0.00, 0.165, 0.50 ]
-funcForm = [2,1,1,1,2]
+knownPos = [-0.50, -0.165, -0.00, 0.165, 0.50]
+funcForm = [2, 1, 1, 1, 2]
# Get fitting parameters
-fitPar = TubeCalibFitParams( ExpectedPositions, ExpectedHeight, ExpectedWidth )
+fitPar = TubeCalibFitParams(ExpectedPositions, ExpectedHeight, ExpectedWidth)
fitPar.setAutomatic(True)
-print "Created objects needed for calibration."
+print("Created objects needed for calibration.")
# == Get the calibration and put results into calibration table ==
# also put peaks into PeakFile
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcForm,
fitPar=fitPar, outputPeak=True)
-print "Got calibration (new positions of detectors) "
+print("Got calibration (new positions of detectors) ")
# == Apply the Calibation ==
-ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
-print "Applied calibration"
-
+mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
+print("Applied calibration")
# == Save workspace ==
-SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps_B1.py")
-print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
+mantid.SaveNexusProcessed(CalibInstWS, 'TubeCalibDemoMapsResult.nxs', "Result of Running TCDemoMaps_B1.py")
+print("saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs")
# == Save Peak File ==
tube.savePeak(peakTable, 'TubeDemoMaps01.txt')
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3.py
index 5413f517d0750a6bf9e7812f43a568e5645a08ed..493a8207be9ea0296fec99a244ad2979d283e877 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
#
# TUBE CALIBRATION DEMONSTRATION PROGRAM FOR MAPS - Execute this
#
@@ -8,26 +8,27 @@
#
import tube
from tube_spec import TubeSpec
-#from tube_calib_fit_params import # To handle fit parameters
+import mantid.simpleapi as mantid
+
+# from tube_calib_fit_params import # To handle fit parameters
# == Set parameters for calibration ==
-filename = 'MAP14919.raw' # Name of calibration run
-rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
-rangeUpper = 10000 #
+filename = 'MAP14919.raw' # Name of calibration run
+rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
+rangeUpper = 10000 #
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent1 = 'C4_window' # Calibrate C4 window
CalibratedComponent2 = 'C3_window' # Calibrate C3 window
-
# Get calibration raw file and integrate it
-rawCalibInstWS = Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
-print "Integrating Workspace"
-CalibInstWS = Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
-DeleteWorkspace(rawCalibInstWS)
-print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+rawCalibInstWS = mantid.Load(filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
+print("Integrating Workspace")
+CalibInstWS = mantid.Integration(rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper)
+mantid.DeleteWorkspace(rawCalibInstWS)
+print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
# == Create Objects needed for calibration ==
@@ -37,22 +38,21 @@ thisTubeSet.setTubeSpecByString(CalibratedComponent1)
thisTubeSet.setTubeSpecByString(CalibratedComponent2)
# Specify the known positions
-knownPos = [-0.50,-0.16,-0.00, 0.16, 0.50 ]
-funcForm = [2,1,1,1,2]
+knownPos = [-0.50, -0.16, -0.00, 0.16, 0.50]
+funcForm = [2, 1, 1, 1, 2]
-print "Created objects needed for calibration."
+print("Created objects needed for calibration.")
# == Get the calibration and put results into calibration table ==
calibrationTable, peakTable = tube.calibrate(CalibInstWS, thisTubeSet, knownPos, funcForm,
outputPeak=True)
-print "Got calibration (new positions of detectors) "
+print("Got calibration (new positions of detectors) ")
# == Apply the Calibation ==
-ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
-print "Applied calibration"
-
+mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
+print("Applied calibration")
# == Save workspace ==
-#SaveNexusProcessed( CalibInstWS, path+'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
-print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
+# SaveNexusProcessed( CalibInstWS, path+'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
+print("saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs")
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3C2.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3C2.py
index e8340cca0de9ad1305e273ffc09afe280b02c8c5..916de7b178c4374b3be97742a9af00adb74eda00 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3C2.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_C4C3C2.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
#
# TUBE CALIBRATION DEMONSTRATION PROGRAM FOR MAPS - Execute this
#
@@ -6,44 +6,43 @@
# specifying them in an array of strings.
import tube
+import mantid.simpleapi as mantid
# == Set parameters for calibration ==
-filename = 'MAP14919.raw' # Name of calibration run
-rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
-rangeUpper = 10000 #
+filename = 'MAP14919.raw' # Name of calibration run
+rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
+rangeUpper = 10000 #
# Set what we want to calibrate (e.g whole intrument or one door )
# Set what we want to calibrate (e.g whole intrument or one door )
-CalibratedComponents = ['C4_window','C3_window','C2_window'] # Calibrate three C windows
-
+CalibratedComponents = ['C4_window', 'C3_window', 'C2_window'] # Calibrate three C windows
# Get calibration raw file and integrate it
-rawCalibInstWS = Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
-print "Integrating Workspace"
-CalibInstWS = Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
-DeleteWorkspace(rawCalibInstWS)
-print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+rawCalibInstWS = mantid.Load(filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
+print("Integrating Workspace")
+CalibInstWS = mantid.Integration(rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper)
+mantid.DeleteWorkspace(rawCalibInstWS)
+print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
# == Create Objects needed for calibration ==
# Specify the known positions
-knownPos = [-0.50,-0.16,-0.00, 0.16, 0.50 ]
-funcForm = [2,1,1,1,2]
+knownPos = [-0.50, -0.16, -0.00, 0.16, 0.50]
+funcForm = [2, 1, 1, 1, 2]
-print "Created objects needed for calibration."
+print("Created objects needed for calibration.")
# == Get the calibration and put results into calibration table ==
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponents, knownPos, funcForm,
outputPeak=True)
-print "Got calibration (new positions of detectors) "
+print("Got calibration (new positions of detectors) ")
# == Apply the Calibation ==
-ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
-print "Applied calibration"
-
+mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
+print("Applied calibration")
# == Save workspace ==
-#SaveNexusProcessed( CalibInstWS, path+'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
-print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
+# SaveNexusProcessed( CalibInstWS, path+'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
+print("saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs")
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_D2.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_D2.py
index 5a725371cdcdd4811124ec2a0ed2d78b6ca8dc67..a59232d971d617dc1d1df65238335c270acaf0e6 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_D2.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_D2.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
#
# TUBE CALIBRATION DEMONSTRATION PROGRAM FOR MAPS - Execute this
#
@@ -7,50 +7,51 @@
#
import tube
from tube_calib_fit_params import TubeCalibFitParams
+import mantid.simpleapi as mantid
+
# == Set parameters for calibration ==
-filename = 'MAP14919.raw' # Calibration run ( found in \\isis\inst$\NDXMAPS\Instrument\data\cycle_09_5 )
+filename = 'MAP14919.raw' # Calibration run ( found in \\isis\inst$\NDXMAPS\Instrument\data\cycle_09_5 )
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent = 'D2_window' # Calibrate D2 window
-
# Get calibration raw file and integrate it
-rawCalibInstWS = Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
-print "Integrating Workspace"
-rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
-rangeUpper = 10000 #
-CalibInstWS = Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
-DeleteWorkspace(rawCalibInstWS)
-print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+rawCalibInstWS = mantid.Load(filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
+print("Integrating Workspace")
+rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
+rangeUpper = 10000 #
+CalibInstWS = mantid.Integration(rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper)
+mantid.DeleteWorkspace(rawCalibInstWS)
+print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
# == Create Objects needed for calibration ==
# The positions of the shadows and ends here are an intelligent guess.
# First array gives positions in Metres and second array gives type 1=Gaussian peak 2=edge.
-knownPos = [-0.65,-0.22,-0.00, 0.22, 0.65 ]
-funcForm = [2,1,1,1,2]
+knownPos = [-0.65, -0.22, -0.00, 0.22, 0.65]
+funcForm = [2, 1, 1, 1, 2]
# Get fitting parameters
# Set initial parameters for peak finding
-ExpectedHeight = -1000.0 # Expected Height of Gaussian Peaks (initial value of fit parameter)
-ExpectedWidth = 8.0 # Expected width of Gaussian peaks in pixels (initial value of fit parameter)
-ExpectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0] # Expected positions of the edges and Gaussian peaks
- # in pixels (initial values of fit parameters)
-fitPar = TubeCalibFitParams( ExpectedPositions, ExpectedHeight, ExpectedWidth)
+ExpectedHeight = -1000.0 # Expected Height of Gaussian Peaks (initial value of fit parameter)
+ExpectedWidth = 8.0 # Expected width of Gaussian peaks in pixels (initial value of fit parameter)
+ExpectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0] # Expected positions of the edges and Gaussian peaks
+# in pixels (initial values of fit parameters)
+fitPar = TubeCalibFitParams(ExpectedPositions, ExpectedHeight, ExpectedWidth)
fitPar.setAutomatic(True)
-print "Created objects needed for calibration."
+print("Created objects needed for calibration.")
# == Get the calibration and put results into calibration table ==
calibrationTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcForm,
- fitPar = fitPar)
-print "Got calibration (new positions of detectors) "
+ fitPar=fitPar)
+print("Got calibration (new positions of detectors) ")
# == Apply the Calibation ==
-ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
-print "Applied calibration"
+mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
+print("Applied calibration")
# == Save workspace ==
-#SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
-#print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
+# SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
+# print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_D2_WideMargins.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_D2_WideMargins.py
index 1131eadedcbc170fec22a0a4121df0f1d8bab222..a5a42ac3e0e2ff7c8a1fbac3456e83f893338502 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_D2_WideMargins.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_D2_WideMargins.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
#
# TUBE CALIBRATION DEMONSTRATION PROGRAM FOR MAPS - Execute this
#
@@ -6,42 +6,41 @@
#
import tube
+import mantid.simpleapi as mantid
# == Set parameters for calibration ==
-filename = 'MAP14919.raw' # Name of calibration run
-rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
-rangeUpper = 10000 #
-
+filename = 'MAP14919.raw' # Name of calibration run
+rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
+rangeUpper = 10000 #
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent = 'D2_window' # Calibrate D2 window
-
# Get calibration raw file and integrate it
-rawCalibInstWS = Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
-print "Integrating Workspace"
-CalibInstWS = Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
-DeleteWorkspace(rawCalibInstWS)
-print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+rawCalibInstWS = mantid.Load(filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
+print("Integrating Workspace")
+CalibInstWS = mantid.Integration(rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper)
+mantid.DeleteWorkspace(rawCalibInstWS)
+print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
# == Create Objects needed for calibration ==
# The positions of the shadows and ends here are an intelligent guess.
-knownPos = [-0.65,-0.22,-0.00, 0.22, 0.65 ]
-funcForm = [2,1,1,1,2]
+knownPos = [-0.65, -0.22, -0.00, 0.22, 0.65]
+funcForm = [2, 1, 1, 1, 2]
-print "Created objects needed for calibration."
+print("Created objects needed for calibration.")
# == Get the calibration and put results into calibration table ==
calibrationTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcForm)
-print "Got calibration (new positions of detectors) "
+print("Got calibration (new positions of detectors) ")
# == Apply the Calibation ==
-ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
-print "Applied calibration"
+mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
+print("Applied calibration")
# == Save workspace ==
-#SaveNexusProcessed( CalibInstWS, path+'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
-#print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
+# SaveNexusProcessed( CalibInstWS, path+'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
+# print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMaps_D4.py b/scripts/Calibration/Examples/TubeCalibDemoMaps_D4.py
index efdb96e9dbbdfb55633e524e7fe4760d4c698ce3..fb89634c6cd1655365e5748e352e38daedfa0e39 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMaps_D4.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMaps_D4.py
@@ -7,6 +7,7 @@
#
import tube
from tube_calib_fit_params import TubeCalibFitParams
+import mantid.simpleapi as mantid
# == Set parameters for calibration ==
@@ -15,13 +16,13 @@ filename = 'MAP14919.raw' # Calibration run ( found in \\isis\inst$\NDXMAPS\Inst
CalibratedComponent = 'D4_window' # Calibrate D4 window
# Get calibration raw file and integrate it
-rawCalibInstWS = Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
-print "Integrating Workspace"
+rawCalibInstWS = mantid.Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
+print("Integrating Workspace")
rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper
rangeUpper = 10000 #
-CalibInstWS = Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
-DeleteWorkspace(rawCalibInstWS)
-print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+CalibInstWS = mantid.Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
+mantid.DeleteWorkspace(rawCalibInstWS)
+print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
# == Create Objects needed for calibration ==
@@ -39,18 +40,18 @@ ExpectedPositions = [4.0, 85.0, 128.0, 165.0, 252.0] # Expected positions of the
fitPar = TubeCalibFitParams( ExpectedPositions, ExpectedHeight, ExpectedWidth)
fitPar.setAutomatic(True)
-print "Created objects needed for calibration."
+print("Created objects needed for calibration.")
# == Get the calibration and put results into calibration table ==
calibrationTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcForm,
fitPar = fitPar)
-print "Got calibration (new positions of detectors) "
+print("Got calibration (new positions of detectors) ")
# == Apply the Calibation ==
-ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
-print "Applied calibration"
+mantid.ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+print("Applied calibration")
# == Save workspace ==
-SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
-print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
+mantid.SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
+print("saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs")
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMerlin.py b/scripts/Calibration/Examples/TubeCalibDemoMerlin.py
index f6b27a28541094f3a1e78a911b6b66a7f1b7e9a8..aa7eeabfd432d0662121e4e3d01ecad45ab71ac4 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMerlin.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMerlin.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
"""
Tube Calibration Demonstration program for MERLIN.
@@ -43,70 +43,72 @@ The previous calibrated instrument view:
.. sectionauthor:: Gesner Passos - ISIS
"""
import numpy
-from mantid.simpleapi import *
+import mantid.simpleapi as mantid
import tube
def analisePeakTable(pTable, peaksName='Peaks'):
- print 'parsing the peak table'
+ print('parsing the peak table')
n = len(pTable)
- peaks = pTable.columnCount() -1
- peaksId = n*['']
- data = numpy.zeros((n,peaks))
+ peaks = pTable.columnCount() - 1
+ peaksId = n * ['']
+ data = numpy.zeros((n, peaks))
line = 0
for row in pTable:
- data_row = [row['Peak%d'%(i)] for i in range(1,peaks+1)]
- data[line,:] = data_row
+ data_row = [row['Peak%d' % (i)] for i in range(1, peaks + 1)]
+ data[line, :] = data_row
peaksId[line] = row['TubeId']
- line+=1
+ line += 1
# data now has all the peaks positions for each tube
# the mean value is the expected value for the peak position for each tube
- expected_peak_pos = numpy.mean(data,axis=0)
- print expected_peak_pos
- #calculate how far from the expected position each peak position is
- distance_from_expected = numpy.abs(data - expected_peak_pos)
+ expected_peak_pos = numpy.mean(data, axis=0)
+ print(expected_peak_pos)
+ # calculate how far from the expected position each peak position is
+ distance_from_expected = numpy.abs(data - expected_peak_pos)
- CreateWorkspace(range(n),distance_from_expected,NSpec=peaks, OutputWorkspace=peaksName)
+ mantid.CreateWorkspace(list(range(n)), distance_from_expected, NSpec=peaks, OutputWorkspace=peaksName)
check = numpy.where(distance_from_expected > 10)[0]
problematic_tubes = list(set(check))
- print 'Tubes whose distance is far from the expected value: ', problematic_tubes
+ print('Tubes whose distance is far from the expected value: ', problematic_tubes)
def calibrateMerlin(filename):
# == Set parameters for calibration ==
- rangeLower = 3000 # Integrate counts in each spectra from rangeLower to rangeUpper
- rangeUpper = 20000 #
+ rangeLower = 3000 # Integrate counts in each spectra from rangeLower to rangeUpper
+ rangeUpper = 20000 #
# Get calibration raw file and integrate it
- rawCalibInstWS = LoadRaw(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
- print "Integrating Workspace"
- CalibInstWS = Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
- DeleteWorkspace(rawCalibInstWS)
- print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+ rawCalibInstWS = mantid.LoadRaw(filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
+ print("Integrating Workspace")
+ CalibInstWS = mantid.Integration(rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper)
+ mantid.DeleteWorkspace(rawCalibInstWS)
+ print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
# the known positions are given in pixels inside the tubes and transformed to provide the positions
# with the center of the tube as the origin
- knownPositions = 2.92713867188*(numpy.array([27.30074322, 92.5, 294.65178585, 362.37861919,
- 512.77103043, 663.41425323, 798.3223896, 930.9, 997.08480835])/1024 - 0.5)
- funcForm = numpy.array([2,2,1,1,1,1,1,2,2],numpy.int8)
+ knownPositions = 2.92713867188 * (numpy.array([27.30074322, 92.5, 294.65178585, 362.37861919,
+ 512.77103043, 663.41425323, 798.3223896, 930.9,
+ 997.08480835]) / 1024 - 0.5)
+ funcForm = numpy.array([2, 2, 1, 1, 1, 1, 1, 2, 2], numpy.int8)
# The calibration will follow different steps for sets of tubes
# For the door9, the best points to define the known positions are the 1st edge, 5 peaks, last edge.
- points7 = knownPositions[[0,2,3,4,5,6,8]]
- points7func = funcForm[[0,2,3,4,5,6,8]]
+ points7 = knownPositions[[0, 2, 3, 4, 5, 6, 8]]
+ points7func = funcForm[[0, 2, 3, 4, 5, 6, 8]]
door9pos = points7
door9func = points7func
- CalibratedComponent = 'MERLIN/door9' # door9
+ CalibratedComponent = 'MERLIN/door9' # door9
# == Get the calibration and put results into calibration table ==
# also put peaks into PeakFile
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, door9pos, door9func,
outputPeak=True,
margin=30,
- rangeList=range(20) # because 20, 21, 22, 23 are defective detectors
+ rangeList=list(range(20))
+ # because 20, 21, 22, 23 are defective detectors
)
- print "Got calibration (new positions of detectors) and put slit peaks into file TubeDemoMerlin01.txt"
+ print("Got calibration (new positions of detectors) and put slit peaks into file TubeDemoMerlin01.txt")
analisePeakTable(peakTable, 'door9_tube1_peaks')
# For the door8, the best points to define the known positions are the 1st edge, 5 peaks, last_edge
@@ -115,118 +117,119 @@ def calibrateMerlin(filename):
CalibratedComponent = 'MERLIN/door8'
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, door8pos,
door8func,
- outputPeak = True, #change to peakTable to append to peakTable
- calibTable = calibrationTable,
- margin = 30)
+ outputPeak=True, # change to peakTable to append to peakTable
+ calibTable=calibrationTable,
+ margin=30)
analisePeakTable(peakTable, 'door8_peaks')
- # For the doors 7,6,5,4, 2, 1 we may use the 9 points
+ # For the doors 7,6,5,4, 2, 1 we may use the 9 points
doorpos = knownPositions
doorfunc = funcForm
- CalibratedComponent = ['MERLIN/door%d'%(i) for i in [7,6,5,4, 2, 1]]
+ CalibratedComponent = ['MERLIN/door%d' % (i) for i in [7, 6, 5, 4, 2, 1]]
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, doorpos,
doorfunc,
- outputPeak = True,
- calibTable = calibrationTable,
- margin = 30)
+ outputPeak=True,
+ calibTable=calibrationTable,
+ margin=30)
analisePeakTable(peakTable, 'door1to7_peaks')
- # The door 3 is a special case, because it is composed by diffent kind of tubes.
- # door 3 tubes: 5_8, 5_7, 5_6, 5_5, 5_4, 5_3, 5_2, 5_1, 4_8, 4_7, 4_6, 4_5, 4_4, 4_3, 4_2, 4_1, 3_8, 3_7, 3_6, 3_5, 3_4
- # obeys the same rules as the doors 7, 6, 5, 4, 2, 1
- # For the tubes 3_3, 3_2, 3_1 -> it is better to skip the central peak
- # For the tubes 1_x (smaller tube below), it is better to take the final part of known positions: peak4,peak5,edge6,edge7
- # For the tubes 2_x (smaller tube above, it is better to take the first part of known positions: edge1, edge2, peak1,peak2
+ # The door 3 is a special case, because it is composed by diffent kind of tubes.
+ # door 3 tubes: 5_8, 5_7, 5_6, 5_5, 5_4, 5_3, 5_2, 5_1, 4_8, 4_7, 4_6, 4_5, 4_4, 4_3, 4_2, 4_1, 3_8, 3_7, 3_6, 3_5, 3_4
+ # obeys the same rules as the doors 7, 6, 5, 4, 2, 1
+ # For the tubes 3_3, 3_2, 3_1 -> it is better to skip the central peak
+ # For the tubes 1_x (smaller tube below), it is better to take the final part of known positions: peak4,peak5,edge6,edge7
+ # For the tubes 2_x (smaller tube above, it is better to take the first part of known positions: edge1, edge2, peak1,peak2
- # NOTE: the smaller tubes they have length = 1.22879882813, but 1024 detectors
- # so we have to correct the known positiosn by multiplying by its lenght and dividing by the longer dimension
+ # NOTE: the smaller tubes they have length = 1.22879882813, but 1024 detectors
+ # so we have to correct the known positiosn by multiplying by its lenght and dividing by the longer dimension
from tube_calib_fit_params import TubeCalibFitParams
- # calibrating tubes 1_x
- CalibratedComponent = ['MERLIN/door3/tube_1_%d'%(i) for i in range(1,9)]
-
- half_diff_center = (2.92713867188 -1.22879882813)/2 # difference among the expected center position for both tubes
-
- # here a little bit of attempts is necessary. The efective center position and lengh is different for the calibrated tube, that
- # is the reason, the calibrated values of the smaller tube does not seems aligned with the others. By, finding the 'best' half_diff_center
- # value, the alignment occurs nicely.
- half_diff_center = 0.835 #
-
- # the knownpositions were given with the center of the bigger tube as origin, to convert
- # to the center of the upper tube as origin is necessary to subtract them with the half_diff_center
- doorpos = knownPositions[[5,6,7,8]] - half_diff_center
- doorfunc = [1,1,2,2]
- # for the smal tubes, automatically searching for the peak position in pixel was not working quite well,
- # so we will give the aproximate position for these tubes through fitPar argument
+ # calibrating tubes 1_x
+ CalibratedComponent = ['MERLIN/door3/tube_1_%d' % (i) for i in range(1, 9)]
+
+ half_diff_center = (
+ 2.92713867188 - 1.22879882813) / 2 # difference among the expected center position for
+ # both tubes here a little bit of attempts is necessary.
+ # The effective center position and lengh is different for the calibrated tube, that is the reason,
+ # the calibrated values of the smaller tube does not seems aligned with the others. By, finding the
+ # 'best' half_diff_center value, the alignment occurs nicely.
+ half_diff_center = 0.835 #
+
+ # the knownpositions were given with the center of the bigger tube as origin, to convert
+ # to the center of the upper tube as origin is necessary to subtract them with the half_diff_center
+ doorpos = knownPositions[[5, 6, 7, 8]] - half_diff_center
+ doorfunc = [1, 1, 2, 2]
+ # for the smal tubes, automatically searching for the peak position in pixel was not working quite well,
+ # so we will give the aproximate position for these tubes through fitPar argument
fitPar = TubeCalibFitParams([216, 527, 826, 989])
fitPar.setAutomatic(True)
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, doorpos,
doorfunc,
- outputPeak = True,
- fitPar = fitPar,
- calibTable = calibrationTable,
- margin = 30)
+ outputPeak=True,
+ fitPar=fitPar,
+ calibTable=calibrationTable,
+ margin=30)
analisePeakTable(peakTable, 'door3_tube1_peaks')
- # calibrating tubes 2_x
- CalibratedComponent = ['MERLIN/door3/tube_2_%d'%(i) for i in range(1,9)]
- # the knownpositions were given with the center of the bigger tube as origin, to convert
- # to the center of the lower tube as origin is necessary to sum them with (len_big - len_small)/2
- doorpos = knownPositions[[0,1,2,3]] + half_diff_center
- # print doorpos
- doorfunc = [2,2,1,1]
+ # calibrating tubes 2_x
+ CalibratedComponent = ['MERLIN/door3/tube_2_%d' % (i) for i in range(1, 9)]
+ # the knownpositions were given with the center of the bigger tube as origin, to convert
+ # to the center of the lower tube as origin is necessary to sum them with (len_big - len_small)/2
+ doorpos = knownPositions[[0, 1, 2, 3]] + half_diff_center
+ # print doorpos
+ doorfunc = [2, 2, 1, 1]
- # for the smal tubes, automatically searching for the peak position in pixel was not working quite well,
- # so we will give the aproximate position for these tubes through fitPar argument
+ # for the smal tubes, automatically searching for the peak position in pixel was not working quite well,
+ # so we will give the aproximate position for these tubes through fitPar argument
fitPar = TubeCalibFitParams([50, 202, 664, 815])
fitPar.setAutomatic(True)
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, doorpos,
doorfunc,
- outputPeak = True,
- calibTable = calibrationTable,
- fitPar = fitPar,
- margin = 30)
+ outputPeak=True,
+ calibTable=calibrationTable,
+ fitPar=fitPar,
+ margin=30)
analisePeakTable(peakTable, 'door3_tube2_peaks')
- # calibrating tubes 3_3,3_2,3_1
- CalibratedComponent = ['MERLIN/door3/tube_3_%d'%(i) for i in [1,2,3]]
- doorpos = knownPositions[[0,1,2,3,5,6,7,8]]
- doorfunc = funcForm[[0,1,2,3,5,6,7,8]]
+ # calibrating tubes 3_3,3_2,3_1
+ CalibratedComponent = ['MERLIN/door3/tube_3_%d' % (i) for i in [1, 2, 3]]
+ doorpos = knownPositions[[0, 1, 2, 3, 5, 6, 7, 8]]
+ doorfunc = funcForm[[0, 1, 2, 3, 5, 6, 7, 8]]
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, doorpos,
doorfunc,
- outputPeak = True,
- calibTable = calibrationTable,
- margin = 30)
+ outputPeak=True,
+ calibTable=calibrationTable,
+ margin=30)
analisePeakTable(peakTable, 'door3_123_peaks')
- # calibrating others inside door3
- # 5_8, 5_7, 5_6, 5_5, 5_4, 5_3, 5_2, 5_1, 4_8, 4_7, 4_6, 4_5, 4_4, 4_3, 4_2, 4_1, 3_8, 3_7, 3_6, 3_5, 3_4
- part_3 = ['MERLIN/door3/tube_3_%d'%(i) for i in [4,5,6,7,8]]
- part_4 = ['MERLIN/door3/tube_4_%d'%(i) for i in range(1,9)]
- part_5 = ['MERLIN/door3/tube_5_%d'%(i) for i in range(1,9)]
+ # calibrating others inside door3
+ # 5_8, 5_7, 5_6, 5_5, 5_4, 5_3, 5_2, 5_1, 4_8, 4_7, 4_6, 4_5, 4_4, 4_3, 4_2, 4_1, 3_8, 3_7, 3_6, 3_5, 3_4
+ part_3 = ['MERLIN/door3/tube_3_%d' % (i) for i in [4, 5, 6, 7, 8]]
+ part_4 = ['MERLIN/door3/tube_4_%d' % (i) for i in range(1, 9)]
+ part_5 = ['MERLIN/door3/tube_5_%d' % (i) for i in range(1, 9)]
CalibratedComponent = part_3 + part_4 + part_5
doorpos = knownPositions
doorfunc = funcForm
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, doorpos,
doorfunc,
- outputPeak = True,
- calibTable = calibrationTable,
- margin = 30)
+ outputPeak=True,
+ calibTable=calibrationTable,
+ margin=30)
analisePeakTable(peakTable, 'door3_peaks')
- # == Apply the Calibation ==
- ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
- print "Applied calibration"
+ # == Apply the Calibation ==
+ mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
+ print("Applied calibration")
- # == Save workspace ==
- #SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoMerlinResult.nxs',"Result of Running TCDemoMerlin.py")
- #print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMerlinResult.nxs"
+ # == Save workspace ==
+ # SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoMerlinResult.nxs',"Result of Running TCDemoMerlin.py")
+ # print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMerlinResult.nxs"
-if __name__=="__main__":
- filename = 'MER12024.raw' # Calibration run ( found in \\isis\inst$\NDXMERLIN\Instrument\data\cycle_11_5 )
+if __name__ == "__main__":
+ filename = 'MER12024.raw' # Calibration run ( found in \\isis\inst$\NDXMERLIN\Instrument\data\cycle_11_5 )
calibrateMerlin(filename)
diff --git a/scripts/Calibration/Examples/TubeCalibDemoMerlin_Simple.py b/scripts/Calibration/Examples/TubeCalibDemoMerlin_Simple.py
index 6631ad1169c75cc3846a009923f2968e2d8c9e16..a7ab13a619276a9dca00095ef3c81543cdf7ccb2 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoMerlin_Simple.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoMerlin_Simple.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
#
# TUBE CALIBRATION DEMONSTRATION PROGRAM FOR MERLIN
#
@@ -15,40 +15,42 @@
import tube
from tube_calib_fit_params import TubeCalibFitParams
import numpy
+import mantid.simpleapi as mantid
RunNumber = 12024
def CalibrateMerlin(RunNumber):
# == Set parameters for calibration ==
- previousDefaultInstrument = config['default.instrument']
- config['default.instrument']="MERLIN"
- filename = str(RunNumber) # Name of calibration run.
- rangeLower = 3000 # Integrate counts in each spectra from rangeLower to rangeUpper
- rangeUpper = 20000 #
+ previousDefaultInstrument = mantid.config['default.instrument']
+ mantid.config['default.instrument'] = "MERLIN"
+ filename = str(RunNumber) # Name of calibration run.
+ rangeLower = 3000 # Integrate counts in each spectra from rangeLower to rangeUpper
+ rangeUpper = 20000 #
# Set parameters for ideal tube.
- Left = 2.0 # Where the left end of tube should be in pixels (target for AP)
- Centre = 512.5 # Where the centre of the tube should be in pixels (target for CP)
- Right = 1023.0 # Where the right of the tube should be in pixels (target for BP)
- ActiveLength = 2.9 # Active length of tube in Metres
+ Left = 2.0 # Where the left end of tube should be in pixels (target for AP)
+ Centre = 512.5 # Where the centre of the tube should be in pixels (target for CP)
+ Right = 1023.0 # Where the right of the tube should be in pixels (target for BP)
+ ActiveLength = 2.9 # Active length of tube in Metres
# Set initial parameters for peak finding
- ExpectedHeight = 1000.0 # Expected Height of Gaussian Peaks (initial value of fit parameter)
- ExpectedWidth = 32.0 # Expected width of centre peak in Pixels (initial value of fit parameter)
- ExpectedPositions = [35.0, 512.0, 989.0] # Expected positions of the edges and peak in pixels (initial values of fit parameters)
+ ExpectedHeight = 1000.0 # Expected Height of Gaussian Peaks (initial value of fit parameter)
+ ExpectedWidth = 32.0 # Expected width of centre peak in Pixels (initial value of fit parameter)
+ ExpectedPositions = [35.0, 512.0,
+ 989.0] # Expected positions of the edges and peak in pixels (initial values of fit parameters)
# Set what we want to calibrate (e.g whole intrument or one door )
CalibratedComponent = 'MERLIN' # Calibrate door 2
# Get calibration raw file and integrate it
- print filename
- rawCalibInstWS = LoadRaw(filename)
+ print(filename)
+ rawCalibInstWS = mantid.LoadRaw(filename)
# 'raw' in 'rawCalibInstWS' means unintegrated.
- print "Integrating Workspace"
- CalibInstWS = Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
- DeleteWorkspace(rawCalibInstWS)
- print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+ print("Integrating Workspace")
+ CalibInstWS = mantid.Integration(rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper)
+ mantid.DeleteWorkspace(rawCalibInstWS)
+ print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
# == Create Objects needed for calibration ==
@@ -60,31 +62,32 @@ def CalibrateMerlin(RunNumber):
##
## for merlin: npixels = 1024
- knownPos = ActiveLength * (numpy.array([Left, Centre, Right])/1024.0 - 0.5)
- funcForm = 3*[1]
+ knownPos = ActiveLength * (numpy.array([Left, Centre, Right]) / 1024.0 - 0.5)
+ funcForm = 3 * [1]
# Get fitting parameters
- fitPar = TubeCalibFitParams( ExpectedPositions, ExpectedHeight, ExpectedWidth, margin=40)
+ fitPar = TubeCalibFitParams(ExpectedPositions, ExpectedHeight, ExpectedWidth, margin=40)
- print "Created objects needed for calibration."
+ print("Created objects needed for calibration.")
# == Get the calibration and put results into calibration table ==
# also put peaks into PeakFile
- calibrationTable,peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcForm,
- outputPeak=True, fitPar=fitPar, plotTube=range(0,280,20))
- print "Got calibration (new positions of detectors) and put slit peaks into file TubeDemoMerlin01.txt"
+ calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcForm,
+ outputPeak=True, fitPar=fitPar, plotTube=list(range(0, 280, 20)))
+ print("Got calibration (new positions of detectors) and put slit peaks into file TubeDemoMerlin01.txt")
# == Apply the Calibation ==
- ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
- print "Applied calibration"
+ mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
+ print("Applied calibration")
# == Save workspace ==
- #SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoMerlinResult.nxs',"Result of Running TubeCalibDemoMerlin_Simple.py")
- #print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMerlinResult.nxs"
+ # SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoMerlinResult.nxs',"Result of Running TubeCalibDemoMerlin_Simple.py")
+ # print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMerlinResult.nxs"
# == Reset dafault instrument ==
- config['default.instrument'] = previousDefaultInstrument
+ mantid.config['default.instrument'] = previousDefaultInstrument
# ==== End of CalibrateMerlin() ====
-CalibrateMerlin( RunNumber )
+
+CalibrateMerlin(RunNumber)
diff --git a/scripts/Calibration/Examples/TubeCalibDemoWish0.py b/scripts/Calibration/Examples/TubeCalibDemoWish0.py
index 515be0cd67a9932d8d2c07b9a36f355557953f38..79607d0f2ef11682b7b37bfb48047625aa47676a 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoWish0.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoWish0.py
@@ -10,24 +10,26 @@
# WISH instrument.
#
import tube
+import mantid.simpleapi as mantid
+
filename = 'WISH00017701.raw' # Calibration run ( found in \\isis\inst$\NDXWISH\Instrument\data\cycle_11_1 )
-rawCalibInstWS = Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
-CalibInstWS = Integration( rawCalibInstWS, RangeLower=1, RangeUpper=20000 )
-DeleteWorkspace(rawCalibInstWS)
-print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+rawCalibInstWS = mantid.Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
+CalibInstWS = mantid.Integration( rawCalibInstWS, RangeLower=1, RangeUpper=20000 )
+mantid.DeleteWorkspace(rawCalibInstWS)
+print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
CalibratedComponent = 'WISH/panel03'
knownPos = [-0.41,-0.31,-0.21,-0.11,-0.02, 0.09, 0.18, 0.28, 0.39 ]
funcForm = 9*[1] # all special points are gaussian peaks
-print "Created objects needed for calibration."
+print("Created objects needed for calibration.")
# Get the calibration and put it into the calibration table
calibrationTable = tube.calibrate(CalibInstWS, CalibratedComponent,
knownPos, funcForm)
-print "Got calibration (new positions of detectors)"
+print("Got calibration (new positions of detectors)")
#Apply the calibration
-ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
-print "Applied calibration"
+mantid.ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+print("Applied calibration")
diff --git a/scripts/Calibration/Examples/TubeCalibDemoWish1.py b/scripts/Calibration/Examples/TubeCalibDemoWish1.py
index b56785e2f74c98966d21e3c465bb5134cd6b3b34..43185f51137ac67585e055973984b3c35af8c81a 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoWish1.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoWish1.py
@@ -10,12 +10,13 @@ reload(tube) # noqa
from tube_spec import TubeSpec
import tube_calib #from tube_calib import constructIdealTubeFromRealTube
from tube_calib_fit_params import TubeCalibFitParams
+import mantid.simpleapi as mantid
filename = 'WISH00017701.raw' # Calibration run ( found in \\isis\inst$\NDXWISH\Instrument\data\cycle_11_1 )
-rawCalibInstWS = Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
-CalibInstWS = Integration( rawCalibInstWS, RangeLower=1, RangeUpper=20000 )
-DeleteWorkspace(rawCalibInstWS)
-print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+rawCalibInstWS = mantid.Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
+CalibInstWS = mantid.Integration( rawCalibInstWS, RangeLower=1, RangeUpper=20000 )
+mantid.DeleteWorkspace(rawCalibInstWS)
+print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
CalibratedComponent = 'WISH/panel03/tube038'
@@ -25,7 +26,7 @@ ExpectedHeight = 2000.0 # Expected Height of Gaussian Peaks (initial value of fi
ExpectedWidth = 32.0 # Expected width of Gaussian peaks in pixels (initial value of fit parameter)
fitPar = TubeCalibFitParams( eP, ExpectedHeight, ExpectedWidth )
fitPar.setAutomatic(True)
-print "Created objects needed for calibration."
+print("Created objects needed for calibration.")
func_form = 9*[1]
# Use first tube as ideal tube
@@ -34,12 +35,12 @@ tube1.setTubeSpecByString('WISH/panel03/tube038')
iTube = tube_calib.constructIdealTubeFromRealTube( CalibInstWS, tube1, fitPar, func_form)
known_pos = iTube.getArray()
-print known_pos
+print(known_pos)
# Get the calibration and put it into the calibration table
calibrationTable = tube.calibrate( CalibInstWS, 'WISH/panel03', known_pos, func_form, fitPar=fitPar)
-print "Got calibration (new positions of detectors)"
+print("Got calibration (new positions of detectors)")
#Apply the calibration
-ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
-print "Applied calibration"
+mantid.ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+print("Applied calibration")
diff --git a/scripts/Calibration/Examples/TubeCalibDemoWish_5panels.py b/scripts/Calibration/Examples/TubeCalibDemoWish_5panels.py
index 93594265bf16c22c96292744245b849fd2c1574b..ce40f500fa8628115d0378736d5dbdfabb66117e 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoWish_5panels.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoWish_5panels.py
@@ -12,7 +12,7 @@ to calibrate the whole instrument.
