Commit a0ba994a authored by Zolnierczuk, Piotr's avatar Zolnierczuk, Piotr
Browse files

bug in writer

parent 880ef877

pysen/inout/writer.py

+20 −26
Original line number Diff line number Diff line
@@ -16,14 +16,16 @@ from ..constants import PICO, NANO, MICRO, ANGSTROM, GAUSS 
from .nexus import MOTORS, B_SENSORS, time_format

from .scans import EchoScan, DiffractionScan, TransmissionScan



# BUNCH OF HARD CODED CONSTANTS

# TO DO: some of this is repeated in nexus.py file (merge!)

# FIXME: BUNCH OF HARD CODED CONSTANTS

PHASE_INDEX = 100



PHASE_UP    = 2 # up phase padding

PHASE_DN    = 1 # down phase padding

PHASES_NPOL = 2+3 # 2xPC for down and 3xPC for up

#

INV_NUMOR   = -999999 # "invalid" numor

#

RE_TRAN  = re.compile('transmission', re.IGNORECASE) # match transmission line

RE_NUMOR = re.compile(r'\d+')



def get_phase_index(scan_index, offset=0):

    "return phase index"
@@ -32,24 +34,22 @@ def get_phase_index(scan_index, offset=0): 
        return updn + offset

    return scan_index%PHASE_INDEX - offset - 1



def make_filename(base, prefix='taco'):

    "make a TACO filename"

    match = re.search(RE_NUMOR, base)

    if match:

        numor = match.group(0)

    else:

        numor = INV_NUMOR

    return f"{prefix}{numor}.dat"





RE_TRAN = re.compile('transmission', re.IGNORECASE)



class TransmissionWriter(TransmissionScan):

    "Convert EPICS/ADARA/NeXus file to transmission .dat file"



    @staticmethod

    def make_filename(base):

        "make diffraction filename"

        root, _ = os.path.splitext(os.path.basename(base)) # remove h5

        root, _ = os.path.splitext(root)                   # remove nxs

        numor = int(root.split('_')[-1])

        return f"transmission_{numor}.dat"



    def save(self, outdir='.'):

        "convert read nexus file to diffrun .dat file"

        transmission_run = self.make_filename(self.info['base'])

        transmission_run = make_filename(self.info['base'], prefix='transmission_')

        with open(os.path.join(outdir, transmission_run), 'wt', encoding='ascii') as fd:

            #

            self.log.info("%s: creating transmission .dat file", transmission_run)
@@ -94,20 +94,14 @@ class TransmissionWriter(TransmissionScan): 
class DiffractionWriter(DiffractionScan):

    "Convert EPICS/ADARA/NeXus file to diffrun .dat file"



    @staticmethod

    def make_filename(base):

        "make diffraction filename"

        root, _ = os.path.splitext(os.path.basename(base)) # remove h5

        root, _ = os.path.splitext(root)                   # remove nxs

        numor = int(root.split('_')[-1])

        return f"diffrun_{numor}.dat"





    def save(self, outdir='.'):

        "convert read nexus file to diffrun .dat file"

        #pylint: disable=too-many-statements

        #FIXME: refactor this

        diffrun = self.make_filename(self.info['base'])

        diffrun = make_filename(self.info['base'], prefix='diffrun_')

        print(self.info['base'])

        outdir='.'

        print(diffrun, outdir)

        with open(os.path.join(outdir, diffrun), 'wt', encoding='ascii') as fd:

            #

            fd.write( "\"############################\"\n")
@@ -170,9 +164,9 @@ class DiffractionWriter(DiffractionScan): 
                fd.write( "\n")



                if not spin_up:

                    if detsum>0:

                    try:

                        fr = upcnt/detsum

                    else:

                    except TypeError:

                        fr = np.nan

                    fd.write(f"\"Q\"   {qmin:g}  ")

                    fd.write(f"\"flip ratio\" {fr:g}\n")

test/test_inout_hdf.py

+1 −1
Original line number Diff line number Diff line 
"""

Python unit test cases for pysen.echo.fit module

Python unit test cases for pysen.echo.converter module

"""

import unittest

import os.path