diff --git a/docs/source/interfaces/Engineering Diffraction.rst b/docs/source/interfaces/Engineering Diffraction.rst
index 89477dfa73a00c494143c17a0cd66574c8f5cce2..f25105692a3eb72adc7cf9b9449c3b47fb8a8c0f 100644
--- a/docs/source/interfaces/Engineering Diffraction.rst
+++ b/docs/source/interfaces/Engineering Diffraction.rst
@@ -121,7 +121,8 @@ a plot for each bank and cropped focusing generates a plot for the single bank o
Clicking the focus button will begin the focusing algorithm for the selected run files. The button and plotting checkbox
will be disabled until the fitting algorithm is complete.
-The focused output files are saved in NeXus, GSS, and raw XYE format to:
+The focused output files are saved in NeXus, GSS, and TOPAS format. The process will also output a CSV file containing
+all numerical sample logs. All of these files are saved to:
`<CHOSEN_OUTPUT_DIRECTORY>/Focus/`
diff --git a/docs/source/release/v5.1.0/diffraction.rst b/docs/source/release/v5.1.0/diffraction.rst
index d4c0041287b2310f43156cddeda2fe8b045647e2..6a86de8a8e6c03acb1590156efefb2db30928069 100644
--- a/docs/source/release/v5.1.0/diffraction.rst
+++ b/docs/source/release/v5.1.0/diffraction.rst
@@ -14,6 +14,10 @@ Powder Diffraction
Engineering Diffraction
-----------------------
+Improvements
+^^^^^^^^^^^^
+- TOPAS files (`.abc`) have replaced the `.dat` files generated when focusing using the GUI.
+- Focusing with the GUI will now generate a CSV containing the averaged values of all numerical sample logs.
Single Crystal Diffraction
--------------------------
diff --git a/scripts/Engineering/gui/engineering_diffraction/tabs/focus/model.py b/scripts/Engineering/gui/engineering_diffraction/tabs/focus/model.py
index 3ca4cb3ffb10fc824d4978a3b71ede70f1e950fd..a744c6995cc5cd64365faa0d8388afde7cc35219 100644
--- a/scripts/Engineering/gui/engineering_diffraction/tabs/focus/model.py
+++ b/scripts/Engineering/gui/engineering_diffraction/tabs/focus/model.py
@@ -6,7 +6,8 @@
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, division, print_function)
-from os import path
+import csv
+from os import path, makedirs
from matplotlib import gridspec
import matplotlib.pyplot as plt
@@ -55,6 +56,7 @@ class FocusModel(object):
# Save the output to the file system.
self._save_output(instrument, sample_path, name, output_workspace_name, rb_num)
output_workspaces.append(workspaces_for_run)
+ self._output_sample_logs(instrument, run_no, sample_workspace, rb_num)
else:
for sample_path in sample_paths:
sample_workspace = path_handling.load_workspace(sample_path)
@@ -64,6 +66,7 @@ class FocusModel(object):
curves_workspace, None, full_calib_workspace, spectrum_numbers)
output_workspaces.append([output_workspace_name])
self._save_output(instrument, sample_path, "cropped", output_workspace_name, rb_num)
+ self._output_sample_logs(instrument, run_no, sample_workspace, rb_num)
# Plot the output
if plot_output:
for ws_names in output_workspaces:
@@ -126,8 +129,8 @@ class FocusModel(object):
rb_num)
self._save_focused_output_files_as_gss(instrument, sample_path, bank, sample_workspace,
rb_num)
- self._save_focused_output_files_as_xye(instrument, sample_path, bank, sample_workspace,
- rb_num)
+ self._save_focused_output_files_as_topas_xye(instrument, sample_path, bank, sample_workspace,
+ rb_num)
def _save_focused_output_files_as_gss(self, instrument, sample_path, bank, sample_workspace,
rb_num):
@@ -153,19 +156,53 @@ class FocusModel(object):
self._generate_output_file_name(instrument, sample_path, bank, ".nxs"))
SaveNexus(InputWorkspace=sample_workspace, Filename=nexus_output_path)
- def _save_focused_output_files_as_xye(self, instrument, sample_path, bank, sample_workspace,
- rb_num):
+ def _save_focused_output_files_as_topas_xye(self, instrument, sample_path, bank,
+ sample_workspace, rb_num):
xye_output_path = path.join(
path_handling.get_output_path(), "Focus",
- self._generate_output_file_name(instrument, sample_path, bank, ".dat"))
- SaveFocusedXYE(InputWorkspace=sample_workspace, Filename=xye_output_path, SplitFiles=False)
+ self._generate_output_file_name(instrument, sample_path, bank, ".abc"))
+ SaveFocusedXYE(InputWorkspace=sample_workspace,
+ Filename=xye_output_path,
+ SplitFiles=False,
+ Format="TOPAS")
if rb_num:
xye_output_path = path.join(
path_handling.get_output_path(), "User", rb_num, "Focus",
- self._generate_output_file_name(instrument, sample_path, bank, ".dat"))
+ self._generate_output_file_name(instrument, sample_path, bank, ".abc"))
SaveFocusedXYE(InputWorkspace=sample_workspace,
Filename=xye_output_path,
- SplitFiles=False)
+ SplitFiles=False,
+ Format="TOPAS")
+
+ @staticmethod
+ def _output_sample_logs(instrument, run_number, workspace, rb_num):
+ def write_to_file():
+ with open(output_path, "w", newline="") as logfile:
+ writer = csv.writer(logfile, ["Sample Log", "Avg Value"])
+ for log in output_dict:
+ writer.writerow([log, output_dict[log]])
+
+ output_dict = {}
+ sample_run = workspace.getRun()
+ log_names = sample_run.keys()
+ # Collect numerical sample logs.