"""
import numpy
-from mantid.simpleapi import *
+import mantid.simpleapi as mantid
import tube
from tube_spec import TubeSpec
@@ -25,28 +25,28 @@ def CalibrateWish(run_per_panel_list):
run_per_panel_list = [ (17706, 'panel01'), (17705, 'panel02'), (17701, 'panel03'), (17702, 'panel04'), (17695, 'panel05')]
'''
# == Set parameters for calibration ==
- previousDefaultInstrument = config['default.instrument']
- config['default.instrument']="WISH"
+ previousDefaultInstrument = mantid.config['default.instrument']
+ mantid.config['default.instrument']="WISH"
# definition of the parameters static for the calibration
lower_tube = numpy.array([-0.41,-0.31,-0.21,-0.11,-0.02, 0.09, 0.18, 0.28, 0.39 ])
upper_tube = numpy.array(lower_tube+0.003)
funcForm = 9*[1] # 9 gaussian peaks
margin = 15
- low_range = range(0,76)
- high_range = range(76,152)
+ low_range = list(range(0,76))
+ high_range = list(range(76,152))
kwargs = {'margin':margin}
# it will copy all the data from the runs to have a single instrument with the calibrated data.
- whole_instrument = LoadRaw(str(run_per_panel_list[0][0]))
- whole_instrument = Integration(whole_instrument)
+ whole_instrument = mantid.LoadRaw(str(run_per_panel_list[0][0]))
+ whole_instrument = mantid.Integration(whole_instrument)
for (run_number, panel_name) in run_per_panel_list:
panel_name = str(panel_name)
run_number = str(run_number)
# load your data and integrate it
- ws = LoadRaw(run_number, OutputWorkspace=panel_name)
- ws = Integration(ws, 1, 20000, OutputWorkspace=panel_name)
+ ws = mantid.LoadRaw(run_number, OutputWorkspace=panel_name)
+ ws = mantid.Integration(ws, 1, 20000, OutputWorkspace=panel_name)
# use the TubeSpec object to be able to copy the data to the whole_instrument
tube_set = TubeSpec(ws)
@@ -63,7 +63,7 @@ def CalibrateWish(run_per_panel_list):
calibrationTable = tube.calibrate(ws, tube_set, upper_tube, funcForm, **kwargs)
kwargs['calibTable'] = calibrationTable
- ApplyCalibration(ws, calibrationTable)
+ mantid.ApplyCalibration(ws, calibrationTable)
# copy data from the current panel to the whole_instrument
for i in range(tube_set.getNumTubes()):
@@ -72,9 +72,9 @@ def CalibrateWish(run_per_panel_list):
# calibrate the whole_instrument with the last calibrated panel which has the calibration accumulation
# of all the others
- CopyInstrumentParameters(run_per_panel_list[-1][1],whole_instrument)
+ mantid.CopyInstrumentParameters(run_per_panel_list[-1][1],whole_instrument)
- config['default.instrument'] = previousDefaultInstrument
+ mantid.config['default.instrument'] = previousDefaultInstrument
# ==== End of CalibrateWish() ====
diff --git a/scripts/Calibration/Examples/TubeCalibDemoWish_Simple.py b/scripts/Calibration/Examples/TubeCalibDemoWish_Simple.py
index f3cfb7e655f795744f1dd645f5241166ceaa6592..48bda575fbeb7af16024f262a1846a6e68e953cd 100644
--- a/scripts/Calibration/Examples/TubeCalibDemoWish_Simple.py
+++ b/scripts/Calibration/Examples/TubeCalibDemoWish_Simple.py
@@ -1,4 +1,4 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
#
# TUBE CALIBRATION DEMONSTRATION PROGRAM FOR WISH
#
@@ -6,67 +6,70 @@
#
import numpy
import tube
-from mantid.simpleapi import *
+import mantid.simpleapi as mantid
-def CalibrateWish( RunNumber, PanelNumber):
+def CalibrateWish(RunNumber, PanelNumber):
'''
:param RunNumber: is the run number of the calibration.
:param PanelNumber: is a string of two-digit number of the panel being calibrated
'''
# == Set parameters for calibration ==
- previousDefaultInstrument = config['default.instrument']
- config['default.instrument']="WISH"
+ previousDefaultInstrument = mantid.config['default.instrument']
+ mantid.config['default.instrument'] = "WISH"
filename = str(RunNumber)
- CalibratedComponent = 'WISH/panel'+PanelNumber
+ CalibratedComponent = 'WISH/panel' + PanelNumber
# Get calibration raw file and integrate it
- print "Loading",filename
- rawCalibInstWS = Load(filename) #'raw' in 'rawCalibInstWS' means unintegrated.
- CalibInstWS = Integration( rawCalibInstWS, RangeLower=1, RangeUpper=20000 )
- DeleteWorkspace(rawCalibInstWS)
- print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
+ print("Loading", filename)
+ rawCalibInstWS = mantid.Load(filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
+ CalibInstWS = mantid.Integration(rawCalibInstWS, RangeLower=1, RangeUpper=20000)
+ mantid.DeleteWorkspace(rawCalibInstWS)
+ print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
# Give y-positions of slit points (gotten for converting first tube's slit point to Y)
# WISH instrument has a particularity. It is composed by a group of upper tubes and lower tubes,
# they are disposed 3 milimiters in difference one among the other
- lower_tube = numpy.array([-0.41,-0.31,-0.21,-0.11,-0.02, 0.09, 0.18, 0.28, 0.39 ])
- upper_tube = numpy.array(lower_tube+0.003)
- funcForm = 9*[1] # 9 gaussian peaks
- print "Created objects needed for calibration."
+ lower_tube = numpy.array([-0.41, -0.31, -0.21, -0.11, -0.02, 0.09, 0.18, 0.28, 0.39])
+ upper_tube = numpy.array(lower_tube + 0.003)
+ funcForm = 9 * [1] # 9 gaussian peaks
+ print("Created objects needed for calibration.")
# Get the calibration and put it into the calibration table
- #calibrate the lower tubes
+ # calibrate the lower tubes
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, lower_tube, funcForm,
- rangeList = range(0,76), outputPeak=True)
+ rangeList=list(range(0, 76)), outputPeak=True)
- #calibrate the upper tubes
+ # calibrate the upper tubes
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, upper_tube, funcForm,
- rangeList = range(76,152),
- calibTable=calibrationTable,#give the calibration table to append data
- outputPeak = peakTable#give peak table to append data
+ rangeList=list(range(76, 152)),
+ calibTable=calibrationTable,
+ # give the calibration table to append data
+ outputPeak=peakTable # give peak table to append data
)
- print "Got calibration (new positions of detectors)"
+ print("Got calibration (new positions of detectors)")
- #Apply the calibration
- ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
- print "Applied calibration"
+ # Apply the calibration
+ mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
+ print("Applied calibration")
# == Save workspace ==
- #uncomment these lines to save the workspace
- #nexusName = "TubeCalibDemoWish"+PanelNumber+"Result.nxs"
- #SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoWishResult.nxs',"Result of Running TubeCalibWishMerlin_Simple.py")
- #print "saved calibrated workspace (CalibInstWS) into Nexus file",nexusName
+ # uncomment these lines to save the workspace
+ # nexusName = "TubeCalibDemoWish"+PanelNumber+"Result.nxs"
+ # SaveNexusProcessed( CalibInstWS, 'TubeCalibDemoWishResult.nxs',"Result of Running TubeCalibWishMerlin_Simple.py")
+ # print "saved calibrated workspace (CalibInstWS) into Nexus file",nexusName
# == Reset dafault instrument ==
- config['default.instrument'] = previousDefaultInstrument
+ mantid.config['default.instrument'] = previousDefaultInstrument
# ==== End of CalibrateWish() ====
+
+
if __name__ == "__main__":
- # this file is found on cycle_11_1
+ # this file is found on cycle_11_1
RunNumber = 17701
PanelNumber = '03'
CalibrateWish(RunNumber, PanelNumber)
diff --git a/scripts/DiamondAttenuationCorrection/FitTrans.py b/scripts/DiamondAttenuationCorrection/FitTrans.py
index e18aeebdae721a3b435c6f046bc4b3b1968f57f2..c10e68ac4b57422cbf3f18ab50608d2604807075 100644
--- a/scripts/DiamondAttenuationCorrection/FitTrans.py
+++ b/scripts/DiamondAttenuationCorrection/FitTrans.py
@@ -59,8 +59,8 @@ def calcDspacing(a, b, c, alp, bet, gam, h, k, l):
sb = np.sin(np.radians(bet))
sg = np.sin(np.radians(gam))
- oneoverdsq = (1.0 - ca**2 - cb**2 - cg**2 + 2 * ca * cb * cg)**(-1) * \
- ((h * sa / a)**2 + (k * sb / b)**2 + (l * sg / c)**2
+ oneoverdsq = (1.0 - ca ** 2 - cb ** 2 - cg ** 2 + 2 * ca * cb * cg) ** (-1) * \
+ ((h * sa / a) ** 2 + (k * sb / b) ** 2 + (l * sg / c) ** 2
+ (2 * k * l / (b * c)) * (cb * cg - ca) + (2 * l * h / (c * a)) * (cg * ca - cb)
+ (2 * h * k / (a * b)) * (ca * cb - cg))
@@ -121,22 +121,22 @@ def forbidden(h, k, l):
result = 0
# condition 1
- if ((h != 0)and (k != 0) and (l != 0)): # general hkl
+ if ((h != 0) and (k != 0) and (l != 0)): # general hkl
term1 = h + k
term2 = h + l # all have to be even
term3 = k + l
- if not((term1 % 2) == 0 and (term2 % 2) == 0 and (term3 % 2) == 0):
+ if not ((term1 % 2) == 0 and (term2 % 2) == 0 and (term3 % 2) == 0):
result = 1
boolresult = bool(result)
return boolresult
else:
result = 0
- #% condition 2
+ # % condition 2
if ((h == 0) and (k != 0) and (l != 0)): # 0kl reflections
term1 = k + l
mod4 = mod(term1, 4)
- if not(mod4 == 0 and mod(k, 2) == 0 and mod(l, 2) == 0):
+ if not (mod4 == 0 and mod(k, 2) == 0 and mod(l, 2) == 0):
result = 1
boolresult = bool(result)
return boolresult
@@ -145,7 +145,7 @@ def forbidden(h, k, l):
# condition 3
if (h == k): # hhl reflections
- if not(mod(h + l, 2) == 0):
+ if not (mod(h + l, 2) == 0):
result = 1
boolresult = bool(result)
return boolresult
@@ -153,9 +153,9 @@ def forbidden(h, k, l):
result = 0
# condition 4
- if ((h == 0) and (k == 0) and (l != 0)): # 00l reflections not including 000
+ if ((h == 0) and (k == 0) and (l != 0)): # 00l reflections not including 000
mod4 = mod(l, 4)
- if not(mod4 == 0):
+ if not (mod4 == 0):
result = 1
boolresult = bool(result)
return boolresult
@@ -191,7 +191,7 @@ def allowedDiamRefs(hmin, hmax, kmin, kmax, lmin, lmax):
# create new array with all h!=0 k!=0 l!=0
hkl = np.zeros(shape=(0, 3))
for i in range(n):
- if not(allhkl[i][0] == 0 and allhkl[i][1] == 0 and allhkl[i][2] == 0):
+ if not (allhkl[i][0] == 0 and allhkl[i][1] == 0 and allhkl[i][2] == 0):
hkl = np.vstack((hkl, [allhkl[i][0], allhkl[i][1], allhkl[i][2]]))
d.append(calcDspacing(3.56683, 3.56683, 3.56683, 90,
90, 90, hkl[k][0], hkl[k][1], hkl[k][2]))
@@ -224,7 +224,7 @@ def getISAWub(fullfilename):
'''
fileID = fullfilename
if fileID == 1:
- print('Error opening file: ' + fullfilename)
+ print(('Error opening file: ' + fullfilename))
f = open(fileID, "r")
lines = f.readlines()
f.close()
@@ -236,7 +236,9 @@ def getISAWub(fullfilename):
UB[i][0], UB[i][1], UB[i][2] = lines[i].split()
UB = UB.transpose()
for i in range(3, 5):
- lattice[i - 3][0], lattice[i - 3][1], lattice[i - 3][2], lattice[i - 3][3], lattice[i - 3][4], lattice[i - 3][5], \
+ lattice[i - 3][0], lattice[i - 3][1], \
+ lattice[i - 3][2], lattice[i - 3][3], \
+ lattice[i - 3][4], lattice[i - 3][5], \
non = lines[i].split()
print('Successfully got UB and lattice')
@@ -260,93 +262,93 @@ def pkintread(hkl, loc):
returns pkint = np. array - 1D vector
'''
- #A = np.genfromtxt('diamond_reflist.csv', delimiter=',', skip_header=True)
+ # A = np.genfromtxt('diamond_reflist.csv', delimiter=',', skip_header=True)
# print A
- A = np.array([[1.00000000e+00, 1.00000000e+00, 1.00000000e+00, 8.00000000e+00,
- 2.06110000e+00, 5.54000000e+04],
- [2.00000000e+00, 2.00000000e+00, 0.00000000e+00, 1.20000000e+01,
- 1.26220000e+00, 7.52000000e+04],
- [3.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 1.07640000e+00, 2.98000000e+04],
- [2.00000000e+00, 2.00000000e+00, 2.00000000e+00, 8.00000000e+00,
- 1.03060000e+00, 2.50000000e-25],
- [4.00000000e+00, 0.00000000e+00, 0.00000000e+00, 6.00000000e+00,
- 8.92500000e-01, 4.05000000e+04],
- [3.00000000e+00, 3.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 8.19000000e-01, 1.61000000e+04],
- [4.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
- 7.28700000e-01, 2.18000000e+04],
- [5.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 6.87000000e-01, 8.64000000e+03],
- [3.00000000e+00, 3.00000000e+00, 3.00000000e+00, 8.00000000e+00,
- 6.87000000e-01, 8.64000000e+03],
- [4.00000000e+00, 4.00000000e+00, 0.00000000e+00, 1.20000000e+01,
- 6.31100000e-01, 1.17000000e+04],
- [5.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
- 6.03400000e-01, 4.65000000e+03],
- [4.00000000e+00, 4.00000000e+00, 2.00000000e+00, 2.40000000e+01,
- 5.95000000e-01, 1.83000000e-12],
- [6.00000000e+00, 2.00000000e+00, 0.00000000e+00, 2.40000000e+01,
- 5.64500000e-01, 6.31000000e+03],
- [5.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
- 5.44400000e-01, 2.50000000e+03],
- [6.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
- 5.38200000e-01, 8.80000000e-26],
- [4.00000000e+00, 4.00000000e+00, 4.00000000e+00, 8.00000000e+00,
- 5.15300000e-01, 3.40000000e+03],
- [5.00000000e+00, 5.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 4.99900000e-01, 1.35000000e+03],
- [7.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 4.99900000e-01, 1.35000000e+03],
- [6.00000000e+00, 4.00000000e+00, 2.00000000e+00, 4.80000000e+01,
- 4.77100000e-01, 1.83000000e+03],
- [7.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
- 4.64800000e-01, 7.25000000e+02],
- [5.00000000e+00, 5.00000000e+00, 3.00000000e+00, 2.40000000e+01,
- 4.64800000e-01, 7.25000000e+02],
- [8.00000000e+00, 0.00000000e+00, 0.00000000e+00, 6.00000000e+00,
- 4.46200000e-01, 9.84000000e+02],
- [7.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
- 4.36100000e-01, 3.90000000e+02],
- [6.00000000e+00, 4.00000000e+00, 4.00000000e+00, 2.40000000e+01,
- 4.32900000e-01, 1.53000000e-13],
- [6.00000000e+00, 6.00000000e+00, 0.00000000e+00, 1.20000000e+01,
- 4.20700000e-01, 5.30000000e+02],
- [8.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
- 4.20700000e-01, 5.30000000e+02],
- [5.00000000e+00, 5.00000000e+00, 5.00000000e+00, 8.00000000e+00,
- 4.12200000e-01, 2.10000000e+02],
- [7.00000000e+00, 5.00000000e+00, 1.00000000e+00, 4.80000000e+01,
- 4.12200000e-01, 2.10000000e+02],
- [6.00000000e+00, 6.00000000e+00, 2.00000000e+00, 2.40000000e+01,
- 4.09500000e-01, 1.98000000e-26],
- [8.00000000e+00, 4.00000000e+00, 0.00000000e+00, 2.40000000e+01,
- 3.99100000e-01, 2.85000000e+02],
- [7.00000000e+00, 5.00000000e+00, 3.00000000e+00, 4.80000000e+01,
- 3.91900000e-01, 1.13000000e+02],
- [9.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 3.91900000e-01, 1.13000000e+02],
- [8.00000000e+00, 4.00000000e+00, 2.00000000e+00, 4.80000000e+01,
- 3.89500000e-01, 4.44000000e-14],
- [6.00000000e+00, 6.00000000e+00, 4.00000000e+00, 2.40000000e+01,
- 3.80600000e-01, 1.53000000e+02],
- [9.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
- 3.74200000e-01, 6.08000000e+01],
- [8.00000000e+00, 4.00000000e+00, 4.00000000e+00, 2.40000000e+01,
- 3.64400000e-01, 8.26000000e+01],
- [9.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
- 3.58800000e-01, 3.27000000e+01],
- [7.00000000e+00, 5.00000000e+00, 5.00000000e+00, 2.40000000e+01,
- 3.58800000e-01, 3.27000000e+01],
- [7.00000000e+00, 7.00000000e+00, 1.00000000e+00, 2.40000000e+01,
- 3.58800000e-01, 3.27000000e+01]])
+ A = np.array([[1.00000000e+00, 1.00000000e+00, 1.00000000e+00, 8.00000000e+00,
+ 2.06110000e+00, 5.54000000e+04],
+ [2.00000000e+00, 2.00000000e+00, 0.00000000e+00, 1.20000000e+01,
+ 1.26220000e+00, 7.52000000e+04],
+ [3.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 1.07640000e+00, 2.98000000e+04],
+ [2.00000000e+00, 2.00000000e+00, 2.00000000e+00, 8.00000000e+00,
+ 1.03060000e+00, 2.50000000e-25],
+ [4.00000000e+00, 0.00000000e+00, 0.00000000e+00, 6.00000000e+00,
+ 8.92500000e-01, 4.05000000e+04],
+ [3.00000000e+00, 3.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 8.19000000e-01, 1.61000000e+04],
+ [4.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
+ 7.28700000e-01, 2.18000000e+04],
+ [5.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 6.87000000e-01, 8.64000000e+03],
+ [3.00000000e+00, 3.00000000e+00, 3.00000000e+00, 8.00000000e+00,
+ 6.87000000e-01, 8.64000000e+03],
+ [4.00000000e+00, 4.00000000e+00, 0.00000000e+00, 1.20000000e+01,
+ 6.31100000e-01, 1.17000000e+04],
+ [5.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
+ 6.03400000e-01, 4.65000000e+03],
+ [4.00000000e+00, 4.00000000e+00, 2.00000000e+00, 2.40000000e+01,
+ 5.95000000e-01, 1.83000000e-12],
+ [6.00000000e+00, 2.00000000e+00, 0.00000000e+00, 2.40000000e+01,
+ 5.64500000e-01, 6.31000000e+03],
+ [5.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
+ 5.44400000e-01, 2.50000000e+03],
+ [6.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
+ 5.38200000e-01, 8.80000000e-26],
+ [4.00000000e+00, 4.00000000e+00, 4.00000000e+00, 8.00000000e+00,
+ 5.15300000e-01, 3.40000000e+03],
+ [5.00000000e+00, 5.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 4.99900000e-01, 1.35000000e+03],
+ [7.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 4.99900000e-01, 1.35000000e+03],
+ [6.00000000e+00, 4.00000000e+00, 2.00000000e+00, 4.80000000e+01,
+ 4.77100000e-01, 1.83000000e+03],
+ [7.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
+ 4.64800000e-01, 7.25000000e+02],
+ [5.00000000e+00, 5.00000000e+00, 3.00000000e+00, 2.40000000e+01,
+ 4.64800000e-01, 7.25000000e+02],
+ [8.00000000e+00, 0.00000000e+00, 0.00000000e+00, 6.00000000e+00,
+ 4.46200000e-01, 9.84000000e+02],
+ [7.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
+ 4.36100000e-01, 3.90000000e+02],
+ [6.00000000e+00, 4.00000000e+00, 4.00000000e+00, 2.40000000e+01,
+ 4.32900000e-01, 1.53000000e-13],
+ [6.00000000e+00, 6.00000000e+00, 0.00000000e+00, 1.20000000e+01,
+ 4.20700000e-01, 5.30000000e+02],
+ [8.00000000e+00, 2.00000000e+00, 2.00000000e+00, 2.40000000e+01,
+ 4.20700000e-01, 5.30000000e+02],
+ [5.00000000e+00, 5.00000000e+00, 5.00000000e+00, 8.00000000e+00,
+ 4.12200000e-01, 2.10000000e+02],
+ [7.00000000e+00, 5.00000000e+00, 1.00000000e+00, 4.80000000e+01,
+ 4.12200000e-01, 2.10000000e+02],
+ [6.00000000e+00, 6.00000000e+00, 2.00000000e+00, 2.40000000e+01,
+ 4.09500000e-01, 1.98000000e-26],
+ [8.00000000e+00, 4.00000000e+00, 0.00000000e+00, 2.40000000e+01,
+ 3.99100000e-01, 2.85000000e+02],
+ [7.00000000e+00, 5.00000000e+00, 3.00000000e+00, 4.80000000e+01,
+ 3.91900000e-01, 1.13000000e+02],
+ [9.00000000e+00, 1.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 3.91900000e-01, 1.13000000e+02],
+ [8.00000000e+00, 4.00000000e+00, 2.00000000e+00, 4.80000000e+01,
+ 3.89500000e-01, 4.44000000e-14],
+ [6.00000000e+00, 6.00000000e+00, 4.00000000e+00, 2.40000000e+01,
+ 3.80600000e-01, 1.53000000e+02],
+ [9.00000000e+00, 3.00000000e+00, 1.00000000e+00, 4.80000000e+01,
+ 3.74200000e-01, 6.08000000e+01],
+ [8.00000000e+00, 4.00000000e+00, 4.00000000e+00, 2.40000000e+01,
+ 3.64400000e-01, 8.26000000e+01],
+ [9.00000000e+00, 3.00000000e+00, 3.00000000e+00, 2.40000000e+01,
+ 3.58800000e-01, 3.27000000e+01],
+ [7.00000000e+00, 5.00000000e+00, 5.00000000e+00, 2.40000000e+01,
+ 3.58800000e-01, 3.27000000e+01],
+ [7.00000000e+00, 7.00000000e+00, 1.00000000e+00, 2.40000000e+01,
+ 3.58800000e-01, 3.27000000e+01]])
diamd = A[:, 4]
- #diamMult = A[:, 3] # unused variable
+ # diamMult = A[:, 3] # unused variable
diamFCalcSq = A[:, 5]
nref = hkl.shape[0]
- #% disp(['there are: ' num2str(nref) ' reflections']);
- #% whos loc
+ # % disp(['there are: ' num2str(nref) ' reflections']);
+ # % whos loc
'''
% [i,j] = size(x);
@@ -363,10 +365,10 @@ def pkintread(hkl, loc):
for i in range(nref):
if loc[i][0] > 0:
- #% satisfies Bragg condition (otherwise ignore)
+ # % satisfies Bragg condition (otherwise ignore)
Fsq = Fsqcalc(loc[i][1], diamd, diamFCalcSq)
- #% Fsq = 1;
- L = (np.sin(np.radians(loc[i][2] / 2.0)))**2 # Lorentz correction
+ # % Fsq = 1;
+ L = (np.sin(np.radians(loc[i][2] / 2.0))) ** 2 # Lorentz correction
R = 1.0 # %dipLam(i)^4; %reflectivity correction
A = 1.0 # %Absorption correction
Ecor = 1
@@ -393,7 +395,7 @@ def Fsqcalc(d, diamd, diamFCalcSq):
% global sf111 sf220 sf311 sf400 sf331
'''
- #n = len(diamd) # unused variable
+ # n = len(diamd) # unused variable
ref = d
dif = abs(diamd - ref)
i = dif.argmin(0) # i is index of diamd closest to d
@@ -496,7 +498,7 @@ def getMANTIDdat_keepbinning(csvfile):
y = []
e = []
if fid < 0:
- print('Error opening file: ' + csvfile)
+ print(('Error opening file: ' + csvfile))
for i in range(1, len(lines)):
a, b, c = lines[i].split(",")
x.append(float(a))
@@ -534,7 +536,7 @@ def findeqvs(hkl):
nperm = len(permcomphkl)
for k in range(nperm):
if refhkl[0] == permcomphkl[k][0] and refhkl[1] == permcomphkl[k][1] and \
- refhkl[2] == permcomphkl[k][2]:
+ refhkl[2] == permcomphkl[k][2]:
eqvlab[j] = lab
lab += 1
@@ -558,8 +560,8 @@ def showx3(x):
global neqv1, eqvlab1, neqv2, eqvlab2
global difa, function_verbose
- #nref1 = hkl1.shape[0] # % number of reflections to integrate over # unused variable
- #nref2 = hkl2.shape[0] # % number of reflections to integrate over # unused variable
+ # nref1 = hkl1.shape[0] # % number of reflections to integrate over # unused variable
+ # nref2 = hkl2.shape[0] # % number of reflections to integrate over # unused variable
# % returns array with same dim as input labelling equivs
eqvlab1, neqv1 = findeqvs(hkl1)
eqvlab2, neqv2 = findeqvs(hkl2)
@@ -569,7 +571,7 @@ def showx3(x):
pkmult2 = x[6 + neqv1:7 + neqv1 + neqv2 - 1]
sf = x[neqv1 + neqv2 + 7 - 1]
pkwid1 = x[neqv1 + neqv2 + 8 - 1]
- #bgd = x[neqv1 + neqv2 + 8 - 1:neqv1 + neqv2 + 9 + 2 - 1] # unused variable
+ # bgd = x[neqv1 + neqv2 + 8 - 1:neqv1 + neqv2 + 9 + 2 - 1] # unused variable
pkwid2 = x[neqv1 + neqv2 + 10]
# % if diamond intensities the same, allow single scale f
relsf = x[neqv1 + neqv2 + 11]
@@ -577,18 +579,18 @@ def showx3(x):
L2 = x[neqv1 + neqv2 + 13]
print('_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/\n')
- print('Setting angles diam {0} : \nalp {1} bet {2} gam {3} \n'.format(
- 1, setang1[0], setang1[1], setang1[2]))
- print('pkmult1: {0}\n'.format(pkmult1))
- print('Setting angles diam {0} : \nalp {1} bet {2} gam {3} \n'.format(
- 2, setang2[0], setang2[1], setang2[2]))
- print('pkmult2: {0}\n'.format(pkmult2))
- print('Scale factor: {0}\n'.format(sf))
- print('pkwid1: {0}\n'.format(pkwid1))
- print('pkwid2: {0}\n'.format(pkwid2))
- print('Rel. scale factor : {0}\n'.format(relsf))
- print('Lambda multiplier: {0}\n'.format(delam))
- print('L2 sample to detector: {0} m\n'.format(L2))
+ print(('Setting angles diam {0} : \nalp {1} bet {2} gam {3} \n'.format(
+ 1, setang1[0], setang1[1], setang1[2])))
+ print(('pkmult1: {0}\n'.format(pkmult1)))
+ print(('Setting angles diam {0} : \nalp {1} bet {2} gam {3} \n'.format(
+ 2, setang2[0], setang2[1], setang2[2])))
+ print(('pkmult2: {0}\n'.format(pkmult2)))
+ print(('Scale factor: {0}\n'.format(sf)))
+ print(('pkwid1: {0}\n'.format(pkwid1)))
+ print(('pkwid2: {0}\n'.format(pkwid2)))
+ print(('Rel. scale factor : {0}\n'.format(relsf)))
+ print(('Lambda multiplier: {0}\n'.format(delam)))
+ print(('L2 sample to detector: {0} m\n'.format(L2)))
print('_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/\n')
@@ -646,7 +648,7 @@ def SimTransOutput3(name, x):
delam = x[neqv1 + neqv2 + 12]
L2 = x[neqv1 + neqv2 + 13]
- shftlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF**2)
+ shftlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF ** 2)
# number of lambda points to calculate over
npt = shftlam.shape[0]
# calculate information for peaks for crystal 1 using hkl,UB1, setang,
@@ -672,47 +674,45 @@ def SimTransOutput3(name, x):
# calculate background profile by multiplying this with coefficients
# themselves
bgdprof = nonzerobgd.dot(X)
- #bgdprof = np.outer(nonzerobgd, X)
+ # bgdprof = np.outer(nonzerobgd, X)
# print bgdprof
- #bgdprof = bgdprof[0, :]
+ # bgdprof = bgdprof[0, :]
# calculate peaks for crystal 1
t1 = np.zeros(npt) # initialise array containing profile
for i in range(nref1):
if pktype == 1:
pkpars1[i][0] = pkpars1[i][0] * delam # linear lambda shift
- sig = pkwid1 * pkpars1[i][0] + pkwid2 * \
- (pkpars1[i][0]**2.) # const del(lambda)/lambda
- extScl = pkpars1[i][0]**0 # lambda dependent extinction effect
+ sig = pkwid1 * pkpars1[i][0] + pkwid2 * (pkpars1[i][0] ** 2.) # const del(lambda)/lambda
+ extScl = pkpars1[i][0] ** 0 # lambda dependent extinction effect
t1 = t1 - extScl * pkmult1[int(eqvlab1[i])] * pkcalcint1[i] * (
- np.exp(-((shftlam - pkpars1[i][0])**2.) / (2 * (sig**2))))
+ np.exp(-((shftlam - pkpars1[i][0]) ** 2.) / (2 * (sig ** 2))))
# calculate peaks for crystal 2
t2 = np.zeros(npt) # initialise array containing profile
for i in range(nref2):
if pktype == 1:
pkpars2[i][0] = pkpars2[i][0] * delam # linear lambda shift
- sig = pkwid1 * pkpars2[i][0] + pkwid2 * \
- (pkpars2[i][0]**2.) # const del(lambda)/lambda
- extScl = pkpars2[i][0]**0 # lambda dependent extinction effect
+ sig = pkwid1 * pkpars2[i][0] + pkwid2 * (pkpars2[i][0] ** 2.) # const del(lambda)/lambda
+ extScl = pkpars2[i][0] ** 0 # lambda dependent extinction effect
t2 = t2 - extScl * pkmult2[int(eqvlab2[i])] * pkcalcint2[i] * (
- np.exp(-(shftlam - pkpars2[i][0])**2. / (2 * (sig**2))))
+ np.exp(-(shftlam - pkpars2[i][0]) ** 2. / (2 * (sig ** 2))))
# calculate final profile
ttot = (bgdprof + sf * t1) * (bgdprof + sf * t2)
- #t1 = 1.0;
+ # t1 = 1.0;
# t2 = 1.0;
# introduce weighting function and calc chi2...
w = np.ones(len(shftlam)) # equal weighting everywhere
- #i1 = np.where(shftlam > 2.15)[0][0]
- #j1 = np.where(shftlam > 2.65)[0][0]
+ # i1 = np.where(shftlam > 2.15)[0][0]
+ # j1 = np.where(shftlam > 2.65)[0][0]
# w[i1:j1] = 5 #extra weighting in region of first peaks
# i1 = find(lam>1.68,1,'first');
# j1 = find(lam>2.05,1,'first');
# w(i1:j1)=5; %extra weighting but not too much
resid = (y - ttot) * w
- chi2 = np.sum(resid**2. / (2 * e**2)) / npt
+ chi2 = np.sum(resid ** 2. / (2 * e ** 2)) / npt
output = 1
if output == 1:
@@ -810,7 +810,7 @@ def SimTrans3(x):
delam = x[neqv1 + neqv2 + 12]
L2 = x[neqv1 + neqv2 + 13]
- shftlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF**2)
+ shftlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF ** 2)
# number of lambda points to calculate over
npt = shftlam.shape[0]
# calculate information for peaks for crystal 1 using hkl,UB1, setang,
@@ -836,51 +836,49 @@ def SimTrans3(x):
# calculate background profile by multiplying this with coefficients
# themselves
bgdprof = nonzerobgd.dot(X)
- #bgdprof = np.outer(nonzerobgd, X)
+ # bgdprof = np.outer(nonzerobgd, X)
# print bgdprof
- #bgdprof = bgdprof[0, :]
+ # bgdprof = bgdprof[0, :]
# calculate peaks for crystal 1
t1 = np.zeros(npt) # initialise array containing profile
for i in range(nref1):
if pktype == 1:
pkpars1[i][0] = pkpars1[i][0] * delam # linear lambda shift
- sig = pkwid1 * pkpars1[i][0] + pkwid2 * \
- (pkpars1[i][0]**2.) # const del(lambda)/lambda
- extScl = pkpars1[i][0]**0 # lambda dependent extinction effect
+ sig = pkwid1 * pkpars1[i][0] + pkwid2 * (pkpars1[i][0] ** 2.) # const del(lambda)/lambda
+ extScl = pkpars1[i][0] ** 0 # lambda dependent extinction effect
t1 = t1 - extScl * pkmult1[int(eqvlab1[i])] * pkcalcint1[i] * (
- np.exp(-((shftlam - pkpars1[i][0])**2.) / (2 * (sig**2))))
+ np.exp(-((shftlam - pkpars1[i][0]) ** 2.) / (2 * (sig ** 2))))
# calculate peaks for crystal 2
t2 = np.zeros(npt) # initialise array containing profile
for i in range(nref2):
if pktype == 1:
pkpars2[i][0] = pkpars2[i][0] * delam # linear lambda shift
- sig = pkwid1 * pkpars2[i][0] + pkwid2 * \
- (pkpars2[i][0]**2.) # const del(lambda)/lambda
- extScl = pkpars2[i][0]**0 # lambda dependent extinction effect
+ sig = pkwid1 * pkpars2[i][0] + pkwid2 * (pkpars2[i][0] ** 2.) # const del(lambda)/lambda
+ extScl = pkpars2[i][0] ** 0 # lambda dependent extinction effect
t2 = t2 - extScl * pkmult2[int(eqvlab2[i])] * pkcalcint2[i] * (
- np.exp(-(shftlam - pkpars2[i][0])**2. / (2 * (sig**2))))
+ np.exp(-(shftlam - pkpars2[i][0]) ** 2. / (2 * (sig ** 2))))
# calculate final profile
ttot = (bgdprof + sf * t1) * (bgdprof + sf * t2)
- #t1 = 1.0;
+ # t1 = 1.0;
# t2 = 1.0;
# introduce weighting function and calc chi2...
w = np.ones(len(shftlam)) # equal weighting everywhere
- #i1 = np.where(shftlam > 2.15)[0][0]
- #j1 = np.where(shftlam > 2.65)[0][0]
+ # i1 = np.where(shftlam > 2.15)[0][0]
+ # j1 = np.where(shftlam > 2.65)[0][0]
# w[i1:j1] = 5 #extra weighting in region of first peaks
# i1 = find(lam>1.68,1,'first');
# j1 = find(lam>2.05,1,'first');
# w(i1:j1)=5; %extra weighting but not too much
resid = (y - ttot) * w
- chi2 = np.sum(resid**2. / (2 * e**2)) / npt
+ chi2 = np.sum(resid ** 2. / (2 * e ** 2)) / npt
# Print if the user wants verbose minimization
if function_verbose == 'y':
- print('Chi^2 ... ' + str(chi2))
+ print(('Chi^2 ... ' + str(chi2)))
return chi2
@@ -921,10 +919,10 @@ def FitTrans():
print('*diamonds allowed to have different dip intensities!*')
if cnstang == 1:
- print(
- '*Diam {0} setting angles constrained to range of +/- {1} about their current values*'.format(1, anglim1))
- print(
- '*Diam {0} setting angles constrained to range of +/- {1} about their current values*'.format(2, anglim2))
+ print((
+ '*Diam {0} setting angles constrained to range of +/- {1} about their current values*'.format(1, anglim1)))
+ print((
+ '*Diam {0} setting angles constrained to range of +/- {1} about their current values*'.format(2, anglim2)))
else:
print('no constraint on setting angles')
@@ -932,13 +930,13 @@ def FitTrans():
print('*intensity multipliers fixed*')
# Get Input Files...
- peaks_file = str(raw_input('Name of file containing diamond peaks: '))
+ peaks_file = str(input('Name of file containing diamond peaks: '))
- run_number = str(raw_input('Input run number for transmission data: '))
+ run_number = str(input('Input run number for transmission data: '))
# Build input filenames
- #fullfilename_ub1 = str(run_number) + 'UB1.dat' # unused variable
- #fullfilename_ub2 = str(run_number) + 'UB2.dat' # unused variable
+ # fullfilename_ub1 = str(run_number) + 'UB1.dat' # unused variable
+ # fullfilename_ub2 = str(run_number) + 'UB2.dat' # unused variable
fullfilename_trans = 'transNorm' + str(run_number) + '.dat'
# get both UB's
@@ -948,13 +946,13 @@ def FitTrans():
# uigetfile('*.dat','Choose UB matrix for upstream diamond:');
# fullfilename = [pathname filename];
# fullfilename_ub1 = 'snap13108UB1.dat'
- #UB1, remainder = getISAWub(fullfilename_ub1)
+ # UB1, remainder = getISAWub(fullfilename_ub1)
# [filename pathname ~] = ...
# uigetfile('*.dat','Choose UB matrix for downstream diamond:');
# fullfilename = [pathname filename];
# fullfilename_ub2 = 'snap13108UB2.dat'
- #UB2, remainder = getISAWub(fullfilename_ub2)
+ # UB2, remainder = getISAWub(fullfilename_ub2)
# get transmission data...
# [filename,pathname,~] = ...
@@ -963,7 +961,7 @@ def FitTrans():
fullfilename_trans = 'transNorm13148.csv'
TOF, yin, ein = getMANTIDdat_keepbinning(fullfilename_trans)
- print('Starting refinement for: ' + fullfilename_trans)
+ print(('Starting refinement for: ' + fullfilename_trans))
# set-up simulation
@@ -982,8 +980,8 @@ def FitTrans():
# rebin transmission data
lam = 0.0039558 * TOF / (L1 + initL2)
- print('wavelength limits: ' +
- str(lam[0]) + ' and ' + str(lam[len(lam) - 1]))
+ print(('wavelength limits: ' +
+ str(lam[0]) + ' and ' + str(lam[len(lam) - 1])))
minlam = 0.8
maxlam = 3.5
imin = np.where(lam >= minlam)[0][0]
@@ -1009,7 +1007,7 @@ def FitTrans():
# initial conditions for crystal 2
setang2 = np.zeros(3)
- #setang2[1:3][0] = 0.0
+ # setang2[1:3][0] = 0.0
a, b, c = pkposcalc(allhkl, UB2, setang2)
pkpars2 = np.column_stack((a, b, c))
@@ -1034,8 +1032,8 @@ def FitTrans():
hkl2 = np.vstack([hkl2, allhkl[i]])
k2 += 1
- print('There are: ' + str(k1) + ' expected dips due to Crystal 1')
- print('There are: ' + str(k2) + ' expected dips due to Crystal 2')
+ print(('There are: ' + str(k1) + ' expected dips due to Crystal 1'))
+ print(('There are: ' + str(k2) + ' expected dips due to Crystal 2'))
# determine equivalents
# returns array with same dim as input labelling equivs
@@ -1058,7 +1056,7 @@ def FitTrans():
pkcalcint2 *= 1e-6
pkmult2 = np.ones(neqv2) # peak intensity multiplier
- relsf = 1.0 # default value
+ relsf = 1.0 # default value
delam = 1.0
L2 = initL2
tbgd = bgd
@@ -1066,38 +1064,37 @@ def FitTrans():
# Either generate, or read variable array from file
# This is one big array with all the parameters to be refined in it.
- prevf = str(raw_input('Look for pars from a previous run ([y]/n)? '))
+ prevf = str(input('Look for pars from a previous run ([y]/n)? '))
if prevf == 'n':
x0 = np.hstack((setang1, pkmult1, setang2, pkmult2, sf,
pkwid, tbgd, pkwid2, relsf, delam, L2))
else:
- # choose which file to use
- parfilename = str(raw_input('Choose file with starting pars: '))
+ # choose which file to use
+ parfilename = str(input('Choose file with starting pars: '))
parfullfilename = parfilename
x0 = dlmread(parfullfilename)
- tog = str(raw_input('Got parameters from: \n' +
- parfilename + '\nUse these ([y]/n)?'))
