The DIALS project provides an extensible framework to analyse X-ray diffraction data. Much of this work is agnostic to the method used to obtain diffraction patterns, and can equally be applied to neutron diffraction data. This repository provides a bridge between data obtained from the ISIS Neutron and Muon source and DIALS, converting raw output to formats that DIALS can read and, additional post-processing for integration into other packages (e.g. Mantid).
git clone [email protected]:dials/isis_utils.git
cd isis_utils
pip install -r requirements.txt
TOFRAW format | ISIS formats | Example data
Raw files can also be read using OpenGenie and Mantid.
Convert single .raw file
python isis_raw_reader.py my_raw_file.raw --convert_to_tofraw
Reading my_raw_file.raw into memory..
Outputting data to my_raw_file.nxs..
Convert multiple .raw files
python isis_raw_reader.py my_raw_file_1.raw my_raw_file_2.raw --convert_to_tofraw
Reading my_raw_file_1.raw into memory..
Outputting data to my_raw_file_1.nxs..
Reading my_raw_file_2.raw into memory..
Outputting data to my_raw_file_2.nxs..
Convert directory of .raw files
python isis_raw_reader.py my_dir/*.raw --convert_to_tofraw
Reading my_dir/my_raw_file_1.raw into memory..
Outputting data to my_dir/my_raw_file_1.nxs..
etc.
Known Issues
Although the data in a generated TOFRAW file aims to be as close as possible to the RAW file, there are some known issues with the conversion used here. This is due to changes/additions/removal of parameters between the two formats, inconsistencies between the two formats, and unknown parameters (the main source of truth for parameter names used when writing this code was Mantid).
The following TOFRAW params are not found (by the author!) in RAW files
raw_data_1/instrument/dae/vetos/fermi_chopper3
raw_data_1/instrument/dae/vetos/fifo
raw_data_1/instrument/dae/vetos/msmode
raw_data_1/instrument/dae/vetos/writing_table_file
raw_data_1/instrument/detector_table_file
raw_data_1/instrument/spectra_table_file
raw_data_1/instrument/dae/type
raw_data_1/instrument/dae/vetos/ISIS_50Hz
raw_data_1/instrument/dae/vetos/TS2_pulse
raw_data_1/instrument/dae/vetos/ext2
raw_data_1/instrument/dae/vetos/ext3
raw_data_1/instrument/moderator/distance
raw_data_1/instrument/source/name
raw_data_1/instrument/source/probe
raw_data_1/instrument/source/type
raw_data_1/measurement/first_run
raw_data_1/measurement/id
raw_data_1/measurement/label
raw_data_1/measurement/subid
raw_data_1/measurement/type
raw_data_1/monitor_events_not_saved
raw_data_1/notes
raw_data_1/periods/good_frames_daq
raw_data_1/periods/highest_used
raw_data_1/periods/labels
raw_data_1/periods/output
raw_data_1/periods/sequences
raw_data_1/periods/total_counts
raw_data_1/run_cycle
raw_data_1/run_log/*
raw_data_1/sample/distance
raw_data_1/sample/id
raw_data_1/sample/name
raw_data_1/sample/shape
raw_data_1/script_name
raw_data_1/seci_config
raw_data_1/selog
raw_data_1/total_counts
raw_data_1/total_uncounted_counts
The following TOFRAW params are not consistent (as far as I can tell!) between formats
detector_1/spectrum_index
raw_data_1/framelog
raw_data_1/instrument/detector_1/distance
raw_data_1/instrument/detector_1/polar_angle
raw_data_1/monitor_/
raw_data_1/periods/proton_charge
raw_data_1/periods/proton_charge_raw
raw_data_1/periods/type
raw_data_1/run_number
raw_data_1/sample/type
E.g. the .raw spectrum_number_table is inconsistent with the .nxs detector_1/spectrum_index. The former gives a 1D array from the top right of each detector moving down each column (i.e for 64x64 detector [64,63,..]). The .nxs index just gives [i for i in range(num pixels)]. When visualising both give the same laue plots, consistent with SXD2001 only when using the indexing e.g. for a 64x64 detector:
np.arange(min_pixel_idx_range, max_pixel_idx_range).reshape(64,64).T
python update_experiment.py mantid_workspace.nxs -take_data dials_experiment.expt
INFO: Update Experiment:mantid_workspace.nxs copied to mantid_workspace_updated.nxs
INFO: Update Experiment:Replacing detector panels in mantid_workspace_updated.nxs with those in dials_experiment.expt
python update_experiment.py mantid_peaks_workspace.nxs -take_data dials_experiment.expt dials_reflection_table.refl
INFO: Update Experiment:mantid_peaks_workspace.nxs copied to mantid_peaks_workspace_updated.nxs
INFO: Update Experiment:Replacing detector panels in mantid_peaks_workspace_updated.nxs with those in dials_experiment.expt
INFO: Update Experiment:Replacing peak table in mantid_peaks_workspace_updated.nxs with table from dials_reflection_table.refl