+ for name in log_names:
+ try:
+ output_dict[name] = sample_run.getPropertyAsSingleValue(name)
+ except ValueError:
+ logger.information(f"Could not convert {name} to a numerical value. It will not be included in the "
+ f"sample logs output file.")
+ focus_dir = path.join(path_handling.get_output_path(), "Focus")
+ if not path.exists(focus_dir):
+ makedirs(focus_dir)
+ output_path = path.join(focus_dir, (instrument + "_" + run_number + "_sample_logs.csv"))
+ write_to_file()
+ if rb_num:
+ focus_user_dir = path.join(path_handling.get_output_path(), "User", rb_num, "Focus")
+ if not path.exists(focus_user_dir):
+ makedirs(focus_user_dir)
+ output_path = path.join(focus_user_dir, (instrument + "_" + run_number + "_sample_logs.csv"))
+ write_to_file()
@staticmethod
def _generate_output_file_name(instrument, sample_path, bank, suffix):
diff --git a/scripts/Engineering/gui/engineering_diffraction/tabs/focus/test/test_focus_model.py b/scripts/Engineering/gui/engineering_diffraction/tabs/focus/test/test_focus_model.py
index 7dd31c555c2d73a993dfb77e288a0c8bc403c432..d117784272767ff41946ec001cff9adf9a8efce7 100644
--- a/scripts/Engineering/gui/engineering_diffraction/tabs/focus/test/test_focus_model.py
+++ b/scripts/Engineering/gui/engineering_diffraction/tabs/focus/test/test_focus_model.py
@@ -7,9 +7,12 @@
from __future__ import (absolute_import, division, print_function)
import unittest
+import tempfile
+import shutil
from os import path
-from mantid.py3compat.mock import patch
+from mantid.py3compat.mock import patch, MagicMock
+from mantid.simpleapi import CreateSampleWorkspace
from Engineering.gui.engineering_diffraction.tabs.focus import model
from Engineering.gui.engineering_diffraction.tabs.common import path_handling
from Engineering.gui.engineering_diffraction.tabs.common.calibration_info import CalibrationInfo
@@ -19,11 +22,15 @@ file_path = "Engineering.gui.engineering_diffraction.tabs.focus.model"
class FocusModelTest(unittest.TestCase):
def setUp(self):
+ self.test_dir = tempfile.mkdtemp()
self.model = model.FocusModel()
self.current_calibration = CalibrationInfo(vanadium_path="/mocked/out/anyway",
sample_path="this_is_mocked_out_too",
instrument="ENGINX")
+ def tearDown(self):
+ shutil.rmtree(self.test_dir)
+
@patch(file_path + ".path_handling.load_workspace")
@patch(file_path + ".vanadium_corrections.Ads.doesExist")
def test_focus_cancelled_if_van_wsp_missing(self, ads_exist, load):
@@ -31,11 +38,12 @@ class FocusModelTest(unittest.TestCase):
self.model.focus_run("307593", ["1", "2"], False, "ENGINX", "0", None)
self.assertEqual(load.call_count, 0)
+ @patch(file_path + ".FocusModel._output_sample_logs")
@patch(file_path + ".Ads")
@patch(file_path + ".FocusModel._save_output")
@patch(file_path + ".FocusModel._run_focus")
@patch(file_path + ".path_handling.load_workspace")
- def test_focus_run_for_each_bank(self, load_focus, run_focus, output, ads):
+ def test_focus_run_for_each_bank(self, load_focus, run_focus, output, ads, logs):
ads.retrieve.return_value = "test_wsp"
banks = ["1", "2"]
load_focus.return_value = "mocked_sample"
@@ -47,11 +55,12 @@ class FocusModelTest(unittest.TestCase):
"305761_" + model.FOCUSED_OUTPUT_WORKSPACE_NAME + banks[-1],
"test_wsp", "test_wsp", banks[-1], None)
+ @patch(file_path + ".FocusModel._output_sample_logs")