+ tog = str(input('Got parameters from: \n' +
+ parfilename + '\nUse these ([y]/n)?'))
if tog == 'n':
x0 = np.hstack((setang1, pkmult1, setang2, pkmult2,
sf, pkwid, tbgd, pkwid2, relsf, delam, L2))
print('discarding pars from previous run')
- print(str(len(x0)) + ' parameters will be refined')
+ print((str(len(x0)) + ' parameters will be refined'))
nvar = len(x0)
- print('number of variables: ' + str(nvar))
- #nref1 = hkl1.shape[0] # unused variable
- #nref2 = hkl2.shape[0] # unused variable
+ print(('number of variables: ' + str(nvar)))
+ # nref1 = hkl1.shape[0] # unused variable
+ # nref2 = hkl2.shape[0] # unused variable
# need to apply correction in the case that pars from previous run had
# fxsamediam==1 and current run also has fxsamediam==1
# to avoid a double multiplication by relsf
if fxsamediam == 1 and x0[neqv1 + neqv2 + 11] != 1:
- x0[6 + neqv1:7 + neqv1 + neqv2 - 1] = x0[3:4 +
- neqv2 - 1] / x0[neqv1 + neqv2 + 11]
- print('Diam 2 peak multipliers reset: ' + str(x0[neqv1 + neqv2 + 11]))
+ x0[6 + neqv1:7 + neqv1 + neqv2 - 1] = x0[3:4 + neqv2 - 1] / x0[neqv1 + neqv2 + 11]
+ print(('Diam 2 peak multipliers reset: ' + str(x0[neqv1 + neqv2 + 11])))
# check starting point
@@ -1113,7 +1110,7 @@ def FitTrans():
plt.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3,
ncol=3, mode="expand", borderaxespad=0.)
plt.show()
- print('Initial chi^2 is: ' + str(chi2))
+ print(('Initial chi^2 is: ' + str(chi2)))
showx3(x0)
@@ -1125,7 +1122,7 @@ def FitTrans():
A[3:4 + neqv1 - 1] = -1.0 # pkmult1 Contrains intensities to be positive
A[4 + neqv1 - 1:6 + neqv1] = 0.0 # setang2 *no constraint
A[6 + neqv1:7 + neqv1 + neqv2 - 1] = -1.0 # pkmult2
- A[6 + neqv1 + neqv2] = -1.0 # sf Scale factor must be +ve
+ A[6 + neqv1 + neqv2] = -1.0 # sf Scale factor must be +ve
A[7 + neqv1 + neqv2] = -1.0 # pkwid peak width must be +ve
A[neqv1 + neqv2 + 8:neqv1 + neqv2 + 9 + 2 - 1] = 0.0 # bgd *no constraint
A[(neqv1 + neqv2 + 10)] = 0.0 # *no constraint
@@ -1139,7 +1136,7 @@ def FitTrans():
Aeq[3:4 + neqv1 - 1] = 0.0 # pkmult1
Aeq[4 + neqv1 - 1:6 + neqv1] = 0.0 # setang2
Aeq[6 + neqv1:7 + neqv1 + neqv2 - 1] = 0.0 # pkmult2
- Aeq[6 + neqv1 + neqv2] = 0.0 # sf
+ Aeq[6 + neqv1 + neqv2] = 0.0 # sf
Aeq[7 + neqv1 + neqv2] = 0.0 # pkwid
Aeq[neqv1 + neqv2 + 8:neqv1 + neqv2 + 9 + 2 - 1] = 0 # unfixed bgd
Aeq[neqv1 + neqv2 + 10] = 0
@@ -1147,7 +1144,7 @@ def FitTrans():
Aeq[neqv1 + neqv2 + 12] = 0
Aeq[neqv1 + neqv2 + 13] = 0
- #beq = 0 # unused variable
+ # beq = 0 # unused variable
# lower bounds
lb = np.zeros(len(x0))
@@ -1155,7 +1152,7 @@ def FitTrans():
lb[3:4 + neqv1 - 1] = 0.5 # pkmult1
lb[4 + neqv1 - 1:6 + neqv1] = -10 # setang2
lb[6 + neqv1:7 + neqv1 + neqv2 - 1] = 0.5 # pkmult2
- lb[6 + neqv1 + neqv2] = 0.0 # sf
+ lb[6 + neqv1 + neqv2] = 0.0 # sf
lb[7 + neqv1 + neqv2] = 0.0005 # pkwid
lb[neqv1 + neqv2 + 8:neqv1 + neqv2 + 9 + 2 - 1] = [0.995, -0.0005] # bgd
lb[neqv1 + neqv2 + 10] = 0.5e-4 # 2nd order pkwid
@@ -1170,7 +1167,7 @@ def FitTrans():
ub[3:4 + neqv1 - 1] = 50 # pkmult1
ub[4 + neqv1 - 1:6 + neqv1] = 10 # setang2
ub[6 + neqv1:7 + neqv1 + neqv2 - 1] = 50 # pkmult2
- ub[6 + neqv1 + neqv2] = 50 # sf
+ ub[6 + neqv1 + neqv2] = 50 # sf
ub[7 + neqv1 + neqv2] = 0.01 # pkwid
ub[neqv1 + neqv2 + 8:neqv1 + neqv2 + 9 + 2 - 1] = [1.005, 0.0005] # bgd
ub[neqv1 + neqv2 + 10] = 1.0e-2 # 2nd order pkwid
@@ -1206,12 +1203,12 @@ def FitTrans():
ub[6 + neqv1:7 + neqv1 + neqv2 - 1] = x0[6 +
neqv1:7 + neqv1 + neqv2 - 1] + 0.01
- prompt = str(raw_input('Enter anything to begin refinement...'))
+ prompt = str(input('Enter anything to begin refinement...'))
print('Refining...\nMight take quite a long time...')
max_number_iterations = int(
- raw_input('Maximum number of iterations for minimization: '))
- function_verbose = str(raw_input('Verbose minimization ([y]/n): '))
+ input('Maximum number of iterations for minimization: '))
+ function_verbose = str(input('Verbose minimization ([y]/n): '))
# make dictionary holding constraints for minimization
# equalities (all must equal 0) and inequalities
@@ -1222,8 +1219,8 @@ def FitTrans():
# bounds have to be list of tuples with (lower, upper) for each parameter
bds = np.vstack((lb, ub)).T
- res = sp.minimize(SimTrans3, x0, method='SLSQP', bounds=bds, constraints=cons, options={'disp': True,
- 'maxiter': max_number_iterations})
+ res = sp.minimize(SimTrans3, x0, method='SLSQP', bounds=bds, constraints=cons,
+ options={'disp': True, 'maxiter': max_number_iterations})
# tolerance limits to put in minimization if you want so : 'ftol': 0.001
@@ -1244,10 +1241,8 @@ def FitTrans():
# len(x)
# neqv1+neqv2+11
# x[neqv1+neqv2+11]
- x[6 + neqv1:7 + neqv1 + neqv2 - 1] = x[3:4 +
- neqv2 - 1] * x[neqv1 + neqv2 + 11]
- print('Diam 2 peak multipliers reset with factor: ' +
- str(x[neqv1 + neqv2 + 11]))
+ x[6 + neqv1:7 + neqv1 + neqv2 - 1] = x[3:4 + neqv2 - 1] * x[neqv1 + neqv2 + 11]
+ print(('Diam 2 peak multipliers reset with factor: ' + str(x[neqv1 + neqv2 + 11])))
else:
# label ensuring I know that run did not use fxsamediam
x[neqv1 + neqv2 + 11] = 1.0
@@ -1261,13 +1256,13 @@ def FitTrans():
# calculate chi2 for best fit
chi2 = SimTrans3(x)
- print('Final Chi2 = ' + str(chi2))
+ print(('Final Chi2 = ' + str(chi2)))
# determine output wavelength range using refined L2 value
- #lamscale = x[neqv1 + neqv2 + 12] # unused variable
+ # lamscale = x[neqv1 + neqv2 + 12] # unused variable
L2 = x[neqv1 + neqv2 + 13]
- outlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF**2)
+ outlam = 0.0039558 * TOF / (L1 + L2) + difa * (TOF ** 2)
fig_name_final = 'Final result ' + run_number
plt.figure(fig_name_final)
@@ -1290,15 +1285,16 @@ def FitTrans():
plt.ylabel('Transmission')
plt.show()
- prompt = str(raw_input('output best fit to file ([y]/n): '))
+ prompt = str(input('output best fit to file ([y]/n): '))
if prompt == 'n':
print('Ending')
else:
fitparname = str(run_number) + '.best_fit_pars3.dat'
np.savetxt(fitparname, x, delimiter=',')
- print('output parameters written to file: \n' + fitparname)
+ print(('output parameters written to file: \n' + fitparname))
ofilename = str(run_number) + '.fitted3.dat'
SimTransOutput3(ofilename, x) # generate output file with fitted data
+
if __name__ == "__main__":
FitTrans()
diff --git a/scripts/Examples/HRPDDialog_Example.py b/scripts/Examples/HRPDDialog_Example.py
index e372796edf2c6de4fc69121638f8b7b3ae24c4fc..60f2dd88c7261fc6b126a045899a9e63da632967 100644
--- a/scripts/Examples/HRPDDialog_Example.py
+++ b/scripts/Examples/HRPDDialog_Example.py
@@ -1,10 +1,13 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
# First a function definition for the Loading algorithms which loads the data and immediately aligns the detectors
+import mantid.simpleapi as mantid
def LoadAndAlign(_type, outputArea):
- LoadRawDialog(OutputWorkspace=outputArea, Message = "Enter path to the file containing the " + _type)
- AlignDetectorsDialog(InputWorkspace=outputArea, OutputWorkspace=outputArea,Message="Enter path to calibration file")
+ mantid.LoadRawDialog(OutputWorkspace=outputArea, Message="Enter path to the file containing the " + _type)
+ mantid.AlignDetectorsDialog(InputWorkspace=outputArea, OutputWorkspace=outputArea,
+ Message="Enter path to calibration file")
+
# ========== The script starts here ============
dataWorkspace = "Vanadium"
@@ -12,31 +15,32 @@ LoadAndAlign("data", dataWorkspace)
LoadAndAlign("empty run", "Empty")
# ==== Just want pure Vanadium so subtract the empty instrument ===
-Minus(LHSWorkspace=dataWorkspace,RHSWorkspace="Empty",OutputWorkspace=dataWorkspace)
+mantid.Minus(LHSWorkspace=dataWorkspace, RHSWorkspace="Empty", OutputWorkspace=dataWorkspace)
# Calculate absorption and correct for it
-transWorkspace="Transmission"
-#The input workspace needs to be in units of wavelength for the CylinderAbsorption algorithm
-ConvertUnits(InputWorkspace=dataWorkspace, OutputWorkspace=dataWorkspace, Target="Wavelength")
-CylinderAbsorptionDialog(InputWorkspace=dataWorkspace, OutputWorkspace=transWorkspace,SampleNumberDensity="0.072",
- ScatteringXSection="5.08",AttenuationXSection="5.1",Message="Enter size parameters")
-Divide(dataWorkspace, transWorkspace, OutputWorkspace=dataWorkspace)
+transWorkspace = "Transmission"
+# The input workspace needs to be in units of wavelength for the CylinderAbsorption algorithm
+mantid.ConvertUnits(InputWorkspace=dataWorkspace, OutputWorkspace=dataWorkspace, Target="Wavelength")
+mantid.CylinderAbsorptionDialog(InputWorkspace=dataWorkspace, OutputWorkspace=transWorkspace,
+ SampleNumberDensity="0.072",
+ ScatteringXSection="5.08", AttenuationXSection="5.1", Message="Enter size parameters")
+mantid.Divide(dataWorkspace, transWorkspace, OutputWorkspace=dataWorkspace)
# === Save as a Nexus file ===
-#SaveNexusProcessDialog(InputWorkspace=sampleWorkspace, message="Enter path to save Nexus file")
+# SaveNexusProcessDialog(InputWorkspace=sampleWorkspace, message="Enter path to save Nexus file")
# === Load the sample data file ===
-sampleWorkspace="Sample"
+sampleWorkspace = "Sample"
LoadAndAlign("sample", sampleWorkspace)
# === Focus the data ===
-ConvertUnits(dataWorkspace,dataWorkspace,'dSpacing')
-alg = DiffractionFocussingDialog(InputWorkspace=dataWorkspace,OutputWorkspace=dataWorkspace)
+mantid.ConvertUnits(dataWorkspace, dataWorkspace, 'dSpacing')
+alg = mantid.DiffractionFocussingDialog(InputWorkspace=dataWorkspace, OutputWorkspace=dataWorkspace)
calibFile = alg.getPropertyValue("GroupingFileName")
-StripPeaks(InputWorkspace=dataWorkspace, OutputWorkspace=dataWorkspace)
+mantid.StripPeaks(InputWorkspace=dataWorkspace, OutputWorkspace=dataWorkspace)
# === Focus the sample ===
-DiffractionFocussing(InputWorkspace=sampleWorkspace,OutputWorkspace=sampleWorkspace,GroupingFileName=calibFile)
+mantid.DiffractionFocussing(InputWorkspace=sampleWorkspace, OutputWorkspace=sampleWorkspace, GroupingFileName=calibFile)
# === The result is the sample corrected by the vandium ===
-resultSpace="Result"
-Divide(sampleWorkspace, dataWorkspace, OutputWorkspace=resultSpace)
+resultSpace = "Result"
+mantid.Divide(sampleWorkspace, dataWorkspace, OutputWorkspace=resultSpace)
diff --git a/scripts/Examples/InstrumentView_Example.py b/scripts/Examples/InstrumentView_Example.py
index 91fe8ee0b8b0941faa4c4f3be6c223e7cc668a68..c20e7f4258e42f6522d86cf2fea40d76f1085864 100644
--- a/scripts/Examples/InstrumentView_Example.py
+++ b/scripts/Examples/InstrumentView_Example.py
@@ -1,24 +1,23 @@
-#pylint: disable=invalid-name
-#
# Example: Instrument view control
#
+import mantid.simpleapi as mantid
# Get some data
-LoadRaw("LOQ48094.raw","LOQTest")
+mantid.LoadRaw("LOQ48094.raw", "LOQTest")
-insView = getInstrumentView("LOQTest")
+insView = mantid.getInstrumentView("LOQTest")
-#insView.changeColorMap("../../../repo/installers/colormaps/Jet.map") # Change to the correct path
+# insView.changeColorMap("../../../repo/installers/colormaps/Jet.map") # Change to the correct path
-insView.setColorMapRange(0.,195)
+insView.setColorMapRange(0., 195)
# Or can set a minimum and maximum separately
-#insView.setColorMapMinValue(1.)
-#insView.setColorMapMaxValue(10.)
+# insView.setColorMapMinValue(1.)
+# insView.setColorMapMaxValue(10.)
# Alter the binning range
-insView.setBinRange(10000,15000)
+insView.setBinRange(10000, 15000)
# Select an individual component
-#insView.selectComponent("main-detector-pixel")
+# insView.selectComponent("main-detector-pixel")
insView.show()
diff --git a/scripts/Examples/PlotAsymmetryByLogValue_Example.py b/scripts/Examples/PlotAsymmetryByLogValue_Example.py
index b9ea09ffbcfdcd48bff7eeb336ccf3b581244492..d1c5abd91f684e7fff8a2e473267b3884d645bb1 100644
--- a/scripts/Examples/PlotAsymmetryByLogValue_Example.py
+++ b/scripts/Examples/PlotAsymmetryByLogValue_Example.py
@@ -1,22 +1,23 @@
-#pylint: disable=invalid-name
# -----------------------------------------------------
-# Runs PlotAssymetryByLogValue algorithm
+# Runs PlotAsymmetryByLogValue algorithm
# and plots the output in MantidPlot using a Python
# dictionary
-#------------------------------------------------------
+# ------------------------------------------------------
+import mantid.simpleapi as mantid
+from six import iteritems
# Execute the algorithm
-alg = PlotAsymmetryByLogValueDialog()
+alg = mantid.PlotAsymmetryByLogValueDialog()
# Get the output workspace
ws = alg.getPropertyValue("OutputWorkspace")
-spectra_plot = { 0 : 'Difference' }
+spectra_plot = {0: 'Difference'}
if int(alg.getPropertyValue("Green")) < 1000:
spectra_plot[1] = 'Red'
spectra_plot[2] = 'Green'
spectra_plot[3] = 'Sum'
-gs = plotSpectrum(ws, spectra_plot.keys())
-for key, value in spectra_plot.iteritems():
+gs = mantid.plotSpectrum(ws, spectra_plot.keys())
+for key, value in iteritems(spectra_plot):
gs.activeLayer().setCurveTitle(key, value)
diff --git a/scripts/Examples/SampleLogs_Demo.py b/scripts/Examples/SampleLogs_Demo.py
index b1c54bb46fd4a8c2cee4d733c21012c674cadcb5..c91da1e28b0efd4f42d481571f4bc607c51078f1 100644
--- a/scripts/Examples/SampleLogs_Demo.py
+++ b/scripts/Examples/SampleLogs_Demo.py
@@ -1,24 +1,24 @@
-#pylint: disable=invalid-name
#
# Example: Retrieving log information from a data set
#
+import mantid.simpleapi as mantid
datadir = "../../../repo/Test/Data/"
rawDataTitle="outputSpace"
# Load the crisp data set which we have log information for
-ws = LoadRaw(Filename = datadir+"Full point detector CRISP dataset/csp79590.raw",OutputWorkspace=rawDataTitle)
+ws = mantid.LoadRaw(Filename = datadir+"Full point detector CRISP dataset/csp79590.raw",OutputWorkspace=rawDataTitle)
if isinstance(ws,tuple):
ws = ws[0]
# This is a grouped file so get the first workspace
-rawWS = mtd[ws.getNames()[0]]
+rawWS = mantid.mtd[ws.getNames()[0]]
logs = rawWS.getRun().getLogData()
# Print all of the log information
for i in range(0, len(logs)):
- print "----- " + logs[i].name + " -------\n" + str(logs[i].value)
+ print("----- " + logs[i].name + " -------\n" + str(logs[i].value))
# Just get a single log by name
status = rawWS.getRun().getLogData("status")
-print status.value
+print(status.value)
diff --git a/scripts/Examples/SimpleMtdCommands_Example.py b/scripts/Examples/SimpleMtdCommands_Example.py
index ed5b145a58cd273a2e98c72643054b2df4fe10a7..c4f2bcdded5305173a5e03faa2359a7429bb7d86 100644
--- a/scripts/Examples/SimpleMtdCommands_Example.py
+++ b/scripts/Examples/SimpleMtdCommands_Example.py
@@ -1,25 +1,26 @@
-#pylint: disable=invalid-name
#
# Example: Basic Mantid commands
#
+import mantid.simpleapi as mantid
+
# Print the available algorithms
-mtdHelp()
+mantid.mtdHelp()
# Print information on a specific algorithm
-mtdHelp(LoadRaw)
+mantid.mtdHelp(mantid.LoadRaw)
# Perform some algorithms
-LoadRaw("HET15869.raw", OutputWorkspace="test")
-ConvertUnits("test","dSpacing", OutputWorkspace="converted")
-Rebin("converted","0.1,0.001,5", OutputWorkspace="rebinned")
+mantid.LoadRaw("HET15869.raw", OutputWorkspace="test")
+mantid.ConvertUnits("test", "dSpacing", OutputWorkspace="converted")
+mantid.Rebin("converted", "0.1,0.001,5", OutputWorkspace="rebinned")
# clear up intermediate workspaces
-DeleteWorkspace("test")
-DeleteWorkspace("converted")
+mantid.DeleteWorkspace("test")
+mantid.DeleteWorkspace("converted")
# extract the one we want
-wksp = mtd['rebinned']
+wksp = mantid.mtd['rebinned']
-print "Rebinned workspace has " + str(wksp.getNumberHistograms()) + " histograms"
-print "Spectrum 450's X data size = " + str(len(wksp.readX(450))) + " bin boundaries"
+print("Rebinned workspace has " + str(wksp.getNumberHistograms()) + " histograms")
+print("Spectrum 450's X data size = " + str(len(wksp.readX(450))) + " bin boundaries")
diff --git a/scripts/Examples/SolidAngle_Example.py b/scripts/Examples/SolidAngle_Example.py
index c6b2bc50220d521ecc0f5cbbced38a60bbda959f..90fcc206f82b169e37a76427738f414492c3734b 100644
--- a/scripts/Examples/SolidAngle_Example.py
+++ b/scripts/Examples/SolidAngle_Example.py
@@ -1,4 +1,3 @@
-#pylint: disable=invalid-name
##-------------------------------------------------------------------------
##
## Example: Calculating the solid angle for a spectrum with respect to the
@@ -6,8 +5,11 @@
##
##-------------------------------------------------------------------------
# Prompt for a raw file to load
+import mantid.simpleapi as mantid
+import math
+
rawWSTitle = "RawFile"
-LoadRawDialog(OutputWorkspace=rawWSTitle)
+mantid.LoadRawDialog(OutputWorkspace=rawWSTitle)
# Get the loaded workspace from Mantid
rawData = mantid.getMatrixWorkspace(rawWSTitle)
@@ -26,11 +28,11 @@ r = detector.getDistance(sample)
twoTheta = detector.getTwoTheta(samplePos, beamPos)*180./math.pi
phi = detector.getPhi()
-print 'R = ' + str(r) + ', TwoTheta = ' + str(twoTheta)+ ', Phi = ' + str(phi)
+print('R = ' + str(r) + ', TwoTheta = ' + str(twoTheta)+ ', Phi = ' + str(phi))
# Check if the spectrum is masked out and calculate the result if not
solidAngle = 0.0
if not rawData.spectrumInfo().isMasked(0):
- sAngle = detector.solidAngle(samplePos)
+ solidAngle = detector.solidAngle(samplePos)
-print "The solid angle of the spectrum located at index " + str(wsIndex) + " is: " + str(sAngle) + " steradians"
+print("The solid angle of the spectrum located at index " + str(wsIndex) + " is: " + str(solidAngle) + " steradians")
diff --git a/scripts/Examples/StripPeaks.py b/scripts/Examples/StripPeaks.py
index 32bd47a83b62412f8ace86f974295bf87d16866a..c36cdb76b4469689efea66dde5b772a0a78b85d6 100644
--- a/scripts/Examples/StripPeaks.py
+++ b/scripts/Examples/StripPeaks.py
@@ -1,20 +1,20 @@
-#pylint: disable=invalid-name
# MantidPlot example script
#
# Using StripPeaks + dialog boxes
#
+import mantid.simpleapi as mantid
-LoadRawDialog(OutputWorkspace="GEM40979")
-alg= AlignDetectorsDialog("GEM40979",OutputWorkspace="aligned")
-DeleteWorkspace("GEM40979")
+mantid.LoadRawDialog(OutputWorkspace="GEM40979")
+alg = mantid.AlignDetectorsDialog("GEM40979", OutputWorkspace="aligned")
+mantid.DeleteWorkspace("GEM40979")
calfile = alg.getPropertyValue("CalibrationFile")
-DiffractionFocussing("aligned",calfile,OutputWorkspace="focussed")
-DeleteWorkspace("aligned")
-StripPeaks("focussed",OutputWorkspace="stripped")
+mantid.DiffractionFocussing("aligned", calfile, OutputWorkspace="focussed")
+mantid.DeleteWorkspace("aligned")
+mantid.StripPeaks("focussed", OutputWorkspace="stripped")
# Plot a spectrum from each remaining workspace
-g1 = plotSpectrum(["focussed","stripped"],5)
+g1 = mantid.plotSpectrum(["focussed", "stripped"], 5)
# Rescale the x-axis to show an interesting region
-g1.activeLayer().setScale(Layer.Bottom,0,2.3)
-print "Done!"
+g1.activeLayer().setScale(Layer.Bottom, 0, 2.3)
+print("Done!")
diff --git a/scripts/Examples/TableWorkspace_Example.py b/scripts/Examples/TableWorkspace_Example.py
index 8c79a9dcb0f585933ad6ed249d72e1736c97dc56..aab4b55aad0073004438752a30082696ce0d2c4e 100644
--- a/scripts/Examples/TableWorkspace_Example.py
+++ b/scripts/Examples/TableWorkspace_Example.py
@@ -1,20 +1,21 @@
-#pylint: disable=invalid-name
# Perform some algorithms
-LoadRaw(Filename="GEM40979.raw",OutputWorkspace="GEM40979")
-AlignDetectors("GEM40979",OutputWorkspace="aligned",CalibrationFile="offsets_2006_cycle064.cal")
-DeleteWorkspace("GEM40979")
-DiffractionFocussing("aligned","offsets_2006_cycle064.cal",OutputWorkspace="focussed")
-DeleteWorkspace("aligned")
-FindPeaks("focussed",PeaksList="peakslist")
+import mantid.simpleapi as mantid
-peaks = mtd["peakslist"]
+mantid.LoadRaw(Filename="GEM40979.raw", OutputWorkspace="GEM40979")
+mantid.AlignDetectors("GEM40979", OutputWorkspace="aligned", CalibrationFile="offsets_2006_cycle064.cal")
+mantid.DeleteWorkspace("GEM40979")
+mantid.DiffractionFocussing("aligned", "offsets_2006_cycle064.cal", OutputWorkspace="focussed")
+mantid.DeleteWorkspace("aligned")
+mantid.FindPeaks("focussed", PeaksList="peakslist")
+
+peaks = mantid.mtd["peakslist"]
help(peaks)
-print "Number of Columns: " + str(peaks.columnCount()) + " , Number of rows: "+ str(peaks.rowCount())
+print("Number of Columns: " + str(peaks.columnCount()) + " , Number of rows: " + str(peaks.rowCount()))
colNames = peaks.getColumnNames()
for i in colNames:
- print i
+ print(i)
for i in range(peaks.rowCount()):
row = peaks.row(i)
- print "Spectrum %d has peak at pos %f" % (row['spectrum'], row['centre'])
+ print("Spectrum %d has peak at pos %f" % (row['spectrum'], row['centre']))
diff --git a/scripts/HFIRPowderReduction/HfirPDReductionControl.py b/scripts/HFIRPowderReduction/HfirPDReductionControl.py
index be3b265ba0fa1198bfed47c7c783c0df216493f9..e826905c598351da8115edb8f4b9f314c8d72ab0 100644
--- a/scripts/HFIRPowderReduction/HfirPDReductionControl.py
+++ b/scripts/HFIRPowderReduction/HfirPDReductionControl.py
@@ -1,4 +1,4 @@
-#pylint: disable=too-many-lines,relative-import,invalid-name,too-many-instance-attributes,too-many-arguments
+# pylint: disable=too-many-lines,relative-import,invalid-name,too-many-instance-attributes,too-many-arguments
############################################################################
#
# HFIR powder reduction control class
@@ -6,21 +6,24 @@
#
############################################################################
import os
-import urllib2
+import urllib.request
+import urllib.error
+import urllib.parse
import math
import numpy
-import HfirUtility as hutil
+from . import HfirUtility as hutil
# Import mantid
import mantid.simpleapi as api
from mantid.simpleapi import AnalysisDataService
-#from mantid.kernel import ConfigService
+# from mantid.kernel import ConfigService
-VanadiumPeakPositions = [0.5044,0.5191,0.5350,0.5526,0.5936,0.6178,0.6453,0.6768,
- 0.7134,0.7566,0.8089,0.8737,0.9571,1.0701,1.2356,1.5133,2.1401]
+
+VanadiumPeakPositions = [0.5044, 0.5191, 0.5350, 0.5526, 0.5936, 0.6178, 0.6453, 0.6768,
+ 0.7134, 0.7566, 0.8089, 0.8737, 0.9571, 1.0701, 1.2356, 1.5133, 2.1401]
class PDRManager(object):
@@ -54,8 +57,8 @@ class PDRManager(object):
self._wavelength = None
- #register startup
- mantid.UsageService.registerFeatureUsage("Interface","HfirPowderReduction",False)
+ # register startup
+ api.UsageService.registerFeatureUsage("Interface", "HfirPowderReduction", False)
return
@@ -88,11 +91,11 @@ class PDRManager(object):
# Sum and average
numpts = self._rawSpiceTableWS.rowCount()
totalcounts = 0
- for irow in xrange(numpts):
+ for irow in range(numpts):
moncounts = self._rawSpiceTableWS.cell(irow, imonitor)
totalcounts += moncounts
- return float(totalcounts)/float(numpts)
+ return float(totalcounts) / float(numpts)
def getProcessedVanadiumWS(self):
"""
@@ -141,7 +144,7 @@ class PDRManager(object):
try:
self.binsize = float(binsize)
except TypeError as e:
- print e
+ print(e)
return
@@ -149,7 +152,7 @@ class PDRManager(object):
""" Set 2 raw SPICE workspaces
"""
# Validate
- if spice_table_ws.id() != 'TableWorkspace' or log_matrix_ws.id() != 'Workspace2D':
+ if spice_table_ws.id() != 'TableWorkspace' or log_matrix_ws.id() != 'Workspace2D':
raise NotImplementedError("Input workspaces for setRawWorkspaces() are not of correct types.")
self._rawSpiceTableWS = spice_table_ws
@@ -213,7 +216,8 @@ class PDRManager(object):
return
-#pylint: disable=too-many-public-methods
+
+# pylint: disable=too-many-public-methods
class HFIRPDRedControl(object):
@@ -224,8 +228,8 @@ class HFIRPDRedControl(object):
""" Initialization
"""
self._myWorkspaceDict = {} # dictionary to manage all the workspaces reduced
- # key = Exp/Scan
- self._myMergedWSDict = {} # key = Exp/Scan list
+ # key = Exp/Scan
+ self._myMergedWSDict = {} # key = Exp/Scan list
self._myWavelengthDict = {}
@@ -238,7 +242,7 @@ class HFIRPDRedControl(object):
"""
if ((expno, scanno) in self._myWorkspaceDict) is False:
raise NotImplementedError("Exp %d Scan %d does not have reduced \
- workspace." % (exp, scan))
+ workspace." % (expno, scanno))
else:
rmanager = self._myWorkspaceDict[(expno, scanno)]
rmanager.applySmoothVanadium(applysmooth)
@@ -276,18 +280,18 @@ class HFIRPDRedControl(object):
# FUTURE: use **args
if xlabel is None:
tempoutws = \
- api.GetSpiceDataRawCountsFromMD(InputWorkspace=datamdws,
- MonitorWorkspace=monitormdws,
- Mode='Detector',
- DetectorID = detid,
- NormalizeByMonitorCounts=normalized)
+ api.GetSpiceDataRawCountsFromMD(InputWorkspace=datamdws,
+ MonitorWorkspace=monitormdws,
+ Mode='Detector',
+ DetectorID=detid,
+ NormalizeByMonitorCounts=normalized)
else:
- print "Plot detector %d's counts vs. sample log %s."%(detid, xlabel)
+ print("Plot detector %d's counts vs. sample log %s." % (detid, xlabel))
tempoutws = \
api.GetSpiceDataRawCountsFromMD(InputWorkspace=datamdws,
MonitorWorkspace=monitormdws,
Mode='Detector',
- DetectorID = detid,
+ DetectorID=detid,
XLabel=xlabel,
NormalizeByMonitorCounts=normalized)
@@ -326,7 +330,7 @@ class HFIRPDRedControl(object):
tempoutws = api.GetSpiceDataRawCountsFromMD(InputWorkspace=datamdws,
MonitorWorkspace=monitormdws,
Mode='Pt.',
- Pt = ptno)
+ Pt=ptno)
vecx = tempoutws.readX(0)[:]
vecy = tempoutws.readY(0)[:]
@@ -343,7 +347,7 @@ class HFIRPDRedControl(object):
# check
if ((expno, scanno) in self._myWorkspaceDict) is False:
raise NotImplementedError("Exp %d Scan %d does not have reduced \
- workspace." % (exp, scan))
+ workspace." % (expno, scanno))
# get data
rmanager = self._myWorkspaceDict[(expno, scanno)]
@@ -382,7 +386,7 @@ class HFIRPDRedControl(object):
# ptnolist = self._getRunNumberList(datamdws=rmanager.datamdws)
# get data
- print "[DB] Plot sample log: XLabel = %s" % (xlabel)
+ print("[DB] Plot sample log: XLabel = %s" % (xlabel))
tempoutws = api.GetSpiceDataRawCountsFromMD(InputWorkspace=datamdws,
MonitorWorkspace=monitormdws,
Mode='Sample Log',
@@ -424,7 +428,7 @@ class HFIRPDRedControl(object):
procVanWs = wsmanager.getProcessedVanadiumWSTemp()
else:
procVanWs = wsmanager.getProcessedVanadiumWS()
- #procVanWs = wsmanager._processedVanWS
+ # procVanWs = wsmanager._processedVanWS
if procVanWs is None:
raise NotImplementedError("Exp %d Scan %d does not have processed vanadium workspace." % (exp, scan))
@@ -470,7 +474,7 @@ class HFIRPDRedControl(object):
wsmanager = self.getWorkspace(exp, scan, raiseexception=True)
if wsmanager.datamdws is None:
self._logError("Unable to rebin the data for exp=%d, scan=%d because either data MD workspace and \
- monitor MD workspace is not present." % (exp, scan))
+ monitor MD workspace is not present." % (exp, scan))
return False
wavelength = wsmanager.getWavelength()
@@ -478,12 +482,12 @@ class HFIRPDRedControl(object):
# Convert the vanadium peaks' position from dSpacing to 2theta
vanpeakpos2theta = []
for peakpos in VanadiumPeakPositions:
- lambda_over_2d = wavelength/2./peakpos
+ lambda_over_2d = wavelength / 2. / peakpos
if abs(lambda_over_2d) <= 1.:
- twotheta = math.asin(lambda_over_2d)*2.*180/math.pi
+ twotheta = math.asin(lambda_over_2d) * 2. * 180 / math.pi
vanpeakpos2theta.append(twotheta)
else:
- print "Vanadium peak %f is out of d-Spacing range." % (peakpos)
+ print("Vanadium peak %f is out of d-Spacing range." % (peakpos))
vanpeakpos2theta = sorted(vanpeakpos2theta)
wsmanager.setVanadiumPeaks(vanpeakpos2theta)
@@ -535,7 +539,7 @@ class HFIRPDRedControl(object):
""" Check whether an Exp/Scan has a reduced workspace
"""
if ((exp, scan) in self._myWorkspaceDict) is False:
- print self._myWorkspaceDict.keys()
+ print(list(self._myWorkspaceDict.keys()))
return False
if self._myWorkspaceDict[(exp, scan)].reducedws is None:
@@ -554,12 +558,12 @@ class HFIRPDRedControl(object):
# load SPICE
tablewsname = basewsname + "_RawTable"
- infowsname = basewsname + "ExpInfo"
+ infowsname = basewsname + "ExpInfo"
api.LoadSpiceAscii(Filename=datafilename,
OutputWorkspace=tablewsname, RunInfoWorkspace=infowsname)
tablews = AnalysisDataService.retrieve(tablewsname)
- infows = AnalysisDataService.retrieve(infowsname)
+ infows = AnalysisDataService.retrieve(infowsname)
if tablews is None or infows is None:
raise NotImplementedError('Unable to retrieve either spice table workspace %s or log workspace %s' % (
tablewsname, infowsname))
@@ -581,7 +585,7 @@ class HFIRPDRedControl(object):
monitormdwslist = []
self._lastWkspToMerge = []
- print "[Checkpoint 0] Scans = ", str(scannolist)
+ print("[Checkpoint 0] Scans = ", str(scannolist))
for scanno in sorted(scannolist):
try:
wsmanager = self.getWorkspace(expno, scanno, True)
@@ -589,21 +593,21 @@ class HFIRPDRedControl(object):
monitormdwslist.append(wsmanager.monitormdws)
self._lastWkspToMerge.append(wsmanager)
except KeyError as ne:
- print '[Error] Unable to retrieve MDWorkspaces for Exp %d Scan %d due to %s.' % (
- expno, scanno, str(ne))
+ print('[Error] Unable to retrieve MDWorkspaces for Exp %d Scan %d due to %s.' % (
+ expno, scanno, str(ne)))
scannolist.remove(scanno)
# ENDFOR
- print "[Checkpoing 1] Scans = ", str(scannolist)
+ print("[Checkpoing 1] Scans = ", str(scannolist))
# Merge and binning
if len(datamdwslist) > 1:
- mg_datamdws = datamdwslist[0] + datamdwslist[1]
+ mg_datamdws = datamdwslist[0] + datamdwslist[1]
mg_monitormdws = monitormdwslist[0] + monitormdwslist[1]
else:
mg_datamdws = datamdwslist[0]
mg_monitormdws = monitormdwslist[0]
- for iw in xrange(2, len(datamdwslist)):
+ for iw in range(2, len(datamdwslist)):
mg_datamdws += datamdwslist[iw]
mg_monitormdws += monitormdwslist[iw]
@@ -659,7 +663,8 @@ class HFIRPDRedControl(object):
if instrument.upper() == 'HB2A':
excldetlist, errmsg = hutil.parseDetExclusionFile(excldetfname)
else:
- raise NotImplementedError('Instrument %s is not supported for parsing excluded detectors file.'%(instrument))
+ raise NotImplementedError(
+ 'Instrument %s is not supported for parsing excluded detectors file.' % (instrument))
return excldetlist, errmsg
@@ -668,13 +673,13 @@ class HFIRPDRedControl(object):
"""
# Get reduction manager
try:
- wsmanager = self._myWorkspaceDict[ (int(expno), int(scanno) )]
+ wsmanager = self._myWorkspaceDict[(int(expno), int(scanno))]
except KeyError:
- raise NotImplementedError("Exp %d Scan %d has not been loaded yet." % (int(expno),int(scanno)))
+ raise NotImplementedError("Exp %d Scan %d has not been loaded yet." % (int(expno), int(scanno)))
# Convert to MDWorkspace
tablews = wsmanager.getRawSpiceTable()
- infows = wsmanager.getRawInfoMatrixWS()
+ infows = wsmanager.getRawInfoMatrixWS()
basewsname = tablews.name().split('_RawTable')[0]
datamdwsname = basewsname + "_DataMD"
@@ -718,7 +723,7 @@ class HFIRPDRedControl(object):
wsmanager = self._myWorkspaceDict[(exp, scan)]
except ValueError:
# type error, return with false
- return False, 'Scan number %s is not integer.'%(str(scan))
+ return False, 'Scan number %s is not integer.' % (str(scan))
except KeyError:
# data has not been reduced yet. Reduce dat
self.reduceSpicePDData(exp, scan, unit='2theta',
@@ -731,7 +736,7 @@ class HFIRPDRedControl(object):
self.reduceSpicePDData(exp, scan, unit='2theta', xmin=min_x, xmax=max_x, binsize=bin_size)
monitorcounts = wsmanager.getAverageMonitorCounts()
- print '[DB] Exp %d Scan %d: average monitor counts = %.5f' % (exp, scan, monitorcounts)
+ print('[DB] Exp %d Scan %d: average monitor counts = %.5f' % (exp, scan, monitorcounts))
# FUTURE: implement method ws_manager.reset_to_normalized() instead
wsmanager.reducedws = wsmanager.reducedws / monitorcounts
# END_FOR(scan)
@@ -758,7 +763,7 @@ class HFIRPDRedControl(object):
wsmanager = self._myWorkspaceDict[(exp, scan)]
except ValueError:
# type error, return with false
- return False, 'Scan number %s is not integer.'%(str(scan))
+ return False, 'Scan number %s is not integer.' % (str(scan))
except KeyError:
# data has not been reduced yet. Reduce dat
self.reduceSpicePDData(exp, scan, unit='2theta',
@@ -771,14 +776,14 @@ class HFIRPDRedControl(object):
self.reduceSpicePDData(exp, scan, unit='2theta', xmin=min_x, xmax=max_x, binsize=bin_size)
monitorcounts = wsmanager.getAverageMonitorCounts()
- print '[DB] Exp %d Scan %d: average monitor counts = %.5f' % (exp, scan, monitorcounts)
+ print('[DB] Exp %d Scan %d: average monitor counts = %.5f' % (exp, scan, monitorcounts))
wsmanager.reducedws = wsmanager.reducedws * monitorcounts
# END_FOR(scan)
return True, ''
def reduceSpicePDData(self, exp, scan, unit, xmin, xmax, binsize, wavelength=None,
- excludeddetlist=None,scalefactor=None):
+ excludeddetlist=None, scalefactor=None):
""" Reduce SPICE powder diffraction data from MDEventWorkspaces
Return - Boolean as reduction is successful or not
"""
@@ -804,14 +809,14 @@ class HFIRPDRedControl(object):
scalefactor = 1.
else:
scalefactor = float(scalefactor)
- print "[DB] Scale factor is %f." % (scalefactor)
+ print("[DB] Scale factor is %f." % (scalefactor))
# Excluded detectors
if excludeddetlist is None:
excludeddetlist = []
else:
- print "[DB] Excluded detectors: %s"%(excludeddetlist), "Convert to numpy array", \
- numpy.array(excludeddetlist)
+ print("[DB] Excluded detectors: %s" % (excludeddetlist), "Convert to numpy array",
+ numpy.array(excludeddetlist))
basewsname = datamdws.name().split("_DataMD")[0]
outwsname = basewsname + "_Reduced"
@@ -819,12 +824,12 @@ class HFIRPDRedControl(object):
InputMonitorWorkspace=monitormdws,
OutputWorkspace=outwsname,
BinningParams=binpar,
- UnitOutput = unit,
+ UnitOutput=unit,
NeutronWaveLength=wavelength,
ExcludedDetectorIDs=numpy.array(excludeddetlist),
ScaleFactor=scalefactor)
- print "[DB] Reduction is finished. Data is in workspace %s. " % (outwsname)
+ print("[DB] Reduction is finished. Data is in workspace %s. " % (outwsname))
# Set up class variable for min/max and
outws = AnalysisDataService.retrieve(outwsname)
@@ -873,11 +878,11 @@ class HFIRPDRedControl(object):
raise e
if detefffname is not None:
localdetefffname = os.path.join(localdatadir, detefffname)
- print "[DB] Detector efficiency file name: %s From %s" % (detefffname, deteffurl)
+ print("[DB] Detector efficiency file name: %s From %s" % (detefffname, deteffurl))
if os.path.exists(localdetefffname) is False:
downloadFile(deteffurl, localdetefffname)
else:
- print "[Info] Detector efficiency file %s exists in directory %s." % (detefffname, localdatadir)
+ print("[Info] Detector efficiency file %s exists in directory %s." % (detefffname, localdatadir))
else:
localdetefffname = None
# ENDIF
@@ -885,14 +890,14 @@ class HFIRPDRedControl(object):
# excluded detectors file
excldetfname, exclurl = hutil.makeExcludedDetectorFileName(exp)
localexcldetfname = os.path.join(localdatadir, excldetfname)
- print "[DB] Excluded det file name: %s From %s" % (excldetfname, exclurl)
+ print("[DB] Excluded det file name: %s From %s" % (excldetfname, exclurl))
if os.path.exists(localexcldetfname) is False:
downloadstatus, errmsg = downloadFile(exclurl, localexcldetfname)
if downloadstatus is False:
localexcldetfname = None
- print "[Error] %s" % (errmsg)
+ print("[Error] %s" % (errmsg))
else:
- print "[Info] Detector exclusion file %s exists in directory %s." % (excldetfname, localdatadir)
+ print("[Info] Detector exclusion file %s exists in directory %s." % (excldetfname, localdatadir))
# Set to ws manager
wsmanager.setWavelength(wavelength)
@@ -926,7 +931,7 @@ class HFIRPDRedControl(object):
wsmanager = self.getWorkspace(exp, scan, raiseexception=True)
if wsmanager.reducedws is None:
raise NotImplementedError("Unable to rebin the data for exp=%d, scan=%d because \
- either data MD workspace and monitor MD workspace is not present." % (exp, scan))
+ either data MD workspace and monitor MD workspace is not present." % (exp, scan))
else:
wksp = wsmanager.reducedws
@@ -955,9 +960,8 @@ class HFIRPDRedControl(object):
# ENDIF
if "topas" in filetype:
- sfilename = sfilename[:-4]+".xye"
+ sfilename = sfilename[:-4] + ".xye"
api.SaveFocusedXYE(InputWorkspace=wksp,
- StartAtBankNumber=info["bank"],
Filename=sfilename,
Format="TOPAS")
# ENDIF
@@ -1000,7 +1004,7 @@ class HFIRPDRedControl(object):
# Get reduced workspace
wsmanager = self.getWorkspace(expno, scanno, raiseexception=True)
vanRun = wsmanager.getProcessedVanadiumWS()
- outws = vanRun.name()+"_smooth"
+ outws = vanRun.name() + "_smooth"
outws = api.FFTSmooth(InputWorkspace=vanRun,
OutputWorkspace=outws,
@@ -1028,7 +1032,7 @@ class HFIRPDRedControl(object):
wksp = wsmanager.reducedws
if wksp is None:
raise NotImplementedError("Unable to rebin the data for exp=%d, scan=%d because either data MD workspace and \
- monitor MD workspace is not present." % (exp, scan))
+ monitor MD workspace is not present." % (exp, scan))
# Convert unit to Time-of-flight by rebinning
xaxis_unit = wksp.getAxis(0).getUnit().unitID()
@@ -1044,7 +1048,7 @@ class HFIRPDRedControl(object):
raise NotImplementedError('No vanadium peaks has been set up.')
# ENDIF
- outwsname = wksp.name()+"_rmVan"
+ outwsname = wksp.name() + "_rmVan"
wksp = api.StripPeaks(InputWorkspace=wksp,
OutputWorkspace=outwsname,
PeakPositions=numpy.array(vanpeakposlist))
@@ -1062,7 +1066,7 @@ class HFIRPDRedControl(object):
tablews.addColumn('double', 'Correction')
for detid in sorted(vancorrdict.keys()):
- tablews.addRow( [detid, vancorrdict[detid]] )
+ tablews.addRow([detid, vancorrdict[detid]])
return tablews
@@ -1074,7 +1078,7 @@ class HFIRPDRedControl(object):
ptnolist = []
numexpinfo = datamdws.getNumExperimentInfo()
- for i in xrange(numexpinfo):
+ for i in range(numexpinfo):
expinfo = datamdws.getExperimentInfo(i)
runid = expinfo.run().getProperty('run_number').value
if runid >= 0:
@@ -1095,9 +1099,10 @@ class HFIRPDRedControl(object):
return rvalue
-#-------------------------------------------------------------------------------
+
+# -------------------------------------------------------------------------------
# External Methods
-#-------------------------------------------------------------------------------
+# -------------------------------------------------------------------------------
def downloadFile(url, localfilepath):
@@ -1109,9 +1114,9 @@ def downloadFile(url, localfilepath):
"""
# open URL
try:
- response = urllib2.urlopen(url)
+ response = urllib.request.urlopen(url)
wbuf = response.read()
- except urllib2.HTTPError as e:
+ except urllib.error.HTTPError as e:
# Unable to download file
if str(e).count('HTTP Error 404') == 1:
return (False, str(e))
diff --git a/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py b/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
index cb0e622476ba439a44369b7fb85c4159d2d24881..51dba73f12d11e3603b7c712d59467a76a123bc1 100644
--- a/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
+++ b/scripts/Inelastic/Direct/ISISDirecInelasticConfig.py
@@ -155,16 +155,17 @@ class UserProperties(object):
else:
pass
- def get_rb_num(self,exp_date):
+ def get_rb_num(self, exp_date):
"""Returns short name of user's RB folder
consisting of string RB and string representation of
RB number e.g. RB1510324,
used on the date specified
"""
return os.path.basename(self._rb_dirs[exp_date])
+
#
- def get_rb_dir(self,exp_date):
+ def get_rb_dir(self, exp_date):
"""Returns full name name of user's RB folder corresponding to the
experiment, with the data provided.
"""
@@ -197,7 +198,7 @@ class UserProperties(object):
raise RuntimeError("User's experiment date is not defined. User undefined")
#
- def get_instrument(self,cycle_date_id):
+ def get_instrument(self, cycle_date_id):
"""Return the instrument, used in the cycle with the date specified"""
return self._instrument[cycle_date_id]
@@ -263,6 +264,7 @@ class UserProperties(object):
if error:
raise RuntimeError("Experiment start date should be defined as"
" a sting in the form YYYYMMDD or YYMMDD but it is: {0}".format(start_date))
+
#
def convert_cycle_int(cycle_int):
@@ -351,6 +353,7 @@ class MantidConfigDirectInelastic(object):
The class have to change/to be amended if the configuration
changes or has additional features.
"""
+
# pylint: disable=too-many-instance-attributes
# It has as many as parameters describing ISIS configuration.
@@ -465,9 +468,10 @@ class MantidConfigDirectInelastic(object):
else:
return False
#
+
#
- def get_user_file_description(self,instr_name=None):
+ def get_user_file_description(self, instr_name=None):
"""returbs full file name (with path) for an xml file which describes
files, which should be copied to a user.
@@ -477,8 +481,8 @@ class MantidConfigDirectInelastic(object):
"""
if self._user:
if not instr_name:
- instr_name = self._user.instrument
- return os.path.join(self._script_repo, 'direct_inelastic',instr_name,
+ instr_name = self._user.instrument
+ return os.path.join(self._script_repo, 'direct_inelastic', instr_name,
self._user_files_descr)
else:
return self._user_files_descr
@@ -504,7 +508,7 @@ class MantidConfigDirectInelastic(object):
return False
#
- def _fullpath_to_copy(self, short_source_file=None, short_target_file=None,cycle_id=None):
+ def _fullpath_to_copy(self, short_source_file=None, short_target_file=None, cycle_id=None):
"""Append full path to source and target files """
if cycle_id:
@@ -526,7 +530,7 @@ class MantidConfigDirectInelastic(object):
return full_source, full_target
#
- def copy_reduction_sample(self, user_file_description=None,cycle_id=None,rb_group=None):
+ def copy_reduction_sample(self, user_file_description=None, cycle_id=None, rb_group=None):
"""copy sample reduction scripts from Mantid script repository
to user folder.
"""
@@ -535,9 +539,9 @@ class MantidConfigDirectInelastic(object):
if rb_group is None:
rb_group = self._user.userID
- info_to_copy = self._parse_user_files_description(user_file_description,cycle_id)
- for source_file,dest_file,subst_list in info_to_copy:
- self._copy_user_file_job(source_file,dest_file,rb_group,subst_list)
+ info_to_copy = self._parse_user_files_description(user_file_description, cycle_id)
+ for source_file, dest_file, subst_list in info_to_copy:
+ self._copy_user_file_job(source_file, dest_file, rb_group, subst_list)
def _copy_and_parse_user_file(self, input_file, output_file, replacemets_list):
"""Method processes file provided for user and replaces list of keywords, describing user
@@ -557,7 +561,7 @@ class MantidConfigDirectInelastic(object):
fh_targ.close()
#
- def _copy_user_file_job(self, input_file, output_file, rb_group,replacement_list=None):
+ def _copy_user_file_job(self, input_file, output_file, rb_group, replacement_list=None):
"""Method copies file provided into the requested destination
and replaces keys specified in replacement list dictionary with their
values if replacement_list is provided.
@@ -576,7 +580,7 @@ class MantidConfigDirectInelastic(object):
self._copy_and_parse_user_file(input_file, output_file, replacement_list)
os.chmod(output_file, 0o777)
- ownership_str = "chown {0}:{1} {2}".format(self._user.userID,rb_group, output_file)
+ ownership_str = "chown {0}:{1} {2}".format(self._user.userID, rb_group, output_file)
if platform.system() != 'Windows':
os.system(ownership_str)
# Set up the file creation and modification dates to the users start date
@@ -584,7 +588,7 @@ class MantidConfigDirectInelastic(object):
file_time = time.mktime(start_date.timetuple())
os.utime(output_file, (file_time, file_time))
- def _get_file_attributes(self, file_node,cycle=None):
+ def _get_file_attributes(self, file_node, cycle=None):
"""processes xml file_node to retrieve file attributes to copy """
source_file = file_node.getAttribute("file_name")
@@ -597,7 +601,7 @@ class MantidConfigDirectInelastic(object):
else:
if "$" in target_file:
target_file = self._user.replace_variables(target_file)
- full_source, full_target = self._fullpath_to_copy(source_file, target_file,cycle)
+ full_source, full_target = self._fullpath_to_copy(source_file, target_file, cycle)
return (full_source, full_target)
@@ -615,13 +619,13 @@ class MantidConfigDirectInelastic(object):
# what should be replaced in the file
source = repl_info.getAttribute("var")
if len(source) == 0:
- raise InvalidArgument(
+ raise ValueError(
'"replace" field of {0} file for instrument {1} has to contain attribute "var" and its value'
.format(self._user_files_descr, self._user.instrument))
# what should be placed instead of the replacement
dest = repl_info.getAttribute("by_var")
if len(dest) == 0:
- raise InvalidArgument(
+ raise ValueError(
'"replace" field of {0} file for instrument {1} has to contain attribute "by_var" and its value'
.format(self._user_files_descr, self._user.instrument))
@@ -630,7 +634,7 @@ class MantidConfigDirectInelastic(object):
dest = self._user.replace_variables(dest)
return (source, dest)
- def _parse_user_files_description(self, job_description_file,cycle_id=None):
+ def _parse_user_files_description(self, job_description_file, cycle_id=None):
""" Method parses xml file used to describe files to provide to user"""
# mainly for debugging purposes
@@ -646,7 +650,7 @@ class MantidConfigDirectInelastic(object):
# have no idea what minidom specific exception is:
# pylint: disable=W0703
except Exception:
- input_file, output_file = self._fullpath_to_copy(None,None,cycle_id)
+ input_file, output_file = self._fullpath_to_copy(None, None, cycle_id)
filenames_to_copy.append((input_file, output_file, None))
return filenames_to_copy
@@ -655,7 +659,7 @@ class MantidConfigDirectInelastic(object):
# go through all files in the description and define file copying operations
for file_node in files_to_copy:
# retrieve file attributes or its default values if the attributes are missing
- input_file, output_file = self._get_file_attributes(file_node,cycle_id)
+ input_file, output_file = self._get_file_attributes(file_node, cycle_id)
if input_file is None:
continue
@@ -715,7 +719,7 @@ class MantidConfigDirectInelastic(object):
users_instruments = theUser.get_all_instruments()
for instr in users_instruments:
if not self.is_inelastic(instr):
- raise RuntimeError('Instrument {0} is not among acceptable instruments'.format(instrument))
+ raise RuntimeError('Instrument {0} is not among acceptable instruments'.format(instr))
self._user = theUser
# pylint: disable=W0201
@@ -830,7 +834,7 @@ class MantidConfigDirectInelastic(object):
self._dynamic_configuration.append('datasearch.directories=' + map_mask_dir + ';' + data_dir)
#
- def generate_config(self,key_users_list=None):
+ def generate_config(self, key_users_list=None):
"""Save generated Mantid configuration file into user's home folder
and copy other files, necessary for Mantid to work properly
"""
@@ -849,19 +853,19 @@ class MantidConfigDirectInelastic(object):
self.make_map_mask_links(user_path)
users_cycles = self._user.get_all_cycles()
- users_rb = self._user.get_all_rb()
+ users_rb = self._user.get_all_rb()
# extract rb folder without path, which gives RB group name
- users_rb = list(map(os.path.basename,users_rb))
+ users_rb = list(map(os.path.basename, users_rb))
#
- for cycle,rb_name in zip(users_cycles,users_rb):
+ for cycle, rb_name in zip(users_cycles, users_rb):
if key_users_list:
key_user = str(key_users_list[rb_name])
if self._fedid.lower() != key_user.lower():
continue
instr = self._user.get_instrument(cycle)
- self.copy_reduction_sample(self.get_user_file_description(instr),cycle,rb_name)
- #
+ self.copy_reduction_sample(self.get_user_file_description(instr), cycle, rb_name)
+ #
#
def make_map_mask_links(self, user_path):
@@ -911,6 +915,7 @@ class MantidConfigDirectInelastic(object):
file_time = time.mktime(start_date.timetuple())
os.utime(config_file_name, (file_time, file_time))
+
# pylint: disable = invalid-name
if __name__ == "__main__":
@@ -947,9 +952,7 @@ if __name__ == "__main__":
# initialize Mantid configuration
# its testing route under main so it rightly imports itself
- #pylint: disable=W0406
- from .ISISDirecInelasticConfig import MantidConfigDirectInelastic, UserProperties
-
+ # pylint: disable=W0406
mcf = MantidConfigDirectInelastic(MantidDir, rootDir, UserScriptRepoDir, MapMaskDir)
print("Successfully initialized ISIS Inelastic Configuration script generator")
diff --git a/scripts/Inelastic/Direct/NonIDF_Properties.py b/scripts/Inelastic/Direct/NonIDF_Properties.py
index 6b1fffb112e70a62e8137ba21c4643b8aef656f7..2029ade3f5b308b68a3124c1b107374b0c1cd797 100644
--- a/scripts/Inelastic/Direct/NonIDF_Properties.py
+++ b/scripts/Inelastic/Direct/NonIDF_Properties.py
@@ -2,6 +2,8 @@
from __future__ import (absolute_import, division, print_function)
from Direct.PropertiesDescriptors import *
from Direct.RunDescriptor import RunDescriptor,RunDescriptorDependent
+from mantid.simpleapi import *
+from mantid import geometry
class NonIDF_Properties(object):
diff --git a/scripts/Inelastic/Direct/PropertiesDescriptors.py b/scripts/Inelastic/Direct/PropertiesDescriptors.py
index 8ba0a0dde6235f6509d4f8fe220beed695aee3cb..2cc58aa0567b55996d54b8c101518b29c2458144 100644
--- a/scripts/Inelastic/Direct/PropertiesDescriptors.py
+++ b/scripts/Inelastic/Direct/PropertiesDescriptors.py
@@ -1,5 +1,5 @@
-#pylint: disable=too-many-lines
-#pylint: disable=invalid-name
+# pylint: disable=too-many-lines
+# pylint: disable=invalid-name
""" File contains collection of Descriptors used to define complex
properties in NonIDF_Properties and PropertyManager classes
"""
@@ -9,44 +9,42 @@ import numpy as np
import math
from collections import Iterable
-from mantid.simpleapi import *
-#pylint: disable=unused-import
-from mantid.kernel import funcinspect
-#pylint: disable=unused-import
-from mantid import api,geometry,config
+import mantid.simpleapi as mantid
+from mantid import api
import Direct.ReductionHelpers as prop_helpers
-#pylint: disable=unused-import
-import Direct.CommonFunctions as common
import collections
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
# Descriptors, providing overloads for complex properties in NonIDF_Properties
# class
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
class PropDescriptor(object):
"""Class provides common custom interface for property descriptors """
def dependencies(self):
"""Returns the list of other properties names, this property depends on"""
return []
-#pylint: disable=unused-argument
- def validate(self,instance, owner):
+ # pylint: disable=unused-argument
+
+ def validate(self, instance, owner):
"""Interface to validate property descriptor,
provided to check properties interaction before long run
Return validation result, errors severity (0 -- fine, 1 -- warning, 2-- error)
and error message if any
"""
- return (True,0,'')
+ return (True, 0, '')
+
+
# end PropDescriptor
-#-----------------------------------------------------------------------------------------
-#-----------------------------------------------------------------------------------------
-#-----------------------------------------------------------------------------------------
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
class SumRuns(PropDescriptor):
@@ -54,25 +52,27 @@ class SumRuns(PropDescriptor):
should be summed.
"""
- def __init__(self,sample_run_prop):
+ def __init__(self, sample_run_prop):
# internal reference to sample run property
self._sample_run = sample_run_prop
# class containing this property
#
self._sum_runs = False
+
#
- def __get__(self,instance,holder_class):
+ def __get__(self, instance, holder_class):
if instance is None:
return self
return self._sum_runs
+
#
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
old_value = self._sum_runs
- if isinstance(value,bool):
+ if isinstance(value, bool):
self._sum_runs = value
- elif isinstance(value,int):
+ elif isinstance(value, int):
if value > 0:
self._sum_runs = True
else:
@@ -81,8 +81,10 @@ class SumRuns(PropDescriptor):
self._sum_runs = bool(value)
#
if old_value != self._sum_runs:
- self._sample_run.notify_sum_runs_changed(old_value,self._sum_runs)
-#--------------------------------------------------------------------------------------------------------------------
+ self._sample_run.notify_sum_runs_changed(old_value, self._sum_runs)
+
+
+# --------------------------------------------------------------------------------------------------------------------
class AvrgAccuracy(PropDescriptor):
@@ -93,14 +95,14 @@ class AvrgAccuracy(PropDescriptor):
def __init__(self):
self._accuracy = 2
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
""" return current number of significant digits"""
if instance is None:
return self
else:
return self._accuracy
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
""" Set up incident energy or range of energies in various formats
or define autoEi"""
val = int(value)
@@ -108,24 +110,24 @@ class AvrgAccuracy(PropDescriptor):
raise ValueError("Averaging accuracy can be only a positive number >= 1")
self._accuracy = val
- def roundoff(self,value):
+ def roundoff(self, value):
"""Round specified sequence for specified number of significant digits"""
- if isinstance(value,Iterable):
+ if isinstance(value, Iterable):
vallist = value
else:
vallist = [value]
rez = []
- lim = 10**(self._accuracy-1)
+ lim = 10 ** (self._accuracy - 1)
- def out(a,b,mult):
- if mult>1:
- return a<b
+ def out(a, b, mult):
+ if mult > 1:
+ return a < b
else:
- return false
+ return False
for val in vallist:
if abs(val) > lim:
- rez.append(round(val,0))
+ rez.append(round(val, 0))
continue
elif abs(val) < lim:
mult = 10
@@ -133,11 +135,11 @@ class AvrgAccuracy(PropDescriptor):
mult = 1
tv = abs(val)
- fin_mult = 1
- while out(tv,lim,mult):
- fin_mult*=mult
- tv *= mult
- fin_rez = math.copysign(round(tv,0)/fin_mult,val)
+ fin_mult = 1
+ while out(tv, lim, mult):
+ fin_mult *= mult
+ tv *= mult
+ fin_rez = math.copysign(round(tv, 0) / fin_mult, val)
rez.append(fin_rez)
if len(rez) == 1:
return rez[0]
@@ -145,7 +147,7 @@ class AvrgAccuracy(PropDescriptor):
return rez
-#--------------------------------------------------------------------------------------------------------------------
+# --------------------------------------------------------------------------------------------------------------------
class IncidentEnergy(PropDescriptor):
"""Provide incident energy or range of incident energies to be processed.
@@ -165,7 +167,7 @@ class IncidentEnergy(PropDescriptor):
self._autoEiRunNumber = None
self._autoEiCalculated = False
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
""" return incident energy or list of incident energies """
if instance is None:
return self
@@ -173,33 +175,33 @@ class IncidentEnergy(PropDescriptor):
return 'AUTO'
else:
return self._incident_energy
-#pylint: disable=too-many-branches
+ # pylint: disable=too-many-branches
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
""" Set up incident energy or range of energies in various formats
or define autoEi"""
if value is not None:
- if isinstance(value,str):
+ if isinstance(value, str):
# Check autoEi
if value.lower() == 'auto':
self._use_autoEi = True
currentRun = instance.sample_run
- if isinstance(currentRun,api.Workspace):
+ if isinstance(currentRun, api.Workspace):
currentRun = currentRun.getRunNumber()
if currentRun != self._autoEiRunNumber or currentRun is None:
self._autoEiRunNumber = currentRun
self._autoEiCalculated = False
- self._incident_energy = 0
+ self._incident_energy = 0
self._cur_iter_en = 0
return
# Ei in string form is provided
else:
if value.find('[') > -1:
energy_list = True
- value = value.replace('[','').replace(']','').strip()
+ value = value.replace('[', '').replace(']', '').strip()
else:
energy_list = False
- en_list = str.split(value,',')
+ en_list = str.split(value, ',')
if len(en_list) > 1:
rez = []
for en_str in en_list:
@@ -212,7 +214,7 @@ class IncidentEnergy(PropDescriptor):
else:
self._incident_energy = float(value)
else:
- if isinstance(value,list):
+ if isinstance(value, list):
rez = []
for val in value:
en_val = float(val)
@@ -228,67 +230,72 @@ class IncidentEnergy(PropDescriptor):
# here we have set specific energy or range of incident energies
self._use_autoEi = False
- if isinstance(self._incident_energy,list):
+ if isinstance(self._incident_energy, list):
self._num_energies = len(self._incident_energy)
else:
self._num_energies = 1
self._cur_iter_en = 0
-#pylint: disable=unused-variable
- ok,sev,message = self.validate(instance)
+ # pylint: disable=unused-variable
+ ok, sev, message = self.validate(instance)
if not ok:
raise KeyError(message)
+
#
def autoEi_mode(self):
"""Return true if energies should be calculated in autoEi mode"""
return self._use_autoEi
+
#
def multirep_mode(self):
""" return true if energy is defined as list of energies or multirep m and false otherwise """
- if isinstance(self._incident_energy,list) or self._use_autoEi:
+ if isinstance(self._incident_energy, list) or self._use_autoEi:
return True
else:
return False
+
#
def getAllEiList(self):
"""Return incident energy(ies) range, defined by the property"""
- if isinstance(self._incident_energy,list):
+ if isinstance(self._incident_energy, list):
return self._incident_energy
else:
- if self._incident_energy==0:
+ if self._incident_energy == 0:
return []
else:
return [self._incident_energy]
+
#
def get_current(self):
""" Return current energy out of range of energies"""
- if isinstance(self._incident_energy,list):
+ if isinstance(self._incident_energy, list):
ind = self._cur_iter_en
return self._incident_energy[ind]
else:
return self._incident_energy
+
#
def next(self):
- if isinstance(self._incident_energy,list):
- self._cur_iter_en +=1
+ if isinstance(self._incident_energy, list):
+ self._cur_iter_en += 1
if self._cur_iter_en >= len(self._incident_energy):
raise StopIteration
else:
raise StopIteration
#
- def set_current_ind(self,ind=None):
+ def set_current_ind(self, ind=None):
""" set current energy value (used in multirep mode) as
energy estimate for the reduction
ind -- if provided, the number of the value in the list of
values (can be used together with enumerate)
"""
- if isinstance(self._incident_energy,list):
+ if isinstance(self._incident_energy, list):
if ind is None:
self._cur_iter_en = 0
else:
@@ -297,9 +304,10 @@ class IncidentEnergy(PropDescriptor):
self._cur_iter_en = ind
else:
self._cur_iter_en = 0
+
#
- def set_auto_Ei(self,monitor_ws,instance,ei_mon_spec=None):
+ def set_auto_Ei(self, monitor_ws, instance, ei_mon_spec=None):
"""Calculate autoEi and set it as input for iterations over energy"""
if not self._use_autoEi:
return
@@ -310,47 +318,50 @@ class IncidentEnergy(PropDescriptor):
self._autoEiCalculated = False
if ei_mon_spec is None:
ei_mon_spec = instance.ei_mon_spectra
- guess_ei_ws = GetAllEi(Workspace=monitor_ws,Monitor1SpecID = ei_mon_spec[0],
- Monitor2SpecID = ei_mon_spec[1])
- guessEi = guess_ei_ws.readX(0)
+ guess_ei_ws = mantid.GetAllEi(Workspace=monitor_ws, Monitor1SpecID=ei_mon_spec[0],
+ Monitor2SpecID=ei_mon_spec[1])
+ guessEi = guess_ei_ws.readX(0)
fin_ei = []
for ei in guessEi:
try:
- ei_ref,_,_,_=GetEi(InputWorkspace=monitor_ws,
- Monitor1Spec=ei_mon_spec[0], Monitor2Spec=ei_mon_spec[1], EnergyEstimate=ei)
+ ei_ref, _, _, _ = mantid.GetEi(InputWorkspace=monitor_ws,
+ Monitor1Spec=ei_mon_spec[0], Monitor2Spec=ei_mon_spec[1],
+ EnergyEstimate=ei)
fin_ei.append(ei_ref)
-#pylint: disable=bare-except
+ # pylint: disable=bare-except
except:
- instance.log("Can not refine guess energy {0:f}. Ignoring it.".format(ei),'warning')
+ instance.log("Can not refine guess energy {0:f}. Ignoring it.".format(ei), 'warning')
if len(fin_ei) == 0:
raise RuntimeError("Was not able to identify auto-energies for workspace: {0}".format(monitor_ws.name()))
# Success! Set up estimated energies
self._autoEiCalculated = True
- self._autoEiRunNumber = newRunNum
+ self._autoEiRunNumber = newRunNum
self._incident_energy = fin_ei
self._num_energies = len(fin_ei)
self._cur_iter_en = 0
# Clear dataservice from unnecessary workspace
- DeleteWorkspace(guess_ei_ws)
+ mantid.DeleteWorkspace(guess_ei_ws)
- def validate(self,instance,owner=None):
- #
- if self._use_autoEi: # nothing much to validate. The ei will be auto if possible
- return (True,0,'')
+ def validate(self, instance, owner=None):
+ #
+ if self._use_autoEi: # nothing much to validate. The ei will be auto if possible
+ return (True, 0, '')
inc_en = self._incident_energy
- if isinstance(inc_en,list):
- for ind,en in enumerate(inc_en):
+ if isinstance(inc_en, list):
+ for ind, en in enumerate(inc_en):
if en <= 0:
- return (False,2,"Incident energy have to be positive number or list of positive numbers.\n"
- "For input argument {0} got negative energy {1}".format(ind,en))
+ return (False, 2, "Incident energy have to be positive number or list of positive numbers.\n"
+ "For input argument {0} got negative energy {1}".format(ind, en))
else:
if inc_en <= 0:
- return (False,2,"Incident energy have to be positive number or list of positive numbers.\n"
- "Got single negative incident energy {0} ".format(inc_en))
- return (True,0,'')
+ return (False, 2, "Incident energy have to be positive number or list of positive numbers.\n"
+ "Got single negative incident energy {0} ".format(inc_en))
+ return (True, 0, '')
+
+
# end IncidentEnergy
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
class EnergyBins(PropDescriptor):
@@ -367,40 +378,41 @@ class EnergyBins(PropDescriptor):
(e.g. prop_man.incident_energy=[100])/
"""
- def __init__(self,IncidentEnergyProp,AccuracyProp):
+ def __init__(self, IncidentEnergyProp, AccuracyProp):
self._incident_energy = IncidentEnergyProp
self._averager = AccuracyProp
self._energy_bins = None
# how close you are ready to rebin w.r.t. the incident energy
self._range = 0.99999
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
"""Binning range for the result of convertToenergy procedure or list of such ranges"""
if instance is None:
return self
return self._energy_bins
- def __set__(self,instance,values):
+ def __set__(self, instance, values):
if values is not None:
- if isinstance(values,str):
- values = values.replace('[','').replace(']','').strip()
+ if isinstance(values, str):
+ values = values.replace('[', '').replace(']', '').strip()
lst = values.split(',')
- self.__set__(instance,lst)
+ self.__set__(instance, lst)
return
else:
value = values
if len(value) != 3:
- raise KeyError("Energy_bin value has to be a tuple of 3 elements or string of 3 comma-separated numbers")
- value = (float(value[0]),float(value[1]),float(value[2]))
+ raise KeyError(
+ "Energy_bin value has to be a tuple of 3 elements or string of 3 comma-separated numbers")
+ value = (float(value[0]), float(value[1]), float(value[2]))
else:
value = None
- #TODO: implement single value settings according to rebin?
+ # TODO: implement single value settings according to rebin?
self._energy_bins = value
- def get_abs_range(self,instance=None):
+ def get_abs_range(self, instance=None):
""" return energies related to incident energies.
"""
- if self._incident_energy.multirep_mode(): # Relative energy
+ if self._incident_energy.multirep_mode(): # Relative energy
ei = self._incident_energy.get_current()
if self._incident_energy.autoEi_mode():
# we need to average ei nicely, as it will give energy jitter otherwise
@@ -412,16 +424,16 @@ class EnergyBins(PropDescriptor):
else:
if instance:
instance.log("*** WARNING! Got energy_bins specified as absolute values in multirep mode.\n"
- " Will normalize these values by max value and treat as relative values ",
+ " Will normalize these values by max value and treat as relative values",
"warning")
mult = self._range / self._energy_bins[2]
- rez = self._calc_relative_range(ei,mult)
+ rez = self._calc_relative_range(ei, mult)
if self._incident_energy.autoEi_mode():
rez = self._averager.roundoff(rez)
return rez
else:
return None
- else: # Absolute energy ranges
+ else: # Absolute energy ranges
if self.is_range_valid():
return self._energy_bins
else:
@@ -431,7 +443,7 @@ class EnergyBins(PropDescriptor):
"warning")
mult = self._range / self._energy_bins[2]
ei = self._incident_energy.get_current()
- return self._calc_relative_range(ei,mult)
+ return self._calc_relative_range(ei, mult)
def is_range_valid(self):
"""Method verifies if binning range is consistent with incident energy """
@@ -440,27 +452,30 @@ class EnergyBins(PropDescriptor):
else:
return self._energy_bins[2] <= self._incident_energy.get_current()
- def _calc_relative_range(self,ei,range_mult=1):
+ def _calc_relative_range(self, ei, range_mult=1):
""" """
mult = range_mult * ei
- return (self._energy_bins[0] * mult ,self._energy_bins[1] * mult,self._energy_bins[2] * mult)
+ return (self._energy_bins[0] * mult, self._energy_bins[1] * mult, self._energy_bins[2] * mult)
- def validate(self,instance,owner):
+ def validate(self, instance, owner):
""" function verifies if the energy binning is consistent with incident energies """
ei = instance.incident_energy
ebin = instance.energy_bins
- if isinstance(ei,list) or owner.incident_energy.autoEi_mode(): # ebin expected to be relative
+ if isinstance(ei, list) or owner.incident_energy.autoEi_mode(): # ebin expected to be relative
if ebin[2] > 1:
- return(False,1,"Binning for multiple energy range should be relative to incident energy. Got ebin_max={0} > 1\n" +
- "Energy range will be normalized and treated as relative range")
+ return (False, 1,
+ "Binning for multiple energy range should be relative to incident energy. Got ebin_max={0} > 1\n" +
+ "Energy range will be normalized and treated as relative range")
else:
if not owner.incident_energy.autoEi_mode() and ebin[2] > ei:
- return (False,2,'Max rebin range {0:f} exceeds incident energy {1:f}'.format(ebin[2],en))
- return(True,0,'')
-#-----------------------------------------------------------------------------------------
+ return (False, 2, 'Max rebin range {0:f} exceeds incident energy {1:f}'.format(ebin[2], ei))
+ return (True, 0, '')
-#end EnergyBins
-#-----------------------------------------------------------------------------------------
+
+# -----------------------------------------------------------------------------------------
+
+# end EnergyBins
+# -----------------------------------------------------------------------------------------
class SaveFileName(PropDescriptor):
@@ -471,11 +486,11 @@ class SaveFileName(PropDescriptor):
used instead.
"""
- def __init__(self,Name=None):
+ def __init__(self, Name=None):
self._file_name = Name
self._custom_print = None
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
# getter functional interface.
if instance is None:
return self
@@ -501,18 +516,18 @@ class SaveFileName(PropDescriptor):
sr = 0
try:
ei = owner.incident_energy.get_current()
- name +='{0:0<5}Ei{1:_<4.2f}meV'.format(sr,ei)
+ name += '{0:0<5}Ei{1:_<4.2f}meV'.format(sr, ei)
if instance.sum_runs:
- name +='sum'
+ name += 'sum'
if owner.monovan_run.run_number():
- name +='_Abs'
- name = name.replace('.','d')
-#pylint: disable=bare-except
+ name += '_Abs'
+ name = name.replace('.', 'd')
+ # pylint: disable=bare-except
except:
name = None
return name
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
if value is None:
self._file_name = None
@@ -521,10 +536,12 @@ class SaveFileName(PropDescriptor):
else:
self._file_name = str(value)
- def set_custom_print(self,routine):
+ def set_custom_print(self, routine):
self._custom_print = routine
-#end SaveFileName
-#-----------------------------------------------------------------------------------------
+
+
+# end SaveFileName
+# -----------------------------------------------------------------------------------------
class InstrumentDependentProp(PropDescriptor):
@@ -532,44 +549,48 @@ class InstrumentDependentProp(PropDescriptor):
which are undefined if no instrument is defined.