@patch(file_path + ".Ads")
@patch(file_path + ".FocusModel._save_output")
@patch(file_path + ".FocusModel._run_focus")
@patch(file_path + ".path_handling.load_workspace")
- def test_focus_run_for_custom_spectra(self, load_focus, run_focus, output, ads):
+ def test_focus_run_for_custom_spectra(self, load_focus, run_focus, output, ads, logs):
ads.retrieve.return_value = "test_wsp"
spectra = "20-50"
load_focus.return_value = "mocked_sample"
@@ -63,6 +72,7 @@ class FocusModelTest(unittest.TestCase):
"305761_" + model.FOCUSED_OUTPUT_WORKSPACE_NAME + "cropped",
"test_wsp", "test_wsp", None, None, spectra)
+ @patch(file_path + ".FocusModel._output_sample_logs")
@patch(file_path + ".Ads")
@patch(file_path + ".FocusModel._save_output")
@patch(file_path + ".FocusModel._plot_focused_workspaces")
@@ -70,7 +80,7 @@ class FocusModelTest(unittest.TestCase):
@patch(file_path + ".path_handling.load_workspace")
@patch(file_path + ".vanadium_corrections.fetch_correction_workspaces")
def test_focus_plotted_when_checked(self, fetch_van, load_focus, run_focus, plot_focus, output,
- ads):
+ ads, logs):
ads.doesExist.return_value = True
fetch_van.return_value = ("mocked_integ", "mocked_curves")
banks = ["1", "2"]
@@ -80,6 +90,7 @@ class FocusModelTest(unittest.TestCase):
self.assertEqual(1, plot_focus.call_count)
+ @patch(file_path + ".FocusModel._output_sample_logs")
@patch(file_path + ".Ads")
@patch(file_path + ".FocusModel._save_output")
@patch(file_path + ".FocusModel._plot_focused_workspaces")
@@ -87,7 +98,7 @@ class FocusModelTest(unittest.TestCase):
@patch(file_path + ".path_handling.load_workspace")
@patch(file_path + ".vanadium_corrections.fetch_correction_workspaces")
def test_focus_not_plotted_when_not_checked(self, fetch_van, load_focus, run_focus, plot_focus,
- output, ads):
+ output, ads, logs):
fetch_van.return_value = ("mocked_integ", "mocked_curves")
banks = ["1", "2"]
load_focus.return_value = "mocked_sample"
@@ -121,6 +132,36 @@ class FocusModelTest(unittest.TestCase):
self.assertEqual(gss.call_count, 2)
self.assertEqual(xye.call_count, 2)
+ @patch(file_path + ".logger")
+ @patch(file_path + ".path_handling.get_output_path")
+ @patch(file_path + ".csv")
+ def test_output_sample_logs_with_rb_number(self, mock_csv, mock_path, mock_logger):
+ mock_writer = MagicMock()
+ mock_csv.writer.return_value = mock_writer
+ mock_path.return_value = self.test_dir
+ ws = CreateSampleWorkspace()
+
+ self.model._output_sample_logs("ENGINX", "00000", ws, "0")
+
+ self.assertEqual(5, len(ws.getRun().keys()))
+ self.assertEqual(1, mock_logger.information.call_count)
+ self.assertEqual(8, mock_writer.writerow.call_count)
+
+ @patch(file_path + ".logger")
+ @patch(file_path + ".path_handling.get_output_path")
+ @patch(file_path + ".csv")
+ def test_output_sample_logs_without_rb_number(self, mock_csv, mock_path, mock_logger):
+ mock_writer = MagicMock()
+ mock_csv.writer.return_value = mock_writer
+ mock_path.return_value = self.test_dir
+ ws = CreateSampleWorkspace()
+
+ self.model._output_sample_logs("ENGINX", "00000", ws, None)
+
+ self.assertEqual(5, len(ws.getRun().keys()))
+ self.assertEqual(1, mock_logger.information.call_count)
+ self.assertEqual(4, mock_writer.writerow.call_count)
+
if __name__ == '__main__':
unittest.main()