"""
- def __init__(self,prop_name):
+ def __init__(self, prop_name):
self._prop_name = prop_name
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
-#pylint: disable=protected-access
+ # pylint: disable=protected-access
if instance._pInstrument is None:
raise KeyError("Attempt to use uninitialized property manager")
else:
- return getattr(instance,self._prop_name)
+ return getattr(instance, self._prop_name)
- def __set__(self,instance,values):
+ def __set__(self, instance, values):
raise AttributeError("Property {0} can not be assigned. It defined by instrument".format(self._prop_name))
-#end InstrumentDependentProp
-#-----------------------------------------------------------------------------------------
+
+
+# end InstrumentDependentProp
+# -----------------------------------------------------------------------------------------
class VanadiumRMM(PropDescriptor):
"""Defines constant static rmm for vanadium."""
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
""" return rmm for vanadium """
return 50.9415
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
raise AttributeError("Can not change vanadium rmm")
-#end VanadiumRMM
-#-----------------------------------------------------------------------------------------
+
+
+# end VanadiumRMM
+# -----------------------------------------------------------------------------------------
# END Descriptors for NonIDF_Properties class
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
# Descriptors, providing overloads for some complex properties in
# PropertyManager
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
class mon2NormalizationEnergyRange(PropDescriptor):
@@ -585,105 +606,112 @@ class mon2NormalizationEnergyRange(PropDescriptor):
def __init__(self):
# default range
- self._relative_range = [0.8,1.2]
+ self._relative_range = [0.8, 1.2]
- def __get__(self,instance,owner):
+ def __get__(self, instance, owner):
""" Return actual energy range from internal relative range and incident energy """
if instance is None:
return self
ei = owner.incident_energy.get_current()
return [self._relative_range[0] * ei, self._relative_range[1] * ei]
- def __set__(self,instance,val):
+ def __set__(self, instance, val):
""" set detector calibration file using various formats """
- if isinstance(val,list):
- self._relative_range = self._check_range(val,instance)
- elif isinstance(val,str):
+ if isinstance(val, list):
+ self._relative_range = self._check_range(val, instance)
+ elif isinstance(val, str):
val = self._parce_string2list(val)
- self.__set__(instance,val)
+ self.__set__(instance, val)
else:
raise KeyError('mon2_norm_energy_range needs to be initialized by two values.\n'
- 'Trying to assign value {0} of unknown type {1}'.format(val,type(val)))
+ 'Trying to assign value {0} of unknown type {1}'.format(val, type(val)))
+
#
- def _check_range(self,val,instance):
+ def _check_range(self, val, instance):
""" method to check if list of values acceptable as ranges """
if len(val) != 2:
- raise KeyError("mon2_norm_energy_range needs to be initialized by lost of two values. Got {0}".format(len(val)))
- self._relative_range = (float(val[0]),float(val[1]))
- ok,sev,message = self.validate(instance)
+ raise KeyError(
+ "mon2_norm_energy_range needs to be initialized by lost of two values. Got {0}".format(len(val)))
+ self._relative_range = (float(val[0]), float(val[1]))
+ ok, sev, message = self.validate(instance)
if not ok:
if sev == 1:
- instance.log(message,'warning')
+ instance.log(message, 'warning')
else:
raise KeyError(message)
return self._relative_range
+
#
- def _parce_string2list(self,val):
+ def _parce_string2list(self, val):
""" method splits input string containing comma into list of strings"""
value = val.strip('[]()')
val = value.split(',')
return val
- def validate(self,instance,owner=None):
+ def validate(self, instance, owner=None):
""" function verifies if the energy range is consistent with incident energies """
en_range = self._relative_range
if len(en_range) != 2:
- return(False,2,'mon2_normalization_energy_range can be initialized by list of two values only.'
- ' Got {0} values'.format(len(range)))
+ return (False, 2, 'mon2_normalization_energy_range can be initialized by list of two values only.'
+ ' Got {0} values'.format(len(range)))
- result = (True,0,'')
+ result = (True, 0, '')
val1 = float(en_range[0])
if val1 < 0.1 or val1 > 0.9:
- message = "Lower mon2_norm_energy_range describes lower limit of energy to integrate neutron signal after the chopper.\n"\
- "The limit is defined as (this value)*incident_energy. Are you sure you want to set this_value to {0}?\n".format(val1)
+ message = "Lower mon2_norm_energy_range describes lower limit of energy to integrate neutron signal after" \
+ " the chopper.\nThe limit is defined as (this value)*incident_energy." \
+ " Are you sure you want to set this_value to {0}?\n".format(val1)
if val1 > 1:
- return(False,2,message)
+ return (False, 2, message)
else:
- result = (False,1,message)
+ result = (False, 1, message)
val2 = float(en_range[1])
if val2 < 1.1 or val2 > 1.9:
- message = "Upper mon2_norm_energy_range describes upper limit of energy to integrate neutron signal after the chopper.\n"\
- "The limit is defined as (this value)*incident_energy. Are you sure you want to set this_value to {0}?\n".format(val2)
+ message = "Upper mon2_norm_energy_range describes upper limit of energy to integrate neutron signal after" \
+ " the chopper.\nThe limit is defined as (this value)*incident_energy." \
+ " Are you sure you want to set this_value to {0}?\n".format(val2)
if val2 > 1:
if result[0]:
- result = (False,1,message)
+ result = (False, 1, message)
else:
- result = (False,1,result[2] + message)
+ result = (False, 1, result[2] + message)
else:
- return (False,2,message)
+ return (False, 2, message)
return result
-#-----------------------------------------------------------------------------------------
+
+# -----------------------------------------------------------------------------------------
class PropertyFromRange(PropDescriptor):
"""Generic descriptor for property, which can have one value from a list of values."""
- def __init__(self,availible_values,default_value):
+ def __init__(self, availible_values, default_value):
self._availible_values = availible_values
- self.__set__(None,default_value)
+ self.__set__(None, default_value)
- def __get__(self,instance,owner):
+ def __get__(self, instance, owner):
""" Return current value for the property with range of values. """
if instance is None:
return self
return self._current_value
- def __set__(self,instance,val):
+ def __set__(self, instance, val):
if val in self._availible_values:
-#pylint: disable=attribute-defined-outside-init
+ # pylint: disable=attribute-defined-outside-init
self._current_value = val
else:
raise KeyError(' Property can not have value {0}'.format(val))
-#-----------------------------------------------------------------------------------------
+
+# -----------------------------------------------------------------------------------------
class DetCalFile(PropDescriptor):
@@ -698,26 +726,26 @@ class DetCalFile(PropDescriptor):
self._det_cal_file = None
self._calibrated_by_run = False
- def __get__(self,instance,owner):
+ def __get__(self, instance, owner):
if instance is None:
return self
return self._det_cal_file
- def __set__(self,instance,val):
+ def __set__(self, instance, val):
""" set detector calibration file using various formats """
- if val is None or isinstance(val,api.Workspace):
- # nothing provided or workspace provided or filename probably provided
- if str(val) in mtd:
- # workspace name provided
- val = mtd[str(val)]
+ if val is None or isinstance(val, api.Workspace):
+ # nothing provided or workspace provided or filename probably provided
+ if str(val) in mantid.mtd:
+ # workspace name provided
+ val = mantid.mtd[str(val)]
self._det_cal_file = val
self._calibrated_by_run = False
return
- if isinstance(val,str):
- if val in mtd:
- val = mtd[val]
+ if isinstance(val, str):
+ if val in mantid.mtd:
+ val = mantid.mtd[val]
self._det_cal_file = val
self._calibrated_by_run = False
return
@@ -729,14 +757,16 @@ class DetCalFile(PropDescriptor):
return
val = intVal
- if isinstance(val,int):
- #if val in instance.all_run_numbers: TODO: retrieve workspace from
- #run numbers
+ if isinstance(val, int):
+ # if val in instance.all_run_numbers: TODO: retrieve workspace from
+ # run numbers
self._det_cal_file = val
self._calibrated_by_run = True
return
- raise NameError('Detector calibration file name can be a workspace name present in Mantid or string describing an file name')
- #if Reducer.det_cal_file != None :
+ raise NameError(
+ 'Detector calibration file name can be a workspace name present in Mantid or string describing an file name')
+
+ # if Reducer.det_cal_file != None :
# if isinstance(Reducer.det_cal_file,str) and not Reducer.det_cal_file
# in mtd : # it is a file
# Reducer.log('Setting detector calibration file to
@@ -744,67 +774,70 @@ class DetCalFile(PropDescriptor):
# else:
# Reducer.log('Setting detector calibration to {0}, which is probably
# a workspace '.format(str(Reducer.det_cal_file)))
- #else:
+ # else:
# Reducer.log('Setting detector calibration to detector block info from
# '+str(sample_run))
def calibrated_by_run(self):
""" reports if the detector calibration is in a run-file or separate file(workspace)"""
return self._calibrated_by_run
-#pylint: disable=unused-argument
- def find_file(self,instance,**kwargs):
+ # pylint: disable=unused-argument
+
+ def find_file(self, instance, **kwargs):
""" Method to find file, correspondent to
current _det_cal_file file hint
"""
if self._det_cal_file is None:
- # nothing to look for
- return (True,"No Detector calibration file defined")
+ # nothing to look for
+ return (True, "No Detector calibration file defined")
- if isinstance(self._det_cal_file,api.Workspace):
- # nothing to do. Workspace used for calibration
- return (True,'Workspace {0} used for detectors calibration'.format(self._det_cal_file.name()))
+ if isinstance(self._det_cal_file, api.Workspace):
+ # nothing to do. Workspace used for calibration
+ return (True, 'Workspace {0} used for detectors calibration'.format(self._det_cal_file.name()))
dcf_val = self._det_cal_file
- if isinstance(dcf_val,str): # it may be string representation of runN
+ if isinstance(dcf_val, str): # it may be string representation of runN
try:
dcf_val = int(dcf_val)
except ValueError:
pass
- if isinstance(dcf_val,int): # this is a run number
+ if isinstance(dcf_val, int): # this is a run number
inst_short_name = instance.short_inst_name
- fac = instance.facility
- zero_padding = fac.instrument(inst_short_name).zeroPadding(dcf_val)
- file_hint = inst_short_name+str(dcf_val).zfill(zero_padding)
+ fac = instance.facility
+ zero_padding = fac.instrument(inst_short_name).zeroPadding(dcf_val)
+ file_hint = inst_short_name + str(dcf_val).zfill(zero_padding)
try:
- file_name = FileFinder.findRuns(file_hint)[0]
-#pylint: disable=bare-except
+ file_name = mantid.FileFinder.findRuns(file_hint)[0]
+ # pylint: disable=bare-except
except:
- return (False,"Can not find run file corresponding to run N: {0}".format(file_hint))
+ return (False, "Can not find run file corresponding to run N: {0}".format(file_hint))
self._det_cal_file = file_name
- return (True,file_name)
+ return (True, file_name)
- # string can be a run number or a file name:
+ # string can be a run number or a file name:
file_name = prop_helpers.findFile(self._det_cal_file)
- if len(file_name) == 0: # it still can be a run number as string
+ if len(file_name) == 0: # it still can be a run number as string
try:
- file_name = FileFinder.findRuns(self._det_cal_file)[0]
-#pylint: disable=bare-except
+ file_name = mantid.FileFinder.findRuns(self._det_cal_file)[0]
+ # pylint: disable=bare-except
except:
- return (False,"Can not find file or run file corresponding to name : {0}".format(self._det_cal_file))
+ return (False, "Can not find file or run file corresponding to name : {0}".format(self._det_cal_file))
else:
pass
self._det_cal_file = file_name
- return (True,file_name)
-#end DetCalFile
-#-----------------------------------------------------------------------------------------
+ return (True, file_name)
+
+
+# end DetCalFile
+# -----------------------------------------------------------------------------------------
class MapMaskFile(PropDescriptor):
"""common method to wrap around an auxiliary file name"""
- def __init__(self,prop_name,file_ext,doc_string=None):
+ def __init__(self, prop_name, file_ext, doc_string=None):
self._file_name = None
self._file_ext = file_ext
self._prop_name = prop_name
@@ -812,37 +845,40 @@ class MapMaskFile(PropDescriptor):
if doc_string is not None:
self.__doc__ = doc_string
- def __get__(self,instance,class_type=None):
+ def __get__(self, instance, class_type=None):
if instance is None:
return self
return self._file_name
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
if value is not None:
-#pylint: disable=unused-variable
+ # pylint: disable=unused-variable
fileName, fileExtension = os.path.splitext(value)
if not fileExtension:
value = value + self._file_ext
self._file_name = value
-#pylint: disable=unused-argument
- def find_file(self,instance,**kwargs):
+ # pylint: disable=unused-argument
+
+ def find_file(self, instance, **kwargs):
""" Method to find file, correspondent to
current MapMaskFile file hint
"""
if self._file_name is None:
- return (True,'No file for {0} is defined'.format(self._prop_name))
+ return (True, 'No file for {0} is defined'.format(self._prop_name))
file_name = prop_helpers.findFile(self._file_name)
- if len(file_name) == 0: # it still can be a run number as string
- return (False,'No file for {0} corresponding to guess: {1} found'.format(self._prop_name,self._file_name))
+ if len(file_name) == 0: # it still can be a run number as string
+ return (False, 'No file for {0} corresponding to guess: {1} found'.format(self._prop_name, self._file_name))
else:
self._file_name = file_name
- return (True,file_name)
-#end MapMaskFile
+ return (True, file_name)
+
+
+# end MapMaskFile
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
class HardMaskPlus(prop_helpers.ComplexProperty):
@@ -856,32 +892,33 @@ class HardMaskPlus(prop_helpers.ComplexProperty):
"""
def __init__(self):
- prop_helpers.ComplexProperty.__init__(self,['use_hard_mask_only','run_diagnostics'])
+ prop_helpers.ComplexProperty.__init__(self, ['use_hard_mask_only', 'run_diagnostics'])
- def __get__(self,instance,class_type=None):
+ def __get__(self, instance, class_type=None):
if instance is None:
return self
return instance.hard_mask_file
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
if value is not None:
-#pylint: disable=unused-variable
+ # pylint: disable=unused-variable
fileName, fileExtension = os.path.splitext(value)
if not fileExtension:
value = value + '.msk'
instance.hard_mask_file = value
- prop_helpers.ComplexProperty.__set__(self,instance.__dict__,[False,True])
+ prop_helpers.ComplexProperty.__set__(self, instance.__dict__, [False, True])
else:
- prop_helpers.ComplexProperty.__set__(self,instance.__dict__,[True,False])
+ prop_helpers.ComplexProperty.__set__(self, instance.__dict__, [True, False])
try:
-#pylint: disable=protected-access
+ # pylint: disable=protected-access
del instance.__changed_properties['hardmaskOnly']
-#pylint: disable=bare-except
+ # pylint: disable=bare-except
except:
pass
-#-----------------------------------------------------------------------------------------
+
+# -----------------------------------------------------------------------------------------
class HardMaskOnly(prop_helpers.ComplexProperty):
@@ -893,32 +930,32 @@ class HardMaskOnly(prop_helpers.ComplexProperty):
"""
def __init__(self):
- prop_helpers.ComplexProperty.__init__(self,['use_hard_mask_only','run_diagnostics'])
+ prop_helpers.ComplexProperty.__init__(self, ['use_hard_mask_only', 'run_diagnostics'])
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
- return prop_helpers.gen_getter(instance.__dict__,'use_hard_mask_only')
+ return prop_helpers.gen_getter(instance.__dict__, 'use_hard_mask_only')
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
if value is None:
use_hard_mask_only = False
instance.hard_mask_file = None
hard_mask_file = None
- elif isinstance(value,bool) or isinstance(value,int):
+ elif isinstance(value, bool) or isinstance(value, int):
use_hard_mask_only = bool(value)
hard_mask_file = instance.hard_mask_file
- elif isinstance(value,str):
- if value.lower() in ['true','yes']:
+ elif isinstance(value, str):
+ if value.lower() in ['true', 'yes']:
use_hard_mask_only = True
- elif value.lower() in ['false','no']:
+ elif value.lower() in ['false', 'no']:
use_hard_mask_only = False
- else: # it is probably a hard mask file provided:
+ else: # it is probably a hard mask file provided:
instance.hard_mask_file = value
use_hard_mask_only = True
hard_mask_file = instance.hard_mask_file
- #end
+ # end
# if no hard mask file is there and use_hard_mask_only is True,
# diagnostics should not run
@@ -926,15 +963,17 @@ class HardMaskOnly(prop_helpers.ComplexProperty):
run_diagnostics = False
else:
run_diagnostics = True
- prop_helpers.ComplexProperty.__set__(self,instance.__dict__,[use_hard_mask_only,run_diagnostics])
+ prop_helpers.ComplexProperty.__set__(self, instance.__dict__, [use_hard_mask_only, run_diagnostics])
try:
-#pylint: disable=protected-access
+ # pylint: disable=protected-access
del instance.__changed_properties['hardmaskPlus']
-#pylint: disable=bare-except
+ # pylint: disable=bare-except
except:
pass
-#end HardMaskOnly
-#-----------------------------------------------------------------------------------------
+
+
+# end HardMaskOnly
+# -----------------------------------------------------------------------------------------
class MonovanIntegrationRange(prop_helpers.ComplexProperty):
@@ -959,75 +998,80 @@ class MonovanIntegrationRange(prop_helpers.ComplexProperty):
integration_range = [monovan_lo_value,monovan_hi_value].
"""
- def __init__(self,DepType=None):
+ def __init__(self, DepType=None):
if DepType:
self._rel_range = False
- prop_helpers.ComplexProperty.__init__(self,['monovan_lo_value','monovan_hi_value'])
+ prop_helpers.ComplexProperty.__init__(self, ['monovan_lo_value', 'monovan_hi_value'])
else:
self._rel_range = True
- prop_helpers.ComplexProperty.__init__(self,['monovan_lo_frac','monovan_hi_frac'])
+ prop_helpers.ComplexProperty.__init__(self, ['monovan_lo_frac', 'monovan_hi_frac'])
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
- if isinstance(instance,dict):
+ if isinstance(instance, dict):
ei = 1
tDict = instance
else:
ei = owner.incident_energy.get_current()
tDict = instance.__dict__
- if self._rel_range: # relative range
+ if self._rel_range: # relative range
if ei is None:
- raise AttributeError('Attempted to obtain relative to ei monovan integration range, but incident energy has not been set')
- rel_range = prop_helpers.ComplexProperty.__get__(self,tDict)
- the_range = [rel_range[0] * ei,rel_range[1] * ei]
+ raise AttributeError(
+ 'Attempted to obtain relative to ei monovan integration range, but incident energy has not been set')
+ rel_range = prop_helpers.ComplexProperty.__get__(self, tDict)
+ the_range = [rel_range[0] * ei, rel_range[1] * ei]
return the_range
- else: # absolute range
- return prop_helpers.ComplexProperty.__get__(self,tDict)
+ else: # absolute range
+ return prop_helpers.ComplexProperty.__get__(self, tDict)
- def __set__(self,instance,value):
- if isinstance(instance,dict):
+ def __set__(self, instance, value):
+ if isinstance(instance, dict):
tDict = instance
else:
tDict = instance.__dict__
if value is None:
if not self._rel_range:
self._rel_range = True
- self._other_prop = ['monovan_lo_frac','monovan_hi_frac']
+ self._other_prop = ['monovan_lo_frac', 'monovan_hi_frac']
else:
if self._rel_range:
self._rel_range = False
- self._other_prop = ['monovan_lo_value','monovan_hi_value']
+ self._other_prop = ['monovan_lo_value', 'monovan_hi_value']
- if isinstance(value,str):
+ if isinstance(value, str):
values = value.split(',')
result = []
- for val in values :
+ for val in values:
result.append(int(val))
value = result
if len(value) != 2:
raise KeyError("monovan_integr_range has to be list of two values, "
- "defining min/max values of integration range or None to use relative to incident energy limits")
- prop_helpers.ComplexProperty.__set__(self,tDict,value)
+ "defining min/max values of integration range or None "
+ "to use relative to incident energy limits")
+
+ prop_helpers.ComplexProperty.__set__(self, tDict, value)
- def validate(self,instance, owner):
+ def validate(self, instance, owner):
""" check if monovan integration range has reasonable value """
if instance.monovan_run is None:
- return (True,0,'')
+ return (True, 0, '')
- the_range = sepf.__get__(instance,owner)
+ the_range = self.__get__(instance, owner)
ei = instance.incident_energy
if the_range[0] >= the_range[1]:
- return (False,2,'monovan integration range limits = [{0}:{1}] are wrong'.format(the_range[0],the_range[1]))
+ return False, 2, 'monovan integration range limits = [{0}:{1}] are wrong'.format(the_range[0], the_range[1])
if the_range[0] < -100 * ei or the_range[0] > 100 * ei:
- return (False,1,'monovan integration is suspiciously wide: [{0}:{1}]. This may be incorrect'
- .format(the_range[0],the_range[1]))
- return (True,0,'')
-#end MonovanIntegrationRange
+ return False, 1, 'monovan integration is suspiciously wide: [{0}:{1}]. ' \
+ 'This may be incorrect'.format(the_range[0], the_range[1])
+ return True, 0, ''
+
+
+# end MonovanIntegrationRange
class EiMonSpectra(prop_helpers.ComplexProperty):
@@ -1039,44 +1083,44 @@ class EiMonSpectra(prop_helpers.ComplexProperty):
def __init__(self):
""" Ei mon spectra is defined as function of two other complex properties"""
- prop_helpers.ComplexProperty.__init__(self,['ei-mon1-spec','ei-mon2-spec'])
+ prop_helpers.ComplexProperty.__init__(self, ['ei-mon1-spec', 'ei-mon2-spec'])
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
- if isinstance(instance,dict):
+ if isinstance(instance, dict):
tDict = instance
else:
tDict = instance.__dict__
- mon_range = prop_helpers.ComplexProperty.__get__(self,tDict)
+ mon_range = prop_helpers.ComplexProperty.__get__(self, tDict)
# Return monitors range, converted into the standard form.
# namely tuple of two monitors or monitors list
- monitors = [0,0]
- for index,mon_val in enumerate(mon_range):
- monitors[index]=self._process_monitors_spectra(mon_val)
- return (monitors[0],monitors[1])
+ monitors = [0, 0]
+ for index, mon_val in enumerate(mon_range):
+ monitors[index] = self._process_monitors_spectra(mon_val)
+ return (monitors[0], monitors[1])
- def __set__(self,instance,value):
- if value is None: # Do nothing
+ def __set__(self, instance, value):
+ if value is None: # Do nothing
return
- if isinstance(instance,dict):
+ if isinstance(instance, dict):
tDict = instance
else:
tDict = instance.__dict__
- if isinstance(value,str):
- val = value.replace('[','').replace(']','').strip()
- if val.find(':')>-1:
+ if isinstance(value, str):
+ val = value.replace('[', '').replace(']', '').strip()
+ if val.find(':') > -1:
val = val.split(':')
else:
val = val.split(',')
else:
val = value
- #end if
+ # end if
if len(val) != 2:
raise KeyError("ei_mon_spectra may be either tuple defining two spectra "
"lists or string, which can be transformed to such lists. Got {0}"
@@ -1088,25 +1132,25 @@ class EiMonSpectra(prop_helpers.ComplexProperty):
if val[1] == 'ei-mon2-spec':
val[1] = tDict['ei-mon2-spec']
#
- prop_helpers.ComplexProperty.__set__(self,tDict,val)
+ prop_helpers.ComplexProperty.__set__(self, tDict, val)
- def need_to_sum_monitors(self,instance):
+ def need_to_sum_monitors(self, instance):
"""Returns True if some monitors are defined as range of spectra to sum
False -- if all monitors are related to one spectra each.
"""
tDict = instance.__dict__
- mon_range = prop_helpers.ComplexProperty.__get__(self,tDict)
+ mon_range = prop_helpers.ComplexProperty.__get__(self, tDict)
# Return monitors range, converted into the standard form.
- need_to_sum =False
+ need_to_sum = False
for mon_val in mon_range:
mon_list = self._process_monitors_spectra(mon_val)
- if isinstance(mon_list,Iterable):
- need_to_sum = True
+ if isinstance(mon_list, Iterable):
+ need_to_sum = True
break
return need_to_sum
#
- def _process_monitors_spectra(self,mon_range):
+ def _process_monitors_spectra(self, mon_range):
"""A method to process any form of monitor spectra list
representation
Called on get rather then on set operation as monitor lists
@@ -1114,12 +1158,12 @@ class EiMonSpectra(prop_helpers.ComplexProperty):
properties and these properties are currently standard properties
"""
- if isinstance(mon_range,str):
+ if isinstance(mon_range, str):
mon_val = mon_range.split(',')
else:
mon_val = mon_range
- if isinstance(mon_val,list) or isinstance(mon_val,tuple):
- rez_spectra=[]
+ if isinstance(mon_val, list) or isinstance(mon_val, tuple):
+ rez_spectra = []
for mon in mon_val:
rez_spectra.append(int(mon))
if len(rez_spectra) == 1:
@@ -1128,11 +1172,12 @@ class EiMonSpectra(prop_helpers.ComplexProperty):
rez_spectra = int(mon_range)
return rez_spectra
-# def validate(self,instance, owner):
+
+# def validate(self,instance, owner):
# """ """
# return (True,0,'')
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
class SpectraToMonitorsList(PropDescriptor):
@@ -1149,43 +1194,45 @@ class SpectraToMonitorsList(PropDescriptor):
def __init__(self):
self._spectra_to_monitors_list = None
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
return self._spectra_to_monitors_list
- def __set__(self,instance,spectra_list):
+ def __set__(self, instance, spectra_list):
""" Sets copy spectra to monitors variable as a list of monitors using different forms of input """
self._spectra_to_monitors_list = self._convert_to_list(spectra_list)
- def _convert_to_list(self,spectra_list):
+ def _convert_to_list(self, spectra_list):
""" convert any spectra_list representation into a list """
if spectra_list is None:
return None
- if isinstance(spectra_list,str):
+ if isinstance(spectra_list, str):
if spectra_list.lower() is 'none':
result = None
else:
spectra = spectra_list.split(',')
result = []
- for spectum in spectra :
+ for spectum in spectra:
result.append(int(spectum))
else:
- if isinstance(spectra_list,list):
+ if isinstance(spectra_list, list):
if len(spectra_list) == 0:
result = None
else:
result = []
- for i in range(0,len(spectra_list)):
+ for i in range(0, len(spectra_list)):
result.append(int(spectra_list[i]))
else:
result = [int(spectra_list)]
return result
-#end SpectraToMonitorsList
-#-----------------------------------------------------------------------------------------
+
+# end SpectraToMonitorsList
+
+# -----------------------------------------------------------------------------------------
class SaveFormat(PropDescriptor):
@@ -1196,19 +1243,19 @@ class SaveFormat(PropDescriptor):
See Mantid documentation for detailed description of the formats.
If set to None, internal saving procedure is not used.
"""
- # formats available for saving the data
- save_formats = ['spe','nxspe','nxs']
+ # formats available for saving the data
+ save_formats = ['spe', 'nxspe', 'nxs']
def __init__(self):
self._save_format = set()
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
return self._save_format
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
""" user can clear save formats by setting save_format=None or save_format = [] or save_format=''
if empty string or empty list is provided as part of the list, all save_format-s set up earlier are cleared"""
@@ -1218,40 +1265,44 @@ class SaveFormat(PropDescriptor):
return
# check string
- if isinstance(value,str):
+ if isinstance(value, str):
value = value.strip('[]().')
subformats = value.split(',')
if len(subformats) > 1:
- self.__set__(instance,subformats)
+ self.__set__(instance, subformats)
return
else:
value = subformats[0]
if value not in SaveFormat.save_formats:
- instance.log("Trying to set saving in unknown format: \"" + str(value) + "\" No saving will occur for this format")
+ instance.log("Trying to set saving in unknown format: \"" + str(
+ value) + "\" No saving will occur for this format")
return
else:
try:
- # set single default save format recursively
+ # set single default save format recursively
for val in value:
- self.__set__(instance,val)
+ self.__set__(instance, val)
return
except:
- raise KeyError(' Attempting to set unknown saving format {0} of type {1}. Allowed values can be spe, nxspe or nxs'
- .format(value,type(value)))
- #end if different types
+ raise KeyError(
+ ' Attempting to set unknown saving format {0} of type {1}. Allowed values can be spe, nxspe or nxs'
+ .format(value, type(value)))
+ # end if different types
self._save_format.add(value)
- def validate(self,instance, owner):
+ def validate(self, instance, owner):
n_formats = len(self._save_format)
if n_formats == 0:
- return (False,1,'No internal save format is defined. Results may be lost')
+ return (False, 1, 'No internal save format is defined. Results may be lost')
else:
- return (True,0,'')
-#end SaveFormat
+ return (True, 0, '')
+
-#-----------------------------------------------------------------------------------------
+# end SaveFormat
+
+# -----------------------------------------------------------------------------------------
class DiagSpectra(PropDescriptor):
@@ -1267,21 +1318,21 @@ class DiagSpectra(PropDescriptor):
def __init__(self):
self._diag_spectra = None
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
return self._diag_spectra
- def __set__(self,instance,spectra_list):
+ def __set__(self, instance, spectra_list):
self._diag_spectra = self._process_spectra_list(spectra_list)
- def _process_spectra_list(self,specta_sring):
+ def _process_spectra_list(self, specta_sring):
""" process IDF description of the spectra string """
if specta_sring is None:
return None
- if isinstance(specta_sring,str):
- if specta_sring.lower() in ['none','no']:
+ if isinstance(specta_sring, str):
+ if specta_sring.lower() in ['none', 'no']:
return None
else:
banks = specta_sring.split(";")
@@ -1289,16 +1340,19 @@ class DiagSpectra(PropDescriptor):
for b in banks:
token = b.split(",") # b = "(,)"
if len(token) != 2:
- raise ValueError("Invalid bank spectra specification in diagnostics properties %s" % specta_sring)
+ raise ValueError(
+ "Invalid bank spectra specification in diagnostics properties %s" % specta_sring)
start = int(token[0].lstrip('('))
end = int(token[1].rstrip(')'))
- bank_spectra.append((start,end))
+ bank_spectra.append((start, end))
return bank_spectra
else:
raise ValueError("Spectra For diagnostics can be a string inthe form (num1,num2);(num3,num4) etc. or None")
-#end class DiagSpectra
-#-----------------------------------------------------------------------------------------
+
+# end class DiagSpectra
+
+# -----------------------------------------------------------------------------------------
class BackbgroundTestRange(PropDescriptor):
@@ -1311,7 +1365,7 @@ class BackbgroundTestRange(PropDescriptor):
def __init__(self):
self._background_test_range = None
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
@@ -1320,31 +1374,34 @@ class BackbgroundTestRange(PropDescriptor):
else:
return instance.bkgd_range
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
if value is None:
self._background_test_range = None
return
- if isinstance(value,str):
- value = str.split(value,',')
+ if isinstance(value, str):
+ value = str.split(value, ',')
if len(value) != 2:
raise ValueError("background test range can be only a 2 element list of floats")
- self._background_test_range = (float(value[0]),float(value[1]))
+ self._background_test_range = (float(value[0]), float(value[1]))
- def validate(self,instance, owner=None):
+ def validate(self, instance, owner=None):
""" validate background test range """
- test_range = self.__get__(instance,owner)
+ test_range = self.__get__(instance, owner)
if test_range is None:
- return (True,0,'')
+ return True, 0, ''
if test_range[0] >= test_range[1]:
- return (False,2,' Background test range: [{0}:{1}] is incorrect '.format(test_range[0],test_range[1]))
+ return False, 2, ' Background test range: [{0}:{1}] is incorrect '.format(test_range[0], test_range[1])
if test_range[0] < 0:
- return (False,2,' Background test range is TOF range, so it can not be negative={0}'.format(test_range[0]))
+ return False, 2, ' Background test range is TOF range, so it can not be negative={0}'.format(test_range[0])
if test_range[1] > 20000:
- return (False,1,' Background test range is TOF range, its max value looks suspiciously big={0}'.format(test_range[1]))
- return (True,0,'')
-#end BackbgroundTestRange
+ return False, 1, ' Background test range is TOF range, its max value looks suspiciously big={0}'.format(
+ test_range[1])
+ return True, 0, ''
+
-#-----------------------------------------------------------------------------------------
+# end BackbgroundTestRange
+
+# -----------------------------------------------------------------------------------------
class MultirepTOFSpectraList(PropDescriptor):
@@ -1358,19 +1415,19 @@ class MultirepTOFSpectraList(PropDescriptor):
def __init__(self):
self._spectra_list = None
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
return self._spectra_list
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
if value is None:
self._spectra_list = None
return
- if isinstance(value,str):
- value = str.split(value,',')
- self.__set__(instance,value)
+ if isinstance(value, str):
+ value = str.split(value, ',')
+ self.__set__(instance, value)
return
if isinstance(value, list):
rez = []
@@ -1379,7 +1436,9 @@ class MultirepTOFSpectraList(PropDescriptor):
else:
rez = [int(value)]
self._spectra_list = rez
-#end MultirepTOFSpectraList
+
+
+# end MultirepTOFSpectraList
class MonoCorrectionFactor(PropDescriptor):
@@ -1398,38 +1457,39 @@ class MonoCorrectionFactor(PropDescriptor):
no changes to the values it depends on were identified.
"""
- def __init__(self,ei_prop,monovan_run_prop):
+ def __init__(self, ei_prop, monovan_run_prop):
self._cor_factor = None
self._mono_run_number = None
self._ei_prop = ei_prop
self.cashed_values = {}
self._mono_run_prop = monovan_run_prop
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
return self._cor_factor
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
self._cor_factor = value
- #
+ #
if value is None:
-#pylint: disable=protected-access
- self._mono_run_prop._in_cash = False # enable monovan run validation if any
+ # pylint: disable=protected-access
+ self._mono_run_prop._in_cash = False # enable monovan run validation if any
+
#
- def set_val_to_cash(self,instance,value):
+ def set_val_to_cash(self, instance, value):
""" """
mono_int_range = instance.monovan_integr_range
cash_id = self._build_cash_val_id(mono_int_range)
self.cashed_values[cash_id] = value
# tell property manager that mono_correction_factor has been modified
# to avoid automatic resetting this property from any workspace
- cp = getattr(instance,'_PropertyManager__changed_properties')
+ cp = getattr(instance, '_PropertyManager__changed_properties')
cp.add('mono_correction_factor')
- def get_val_from_cash(self,instance):
+ def get_val_from_cash(self, instance):
mono_int_range = instance.monovan_integr_range
cash_id = self._build_cash_val_id(mono_int_range)
if cash_id in self.cashed_values:
@@ -1437,7 +1497,7 @@ class MonoCorrectionFactor(PropDescriptor):
else:
return None
- def set_cash_mono_run_number(self,new_value):
+ def set_cash_mono_run_number(self, new_value):
if new_value is None:
self.cashed_values = {}
self._mono_run_number = None
@@ -1446,20 +1506,22 @@ class MonoCorrectionFactor(PropDescriptor):
self.cashed_values = {}
self._mono_run_number = int(new_value)
- def _build_cash_val_id(self,mono_int_range):
+ def _build_cash_val_id(self, mono_int_range):
ei = self._ei_prop.get_current()
- cash_id = "Ei={0:0>9.4e}:Int({1:0>9.4e}:{2:0>9.5e}):Run{3}".\
- format(ei,mono_int_range[0],mono_int_range[1],self._mono_run_number)
+ cash_id = "Ei={0:0>9.4e}:Int({1:0>9.4e}:{2:0>9.5e}):Run{3}". \
+ format(ei, mono_int_range[0], mono_int_range[1], self._mono_run_number)
return cash_id
- def validate(self,instance, owner=None):
+ def validate(self, instance, owner=None):
if self._cor_factor is None:
- return (True,0,'')
+ return (True, 0, '')
if self._cor_factor <= 0:
- return (False,2,'Mono-correction factor has to be positive if specified: {0}'.format(self._cor_factor))
- return (True,0,'')
-#end MonoCorrectionFactor
+ return (False, 2, 'Mono-correction factor has to be positive if specified: {0}'.format(self._cor_factor))
+ return (True, 0, '')
+
+
+# end MonoCorrectionFactor
class MotorLogName(PropDescriptor):
@@ -1474,22 +1536,24 @@ class MotorLogName(PropDescriptor):
def __init__(self):
self._log_names = []
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
return self._log_names
- def __set__(self,instance,value):
- if isinstance(value,str):
+ def __set__(self, instance, value):
+ if isinstance(value, str):
val_list = value.split(';')
- elif isinstance(value,list):
+ elif isinstance(value, list):
val_list = []
for val in value:
val_list.append(str(val))
else:
val_list = [str(value)]
self._log_names = val_list
-#end MotorLogName
+
+
+# end MotorLogName
class MotorOffset(PropDescriptor):
@@ -1501,19 +1565,21 @@ class MotorOffset(PropDescriptor):
def __init__(self):
self._offset = None
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
return self._offset
- def __set__(self,instance,value):
+ def __set__(self, instance, value):
# we do not need to analyze for None or empty list
# as all this is implemented within generic setter
if value is None:
self._offset = None
else:
self._offset = float(value)
-#end MotorOffset
+
+
+# end MotorOffset
class RotationAngle(PropDescriptor):
@@ -1526,7 +1592,7 @@ class RotationAngle(PropDescriptor):
the value specified is used and stored in NXSPE files.
"""
- def __init__(self,MotorLogNamesClass,Motor_Offset):
+ def __init__(self, MotorLogNamesClass, Motor_Offset):
self._mot_offset = Motor_Offset
self._motor_log = MotorLogNamesClass
# user may override value derived
@@ -1539,7 +1605,7 @@ class RotationAngle(PropDescriptor):
self._log_ws_name = None
#
- def __get__(self,instance,owner=None):
+ def __get__(self, instance, owner=None):
if instance is None:
return self
@@ -1547,52 +1613,52 @@ class RotationAngle(PropDescriptor):
return self._own_psi_value
return self.read_psi_from_workspace(self._log_ws_name)
- def __set__(self,instance,value):
- if isinstance(value,str):
- if value in mtd: ## its workspace
+ def __set__(self, instance, value):
+ if isinstance(value, str):
+ if value in mantid.mtd: ## its workspace
self._log_ws_name = value
self._own_psi_value = None
- else: # it is string representation of psi. Should be
+ else: # it is string representation of psi. Should be
# convertible to number.
self._own_psi_value = float(value)
- elif isinstance(value,api.Workspace):
+ elif isinstance(value, api.Workspace):
self._log_ws_name = value.name()
self._own_psi_value = None
- elif value is None: # clear all
+ elif value is None: # clear all
self._own_psi_value = None
- else: #own psi value
+ else: # own psi value
self._own_psi_value = float(value)
- def _read_ws_logs(self,external_ws=None):
+ def _read_ws_logs(self, external_ws=None):
"""read specified workspace logs from workspace
provided either internally or externally
"""
working_ws = external_ws
if working_ws is None:
- working_ws = mtd[self._log_ws_name]
+ working_ws = mantid.mtd[self._log_ws_name]
if working_ws is None:
raise RuntimeError("No workspace provided. Can not read logs to identify psi")
else:
- if isinstance(external_ws,str):
- working_ws = mtd[external_ws]
+ if isinstance(external_ws, str):
+ working_ws = mantid.mtd[external_ws]
value = None
-#pylint: disable=protected-access
+ # pylint: disable=protected-access
log_names = self._motor_log._log_names
for name in log_names:
try:
value = working_ws.getRun().getLogData(name).timeAverageValue()
break
-#pylint: disable=bare-except
+ # pylint: disable=bare-except
except:
pass
return value
- def read_psi_from_workspace(self,workspace):
+ def read_psi_from_workspace(self, workspace):
"""Independent method to read rotation angle from workspace and
previously set log and offset parameters
"""
-#pylint: disable=protected-access
+ # pylint: disable=protected-access
offset = self._mot_offset._offset
if offset is None:
return np.NaN
@@ -1603,10 +1669,11 @@ class RotationAngle(PropDescriptor):
return offset + log_val
def dependencies(self):
- return ['motor_log_names','motor_offset']
-#end RotationAngle
+ return ['motor_log_names', 'motor_offset']
+
+# end RotationAngle
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
# END Descriptors for PropertyManager itself
-#-----------------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------------------
diff --git a/scripts/Inelastic/Direct/PropertyManager.py b/scripts/Inelastic/Direct/PropertyManager.py
index 22fb7840ad2c49959c1bace7ecb5a6d40985f934..5eceaa888cf692874df451d9b14df2d3c37a229e 100644
--- a/scripts/Inelastic/Direct/PropertyManager.py
+++ b/scripts/Inelastic/Direct/PropertyManager.py
@@ -2,9 +2,9 @@
from __future__ import (absolute_import, division, print_function)
from Direct.NonIDF_Properties import *
-from collections import OrderedDict,Iterable
+from collections import OrderedDict, Iterable
from six import iteritems
-
+from mantid.kernel import funcinspect
class PropertyManager(NonIDF_Properties):
""" Class defines the interface for Direct inelastic reduction with properties
@@ -302,15 +302,12 @@ class PropertyManager(NonIDF_Properties):
""" Method returns list of monitors ID used during reduction """
used_mon=set()
- for case in common.switch(self.normalise_method):
- if case('monitor-1'):
- used_mon.add(self.mon1_norm_spec)
- break
- if case('monitor-2'):
- used_mon.add(self.mon2_norm_spec)
- break
- if case(): # default, could also just omit condition or 'if True'
- pass
+ if self.normalise_method == 'monitor-1':
+ used_mon.add(self.mon1_norm_spec)
+ elif self.normalise_method == 'monitor-2':
+ used_mon.add(self.mon2_norm_spec)
+ else: # default, could also just omit condition or 'if True'
+ pass
#
def add_ei_monitors(used_mon,ei_mon_list):
diff --git a/scripts/Inelastic/Direct/RunDescriptor.py b/scripts/Inelastic/Direct/RunDescriptor.py
index b3b30a06a1ff19084b0f0984e6447f11d139c62b..9dc9e8307295668dce80d37979f36cfd3a78de8c 100644
--- a/scripts/Inelastic/Direct/RunDescriptor.py
+++ b/scripts/Inelastic/Direct/RunDescriptor.py
@@ -5,6 +5,7 @@
from __future__ import (absolute_import, division, print_function)
from mantid.simpleapi import *
+from mantid.kernel import funcinspect
from Direct.PropertiesDescriptors import *
import re
import collections
diff --git a/scripts/Interface/reduction_gui/reduction/inelastic/dgs_reduction_script.py b/scripts/Interface/reduction_gui/reduction/inelastic/dgs_reduction_script.py
index 5591e7f647fc7b0bc9a89a6772faa41d33f2e20a..4c99c1074664996b7e0dd5b210a7a0c70738133b 100644
--- a/scripts/Interface/reduction_gui/reduction/inelastic/dgs_reduction_script.py
+++ b/scripts/Interface/reduction_gui/reduction/inelastic/dgs_reduction_script.py
@@ -100,10 +100,7 @@ class DgsReductionScripter(BaseReductionScripter):
options += subitem
if '_spe' in output_workspace:
- output_workspace_name = 'live_spe'
output_workspace = 'OutputWorkspace="live_spe"'
- else:
- output_workspace_name = output_workspace.split('"')[1]
script = """StartLiveData(UpdateEvery='10',Instrument='"""
script += self.instrument_name
diff --git a/scripts/Interface/reduction_gui/reduction/output_script.py b/scripts/Interface/reduction_gui/reduction/output_script.py
index ce485383ee73da01f4dcc8ee4eddc9506cfcde2f..a1dc06f729158ae1d5ec5916f3020e5453647919 100644
--- a/scripts/Interface/reduction_gui/reduction/output_script.py
+++ b/scripts/Interface/reduction_gui/reduction/output_script.py
@@ -1,5 +1,6 @@
#pylint: disable=invalid-name
from scripter import BaseScriptElement
+import sys
# Check whether we are running in MantidPlot
IS_IN_MANTIDPLOT = False
diff --git a/scripts/Interface/reduction_gui/reduction/reflectometer/refl_sf_calculator.py b/scripts/Interface/reduction_gui/reduction/reflectometer/refl_sf_calculator.py
index 2f6aa39f0c87a6090c653599e721b0d702f811ee..db262d8cd71e1e85380d3efd74f9b281e77cf1f4 100644
--- a/scripts/Interface/reduction_gui/reduction/reflectometer/refl_sf_calculator.py
+++ b/scripts/Interface/reduction_gui/reduction/reflectometer/refl_sf_calculator.py
@@ -156,7 +156,7 @@ class REFLSFCalculatorScripter(BaseReductionScripter):
_script = self.create_script(script_part2)
if _script == '':
- print 'Please define a Scaling Factor File Name'
+ print('Please define a Scaling Factor File Name')
raise RuntimeError
script += _script
@@ -175,14 +175,14 @@ class REFLSFCalculatorScripter(BaseReductionScripter):
if HAS_MANTID:
script = self.to_script(None)
- print script
+ print(script)
try:
t0 = time.time()
- exec script
+ exec(script)
delta_t = time.time()-t0
- print REF_RED_OUTPUT_MESSAGE
- print "SF calculation time: %5.2g sec" % delta_t
+ print("REF_RED_OUTPUT_MESSAGE")
+ print("SF calculation time: %5.2g sec" % delta_t)
# Update scripter
for item in self._observers:
if item.state() is not None:
@@ -196,6 +196,6 @@ class REFLSFCalculatorScripter(BaseReductionScripter):
item.state().update()
except:
pass
- raise RuntimeError(sys.exc_value)
+ raise RuntimeError(sys.exc_info()[1])
else:
raise RuntimeError("SF calculation could not be executed: Mantid could not be imported")
diff --git a/scripts/Interface/reduction_gui/reduction/reflectometer/refl_sf_calculator_data_script.py b/scripts/Interface/reduction_gui/reduction/reflectometer/refl_sf_calculator_data_script.py
index 1d79a37982c377cb9182dddfd30a8bab1adda390..ea85b3fc56911cdce8851e3fd192150ebfa73446 100644
--- a/scripts/Interface/reduction_gui/reduction/reflectometer/refl_sf_calculator_data_script.py
+++ b/scripts/Interface/reduction_gui/reduction/reflectometer/refl_sf_calculator_data_script.py
@@ -89,9 +89,7 @@ class DataSets(BaseScriptElement):
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
self.from_xml_element(dom)
- element_list = dom.getElementsByTagName("RefLSFCalculator")
- if len(element_list)>0:
- instrument_dom = element_list[0]
+ dom.getElementsByTagName("RefLSFCalculator")
def from_xml_element(self, instrument_dom):
"""
diff --git a/scripts/Interface/reduction_gui/reduction/reflectometer/refm_data_script.py b/scripts/Interface/reduction_gui/reduction/reflectometer/refm_data_script.py
index 2e86224f60fb60818b47c2f0d8598db9ec2be596..30ece94dd30c7b10d75101ee91d635e083bb382c 100644
--- a/scripts/Interface/reduction_gui/reduction/reflectometer/refm_data_script.py
+++ b/scripts/Interface/reduction_gui/reduction/reflectometer/refm_data_script.py
@@ -234,9 +234,7 @@ class DataSets(BaseScriptElement):
self.reset()
dom = xml.dom.minidom.parseString(xml_str)
self.from_xml_element(dom)
- element_list = dom.getElementsByTagName("RefMData")
- if len(element_list) > 0:
- instrument_dom = element_list[0]
+ dom.getElementsByTagName("RefMData")
def from_xml_element(self, instrument_dom):
"""
diff --git a/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py b/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
index d06336dbf6016858ef24eb2876b315f68085f6ca..1116c5b1cd9289691de4c4abf961b0012794f6fc 100644
--- a/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
+++ b/scripts/Interface/reduction_gui/widgets/reflectometer/base_ref_reduction.py
@@ -2,11 +2,13 @@
import math
import time
import sys
+import os
from functools import partial
import numpy as np
from PyQt4 import QtGui, QtCore
import reduction_gui.widgets.util as util
from reduction_gui.widgets.base_widget import BaseWidget
+
# from launch_peak_back_selection_1d import DesignerMainWindow
IS_IN_MANTIDPLOT = False
@@ -14,12 +16,12 @@ try:
# from MantidFramework import *
# mtd.initialise(False)
# from mantidsimple import *
- from mantid.simpleapi import *
+ import mantid.simpleapi as mantid
from reduction.instruments.reflectometer import data_manipulation
IS_IN_MANTIDPLOT = True
-except ImportError, e:
- logger.error(e.message())
+except ImportError as e:
+ mantid.logger.error(e)
class BaseRefWidget(BaseWidget):
@@ -57,14 +59,16 @@ class BaseRefWidget(BaseWidget):
# Validators
self._summary.data_peak_from_pixel.setValidator(QtGui.QIntValidator(self._summary.data_peak_from_pixel))
self._summary.data_peak_to_pixel.setValidator(QtGui.QIntValidator(self._summary.data_peak_to_pixel))
- self._summary.data_background_from_pixel1.setValidator(QtGui.QIntValidator(self._summary.data_background_from_pixel1))
- self._summary.data_background_to_pixel1.setValidator(QtGui.QIntValidator(self._summary.data_background_to_pixel1))
+ self._summary.data_background_from_pixel1.setValidator(
+ QtGui.QIntValidator(self._summary.data_background_from_pixel1))
+ self._summary.data_background_to_pixel1.setValidator(
+ QtGui.QIntValidator(self._summary.data_background_to_pixel1))
self._summary.data_from_tof.setValidator(QtGui.QIntValidator(self._summary.data_from_tof))
self._summary.data_to_tof.setValidator(QtGui.QIntValidator(self._summary.data_to_tof))
self._summary.dq0.setValidator(QtGui.QDoubleValidator(self._summary.dq0))
self._summary.dq_over_q.setValidator(QtGui.QDoubleValidator(self._summary.dq_over_q))
-# self._summary.overlapValueMeanRadioButton(QtGui.setChecked(False)
-# self._summary.overlapValueLowestErrorRadioButton.setChecked(True)
+ # self._summary.overlapValueMeanRadioButton(QtGui.setChecked(False)
+ # self._summary.overlapValueLowestErrorRadioButton.setChecked(True)
self._summary.x_min_edit.setValidator(QtGui.QDoubleValidator(self._summary.x_min_edit))
self._summary.x_max_edit.setValidator(QtGui.QDoubleValidator(self._summary.x_max_edit))
@@ -75,12 +79,15 @@ class BaseRefWidget(BaseWidget):
self._summary.q_min_edit.setValidator(QtGui.QDoubleValidator(self._summary.q_min_edit))
self._summary.angle_offset_edit.setValidator(QtGui.QDoubleValidator(self._summary.angle_offset_edit))
- self._summary.angle_offset_error_edit.setValidator(QtGui.QDoubleValidator(self._summary.angle_offset_error_edit))
+ self._summary.angle_offset_error_edit.setValidator(
+ QtGui.QDoubleValidator(self._summary.angle_offset_error_edit))
self._summary.norm_peak_from_pixel.setValidator(QtGui.QIntValidator(self._summary.norm_peak_from_pixel))
self._summary.norm_peak_to_pixel.setValidator(QtGui.QIntValidator(self._summary.norm_peak_to_pixel))
- self._summary.norm_background_from_pixel1.setValidator(QtGui.QIntValidator(self._summary.norm_background_from_pixel1))
- self._summary.norm_background_to_pixel1.setValidator(QtGui.QIntValidator(self._summary.norm_background_to_pixel1))
+ self._summary.norm_background_from_pixel1.setValidator(
+ QtGui.QIntValidator(self._summary.norm_background_from_pixel1))
+ self._summary.norm_background_to_pixel1.setValidator(
+ QtGui.QIntValidator(self._summary.norm_background_to_pixel1))
# Event connections
self.connect(self._summary.data_run_number_edit, QtCore.SIGNAL("returnPressed()"),
@@ -225,7 +232,7 @@ class BaseRefWidget(BaseWidget):
This retrieve the metadata from the data event NeXus filename
"""
_full_file_name = filename
- tmpWks = LoadEventNexus(Filename=_full_file_name,MetaDataOnly='1')
+ tmpWks = mantid.LoadEventNexus(Filename=_full_file_name, MetaDataOnly='1')
isSi = False
@@ -257,7 +264,7 @@ class BaseRefWidget(BaseWidget):
except:
s2w = mt_run.getProperty('S2HWidth').value[0]
- return [tthd,ths, lambda_requested, s1h, s2h, s1w, s2w, isSi]
+ return [tthd, ths, lambda_requested, s1h, s2h, s1w, s2w, isSi]
def data_run_number_validated(self):
"""
@@ -265,30 +272,30 @@ class BaseRefWidget(BaseWidget):
number and will retrieve some of the metadata and display them
in the metadata box
"""
-# self._summary.data_run_number_processing.show()
+ # self._summary.data_run_number_processing.show()
run_number = self._summary.data_run_number_edit.text()
try:
- _file = FileFinder.findRuns("REF_L%d"%int(run_number))[0]
+ _file = mantid.FileFinder.findRuns("REF_L%d" % int(run_number))[0]
- metadata= self.getMetadata(_file)
+ metadata = self.getMetadata(_file)
- #tthd
+ # tthd
tthd_value = metadata[0]
tthd_value_string = '{0:.2f}'.format(tthd_value)
self._summary.tthd_value.setText(tthd_value_string)
- #ths
+ # ths
ths_value = metadata[1]
ths_value_string = '{0:.2f}'.format(ths_value)
self._summary.ths_value.setText(ths_value_string)
- #lambda requested
+ # lambda requested
lambda_value = metadata[2]
lambda_value_string = '{0:.2f}'.format(lambda_value)
self._summary.lambda_request.setText(lambda_value_string)
- #s1h, s2h, s1w and s2w
+ # s1h, s2h, s1w and s2w
s1h_value = metadata[3]
s1h_value_string = '{0:.2f}'.format(s1h_value)
self._summary.s1h.setText(s1h_value_string)
@@ -309,17 +316,17 @@ class BaseRefWidget(BaseWidget):
self._summary.s2w.setText(s2w_value_string)
isSi = metadata[7]
- print isSi
+ print(isSi)
if isSi:
self._summary.label_25.setText("Si height:")
self._summary.label_27.setText("Si width:")
else:
self._summary.label25.setText("S2 height:")
self._summary.label27.setText("S2 width:")
-# self._summary.data_run_number_processing.hide()
+ # self._summary.data_run_number_processing.hide()
except:
pass
-# self._summary.data_run_number_processing.hide()
+ # self._summary.data_run_number_processing.hide()
def _output_dir_browse(self):
output_dir = QtGui.QFileDialog.getExistingDirectory(self, "Output Directory - Choose a directory",
@@ -334,22 +341,22 @@ class BaseRefWidget(BaseWidget):
This method will do an weighted average of the value when
their x-axis is within a given range (precision)
"""
- _precision = 0.1/100. #0.1%
+ _precision = 0.1 / 100. # 0.1%
new_x_axis = []
new_y_axis = []
new_e_axis = []
-# if self.bDEBUG:
-# print 'x_axis before _smooth_x_axis:'
-# print x_axis
+ # if self.bDEBUG:
+ # print 'x_axis before _smooth_x_axis:'
+ # print x_axis
sz = len(x_axis)
- i=0
- while i < sz-1:
+ i = 0
+ while i < sz - 1:
_left_x = x_axis[i]
- _right_x = x_axis[i+1]
+ _right_x = x_axis[i + 1]
bCalAverage = False
if _left_x == _right_x:
@@ -367,26 +374,26 @@ class BaseRefWidget(BaseWidget):
if bCalAverage:
- #average the two values
- _right_e = e_axis[i+1]
+ # average the two values
+ _right_e = e_axis[i + 1]
_right_e2 = _right_e * _right_e
- _right_y = y_axis[i+1]
+ _right_y = y_axis[i + 1]
if _left_e2 == 0. or _right_e2 == 0.:
_y = 0.
_e = 0.
else:
- _error = 1./_left_e2 + 1./_right_e2
+ _error = 1. / _left_e2 + 1. / _right_e2
_x = (_left_x + _right_x) / 2.
- _y = (_left_y/_left_e2 + _right_y/_right_e2) / _error
- _e = math.sqrt(1./_error)
+ _y = (_left_y / _left_e2 + _right_y / _right_e2) / _error
+ _e = math.sqrt(1. / _error)
new_x_axis.append(_x)
new_y_axis.append(_y)
new_e_axis.append(_e)
- i+=1
+ i += 1
else:
@@ -394,12 +401,12 @@ class BaseRefWidget(BaseWidget):
new_y_axis.append(y_axis[i])
new_e_axis.append(e_axis[i])
- i+=1
+ i += 1
-# if self.bDEBUG:
-# print
-# print 'x-axis after _smooth_x_axis:'
-# print new_x_axis
+ # if self.bDEBUG:
+ # print
+ # print 'x-axis after _smooth_x_axis:'
+ # print new_x_axis
self.x_axis = new_x_axis
self.y_axis = new_y_axis
@@ -420,7 +427,7 @@ class BaseRefWidget(BaseWidget):
dataDen = 0
for i in range(sz):
if error_array[i] != 0:
- tmpFactor = 1./float((pow(error_array[i], 2)))
+ tmpFactor = 1. / float((pow(error_array[i], 2)))
dataDen += tmpFactor
if dataDen == 0:
@@ -428,7 +435,7 @@ class BaseRefWidget(BaseWidget):
mean_error = 0
else:
mean = float(dataNum) / float(dataDen)
- mean_error = math.sqrt(1/dataDen)
+ mean_error = math.sqrt(1 / dataDen)
return [mean, mean_error]
@@ -438,7 +445,7 @@ class BaseRefWidget(BaseWidget):
the weighted mean
"""
- ws_list = AnalysisDataService.getObjectNames()
+ ws_list = mantid.AnalysisDataService.getObjectNames()
scaled_ws_list = []
# Get the list of scaled histos
@@ -455,19 +462,19 @@ class BaseRefWidget(BaseWidget):
# Convert each histo to histograms and rebin to final binning
for ws in scaled_ws_list:
new_name = "%s_histo" % ws
- ConvertToHistogram(InputWorkspace=ws, OutputWorkspace=new_name)
- Rebin(InputWorkspace=new_name, Params=binning_parameters,
- OutputWorkspace=new_name)
+ mantid.ConvertToHistogram(InputWorkspace=ws, OutputWorkspace=new_name)
+ mantid.Rebin(InputWorkspace=new_name, Params=binning_parameters,
+ OutputWorkspace=new_name)
# Take the first rebinned histo as our output
- data_y = mtd[scaled_ws_list[0]+'_histo'].dataY(0)
- data_e = mtd[scaled_ws_list[0]+'_histo'].dataE(0)
+ data_y = mantid.mtd[scaled_ws_list[0] + '_histo'].dataY(0)
+ data_e = mantid.mtd[scaled_ws_list[0] + '_histo'].dataE(0)
# Add in the other histos, averaging the overlaps
for scaled_ws in scaled_ws_list:
y_val_index = 0
- data_y_i = mtd[scaled_ws +'_histo'].dataY(0)
- data_e_i = mtd[scaled_ws+'_histo'].dataE(0)
+ data_y_i = mantid.mtd[scaled_ws + '_histo'].dataY(0)
+ data_e_i = mantid.mtd[scaled_ws + '_histo'].dataE(0)
for y_val in data_y_i:
y_val_index += 1
if data_y[y_val_index] > 0 and y_val > 0:
@@ -478,7 +485,7 @@ class BaseRefWidget(BaseWidget):
data_y[y_val_index] = y_val
data_e[y_val_index] = data_e_i[y_val_index]
- return scaled_ws_list[0]+'_histo'
+ return scaled_ws_list[0] + '_histo'
def _produce_y_of_same_x_(self, isUsingLessErrorValue):
"""
@@ -486,7 +493,7 @@ class BaseRefWidget(BaseWidget):
the weighted mean
"""
- ws_list = AnalysisDataService.getObjectNames()
+ ws_list = mantid.AnalysisDataService.getObjectNames()
scaled_ws_list = []
# Get the list of scaled histos
@@ -502,17 +509,13 @@ class BaseRefWidget(BaseWidget):
# DEBUGGING ONLY
_file_number = 0
-# print '=========== BEFORE REBINING =========='
+ # print '=========== BEFORE REBINING =========='
for ws in scaled_ws_list:
# print 'file_number: ' , file_number
- data_y = mtd[ws].dataY(0)
+ data_y = mantid.mtd[ws].dataY(0)
# cleanup data 0-> NAN
- for y_val in data_y:
- # print '-> data_y[j]: ' , data_y[j] , ' data_e[j]: ' , data_y[j]
- if y_val < 1e-12:
- _y_val = np.nan
-
+ data_y = [np.nan if y_val < 1e-12 else y_val for y_val in data_y]
_file_number += 1
# END OF DEBUGGING ONLY
@@ -520,38 +523,38 @@ class BaseRefWidget(BaseWidget):
# Convert each histo to histograms and rebin to final binning
for ws in scaled_ws_list:
new_name = "%s_histo" % ws
- ConvertToHistogram(InputWorkspace=ws, OutputWorkspace=new_name)
-# mtd[new_name].setDistribution(True)
- Rebin(InputWorkspace=new_name, Params=binning_parameters,
- OutputWorkspace=new_name)
+ mantid.ConvertToHistogram(InputWorkspace=ws, OutputWorkspace=new_name)
+ # mtd[new_name].setDistribution(True)
+ mantid.Rebin(InputWorkspace=new_name, Params=binning_parameters,
+ OutputWorkspace=new_name)
# Take the first rebinned histo as our output
- data_y = mtd[scaled_ws_list[0]+'_histo'].dataY(0)
- data_e = mtd[scaled_ws_list[0]+'_histo'].dataE(0)
+ data_y = mantid.mtd[scaled_ws_list[0] + '_histo'].dataY(0)
+ data_e = mantid.mtd[scaled_ws_list[0] + '_histo'].dataE(0)
# skip first 3 points and last one
skip_index = 0
point_to_skip = 3
-# print '============ AFTER REBINING ================' #DEBUGGING ONLY
+ # print '============ AFTER REBINING ================' #DEBUGGING ONLY
# Add in the other histos, averaging the overlaps
for i in range(1, len(scaled_ws_list)):
-# print 'i: ' , i
+ # print 'i: ' , i
skip_point = True
can_skip_last_point = False
- data_y_i = mtd[scaled_ws_list[i]+'_histo'].dataY(0)
- data_e_i = mtd[scaled_ws_list[i]+'_histo'].dataE(0)
- for j in range(len(data_y_i)-1):
+ data_y_i = mantid.mtd[scaled_ws_list[i] + '_histo'].dataY(0)
+ data_e_i = mantid.mtd[scaled_ws_list[i] + '_histo'].dataE(0)
+ for j in range(len(data_y_i) - 1):
-# print '-> j: ' , j
+ # print '-> j: ' , j
if data_y_i[j] > 0:
-# print ' data_y_i[j]: ', data_y_i[j], ' data_e_i[j]: ' , data_e_i[j]
+ # print ' data_y_i[j]: ', data_y_i[j], ' data_e_i[j]: ' , data_e_i[j]
can_skip_last_point = True
if skip_point:
@@ -562,10 +565,10 @@ class BaseRefWidget(BaseWidget):
else:
continue
- if can_skip_last_point and (data_y_i[j+1]==0):
+ if can_skip_last_point and (data_y_i[j + 1] == 0):
break
- if data_y[j]>0 and data_y_i[j]>0:
+ if data_y[j] > 0 and data_y_i[j] > 0:
if isUsingLessErrorValue:
if data_e[j] > data_e_i[j]:
@@ -574,33 +577,33 @@ class BaseRefWidget(BaseWidget):
else:
[data_y[j], data_e[j]] = self.weightedMean([data_y[j], data_y_i[j]], [data_e[j], data_e_i[j]])
- elif (data_y[j] == 0) and (data_y_i[j]>0):
+ elif (data_y[j] == 0) and (data_y_i[j] > 0):
data_y[j] = data_y_i[j]
data_e[j] = data_e_i[j]
- return scaled_ws_list[0]+'_histo'
+ return scaled_ws_list[0] + '_histo'
def _create_ascii_clicked(self):
"""
Reached by the 'Create ASCII' button
"""
- #make sure there is the right output workspace called '
-# if not mtd.workspaceExists('ref_combined'):
-# print 'Workspace "ref_combined" does not exist !'
-# return
+ # make sure there is the right output workspace called '
+ # if not mtd.workspaceExists('ref_combined'):
+ # print 'Workspace "ref_combined" does not exist !'
+ # return
- #get default output file name
+ # get default output file name
run_number = self._summary.data_run_number_edit.text()
default_file_name = 'REFL_' + run_number + '_combined_data.txt'
- #retrieve name of the output file
+ # retrieve name of the output file
file_name = QtGui.QFileDialog.getSaveFileName(self, "Select or define a ASCII file name", default_file_name,
"(*.txt)")
if str(file_name).strip() == '':
return
- #check the status of the 4th column switch
+ # check the status of the 4th column switch
_with_4th_flag = self._summary.fourth_column_switch.isChecked()
text = []
if _with_4th_flag:
@@ -613,36 +616,36 @@ class BaseRefWidget(BaseWidget):
else:
text = ['#Q(1/Angstrom) R delta_R']
-# #rebinned using output factors
-# q_min = float(self._summary.q_min_edit.text())
-# q_bin = -float(self._summary.q_step_edit.text())
-#
-# mt = mtd['ref_combined']
-# x_axis = mt.readX(0)[:]
-# q_max = float(x_axis[-1])
-#
-# q_binning = [q_min, q_bin, q_max]
-# Rebin(InputWorkspace='ref_combined',
-# OutputWorkspace='ref_combined',
-# Params=q_binning)
-
- #using mean or value with less error
+ # #rebinned using output factors
+ # q_min = float(self._summary.q_min_edit.text())
+ # q_bin = -float(self._summary.q_step_edit.text())
+ #
+ # mt = mtd['ref_combined']
+ # x_axis = mt.readX(0)[:]
+ # q_max = float(x_axis[-1])
+ #
+ # q_binning = [q_min, q_bin, q_max]
+ # Rebin(InputWorkspace='ref_combined',
+ # OutputWorkspace='ref_combined',
+ # Params=q_binning)
+
+ # using mean or value with less error
_overlap_less_error_flag = self._summary.overlapValueLowestErrorRadioButton.isChecked()
wks_file_name = self._produce_y_of_same_x_(_overlap_less_error_flag)
-# print 'wks_file_name: ' , wks_file_name
+ # print 'wks_file_name: ' , wks_file_name
-# mt = mtd['ref_combined']
-# x_axis = mt.readX(0)[:]
-# y_axis = mt.readY(0)[:]
-# e_axis = mt.readE(0)[:]
-#
-# self._smooth_x_axis(x_axis, y_axis, e_axis)
+ # mt = mtd['ref_combined']
+ # x_axis = mt.readX(0)[:]
+ # y_axis = mt.readY(0)[:]
+ # e_axis = mt.readE(0)[:]
+ #
+ # self._smooth_x_axis(x_axis, y_axis, e_axis)
- x_axis = mtd[wks_file_name].readX(0)[:]
- y_axis = mtd[wks_file_name].readY(0)[:]
- e_axis = mtd[wks_file_name].readE(0)[:]
+ x_axis = mantid.mtd[wks_file_name].readX(0)[:]
+ y_axis = mantid.mtd[wks_file_name].readY(0)[:]
+ e_axis = mantid.mtd[wks_file_name].readE(0)[:]
- sz = len(x_axis)-1
+ sz = len(x_axis) - 1
for i in range(sz):
# do not display data where R=0
if y_axis[i] > 1e-15:
@@ -654,7 +657,7 @@ class BaseRefWidget(BaseWidget):
_line += ' ' + _precision
text.append(_line)
- f=open(file_name,'w')
+ f = open(file_name, 'w')
for _line in text:
f.write(_line + '\n')
@@ -669,7 +672,7 @@ class BaseRefWidget(BaseWidget):
self._summary.cfg_scaling_factor_file_name.setText(file_name)
self.retrieve_list_of_incident_medium(file_name)
except:
- print 'Invalid file format (' + file_name + ')'
+ print('Invalid file format (' + file_name + ')')
def variable_value_splitter(self, variable_value):
"""
@@ -679,7 +682,7 @@ class BaseRefWidget(BaseWidget):
_split = variable_value.split('=')
variable = _split[0]
value = _split[1]
- return {'variable':variable, 'value':value}
+ return {'variable': variable, 'value': value}
def retrieve_list_of_incident_medium(self, cfg_file_name):
"""
@@ -687,7 +690,7 @@ class BaseRefWidget(BaseWidget):
populate the Incident Medium dropbox with the list of incident medium
found
"""
- f=open(cfg_file_name,'r')
+ f = open(cfg_file_name, 'r')
text = f.readlines()
list_incident_medium = []
for _line in text:
@@ -761,7 +764,7 @@ class BaseRefWidget(BaseWidget):
m.data_files = ["runNumber"]
reduce_script = m.to_script(True)
- content = "# Script automatically generated by Mantid on %s\n" % time.ctime()
+ content = "# Script automatically generated by Mantid on %s\n" % time.ctime()
content += "import sys\n"
content += "import os\n"
content += "if (os.environ.has_key(\"MANTIDPATH\")):\n"
@@ -794,7 +797,7 @@ class BaseRefWidget(BaseWidget):
xml_str += " <timestamp>%s</timestamp>\n" % time.ctime()
xml_str += " <python_version>%s</python_version>\n" % sys.version
if IS_IN_MANTIDPLOT:
- xml_str += " <mantid_version>%s</mantid_version>\n" % mantid_build_version()
+ xml_str += " <mantid_version>%s</mantid_version>\n" % mantid.mantid_build_version()
xml_str += m.to_xml()
xml_str += "</Reduction>\n"
@@ -817,7 +820,7 @@ class BaseRefWidget(BaseWidget):
content += " CommentIndicator='# ')\n"
home_dir = os.path.expanduser('~')
- f=open(os.path.join(home_dir,"reduce_%s.py" % self.instrument_name),'w')
+ f = open(os.path.join(home_dir, "reduce_%s.py" % self.instrument_name), 'w')
f.write(content)
f.close()
@@ -825,23 +828,23 @@ class BaseRefWidget(BaseWidget):
def _report_error(error=None):
message = ""
if error is not None:
- message += error+'\n\n'
+ message += error + '\n\n'
else:
message += "The automated reduction script could not be saved.\n\n"
message += "Your script has been saved in your home directory:\n"
- message += os.path.join(home_dir,"reduce_%s.py" % self.instrument_name)
+ message += os.path.join(home_dir, "reduce_%s.py" % self.instrument_name)
message += "\n\nTry copying it by hand in %s\n" % sns_path
QtGui.QMessageBox.warning(self, "Error saving automated reduction script", message)
sns_path = "/SNS/%s/shared/autoreduce" % self.instrument_name
if os.path.isdir(sns_path):
if os.access(sns_path, os.W_OK):
- file_path = os.path.join(sns_path,"reduce_%s.py" % self.instrument_name)
+ file_path = os.path.join(sns_path, "reduce_%s.py" % self.instrument_name)
if os.path.isfile(file_path) and not os.access(file_path, os.W_OK):
_report_error("You do not have permissions to overwrite %s." % file_path)
return
try:
- f = open(file_path,'w')
+ f = open(file_path, 'w')
f.write(content)
f.close()
QtGui.QMessageBox.information(self, "Automated reduction script saved",
@@ -865,12 +868,12 @@ class BaseRefWidget(BaseWidget):
self._summary.auto_reduce_btn.hide()
def _remove_item(self):
- if self._summary.angle_list.count()==0:
+ if self._summary.angle_list.count() == 0:
return
self._summary.angle_list.setEnabled(False)
self._summary.remove_btn.setEnabled(False)
row = self._summary.angle_list.currentRow()
- if row>=0:
+ if row >= 0:
self._summary.angle_list.takeItem(row)
self._summary.angle_list.setEnabled(True)
self._summary.remove_btn.setEnabled(True)
@@ -981,7 +984,7 @@ class BaseRefWidget(BaseWidget):
self._summary.tof_max_label.setEnabled(is_checked)
self._summary.data_to_tof.setEnabled(is_checked)
self._summary.tof_max_label2.setEnabled(is_checked)
- #self._summary.plot_tof_btn.setEnabled(is_checked)
+ # self._summary.plot_tof_btn.setEnabled(is_checked)
self._edit_event(None, self._summary.tof_range_switch)
@@ -1001,40 +1004,40 @@ class BaseRefWidget(BaseWidget):
For REFM, this is X
For REFL, this is Y
"""
-# run_number = self._summary.data_run_number_edit.text()
-# f = FileFinder.findRuns("%s%s" % (self.instrument_name, str(run_number)))[0]
-#
-# #range_min = int(min_ctrl.text())
-# #range_max = int(max_ctrl.text())
-#
-# # For REFL, Y is high-res
-# is_pixel_y = True
-# is_high_res = True
-# isPeak = True
-# min, max = data_manipulation.counts_vs_pixel_distribution(f, is_pixel_y=is_pixel_y,
-# high_res=is_high_res,
-# instrument=self.short_name,
-# isPeak=isPeak)
-#
-# # for low res
-# is_high_res = False
-# is_pixel_y = False
-# min, max = data_manipulation.counts_vs_pixel_distribution(f, is_pixel_y=is_pixel_y,
-# high_res=is_high_res,
-# instrument=self.short_name,
-# isPeak=isPeak)
-#
-#
-# basename = os.path.basename(f)
-# wk1 = "Peak - " + basename + " - Y pixel "
-# wk2 = "Peak - " + basename + " - X pixel "
-# dmw = DesignerMainWindow(parent=self, wk1=wk1, wk2=wk2, type='data')
-#
-# # show it
-# dmw.show()
-# # start the Qt main loop execution, existing from this script
-# # with the same return code of Qt application
-## sys.exit(app.exec_())
+ # run_number = self._summary.data_run_number_edit.text()
+ # f = FileFinder.findRuns("%s%s" % (self.instrument_name, str(run_number)))[0]
+ #
+ # #range_min = int(min_ctrl.text())
+ # #range_max = int(max_ctrl.text())
+ #
+ # # For REFL, Y is high-res
+ # is_pixel_y = True
+ # is_high_res = True
+ # isPeak = True
+ # min, max = data_manipulation.counts_vs_pixel_distribution(f, is_pixel_y=is_pixel_y,
+ # high_res=is_high_res,
+ # instrument=self.short_name,
+ # isPeak=isPeak)
+ #
+ # # for low res
+ # is_high_res = False
+ # is_pixel_y = False
+ # min, max = data_manipulation.counts_vs_pixel_distribution(f, is_pixel_y=is_pixel_y,
+ # high_res=is_high_res,
+ # instrument=self.short_name,
+ # isPeak=isPeak)
+ #
+ #
+ # basename = os.path.basename(f)
+ # wk1 = "Peak - " + basename + " - Y pixel "
+ # wk2 = "Peak - " + basename + " - X pixel "
+ # dmw = DesignerMainWindow(parent=self, wk1=wk1, wk2=wk2, type='data')
+ #
+ # # show it
+ # dmw.show()
+ # # start the Qt main loop execution, existing from this script
+ # # with the same return code of Qt application
+ ## sys.exit(app.exec_())
_minimum, _maximum = self._integrated_plot(True,
self._summary.data_run_number_edit,
@@ -1080,73 +1083,73 @@ class BaseRefWidget(BaseWidget):
"""
# retrieve name of workspace first
- run_number = self._summary.data_run_number_edit.text()
- file_path = FileFinder.findRuns("%s%s" % (self.instrument_name, str(run_number)))[0]
+ run_number = self._summary.data_run_number_edit.text()
+ file_path = mantid.FileFinder.findRuns("%s%s" % (self.instrument_name, str(run_number)))[0]
basename = os.path.basename(file_path)
-# if self.instrument_name == 'REF_L':
-# ws_output_base = "Pixel Y vs TOF" + " - " + basename
-# else:
-# ws_output_base = "Pixel X vs TOF" + " - " + basename
-
-# if (self.instrument_name == 'REF_L'):
-# if isPeak:
-# type = 'Peak'
-# else:
-# type = 'Background'
-# if is_pixel_y is False:
-# x_title = "X pixel"
-# else:
-# x_title = "Y pixel"
-# ws_output_base = type + " - " + basename + " - " + x_title
-# else:
-# ws_output_base = "Counts vs TOF - %s" % basename
-# x_title = "Y pixel"
-# if is_pixel_y is False:
-# ws_output_base = "Counts vs X pixel - %s" % basename
-# x_title = "X pixel"
-
-# range_min = int(self._summary.data_from_tof.text())
-# range_max = int(self._summary.data_to_tof.text())
+ # if self.instrument_name == 'REF_L':
+ # ws_output_base = "Pixel Y vs TOF" + " - " + basename
+ # else:
+ # ws_output_base = "Pixel X vs TOF" + " - " + basename
+
+ # if (self.instrument_name == 'REF_L'):
+ # if isPeak:
+ # type = 'Peak'
+ # else:
+ # type = 'Background'
+ # if is_pixel_y is False:
+ # x_title = "X pixel"
+ # else:
+ # x_title = "Y pixel"
+ # ws_output_base = type + " - " + basename + " - " + x_title
+ # else:
+ # ws_output_base = "Counts vs TOF - %s" % basename
+ # x_title = "Y pixel"
+ # if is_pixel_y is False:
+ # ws_output_base = "Counts vs X pixel - %s" % basename
+ # x_title = "X pixel"
+
+ # range_min = int(self._summary.data_from_tof.text())
+ # range_max = int(self._summary.data_to_tof.text())
ws_output_base = "Peak - " + basename + " - Y pixel _2D"
-# if mtd.workspaceExists(ws_output_base):
-# mtd.deleteWorkspace(ws_output_base)
-# ws_output_base_1 = "__" + self.instrument_name + "_" + str(run_number) + "_event.nxs"
-# mtd.deleteWorkspace(ws_output_base_1)
-# ws_output_base_2 = "__" + self.instrument_name + "_" + str(run_number) + "_event.nxs_all"
-# mtd.deleteWorkspace(ws_output_base_2)
-# ws_output_base_3 = "Peak - " + self.instrument_name + "_" + str(run_number) + "_event.nxs - Y pixel "
-# mtd.deleteWorkspace(ws_output_base_3)
-
- if mtd.doesExist(ws_output_base):
- DeleteWorkspace(ws_output_base)
+ # if mtd.workspaceExists(ws_output_base):
+ # mtd.deleteWorkspace(ws_output_base)
+ # ws_output_base_1 = "__" + self.instrument_name + "_" + str(run_number) + "_event.nxs"
+ # mtd.deleteWorkspace(ws_output_base_1)
+ # ws_output_base_2 = "__" + self.instrument_name + "_" + str(run_number) + "_event.nxs_all"
+ # mtd.deleteWorkspace(ws_output_base_2)
+ # ws_output_base_3 = "Peak - " + self.instrument_name + "_" + str(run_number) + "_event.nxs - Y pixel "
+ # mtd.deleteWorkspace(ws_output_base_3)
+
+ if mantid.mtd.doesExist(ws_output_base):
+ mantid.DeleteWorkspace(ws_output_base)
ws_output_base_1 = "__" + self.instrument_name + "_" + str(run_number) + "_event.nxs"
- DeleteWorkspace(ws_output_base_1)
+ mantid.DeleteWorkspace(ws_output_base_1)
ws_output_base_2 = "__" + self.instrument_name + "_" + str(run_number) + "_event.nxs_all"
- DeleteWorkspace(ws_output_base_2)
+ mantid.DeleteWorkspace(ws_output_base_2)
ws_output_base_3 = "Peak - " + self.instrument_name + "_" + str(run_number) + "_event.nxs - Y pixel "
- DeleteWorkspace(ws_output_base_3)
+ mantid.DeleteWorkspace(ws_output_base_3)
data_manipulation.counts_vs_pixel_distribution(file_path,
is_pixel_y=True,
callback=None,
instrument='REFL')
-# def call_back(peakmin, peakmax, backmin, backmax, tofmin, tofmax):
-# print 'Inside the call_back on the python side'
-# self._summary.data_peak_from_pixel.setText("%-d" % int(peakmin))
-# self._summary.data_peak_to_pixel.setText("%-d" % int(peakmax))
-# self._summary.data_background_from_pixel1.setText("%-d" % int(backmin))
-# self._summary.data_background_to_pixel1.setText("%-d" % int(backmax))
-# self._summary.x_min_edit.setText("%-d" % int(tofmin))
-# self._summary.x_max_edit.setText("%-d" % int(tofmax))
+ # def call_back(peakmin, peakmax, backmin, backmax, tofmin, tofmax):
+ # print 'Inside the call_back on the python side'
+ # self._summary.data_peak_from_pixel.setText("%-d" % int(peakmin))
+ # self._summary.data_peak_to_pixel.setText("%-d" % int(peakmax))
+ # self._summary.data_background_from_pixel1.setText("%-d" % int(backmin))
+ # self._summary.data_background_to_pixel1.setText("%-d" % int(backmax))
+ # self._summary.x_min_edit.setText("%-d" % int(tofmin))
+ # self._summary.x_max_edit.setText("%-d" % int(tofmax))
# mantidplot.app should be used instead of _qti.app (it's just an alias)
- #mantidplot.app.connect(mantidplot.app.mantidUI, QtCore.SIGNAL("python_peak_back_tof_range_update(double,double,
+ # mantidplot.app.connect(mantidplot.app.mantidUI, QtCore.SIGNAL("python_peak_back_tof_range_update(double,double,
# double,double,double,double)"), call_back)
- #mantidplot.app.connect(mantidplot.app.RefDetectorViewer, QtCore.SIGNAL("python_peak_back_tof_range_update
+ # mantidplot.app.connect(mantidplot.app.RefDetectorViewer, QtCore.SIGNAL("python_peak_back_tof_range_update
# (double,double,double,double,double,double)"), call_back)
peak_min = int(self._summary.data_peak_from_pixel.text())
@@ -1174,40 +1177,40 @@ class BaseRefWidget(BaseWidget):
def _norm_count_vs_y(self):
-# run_number = self._summary.norm_run_number_edit.text()
-# f = FileFinder.findRuns("%s%s" % (self.instrument_name, str(run_number)))[0]
-#
-# #range_min = int(min_ctrl.text())
-# #range_max = int(max_ctrl.text())
-#
-# # For REFL, Y is high-res
-# is_pixel_y = True
-# is_high_res = True
-# isPeak = True
-# min, max = data_manipulation.counts_vs_pixel_distribution(f, is_pixel_y=is_pixel_y,
-# high_res=is_high_res,
-# instrument=self.short_name,
-# isPeak=isPeak)
-#
-# # for low res
-# is_high_res = False
-# is_pixel_y = False
-# min, max = data_manipulation.counts_vs_pixel_distribution(f, is_pixel_y=is_pixel_y,
-# high_res=is_high_res,
-# instrument=self.short_name,
-# isPeak=isPeak)
-#
-#
-# basename = os.path.basename(f)
-# wk1 = "Peak - " + basename + " - Y pixel "
-# wk2 = "Peak - " + basename + " - X pixel "
-# dmw = DesignerMainWindow(parent=self, wk1=wk1, wk2=wk2, type='norm')
-#
-# # show it
-# dmw.show()
-
-# dmw = DesignerMainWindow(self, 'norm')
-# dmw.show()
+ # run_number = self._summary.norm_run_number_edit.text()
+ # f = FileFinder.findRuns("%s%s" % (self.instrument_name, str(run_number)))[0]
+ #
+ # #range_min = int(min_ctrl.text())
+ # #range_max = int(max_ctrl.text())
+ #
+ # # For REFL, Y is high-res
+ # is_pixel_y = True
+ # is_high_res = True
+ # isPeak = True
+ # min, max = data_manipulation.counts_vs_pixel_distribution(f, is_pixel_y=is_pixel_y,
+ # high_res=is_high_res,
+ # instrument=self.short_name,
+ # isPeak=isPeak)
+ #
+ # # for low res
+ # is_high_res = False
+ # is_pixel_y = False
+ # min, max = data_manipulation.counts_vs_pixel_distribution(f, is_pixel_y=is_pixel_y,
+ # high_res=is_high_res,
+ # instrument=self.short_name,
+ # isPeak=isPeak)
+ #
+ #
+ # basename = os.path.basename(f)
+ # wk1 = "Peak - " + basename + " - Y pixel "
+ # wk2 = "Peak - " + basename + " - X pixel "
+ # dmw = DesignerMainWindow(parent=self, wk1=wk1, wk2=wk2, type='norm')
+ #
+ # # show it
+ # dmw.show()
+
+ # dmw = DesignerMainWindow(self, 'norm')
+ # dmw.show()
_minimum, _maximum = self._integrated_plot(True,
self._summary.norm_run_number_edit,
self._summary.norm_peak_from_pixel,
@@ -1262,7 +1265,7 @@ class BaseRefWidget(BaseWidget):
return None, None
try:
- f = FileFinder.findRuns("%s%s" % (self.instrument_name, str(file_ctrl.text())))[0]
+ f = mantid.FileFinder.findRuns("%s%s" % (self.instrument_name, str(file_ctrl.text())))[0]
range_min = int(min_ctrl.text())
range_max = int(max_ctrl.text())
@@ -1273,7 +1276,7 @@ class BaseRefWidget(BaseWidget):
# For REFL, Y is high-res
- is_pixel_y = is_high_res
+ is_pixel_y = is_high_res
# For REFM it's the other way around
if self.short_name == "REFM":
is_pixel_y = not is_pixel_y
@@ -1287,15 +1290,16 @@ class BaseRefWidget(BaseWidget):
isPeak=isPeak)
return minimum, maximum
- except IOError, e:
- logger.error("Could not find file: " + e.filename())
+ except IOError as e:
+ mantid.logger.error("Could not find file: " + e)
def _plot_tof(self):
if not IS_IN_MANTIDPLOT:
return
try:
- f = FileFinder.findRuns("%s%s" % (self.instrument_name, str(self._summary.norm_run_number_edit.text())))[0]
-# print FileFinder.findRuns("%s%s" % (self.instrument_name, str(self._summary.norm_run_number_edit.text())))
+ f = mantid.FileFinder.findRuns("%s%s" %
+ (self.instrument_name, str(self._summary.norm_run_number_edit.text())))[0]
+ # print FileFinder.findRuns("%s%s" % (self.instrument_name, str(self._summary.norm_run_number_edit.text())))
range_min = int(self._summary.data_from_tof.text())
range_max = int(self._summary.data_to_tof.text())
@@ -1315,14 +1319,14 @@ class BaseRefWidget(BaseWidget):
# Check whether it's already in the list
run_numbers = self._summary.data_run_number_edit.text()
list_items = self._summary.angle_list.findItems(run_numbers, QtCore.Qt.MatchFixedString)
- if len(list_items)>0:
+ if len(list_items) > 0:
list_items[0].setData(QtCore.Qt.UserRole, state)
in_list = True
- #loop over all the already defined states and give all of them the
- #same Qmin, Qsteps, Angle offset, scaling factor config file name
- #and incident medium
- i=0
+ # loop over all the already defined states and give all of them the
+ # same Qmin, Qsteps, Angle offset, scaling factor config file name
+ # and incident medium
+ i = 0
while i < self._summary.angle_list.count():
current_item = self._summary.angle_list.item(i)
@@ -1345,7 +1349,7 @@ class BaseRefWidget(BaseWidget):
state.geometry_correction_switch = self._summary.geometry_correction_switch.isChecked()
- #incident medium
+ # incident medium
_incident_medium_list = [str(self._summary.incident_medium_combobox.itemText(j))
for j in range(self._summary.incident_medium_combobox.count())]
_incident_medium_index_selected = self._summary.incident_medium_combobox.currentIndex()
@@ -1359,12 +1363,12 @@ class BaseRefWidget(BaseWidget):
state.overlap_lowest_error = self._summary.overlapValueLowestErrorRadioButton.isChecked()
state.overlap_mean_value = self._summary.overlapValueMeanRadioButton.isChecked()
- #4th column (precision)
+ # 4th column (precision)
state.fourth_column_dq0 = self._summary.dq0.text()
state.fourth_column_dq_over_q = self._summary.dq_over_q.text()
current_item.setData(QtCore.Qt.UserRole, state)
- i+=1
+ i += 1
else:
item_widget = QtGui.QListWidgetItem(run_numbers, self._summary.angle_list)
@@ -1377,7 +1381,7 @@ class BaseRefWidget(BaseWidget):
state.geometry_correction_switch = self._summary.geometry_correction_switch.isChecked()
- #incident medium
+ # incident medium
_incident_medium_list = [str(self._summary.incident_medium_combobox.itemText(j))
for j in range(self._summary.incident_medium_combobox.count())]
_incident_medium_index_selected = self._summary.incident_medium_combobox.currentIndex()
@@ -1400,11 +1404,11 @@ class BaseRefWidget(BaseWidget):
self._reset_warnings()
def _angle_changed(self):
- if self._summary.angle_list.count()==0:
+ if self._summary.angle_list.count() == 0:
return
self._summary.angle_list.setEnabled(False)
self._summary.remove_btn.setEnabled(False)
- current_item = self._summary.angle_list.currentItem()
+ current_item = self._summary.angle_list.currentItem()
if current_item is not None:
state = current_item.data(QtCore.Qt.UserRole)
self.set_editing_state(state)
@@ -1418,22 +1422,22 @@ class BaseRefWidget(BaseWidget):
@param state: data object
"""
self._summary.angle_list.clear()
- if len(state.data_sets)==1 and state.data_sets[0].data_files[0]==0:
+ if len(state.data_sets) == 1 and state.data_sets[0].data_files[0] == 0:
pass
else:
for item in state.data_sets:
if item is not None:
- item_widget = QtGui.QListWidgetItem(unicode(str(','.join([str(i) for i in item.data_files]))),
+ item_widget = QtGui.QListWidgetItem(str(str(','.join([str(i) for i in item.data_files]))),
self._summary.angle_list)
item_widget.setData(QtCore.Qt.UserRole, item)
- if len(state.data_sets)>0:
+ if len(state.data_sets) > 0:
self.set_editing_state(state.data_sets[0])
self._summary.angle_list.setCurrentRow(0, QtGui.QItemSelectionModel.Select)
-# # Common Q binning
-# self._summary.q_min_edit.setText(str(state.data_sets[0].q_min))
-# self._summary.log_scale_chk.setChecked(state.data_sets[0].q_step<0)
+ # # Common Q binning
+ # self._summary.q_min_edit.setText(str(state.data_sets[0].q_min))
+ # self._summary.log_scale_chk.setChecked(state.data_sets[0].q_step<0)
# Common angle offset
if hasattr(state.data_sets[0], "angle_offset"):
@@ -1444,7 +1448,7 @@ class BaseRefWidget(BaseWidget):
def set_editing_state(self, state):
self._summary.q_min_edit.setText(str(state.q_min))
- self._summary.log_scale_chk.setChecked(state.q_step<0)
+ self._summary.log_scale_chk.setChecked(state.q_step < 0)
self._summary.incident_medium_combobox.clear()
_incident_medium_str = str(state.incident_medium_list[0])
@@ -1453,35 +1457,35 @@ class BaseRefWidget(BaseWidget):
self._summary.incident_medium_combobox.addItem(str(item))
self._summary.incident_medium_combobox.setCurrentIndex(state.incident_medium_index_selected)
- #Peak from/to pixels
+ # Peak from/to pixels
self._summary.data_peak_from_pixel.setText(str(state.DataPeakPixels[0]))
self._summary.data_peak_to_pixel.setText(str(state.DataPeakPixels[1]))
- #data low resolution range
+ # data low resolution range
self._summary.data_low_res_range_switch.setChecked(state.data_x_range_flag)
self._summary.x_min_edit.setText(str(state.data_x_range[0]))
self._summary.x_max_edit.setText(str(state.data_x_range[1]))
self._data_low_res_clicked(state.data_x_range_flag)
- #data metadata
+ # data metadata
self._summary.tthd_value.setText(str(state.tthd_value))
self._summary.ths_value.setText(str(state.ths_value))
- #norm low resolution range
+ # norm low resolution range
self._summary.norm_low_res_range_switch.setChecked(state.norm_x_range_flag)
self._summary.norm_x_min_edit.setText(str(state.norm_x_range[0]))
self._summary.norm_x_max_edit.setText(str(state.norm_x_range[1]))
self._norm_low_res_clicked(state.data_x_range_flag)
- #Background flag
+ # Background flag
self._summary.data_background_switch.setChecked(state.DataBackgroundFlag)
self._data_background_clicked(state.DataBackgroundFlag)
- #Background from/to pixels
+ # Background from/to pixels
self._summary.data_background_from_pixel1.setText(str(state.DataBackgroundRoi[0]))
self._summary.data_background_to_pixel1.setText(str(state.DataBackgroundRoi[1]))
- #from TOF and to TOF
+ # from TOF and to TOF
self._summary.data_from_tof.setText(str(int(state.DataTofRange[0])))
self._summary.data_to_tof.setText(str(int(state.DataTofRange[1])))
@@ -1496,13 +1500,13 @@ class BaseRefWidget(BaseWidget):
self._summary.norm_background_from_pixel1.setText(str(state.NormBackgroundRoi[0]))
self._summary.norm_background_to_pixel1.setText(str(state.NormBackgroundRoi[1]))
- #normalization flag
+ # normalization flag
self._summary.norm_switch.setChecked(state.NormFlag)
self._norm_clicked(state.NormFlag)
# Q binning
self._summary.q_min_edit.setText(str(state.q_min))
- self._summary.log_scale_chk.setChecked(state.q_step<0)
+ self._summary.log_scale_chk.setChecked(state.q_step < 0)
self._summary.q_step_edit.setText(str(math.fabs(state.q_step)))
# overlap ascii values
@@ -1511,10 +1515,10 @@ class BaseRefWidget(BaseWidget):
# Output directory
if hasattr(state, "output_dir"):
- if len(str(state.output_dir).strip())>0:
+ if len(str(state.output_dir).strip()) > 0:
self._summary.outdir_edit.setText(str(state.output_dir))
- #scaling factor file and options
+ # scaling factor file and options
self._summary.use_sf_config_switch.setChecked(state.scaling_factor_file_flag)
self._summary.cfg_scaling_factor_file_name.setText(str(state.scaling_factor_file))
self._summary.slits_width_flag.setChecked(state.slits_width_flag)
@@ -1526,6 +1530,6 @@ class BaseRefWidget(BaseWidget):
self._reset_warnings()
self._summary.data_run_number_edit.setText(str(','.join([str(i) for i in state.data_files])))
- #4th column (precision)
+ # 4th column (precision)
self._summary.fourth_column_switch.setChecked(state.fourth_column_flag)
self._fourth_column_clicked(state.fourth_column_flag)
diff --git a/scripts/Interface/ui/reflectometer/refl_gui.py b/scripts/Interface/ui/reflectometer/refl_gui.py
index 8de9d8c0aeeb0baf9c40641ffcb4dfa09f8eec92..99c39eb0152226ea27054ef8f9a509da977089b6 100644
--- a/scripts/Interface/ui/reflectometer/refl_gui.py
+++ b/scripts/Interface/ui/reflectometer/refl_gui.py
@@ -4,7 +4,7 @@
try:
from mantidplot import *
except ImportError:
- canMantidPlot = False #
+ canMantidPlot = False #
import ui_refl_window
import refl_save
@@ -35,7 +35,6 @@ canMantidPlot = True
class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
-
current_instrument = None
current_table = None
current_polarisation_method = None
@@ -81,25 +80,27 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
self.__group_tof_workspaces_key = "group_tof_workspaces"
self.__stitch_right_key = "stitch_right"
- #Setup instrument with defaults assigned.
+ # Setup instrument with defaults assigned.
self.instrument_list = ['INTER', 'SURF', 'CRISP', 'POLREF', 'OFFSPEC']
self.polarisation_instruments = ['CRISP', 'POLREF']
self.polarisation_options = {'None': PolarisationCorrection.NONE,
'1-PNR': PolarisationCorrection.PNR,
'2-PA': PolarisationCorrection.PA}
- #Set the live data settings, use default if none have been set before
+ # Set the live data settings, use default if none have been set before
settings = QtCore.QSettings()
settings.beginGroup(self.__live_data_settings)
self.live_method = settings.value(self.__live_data_method_key, "", type=str)
self.live_freq = settings.value(self.__live_data_frequency_key, 0, type=float)
if not self.live_freq:
- logger.information("No settings were found for Update frequency of loading live data, Loading default of 60 seconds")
+ logger.information(
+ "No settings were found for Update frequency of loading live data, Loading default of 60 seconds")
self.live_freq = float(60)
settings.setValue(self.__live_data_frequency_key, self.live_freq)
if not self.live_method:
- logger.information("No settings were found for Accumulation Method of loading live data, Loading default of \"Add\"")
+ logger.information(
+ "No settings were found for Accumulation Method of loading live data, Loading default of \"Add\"")
self.live_method = "Add"
settings.setValue(self.__live_data_method_key, self.live_method)
settings.endGroup()
@@ -108,8 +109,8 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
self.__alg_migrate = settings.value(self.__alg_migration_key, True, type=bool)
if self.__alg_migrate:
- self.__alg_use = True # We will use the algorithms by default rather than the quick scripts
- self.__alg_migrate = False # Never do this again. We only want to reset once.
+ self.__alg_use = True # We will use the algorithms by default rather than the quick scripts
+ self.__alg_migrate = False # Never do this again. We only want to reset once.
else:
self.__alg_use = settings.value(self.__ads_use_key, True, type=bool)
@@ -126,7 +127,7 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
settings.endGroup()
del settings
- #register startup
+ # register startup
UsageService.registerFeatureUsage("Interface", "ISIS Reflectomety", False)
def __del__(self):
@@ -194,16 +195,17 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
self.textRB.clear()
self._populate_runs_list()
self.current_instrument = self.instrument_list[instrument]
- self.comboPolarCorrect.setEnabled(self.current_instrument in self.polarisation_instruments) # Enable as appropriate
- self.comboPolarCorrect.setCurrentIndex(self.comboPolarCorrect.findText('None')) # Reset to None
+ self.comboPolarCorrect.setEnabled(
+ self.current_instrument in self.polarisation_instruments) # Enable as appropriate
+ self.comboPolarCorrect.setCurrentIndex(self.comboPolarCorrect.findText('None')) # Reset to None
def _table_modified(self, row, column):
"""
sets the modified flag when the table is altered
"""
- #Sometimes users enter leading or trailing whitespace into a cell.
- #Let's remove it for them automatically.
+ # Sometimes users enter leading or trailing whitespace into a cell.
+ # Let's remove it for them automatically.
item = self.tableMain.item(row, column)
item.setData(0, str.strip(str(item.data(0))))
@@ -248,7 +250,7 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
config['default.instrument'] = 'INTER'
self.current_instrument = config['default.instrument'].upper()
- #Setup polarisation options with default assigned
+ # Setup polarisation options with default assigned
self.comboPolarCorrect.clear()
self.comboPolarCorrect.addItems(self.polarisation_options.keys())
self.comboPolarCorrect.setCurrentIndex(self.comboPolarCorrect.findText('None'))
@@ -266,7 +268,7 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
"""
Reset the plot buttons and stitch checkboxes back to thier defualt state
"""
- #switches from current to true, to false to make sure stateChanged fires
+ # switches from current to true, to false to make sure stateChanged fires
self.checkTickAll.setCheckState(2)
self.checkTickAll.setCheckState(0)
for row in range(self.tableMain.rowCount()):
@@ -287,7 +289,7 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
"""
Initialise the table. Clearing all data and adding the checkboxes and plot buttons
"""
- #first check if the table has been changed before clearing it
+ # first check if the table has been changed before clearing it
if self.mod_flag:
ret, _saved = self._save_check()
if ret == QtGui.QMessageBox.RejectRole:
@@ -425,7 +427,7 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
search_alg = AlgorithmManager.create('CatalogGetDataFiles')
search_alg.initialize()
- search_alg.setChild(True) # Keeps the results table out of the ADS
+ search_alg.setChild(True) # Keeps the results table out of the ADS
search_alg.setProperty('InvestigationId', str(self.textRB.text()))
search_alg.setProperty('Session', active_session_id)
search_alg.setPropertyValue('OutputWorkspace', '_dummy')
@@ -440,7 +442,7 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
description = row['Description']
run_number = re.search(r'[1-9]\d+', file_name).group()
- if bool(re.search('(raw)$', file_name, re.IGNORECASE)): # Filter to only display and map raw files.
+ if bool(re.search('(raw)$', file_name, re.IGNORECASE)): # Filter to only display and map raw files.
title = (run_number + ': ' + description).strip()
self.icat_file_map[title] = (file_id, run_number, file_name)
self.listMain.addItem(title)
@@ -476,7 +478,8 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
"No target cells to autofill. Rows to be filled should contain a run number in their "
"first cell, and start from directly below the selected line.")
else:
- QtGui.QMessageBox.critical(self.tableMain, 'Cannot perform Autofill', "Selected cells must all be in the same row.")
+ QtGui.QMessageBox.critical(self.tableMain, 'Cannot perform Autofill',
+ "Selected cells must all be in the same row.")
else:
QtGui.QMessageBox.critical(self.tableMain, 'Cannot perform Autofill', "There are no source cells selected.")
@@ -503,7 +506,8 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
"""
cells = self.tableMain.selectedItems()
if not cells:
- print 'nothing to copy'
+ print
+ 'nothing to copy'
return
# first discover the size of the selection and initialise a list
mincol = cells[0].column()
@@ -522,7 +526,7 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
colsize = maxcol - mincol + 1
rowsize = maxrow - minrow + 1
selection = [['' for x in range(colsize)] for y in range(rowsize)]
- #now fill that list
+ # now fill that list
for cell in cells:
row = cell.row()
col = cell.column()
@@ -557,20 +561,21 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
pastedcols = len(pastedcells[0])
pastedrows = len(pastedcells)
if len(selected) > 1:
- #discover the size of the selection
+ # discover the size of the selection
mincol = selected[0].column()
if mincol > self.scale_col:
logger.error("Cannot copy, all cells out of range")
return
minrow = selected[0].row()
- #now fill that list
+ # now fill that list
for cell in selected:
row = cell.row()
col = cell.column()
- if col < self.stitch_col and (col - mincol) < pastedcols and (row - minrow) < pastedrows and len(pastedcells[row - minrow]):
+ if col < self.stitch_col and (col - mincol) < pastedcols and (row - minrow) < pastedrows and len(
+ pastedcells[row - minrow]):
cell.setText(pastedcells[row - minrow][col - mincol])
elif selected:
- #when only a single cell is selected, paste all the copied item up until the table limits
+ # when only a single cell is selected, paste all the copied item up until the table limits
cell = selected[0]
currow = cell.row()
homecol = cell.column()
@@ -585,11 +590,11 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
curcell.setText(col)
curcol += 1
else:
- #the row has hit the end of the editable cells
+ # the row has hit the end of the editable cells
break
currow += 1
else:
- #it's dropped off the bottom of the table
+ # it's dropped off the bottom of the table
break
else:
logger.warning("Cannot paste, no editable cells selected")
@@ -609,18 +614,18 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
continue
else:
theta = 0
- split_title.append(theta) # Append a dummy theta value.
+ split_title.append(theta) # Append a dummy theta value.
if len(split_title) < 4:
dqq = 0
- split_title.append(dqq) # Append a dummy dq/q value.
- tup = tup + (split_title,) # Tuple of lists containing (run number, title, theta, dq/q)
+ split_title.append(dqq) # Append a dummy dq/q value.
+ tup = tup + (split_title,) # Tuple of lists containing (run number, title, theta, dq/q)
tupsort = sorted(tup, key=itemgetter(1, 2)) # now sorted by title then theta
row = 0
- for _key, group in itertools.groupby(tupsort, lambda x: x[1]): # now group by title
+ for _key, group in itertools.groupby(tupsort, lambda x: x[1]): # now group by title
col = 0
- dqq = 0 # only one value of dqq per row
- run_angle_pairs_of_title = list() # for storing run_angle pairs all with the same title
+ dqq = 0 # only one value of dqq per row
+ run_angle_pairs_of_title = list() # for storing run_angle pairs all with the same title
for object in group: # loop over all with equal title
run_no = object[0]
@@ -668,7 +673,8 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
save_location = config['defaultsave.directory']
- CatalogDownloadDataFiles(file_id, FileNames=file_name, DownloadPath=save_location, Session=active_session_id)
+ CatalogDownloadDataFiles(file_id, FileNames=file_name, DownloadPath=save_location,
+ Session=active_session_id)
current_search_dirs = config.getDataSearchDirs()
@@ -689,7 +695,7 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
"""
Process has been pressed, check what has been selected then pass the selection (or whole table) to quick
"""
-#--------- If "Process" button pressed, convert raw files to IvsLam and IvsQ and combine if checkbox ticked -------------
+ # --------- If "Process" button pressed, convert raw files to IvsLam and IvsQ and combine if checkbox ticked -------------
_overallQMin = float("inf")
_overallQMax = float("-inf")
try:
@@ -731,7 +737,8 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
if self.tableMain.item(row, 15).text() == '':
loadedRun = None
if load_live_runs.is_live_run(runno[0]):
- loadedRun = load_live_runs.get_live_data(config['default.instrument'], frequency=self.live_freq,
+ loadedRun = load_live_runs.get_live_data(config['default.instrument'],
+ frequency=self.live_freq,
accumulation=self.live_method)
else:
Load(Filename=runno[0], OutputWorkspace="_run")
@@ -742,19 +749,19 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
if len(two_theta_str) > 0:
two_theta = float(two_theta_str)
- #Make sure we only ever run calculate resolution on a non-group workspace.
- #If we're given a group workspace, we can just run it on the first member of the group instead
+ # Make sure we only ever run calculate resolution on a non-group workspace.
+ # If we're given a group workspace, we can just run it on the first member of the group instead
thetaRun = loadedRun
if isinstance(thetaRun, WorkspaceGroup):
thetaRun = thetaRun[0]
dqq, two_theta = CalculateResolution(Workspace=thetaRun, TwoTheta=two_theta)
- #Put the calculated resolution into the table
+ # Put the calculated resolution into the table
resItem = QtGui.QTableWidgetItem()
resItem.setText(str(dqq))
self.tableMain.setItem(row, 15, resItem)
- #Update the value for two_theta in the table
+ # Update the value for two_theta in the table
ttItem = QtGui.QTableWidgetItem()
ttItem.setText(str(two_theta))
self.tableMain.setItem(row, 1, ttItem)
@@ -762,8 +769,9 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
logger.notice("Calculated resolution: " + str(dqq))
except:
self.statusMain.clearMessage()
- logger.error("Failed to calculate dq/q because we could not find theta in the workspace's sample log. "
- "Try entering theta or dq/q manually.")
+ logger.error(
+ "Failed to calculate dq/q because we could not find theta in the workspace's sample log. "
+ "Try entering theta or dq/q manually.")
return
else:
dqq = float(self.tableMain.item(row, 15).text())
@@ -787,7 +795,7 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
theta, qmin, qmax, _wlam, wqBinnedAndScaled, _wqUnBinnedAndUnScaled = \
self._do_run(runno[i], row, i)
if not first_wq:
- first_wq = wqBinnedAndScaled # Cache the first Q workspace
+ first_wq = wqBinnedAndScaled # Cache the first Q workspace
theta = round(theta, 3)
qmin = round(qmin, 3)
qmax = round(qmax, 3)
@@ -833,9 +841,9 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
if Qmin < _overallQMin:
_overallQMin = Qmin
- _wcomb = combineDataMulti(wksp, outputwksp, overlapLow, overlapHigh,
- _overallQMin, _overallQMax, -dqq, 1, keep=True,
- scale_right=self.__scale_right)
+ combineDataMulti(wksp, outputwksp, overlapLow, overlapHigh,
+ _overallQMin, _overallQMax, -dqq, 1, keep=True,
+ scale_right=self.__scale_right)
# Enable the plot button
plotbutton = self.tableMain.cellWidget(row, self.plot_col).children()[1]
@@ -860,7 +868,7 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
return
import unicodedata
- #make sure the required data can be retrieved properly
+ # make sure the required data can be retrieved properly
try:
runno_u = plotbutton.property('runno')
runno = []
@@ -924,8 +932,8 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
outputwksp = runno[0] + '_' + runno[2][3:]
if not getWorkspace(outputwksp, report_error=False):
# Stitching has not been done as part of processing, so we need to do it here.
- _wcomb = combineDataMulti(wkspBinned, outputwksp, overlapLow, overlapHigh, Qmin, Qmax, -dqq, 1,
- keep=True, scale_right=self.__scale_right)
+ combineDataMulti(wkspBinned, outputwksp, overlapLow, overlapHigh, Qmin, Qmax, -dqq, 1,
+ keep=True, scale_right=self.__scale_right)
Qmin = min(getWorkspace(outputwksp).readX(0))
Qmax = max(getWorkspace(outputwksp).readX(0))
@@ -985,7 +993,8 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
loadedRun = runno
if load_live_runs.is_live_run(runno):
- load_live_runs.get_live_data(config['default.instrument'], frequency=self.live_freq, accumulation=self.live_method)
+ load_live_runs.get_live_data(config['default.instrument'], frequency=self.live_freq,
+ accumulation=self.live_method)
wlam, wq, th, wqBinned = None, None, None, None
# Only make a transmission workspace if we need one.
@@ -996,12 +1005,15 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
if size == 1:
trans1 = converter.get_workspace_from_list(0)
- transmission_ws = CreateTransmissionWorkspaceAuto(FirstTransmissionRun=trans1, OutputWorkspace=out_ws_name,
- Params=0.02, StartOverlap=10.0, EndOverlap=12.0, Version=1)
+ transmission_ws = CreateTransmissionWorkspaceAuto(FirstTransmissionRun=trans1,
+ OutputWorkspace=out_ws_name,
+ Params=0.02, StartOverlap=10.0, EndOverlap=12.0,
+ Version=1)
elif size == 2:
trans1 = converter.get_workspace_from_list(0)
trans2 = converter.get_workspace_from_list(1)
- transmission_ws = CreateTransmissionWorkspaceAuto(FirstTransmissionRun=trans1, OutputWorkspace=out_ws_name,
+ transmission_ws = CreateTransmissionWorkspaceAuto(FirstTransmissionRun=trans1,
+ OutputWorkspace=out_ws_name,
SecondTransmissionRun=trans2, Params=0.02,
StartOverlap=10.0, EndOverlap=12.0, Version=1)
else:
@@ -1012,11 +1024,11 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
if self.__alg_use:
if self.tableMain.item(row, self.scale_col).text():
- factor=float(self.tableMain.item(row, self.scale_col).text())
+ factor = float(self.tableMain.item(row, self.scale_col).text())
else:
- factor=1.0
+ factor = 1.0
if self.tableMain.item(row, 15).text():
- Qstep=float(self.tableMain.item(row, 15).text())
+ Qstep = float(self.tableMain.item(row, 15).text())
else:
Qstep = None
if len(self.tableMain.item(row, which * 5 + 3).text()) > 0:
@@ -1036,7 +1048,7 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
thetaGroup = []
group_trans_ws = transmission_ws
for i in range(0, ws.size()):
- #If the transmission workspace is a group, we'll use it pair-wise with the tof workspace group
+ # If the transmission workspace is a group, we'll use it pair-wise with the tof workspace group
if isinstance(transmission_ws, WorkspaceGroup):
group_trans_ws = transmission_ws[i]
@@ -1047,9 +1059,9 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
alg.setProperty("FirstTransmissionRun", group_trans_ws)
if angle is not None:
alg.setProperty("ThetaIn", angle)
- alg.setProperty("OutputWorkspaceBinned", runno+'_IvsQ_binned_'+str(i+1))
- alg.setProperty("OutputWorkspace", runno+'_IvsQ_'+str(i+1))
- alg.setProperty("OutputWorkspaceWavelength", runno+'_IvsLam_'+str(i+1))
+ alg.setProperty("OutputWorkspaceBinned", runno + '_IvsQ_binned_' + str(i + 1))
+ alg.setProperty("OutputWorkspace", runno + '_IvsQ_' + str(i + 1))
+ alg.setProperty("OutputWorkspaceWavelength", runno + '_IvsLam_' + str(i + 1))
alg.setProperty("ScaleFactor", factor)
if Qstep is not None:
alg.setProperty("MomentumTransferStep", Qstep)
@@ -1058,9 +1070,9 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
if Qmax is not None:
alg.setProperty("MomentumTransferMax", Qmax)
alg.execute()
- wqBinned = mtd[runno+'_IvsQ_binned_'+str(i+1)]
- wq = mtd[runno+'_IvsQ_'+str(i+1)]
- wlam = mtd[runno+'_IvsLam_'+str(i+1)]
+ wqBinned = mtd[runno + '_IvsQ_binned_' + str(i + 1)]
+ wq = mtd[runno + '_IvsQ_' + str(i + 1)]
+ wlam = mtd[runno + '_IvsLam_' + str(i + 1)]
th = alg.getProperty("ThetaIn").value
wqGroupBinned.append(wqBinned)
@@ -1068,9 +1080,9 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
wlamGroup.append(wlam)
thetaGroup.append(th)
- wqBinned = GroupWorkspaces(InputWorkspaces=wqGroupBinned, OutputWorkspace=runno+'_IvsQ_binned')
- wq = GroupWorkspaces(InputWorkspaces=wqGroup, OutputWorkspace=runno+'_IvsQ')
- wlam = GroupWorkspaces(InputWorkspaces=wlamGroup, OutputWorkspace=runno+'_IvsLam')
+ wqBinned = GroupWorkspaces(InputWorkspaces=wqGroupBinned, OutputWorkspace=runno + '_IvsQ_binned')
+ wq = GroupWorkspaces(InputWorkspaces=wqGroup, OutputWorkspace=runno + '_IvsQ')
+ wlam = GroupWorkspaces(InputWorkspaces=wlamGroup, OutputWorkspace=runno + '_IvsLam')
th = thetaGroup[0]
else:
alg = AlgorithmManager.create("ReflectometryReductionOneAuto")
@@ -1080,9 +1092,9 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
alg.setProperty("FirstTransmissionRun", transmission_ws)
if angle is not None:
alg.setProperty("ThetaIn", angle)
- alg.setProperty("OutputWorkspaceBinned", runno+'_IvsQ_binned')
- alg.setProperty("OutputWorkspace", runno+'_IvsQ')
- alg.setProperty("OutputWorkspaceWavelength", runno+'_IvsLam')
+ alg.setProperty("OutputWorkspaceBinned", runno + '_IvsQ_binned')
+ alg.setProperty("OutputWorkspace", runno + '_IvsQ')
+ alg.setProperty("OutputWorkspaceWavelength", runno + '_IvsLam')
alg.setProperty("ScaleFactor", factor)
if Qstep is not None:
alg.setProperty("MomentumTransferStep", Qstep)
@@ -1091,9 +1103,9 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
if Qmax is not None:
alg.setProperty("MomentumTransferMax", Qmax)
alg.execute()
- wqBinned = mtd[runno+'_IvsQ_binned']
- wq = mtd[runno+'_IvsQ']
- wlam = mtd[runno+'_IvsLam']
+ wqBinned = mtd[runno + '_IvsQ_binned']
+ wq = mtd[runno + '_IvsQ']
+ wlam = mtd[runno + '_IvsLam']
th = alg.getProperty("ThetaIn").value
cleanup()
@@ -1150,11 +1162,13 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
"""
filename = ''
if failsave:
- #this is an emergency autosave as the program is failing
- logger.error("The ISIS Reflectonomy GUI has encountered an error, it will now attempt to save a copy of your work.")
+ # this is an emergency autosave as the program is failing
+ logger.error(
+ "The ISIS Reflectonomy GUI has encountered an error, it will now attempt to save a copy of your work.")
msgBox = QtGui.QMessageBox()
- msgBox.setText("The ISIS Reflectonomy GUI has encountered an error, it will now attempt to save a copy of your work.\n"
- "Please check the log for details.")
+ msgBox.setText(
+ "The ISIS Reflectonomy GUI has encountered an error, it will now attempt to save a copy of your work.\n"
+ "Please check the log for details.")
msgBox.setStandardButtons(QtGui.QMessageBox.Ok)
msgBox.setIcon(QtGui.QMessageBox.Critical)
msgBox.setDefaultButton(QtGui.QMessageBox.Ok)
@@ -1211,11 +1225,11 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
loadDialog.setNameFilter("Table Files (*.tbl);;All files (*)")
if loadDialog.exec_():
try:
- #before loading make sure you give them a chance to save
+ # before loading make sure you give them a chance to save
if self.mod_flag:
ret, _saved = self._save_check()
if ret == QtGui.QMessageBox.RejectRole:
- #if they hit cancel abort the load
+ # if they hit cancel abort the load
self.loading = False
return
self._reset_table()
@@ -1244,14 +1258,15 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
if filename:
if self.mod_flag:
msgBox = QtGui.QMessageBox()
- msgBox.setText("The table has been modified. Are you sure you want to reload the table and lose your changes?")
+ msgBox.setText(
+ "The table has been modified. Are you sure you want to reload the table and lose your changes?")
msgBox.setStandardButtons(QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
msgBox.setIcon(QtGui.QMessageBox.Question)
msgBox.setDefaultButton(QtGui.QMessageBox.Yes)
msgBox.setEscapeButton(QtGui.QMessageBox.No)
ret = msgBox.exec_()
if ret == QtGui.QMessageBox.No:
- #if they hit No abort the reload
+ # if they hit No abort the reload
self.loading = False
return
try:
@@ -1291,12 +1306,12 @@ class ReflGui(QtGui.QMainWindow, ui_refl_window.Ui_windowRefl):
"""
try:
- dialog_controller = refl_options.ReflOptions(def_method = self.live_method, def_freq = self.live_freq,
- def_alg_use = self.__alg_use, def_icat_download=self.__icat_download,
- def_group_tof_workspaces = self.__group_tof_workspaces,
+ dialog_controller = refl_options.ReflOptions(def_method=self.live_method, def_freq=self.live_freq,
+ def_alg_use=self.__alg_use,
+ def_icat_download=self.__icat_download,
+ def_group_tof_workspaces=self.__group_tof_workspaces,
def_stitch_right=self.__scale_right)
if dialog_controller.exec_():
-
# Fetch the settings back off the controller
self.live_freq = dialog_controller.frequency()
self.live_method = dialog_controller.method()
diff --git a/scripts/LargeScaleStructures/REF_L_geometry.py b/scripts/LargeScaleStructures/REF_L_geometry.py
index 8d180316e273c59f84844b8113cdb1cdace8ddfd..33e09c635349798f747f87c333e0c5bc7fd65c25 100644
--- a/scripts/LargeScaleStructures/REF_L_geometry.py
+++ b/scripts/LargeScaleStructures/REF_L_geometry.py
@@ -1,6 +1,7 @@
#pylint: disable=invalid-name
from __future__ import (absolute_import, division, print_function)
from .geometry_writer import MantidGeom
+import mantid.simpleapi as mantid
NUM_PIXELS_PER_TUBE = 304
NUM_TUBES = 256
@@ -15,10 +16,10 @@ def create_grouping(workspace=None):
## Integrated over X
if workspace is not None:
- if mtd[workspace].getInstrument().hasParameter("number-of-x-pixels"):
- npix_x = int(mtd[workspace].getInstrument().getNumberParameter("number-of-x-pixels")[0])
- if mtd[workspace].getInstrument().hasParameter("number-of-y-pixels"):
- npix_y = int(mtd[workspace].getInstrument().getNumberParameter("number-of-y-pixels")[0])
+ if mantid.mtd[workspace].getInstrument().hasParameter("number-of-x-pixels"):
+ npix_x = int(mantid.mtd[workspace].getInstrument().getNumberParameter("number-of-x-pixels")[0])
+ if mantid.mtd[workspace].getInstrument().hasParameter("number-of-y-pixels"):
+ npix_y = int(mantid.mtd[workspace].getInstrument().getNumberParameter("number-of-y-pixels")[0])
f = open("REFL_Detector_Grouping_Sum_X_rot.xml",'w')
f.write("<detector-grouping description=\"Integrated over X\">\n")
diff --git a/scripts/MantidIPython/__init__.py b/scripts/MantidIPython/__init__.py
index 4ede76d88d070c30442eb2eeda0ed3d9098acbde..831824e6114261387169bae1de844b987c996b0a 100644
--- a/scripts/MantidIPython/__init__.py
+++ b/scripts/MantidIPython/__init__.py
@@ -21,10 +21,8 @@
Some tools for use in ipython notebooks generated by Mantid.
"""
-from MantidIPython.plot_functions import *
-import warnings
-import mantid.kernel
-
-# Check if the version of Mantid being used matches the version which created the notebook.
-if "3.5.20160108.1509" != mantid.kernel.version_str():
- warnings.warn("Version of Mantid being used does not match version which created the notebook.")
+# Suppress warnings about unused import as these
+# imports are important for iPython
+from MantidIPython.plot_functions import * # noqa: F401
+import warnings # noqa: F401
+import mantid.kernel # noqa: F401
diff --git a/scripts/SANS/ISISCommandInterface.py b/scripts/SANS/ISISCommandInterface.py
index de531bac0a104ea2445f42825e27e7920e9ef022..0a81425fa643b98485a6b37b13bf2b7d620f2b44 100644
--- a/scripts/SANS/ISISCommandInterface.py
+++ b/scripts/SANS/ISISCommandInterface.py
@@ -980,7 +980,6 @@ def DisplayMask(mask_worksp=None):
"""
# this will be copied from a sample work space if one exists
counts_data = None
- _instrument = ReductionSingleton().instrument
if not mask_worksp:
mask_worksp = '__CurrentMask'
diff --git a/scripts/TemporaryREF_MScripts/testCenterREF_M.py b/scripts/TemporaryREF_MScripts/testCenterREF_M.py
index b29ff2c92b3cc3decc38fa289c298bf6a3d8e58b..65053f0c0e3f97849437c3c7d2625fb6a77ac2ce 100644
--- a/scripts/TemporaryREF_MScripts/testCenterREF_M.py
+++ b/scripts/TemporaryREF_MScripts/testCenterREF_M.py
@@ -30,12 +30,12 @@ atangle=mantid.simpleapi.LoadEventNexus('REF_M_22710',NXentryName='entry-Off_Off
mantid.simpleapi.MoveInstrumentComponent(Workspace=atangle,ComponentName="DetectorArm",X=0,Y=translation,Z=1,RelativePosition=1)
mantid.simpleapi.RotateInstrumentComponent(Workspace=atangle,ComponentName="DetectorArm",X=0,Y=1,Z=0,Angle=rotation,RelativeRotation=1)
-central=ConvertUnits(central,Target="Wavelength",EMode="Elastic")
-central=Rebin(central,"3.5,0.1,7")
+central=mantid.simpleapi.ConvertUnits(central,Target="Wavelength",EMode="Elastic")
+central=mantid.simpleapi.Rebin(central,"3.5,0.1,7")
-atangle=ConvertUnits(atangle,Target="Wavelength",EMode="Elastic")
-atangle=Rebin(atangle,"3.5,0.1,7")
+atangle=mantid.simpleapi.ConvertUnits(atangle,Target="Wavelength",EMode="Elastic")
+atangle=mantid.simpleapi.Rebin(atangle,"3.5,0.1,7")
-csum=SumSpectra(central)
-asum=SumSpectra(atangle)
+csum=mantid.simpleapi.SumSpectra(central)
+asum=mantid.simpleapi.SumSpectra(atangle)
normalized=asum/csum
diff --git a/scripts/Vates/Diffraction_Workflow.py b/scripts/Vates/Diffraction_Workflow.py
index 4ce3ad2480457bffbd9d6c7a104e7890eeaabb54..e9114ebcd1d30c7338f87953b9f6ee4d44f125e4 100644
--- a/scripts/Vates/Diffraction_Workflow.py
+++ b/scripts/Vates/Diffraction_Workflow.py
@@ -1,84 +1,88 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
# Basic parameters for Triphylite Crystal
-#Name of the workspaces to create
+# Name of the workspaces to create
+import mantid.simpleapi as mantid
+
ws_name = "TOPAZ_3132"
-filename = ws_name +"_event.nxs"
-ws = LoadEventNexus(Filename=filename,FilterByTofMin=3000, FilterByTofMax=16000)
+filename = ws_name + "_event.nxs"
+ws = mantid.LoadEventNexus(Filename=filename, FilterByTofMin=3000, FilterByTofMax=16000)
# ------------------------------------------------------------------------------------------------------------------------------------------
# Part 1. Basic Reduction
# Spherical Absorption and Lorentz Corrections
-ws = AnvredCorrection(InputWorkspace=ws, LinearScatteringCoef=0.451, LinearAbsorptionCoef=0.993, Radius=0.14)
+ws = mantid.AnvredCorrection(InputWorkspace=ws, LinearScatteringCoef=0.451, LinearAbsorptionCoef=0.993, Radius=0.14)
# Convert to Q space
-LabQ = ConvertToDiffractionMDWorkspace(InputWorkspace=ws, LorentzCorrection='0',
- OutputDimensions='Q (lab frame)', SplitInto=2, SplitThreshold=150)
+LabQ = mantid.ConvertToDiffractionMDWorkspace(InputWorkspace=ws, LorentzCorrection='0',
+ OutputDimensions='Q (lab frame)', SplitInto=2, SplitThreshold=150)
# Find peaks
-PeaksLattice = FindPeaksMD(InputWorkspace=LabQ,MaxPeaks=100)
+PeaksLattice = mantid.FindPeaksMD(InputWorkspace=LabQ, MaxPeaks=100)
# 3d integration to centroid peaks
-PeaksLattice = CentroidPeaksMD(InputWorkspace=LabQ,
- PeakRadius=0.12, PeaksWorkspace=PeaksLattice)
+PeaksLattice = mantid.CentroidPeaksMD(InputWorkspace=LabQ,
+ PeakRadius=0.12, PeaksWorkspace=PeaksLattice)
# Find the UB matrix using the peaks and known lattice parameters
-FindUBUsingLatticeParameters(PeaksWorkspace=PeaksLattice, a=10.3522, b=6.0768, c=4.7276,
- alpha=90, beta=90, gamma=90, NumInitial=20, Tolerance=0.12)
+mantid.FindUBUsingLatticeParameters(PeaksWorkspace=PeaksLattice, a=10.3522, b=6.0768, c=4.7276,
+ alpha=90, beta=90, gamma=90, NumInitial=20, Tolerance=0.12)
# And index to HKL
-IndexPeaks(PeaksWorkspace=PeaksLattice, Tolerance=0.12)
+mantid.IndexPeaks(PeaksWorkspace=PeaksLattice, Tolerance=0.12)
# Integrate peaks in Q space using spheres
-PeaksLattice_Integrated = IntegratePeaksMD(InputWorkspace=LabQ,PeakRadius=0.12,
- BackgroundOuterRadius=0.18,BackgroundInnerRadius=0.15,
- PeaksWorkspace=PeaksLattice)
+PeaksLattice_Integrated = mantid.IntegratePeaksMD(InputWorkspace=LabQ, PeakRadius=0.12,
+ BackgroundOuterRadius=0.18, BackgroundInnerRadius=0.15,
+ PeaksWorkspace=PeaksLattice)
# Save for SHELX
-SaveHKL(InputWorkspace=PeaksLattice, Filename=ws_name + '.hkl')
+mantid.SaveHKL(InputWorkspace=PeaksLattice, Filename=ws_name + '.hkl')
# ------------------------------------------------------------------------------------------------------------------------------------------
# Part 2. Alternative/Advanced Processing Steps
# Find peaks again for FFT
-PeaksLatticeFFT = FindPeaksMD(InputWorkspace=LabQ, MaxPeaks=100)
+PeaksLatticeFFT = mantid.FindPeaksMD(InputWorkspace=LabQ, MaxPeaks=100)
# 3d integration to centroid peaks
-PeaksLatticeFFT = CentroidPeaksMD(InputWorkspace=LabQ,
- PeakRadius=0.12, PeaksWorkspace=PeaksLatticeFFT)
+PeaksLatticeFFT = mantid.CentroidPeaksMD(InputWorkspace=LabQ,
+ PeakRadius=0.12, PeaksWorkspace=PeaksLatticeFFT)
# Find the UB matrix using FFT
-FindUBUsingFFT(PeaksWorkspace=PeaksLatticeFFT, MinD=3.0, MaxD=14.0)
+mantid.FindUBUsingFFT(PeaksWorkspace=PeaksLatticeFFT, MinD=3.0, MaxD=14.0)
# And index to HKL
-IndexPeaks(PeaksWorkspace=PeaksLatticeFFT, Tolerance=0.12)
+mantid.IndexPeaks(PeaksWorkspace=PeaksLatticeFFT, Tolerance=0.12)
# Integrate peaks in Q space using spheres
-PeaksLatticeFFT = IntegratePeaksMD(InputWorkspace=LabQ, PeakRadius=0.12,
- BackgroundOuterRadius=0.18,BackgroundInnerRadius=0.15,
- PeaksWorkspace=PeaksLatticeFFT)
+PeaksLatticeFFT = mantid.IntegratePeaksMD(InputWorkspace=LabQ, PeakRadius=0.12,
+ BackgroundOuterRadius=0.18, BackgroundInnerRadius=0.15,
+ PeaksWorkspace=PeaksLatticeFFT)
# Save for SHELX
-SaveHKL(InputWorkspace=PeaksLatticeFFT, Filename=ws_name + '.hkl')
+mantid.SaveHKL(InputWorkspace=PeaksLatticeFFT, Filename=ws_name + '.hkl')
# ------------------------------------------------------------------------------------------------------------------------------------------
# Part 3. Utilising the UB
# Copy the UB matrix back to the original workspace
-CopySample(InputWorkspace=PeaksLattice, OutputWorkspace=ws,
- CopyName='0',CopyMaterial='0',CopyEnvironment='0',CopyShape='0', CopyLattice=1)
+mantid.CopySample(InputWorkspace=PeaksLattice, OutputWorkspace=ws,
+ CopyName='0', CopyMaterial='0', CopyEnvironment='0', CopyShape='0', CopyLattice=1)
# Convert to reciprocal space, in the sample frame
-HKL = ConvertToDiffractionMDWorkspace(InputWorkspace=ws,
- OutputDimensions='HKL',LorentzCorrection='0', SplitInto='2',SplitThreshold='150')
+HKL = mantid.ConvertToDiffractionMDWorkspace(InputWorkspace=ws,
+ OutputDimensions='HKL', LorentzCorrection='0', SplitInto='2',
+ SplitThreshold='150')
# ------------------------------------------------------------------------------------------------------------------------------------------
# Part 4. Displaying
# Bin to a regular grid
-Binned = BinMD(InputWorkspace=HKL,AlignedDim0='[H,0,0], -15, 5, 150',AlignedDim1='[0,K,0], -0, 10, 50',AlignedDim2='[0,0,L], 0, 12, 150')
+Binned = mantid.BinMD(InputWorkspace=HKL, AlignedDim0='[H,0,0], -15, 5, 150', AlignedDim1='[0,K,0], -0, 10, 50',
+ AlignedDim2='[0,0,L], 0, 12, 150')
# Show in slice Viewer
-sv = plotSlice(Binned, xydim=('[H,0,0]','[0,0,L]'), slicepoint=[0, +9, 0], colorscalelog=True)
-sv.setColorMapBackground(0,0,0)
+sv = mantid.plotSlice(Binned, xydim=('[H,0,0]', '[0,0,L]'), slicepoint=[0, +9, 0], colorscalelog=True)
+sv.setColorMapBackground(0, 0, 0)
diff --git a/scripts/Vates/Inelastic_Workflow.py b/scripts/Vates/Inelastic_Workflow.py
index 4a3f6b9edff32c8e6a60ecce51625393d5e59491..3a501525d06274be34fae2b3467a010c975a4031 100644
--- a/scripts/Vates/Inelastic_Workflow.py
+++ b/scripts/Vates/Inelastic_Workflow.py
@@ -1,27 +1,29 @@
-#pylint: disable=invalid-name
-#Common names
+# pylint: disable=invalid-name
+# Common names
+import mantid.simpleapi as mantid
+
filename = 'fe_demo_30.sqw'
-ws_in ='fe_demo_30'
+ws_in = 'fe_demo_30'
-#Load an SQW file and internally convert to a Multidimensional event workspace (MDEW)
-if not mtd.doesExist(ws_in):
- LoadSQW(filename, OutputWorkspace=ws_in)
+# Load an SQW file and internally convert to a Multidimensional event workspace (MDEW)
+if not mantid.mtd.doesExist(ws_in):
+ mantid.LoadSQW(filename, OutputWorkspace=ws_in)
-#Bin the workspace in an axis aligned manner. Creates a Histogrammed MD workspace.
-BinMD(InputWorkspace=ws_in,OutputWorkspace='binned_axis_aligned',AxisAligned=True,
- AlignedDim0='Q_\\zeta,-1.5,5,100',
- AlignedDim1='Q_\\xi,-6,6,100',
- AlignedDim2='Q_\\eta,-6,6,100',
- AlignedDim3='E,0,150,30')
+# Bin the workspace in an axis aligned manner. Creates a Histogrammed MD workspace.
+mantid.BinMD(InputWorkspace=ws_in, OutputWorkspace='binned_axis_aligned', AxisAligned=True,
+ AlignedDim0='Q_\\zeta,-1.5,5,100',
+ AlignedDim1='Q_\\xi,-6,6,100',
+ AlignedDim2='Q_\\eta,-6,6,100',
+ AlignedDim3='E,0,150,30')
-#Bin the workpace using a coordinate transformation to rotate the output.. Creates a Histogrammed MD workspace.
-BinMD(InputWorkspace=ws_in,OutputWorkspace='binned_rotated',AxisAligned=False,
- BasisVector0='Qx,Ang,1,0.5,0,0,1,100',
- BasisVector1='Qy,Ang,-0.5,1,0,0,1,100',
- BasisVector2='Qz,Ang,0,0,1.25,0,1,100',
- Origin='0,0,0,0')
+# Bin the workpace using a coordinate transformation to rotate the output.. Creates a Histogrammed MD workspace.
+mantid.BinMD(InputWorkspace=ws_in, OutputWorkspace='binned_rotated', AxisAligned=False,
+ BasisVector0='Qx,Ang,1,0.5,0,0,1,100',
+ BasisVector1='Qy,Ang,-0.5,1,0,0,1,100',
+ BasisVector2='Qz,Ang,0,0,1.25,0,1,100',
+ Origin='0,0,0,0')
-#Save the MDEW workspace in the MDEW nexus format.
-SaveMD(ws_in, Filename='MDEW_fe_demo_30.nxs')
+# Save the MDEW workspace in the MDEW nexus format.
+mantid.SaveMD(ws_in, Filename='MDEW_fe_demo_30.nxs')
-#Could reload the MDEW at this point.
+# Could reload the MDEW at this point.
diff --git a/scripts/Vates/SXD_NaCl.py b/scripts/Vates/SXD_NaCl.py
index 9d418ba063867b2aa8fa6107b69467185bc684a0..3bfe353accddbca0769f58d17d01c383d836905f 100644
--- a/scripts/Vates/SXD_NaCl.py
+++ b/scripts/Vates/SXD_NaCl.py
@@ -1,4 +1,5 @@
from __future__ import (absolute_import, division, print_function)
+import mantid.simpleapi as mantid
def reportUnitCell(peaks_ws):
@@ -15,26 +16,27 @@ def reportUnitCell(peaks_ws):
#
# Exclude the monitors when loading the raw SXD file. This avoids
#
-Load(Filename='SXD23767.raw',OutputWorkspace='SXD23767',LoadMonitors='Exclude')
+mantid.Load(Filename='SXD23767.raw', OutputWorkspace='SXD23767', LoadMonitors='Exclude')
#
# A lower SplitThreshold, with a reasonable bound on the recursion depth, helps find weaker peaks at higher Q.
#
-QLab = ConvertToDiffractionMDWorkspace(InputWorkspace='SXD23767', OutputDimensions='Q (lab frame)',
- SplitThreshold=50, LorentzCorrection='1',
- MaxRecursionDepth='13',Extents='-15,15,-15,15,-15,15')
+QLab = mantid.ConvertToDiffractionMDWorkspace(InputWorkspace='SXD23767', OutputDimensions='Q (lab frame)',
+ SplitThreshold=50, LorentzCorrection='1',
+ MaxRecursionDepth='13', Extents='-15,15,-15,15,-15,15')
#
# NaCl has a relatively small unit cell, so the distance between peaks is relatively large. Setting the PeakDistanceThreshold
# higher avoids finding high count regions on the sides of strong peaks as separate peaks.
#
-peaks_qLab = FindPeaksMD(InputWorkspace='QLab', MaxPeaks=300, DensityThresholdFactor=10,PeakDistanceThreshold=1.0)
+peaks_qLab = mantid.FindPeaksMD(InputWorkspace='QLab', MaxPeaks=300, DensityThresholdFactor=10,
+ PeakDistanceThreshold=1.0)
#
# Fewer peaks index if Centroiding is used. This indicates that there may be an error in the centroiding algorithm,
# since the peaks seem to be less accurate.
#
-#peaks_qLab = CentroidPeaksMD(InputWorkspace='QLab',PeaksWorkspace=peaks_qLab)
+# peaks_qLab = CentroidPeaksMD(InputWorkspace='QLab',PeaksWorkspace=peaks_qLab)
use_fft = True
use_cubic_lat_par = False
@@ -44,32 +46,33 @@ use_Niggli_lat_par = False
# Note: Reduced tolerance on FindUBUsingFFT will omit peaks not near the lattice. This seems to help
# find the Niggli cell correctly, with all angle 60 degrees, and all sides 3.99
#
-if use_fft:
- FindUBUsingFFT(PeaksWorkspace=peaks_qLab, MinD='3', MaxD='5',Tolerance=0.08)
+if use_fft:
+ mantid.FindUBUsingFFT(PeaksWorkspace=peaks_qLab, MinD='3', MaxD='5', Tolerance=0.08)
print('\nNiggli cell found from FindUBUsingFFT:')
if use_cubic_lat_par:
- FindUBUsingLatticeParameters(PeaksWorkspace=peaks_qLab, a=5.6402,b=5.6402,c=5.6402,
- alpha=90,beta=90,gamma=90,NumInitial=25,Tolerance=0.12)
+ mantid.FindUBUsingLatticeParameters(PeaksWorkspace=peaks_qLab, a=5.6402, b=5.6402, c=5.6402,
+ alpha=90, beta=90, gamma=90, NumInitial=25, Tolerance=0.12)
print('\nCubic cell found directly from FindUBUsingLatticeParameters')
if use_Niggli_lat_par:
- FindUBUsingLatticeParameters(PeaksWorkspace=peaks_qLab, a=3.9882,b=3.9882,c=3.9882,
- alpha=60,beta=60,gamma=60,NumInitial=25,Tolerance=0.12)
+ mantid.FindUBUsingLatticeParameters(PeaksWorkspace=peaks_qLab, a=3.9882, b=3.9882, c=3.9882,
+ alpha=60, beta=60, gamma=60, NumInitial=25, Tolerance=0.12)
print('\nNiggli cell found from FindUBUsingLatticeParameters:')
reportUnitCell(peaks_qLab)
-IndexPeaks(PeaksWorkspace=peaks_qLab,Tolerance=0.12,RoundHKLs=1)
+mantid.IndexPeaks(PeaksWorkspace=peaks_qLab, Tolerance=0.12, RoundHKLs=1)
if use_fft or use_Niggli_lat_par:
- ShowPossibleCells(PeaksWorkspace=peaks_qLab,MaxScalarError='0.5')
- SelectCellOfType(PeaksWorkspace=peaks_qLab, CellType='Cubic', Centering='F', Apply=True)
+ mantid.ShowPossibleCells(PeaksWorkspace=peaks_qLab, MaxScalarError='0.5')
+ mantid.SelectCellOfType(PeaksWorkspace=peaks_qLab, CellType='Cubic', Centering='F', Apply=True)
-peaks_qLab_Integrated = IntegratePeaksMD(InputWorkspace=QLab, PeaksWorkspace=peaks_qLab, PeakRadius=0.2,
- BackgroundInnerRadius=0.3, BackgroundOuterRadius=0.4)
+peaks_qLab_Integrated = mantid.IntegratePeaksMD(InputWorkspace=QLab, PeaksWorkspace=peaks_qLab, PeakRadius=0.2,
+ BackgroundInnerRadius=0.3, BackgroundOuterRadius=0.4)
-binned=BinMD(InputWorkspace=QLab,AlignedDim0='Q_lab_x,-15,15,200',AlignedDim1='Q_lab_y,-15,15,200',AlignedDim2='Q_lab_z,-15,15,200')
+binned = mantid.BinMD(InputWorkspace=QLab, AlignedDim0='Q_lab_x,-15,15,200', AlignedDim1='Q_lab_y,-15,15,200',
+ AlignedDim2='Q_lab_z,-15,15,200')
print('The final result is:')
reportUnitCell(peaks_qLab)
diff --git a/scripts/reducer_singleton.py b/scripts/reducer_singleton.py
index c22114225429a55453059a77de500a956ae799e9..b0fdb5d7bc21e06a069041a3246466f3fe7cc738 100644
--- a/scripts/reducer_singleton.py
+++ b/scripts/reducer_singleton.py
@@ -1,8 +1,9 @@
-#pylint: disable=invalid-name
+# pylint: disable=invalid-name
import random
import string
import os
import mantid
+import time
from isis_instrument import BaseInstrument
@@ -11,6 +12,7 @@ class ReductionStep(object):
"""
Base class for reduction steps
"""
+
@classmethod
def delete_workspaces(cls, workspace):
"""
@@ -25,8 +27,9 @@ class ReductionStep(object):
"""
Generate a unique name for an internal workspace
"""
- random_str = ''.join(random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
- return "__"+descriptor+"_"+extract_workspace_name(filepath)+"_"+random_str
+ random_str = ''.join(
+ random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
+ return "__" + descriptor + "_" + os.path.basename(filepath) + "_" + random_str
def execute(self, reducer, inputworkspace=None, outputworkspace=None):
"""
@@ -64,14 +67,16 @@ class Reducer(object):
output_workspaces = []
def __init__(self):
- self.UID = ''.join(random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
+ self.UID = ''.join(
+ random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
self._reduction_steps = []
def set_instrument(self, configuration):
if issubclass(configuration.__class__, BaseInstrument):
self.instrument = configuration
else:
- raise RuntimeError("Reducer.set_instrument expects an %s object, found %s" % (Instrument, configuration.__class__))
+ raise RuntimeError(
+ "Reducer.set_instrument expects an %s object, found %s" % (BaseInstrument, configuration.__class__))
def set_data_path(self, path):
"""
@@ -131,7 +136,7 @@ class Reducer(object):
self.pre_process()
# Go through the list of files to be reduced
- #for file_ws in self._data_files:
+ # for file_ws in self._data_files:
# for item in self._reduction_steps:
# try:
# result = item.execute(self, file_ws)
@@ -141,7 +146,7 @@ class Reducer(object):
# self.log_text += "\n%s\n" % sys.exc_value
# raise
- #any clean up, possibly removing workspaces
+ # any clean up, possibly removing workspaces
self.post_process()
# Determine which directory to use
@@ -152,8 +157,8 @@ class Reducer(object):
else:
output_dir = os.path.expanduser('~')
- self.log_text += "Reduction completed in %g sec\n" % (time.time()-t_0)
- log_path = os.path.join(output_dir,"%s_reduction.log" % instrument_name)
+ self.log_text += "Reduction completed in %g sec\n" % (time.time() - t_0)
+ log_path = os.path.join(output_dir, "%s_reduction.log" % instrument_name)
self.log_text += "Log saved to %s" % log_path
# Write the log to file
diff --git a/scripts/reduction/reducer.py b/scripts/reduction/reducer.py
index 383d3763fb79450591d1f73830240f50479aa017..0854667337f60305e66c3d5a3275ab5abea4e606 100644
--- a/scripts/reduction/reducer.py
+++ b/scripts/reduction/reducer.py
@@ -24,12 +24,11 @@ import os
import sys
import time
import types
+import uuid
from reduction.instrument import Instrument
-import mantid
-from mantid import simpleapi
+import mantid.simpleapi as mantid
import warnings
import inspect
-import random
from reduction.find_data import find_data
@@ -79,7 +78,7 @@ def validate_loader(func):
if data_file is None:
return
else:
- raise RuntimeError("SANSReductionSteps.LoadRun doesn't recognize workspace handle %s" % workspace)
+ raise RuntimeError("SANSReductionSteps.LoadRun doesn't recognize workspace handle %s" % inputworkspace)
else:
data_file = self._data_file
@@ -107,7 +106,7 @@ def validate_loader(func):
kwargs[kwargs["AlternateName"]] = data_file
self.algorithm = alg
- simpleapi.set_properties(alg, *(), **kwargs)
+ mantid.set_properties(alg, *(), **kwargs)
alg.execute()
if "OutputMessage" in propertyOrder:
return alg.getPropertyValue("OutputMessage")
@@ -146,7 +145,7 @@ def validate_loader(func):
if data_file is None:
return
else:
- raise RuntimeError("SANSReductionSteps.LoadRun doesn't recognize workspace handle %s" % workspace)
+ raise RuntimeError("SANSReductionSteps.LoadRun doesn't recognize workspace handle %s" % inputworkspace)
else:
data_file = self._data_file
@@ -255,7 +254,7 @@ def validate_step(func):
kwargs["OutputWorkspace"] = outputworkspace
self.algorithm = alg
- simpleapi.set_properties(alg, *(), **kwargs)
+ mantid.set_properties(alg, *(), **kwargs)
alg.execute()
if "OutputMessage" in propertyOrder:
return alg.getPropertyValue("OutputMessage")
@@ -335,8 +334,8 @@ class Reducer(object):
output_workspaces = []
def __init__(self):
- self.UID = ''.join(
- random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
+ # Generate UUID and trim to 5 chars
+ self.UID = str(uuid.uuid1())[:5]
self.property_manager = "__reduction_parameters_" + self.UID
self._data_files = {}
self._reduction_steps = []
@@ -366,8 +365,8 @@ class Reducer(object):
Removes all workspace flagged as dirty, use when a reduction aborts with errors
"""
for bad_data in self._dirty:
- if bad_data in mtd:
- simpleapi.DeleteWorkspace(Workspace=bad_data)
+ if bad_data in mantid.mtd:
+ mantid.DeleteWorkspace(Workspace=bad_data)
else:
mantid.logger.notice('reducer: Could not access tainted workspace ' + bad_data)
@@ -454,7 +453,7 @@ class Reducer(object):
TODO: this needs to be an ordered list
"""
if data_file is None:
- if workspace in mtd:
+ if workspace in mantid.mtd:
self._data_files[workspace] = None
return
else:
@@ -555,8 +554,7 @@ class ReductionStep(object):
"""
Generate a unique name for an internal workspace
"""
- random_str = ''.join(
- random.choice(string.ascii_lowercase + string.ascii_uppercase + string.digits) for x in range(5))
+ random_str = str(uuid.uuid1())[:5]
return "__" + descriptor + "_" + extract_workspace_name(filepath) + "_" + random_str
def execute(self, reducer, inputworkspace=None, outputworkspace=None):
diff --git a/scripts/reduction_workflow/command_interface.py b/scripts/reduction_workflow/command_interface.py
index c75684cba6d4036d55f89bcff1ddd3bcd5471621..490fe35491c5f6fc1e1abeb0d30b4e3f78540c40 100644
--- a/scripts/reduction_workflow/command_interface.py
+++ b/scripts/reduction_workflow/command_interface.py
@@ -8,8 +8,7 @@ from reduction_workflow.reducer import Reducer
class ReductionSingleton(object):
""" Singleton reduction class """
-
- ## storage for the instance reference
+ # storage for the instance reference
__instance = None
def __init__(self):
@@ -66,7 +65,8 @@ class ReductionSingleton(object):
def get_property_manager(name):
- prop_mng = PropertyManagerDataService.retrieve(name)
+ # prop_mng = mantid.PropertyManagerDataService.retrieve(name)
+ pass
## List of user commands ######################################################
diff --git a/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py b/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py
index a00031304af16f927baa590a57cff84c0e74fc85..8a5a5326a2acded2a3014fd45971abae9853c9cd 100644
--- a/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py
+++ b/scripts/reduction_workflow/instruments/sans/hfir_command_interface.py
@@ -8,13 +8,17 @@ List of common user commands for HFIR SANS
import os.path
import mantid
-from reduction_workflow.command_interface import ReductionSingleton, Clear, OutputPath, Reduce1D, Reduce, AppendDataFile, ClearDataFiles
+from reduction_workflow.command_interface import ReductionSingleton, Clear
from reduction_workflow.find_data import find_data
from reduction_workflow.instruments.sans import hfir_instrument
from mantid.kernel import Logger
from mantid.simpleapi import Load
+# The following imports allow users to import this file and have all functionality automatically imported
+# Do not remove these imports as it will break user scripts which rely on them
+from reduction_workflow.command_interface import OutputPath, Reduce1D, Reduce, \
+ AppendDataFile, ClearDataFiles # noqa: F401
def BIOSANS():
Clear()
diff --git a/scripts/reduction_workflow/instruments/sans/sns_command_interface.py b/scripts/reduction_workflow/instruments/sans/sns_command_interface.py
index 5adfdacd89f0fe096406df999f7433f1ec0c2a1b..ae30908e0f8ab998ef21285833a77f75bd2210c3 100644
--- a/scripts/reduction_workflow/instruments/sans/sns_command_interface.py
+++ b/scripts/reduction_workflow/instruments/sans/sns_command_interface.py
@@ -5,38 +5,37 @@
# Import the specific commands that we need - some of these are used in systemtests
from reduction_workflow.command_interface import *
-from hfir_command_interface import DarkCurrent, NoDarkCurrent, NoNormalization
-from hfir_command_interface import SolidAngle, NoSolidAngle
-from hfir_command_interface import DirectBeamCenter, ScatteringBeamCenter
+from hfir_command_interface import SolidAngle
from hfir_command_interface import SetBeamCenter as BaseSetBeamCenter
-from hfir_command_interface import SensitivityCorrection, SetSensitivityBeamCenter
-from hfir_command_interface import SensitivityDirectBeamCenter, SensitivityScatteringBeamCenter
-from hfir_command_interface import NoSensitivityCorrection, DivideByThickness
+# The following imports allow users to import this file and have all functionality automatically imported
+# Do not remove these imports as it will break user scripts which rely on them
-from hfir_command_interface import IQxQy, NoIQxQy, SaveIq, NoSaveIq, SaveIqAscii
+from hfir_command_interface import DarkCurrent, NoDarkCurrent, NoNormalization, NoSolidAngle # noqa: F401
+from hfir_command_interface import DirectBeamCenter, ScatteringBeamCenter # noqa: F401
+from hfir_command_interface import SensitivityCorrection, SetSensitivityBeamCenter # noqa: F401
+from hfir_command_interface import SensitivityDirectBeamCenter, SensitivityScatteringBeamCenter # noqa: F401
+from hfir_command_interface import NoSensitivityCorrection, DivideByThickness # noqa: F401
-from hfir_command_interface import DirectBeamTransmission, TransmissionDarkCurrent
-from hfir_command_interface import ThetaDependentTransmission
-from hfir_command_interface import SetTransmissionBeamCenter, TransmissionDirectBeamCenter
-from hfir_command_interface import SetTransmission, NoTransmission
+from hfir_command_interface import IQxQy, NoIQxQy, SaveIq, NoSaveIq, SaveIqAscii # noqa: F401
-from hfir_command_interface import Background, NoBackground, NoBckTransmission
-from hfir_command_interface import SetBckTransmission, BckDirectBeamTransmission
-from hfir_command_interface import SetBckTransmissionBeamCenter, BckThetaDependentTransmission
-from hfir_command_interface import BckTransmissionDirectBeamCenter, BckTransmissionDarkCurrent
+from hfir_command_interface import DirectBeamTransmission, TransmissionDarkCurrent # noqa: F401
+from hfir_command_interface import ThetaDependentTransmission # noqa: F401
+from hfir_command_interface import SetTransmissionBeamCenter, TransmissionDirectBeamCenter # noqa: F401
+from hfir_command_interface import SetTransmission, NoTransmission # noqa: F401
-from hfir_command_interface import SetSampleDetectorOffset, SetSampleDetectorDistance
-from hfir_command_interface import Mask, MaskRectangle, MaskDetectors, MaskDetectorSide
-from hfir_command_interface import SetAbsoluteScale, SetDirectBeamAbsoluteScale
+from hfir_command_interface import Background, NoBackground, NoBckTransmission # noqa: F401
+from hfir_command_interface import SetBckTransmission, BckDirectBeamTransmission # noqa: F401
+from hfir_command_interface import SetBckTransmissionBeamCenter, BckThetaDependentTransmission # noqa: F401
+from hfir_command_interface import BckTransmissionDirectBeamCenter, BckTransmissionDarkCurrent # noqa: F401
+
+from hfir_command_interface import SetSampleDetectorOffset, SetSampleDetectorDistance # noqa: F401
+from hfir_command_interface import Mask, MaskRectangle, MaskDetectors, MaskDetectorSide # noqa: F401
+from hfir_command_interface import SetAbsoluteScale, SetDirectBeamAbsoluteScale # noqa: F401
from hfir_command_interface import Stitch
-#from mantid.api import AlgorithmManager
-#from mantid.kernel import Logger
-#import mantid.simpleapi as simpleapi
from reduction_workflow.find_data import find_data
-
def EQSANS(keep_events=False, property_manager=None):
Clear()
ReductionSingleton().set_instrument("EQSANS",