Fix bugs from past refactoring that went unnoticed

one_key() was not defined for me too. Is that because I am using an older version of extra-data? Not sure if this was because of my hack to fix the issue or an issue in itself.

I also tried it and I get another issue. I tested with:

/gpfs/exfel/data/scratch/danilo/envs/pes_to_spec/bin/exdf-reduce /gpfs/exfel/exp/SA3/202330/p900331/raw/r0070 --remove-sources SA3_XTD10_VAC/MDL/GATT_PHYSICS_UNIT SA3_XTD10_VAC/MDL/GATT_TRANSMISSION_MONITOR SCS_XTD10_IMGES/MOTOR/SWITCH_OPTICS SA3_XTD10_VAC/GAUGE/G30490D_IN SCS_XTD10_IMGES/ACTRL/MCP_GAIN SCS_XTD10_ESLIT/MDL/MAIN SCS_XTD10_IMGES/MOTOR/NAVITAR_ZOOM SA3_XTD10_VAC/MDL/GATT_P_CELL SA3_XTD10_VSLIT/MDL/BLADE SA3_XTD10_MONO/MDL/PHOTON_ENERGY SA3_XTD10_MIRR-2/MDL/FOCUS_POSITION SCS_XTD10_IMGES/MOTOR/SCREEN SA3_XTD10_VAC/GAUGE/G30480D_IN SA3_XTD10_VAC/DCTRL/AR_MODE_OK SA3_XTD10_UND/DOOCS/PHOTON_ENERGY_COLOR3 SA3_XTD10_VAC/DCTRL/D6_APERT_IN_OK SA3_XTD10_MONO/MOTOR/GRATING_AX SCS_XTD10_IMGES/CAM/BEAMVIEW_NAVITAR:daqOutput SA3_XTD10_UND/DOOCS/PHOTON_ENERGY SCS_XTD10_HSLIT/MDL/BLADE SCS_XTD10_IMGES/PROC/BEAMVIEW_NAVITAR SA3_XTD10_VAC/GAUGE/G30470D_IN SA3_XTD10_VAC/DCTRL/D12_APERT_IN_OK SA3_BR_UTC/MDL/BUNCHPATTERN_DECODER SA3_XTD10_VAC/DCTRL/N2_MODE_OK SA3_XTD10_PES/GAUGE/G30300F SA3_XTD10_MIRR-2/MOTOR/BENDER SQS_XTD10_ESLIT/MDL/MAIN SCS_XTD10_IMGES/DCTRL/LED_POWER SCS_XTD10_IMGES/MOTOR/NAVITAR_FOCUS SA3_XTD4_UND/DOOCS/UNDULATOR_CELLS SCS_XTD10_IMGES/CAM/BEAMVIEW_NAVITAR SCS_XTD10_IMGES/PROC/BEAMVIEW_NAVITAR:output SA3_XTD10_VAC/GAUGE/G30510C SA3_XTD10_UND/DOOCS/PHOTON_ENERGY_COLOR2 -o /gpfs/exfel/data/scratch/danilo/vspaper_data/dataset_A_test

Traceback:

Traceback (most recent call last):
  File "/gpfs/exfel/data/scratch/danilo/envs/pes_to_spec/bin/exdf-reduce", line 8, in <module>
    sys.exit(main())
  File "/gpfs/exfel/data/scratch/danilo/envs/pes_to_spec/lib/python3.9/site-packages/exdf/cli/reduce.py", line 254, in main
    writer.write_collection(output_path)
  File "/gpfs/exfel/data/scratch/danilo/envs/pes_to_spec/lib/python3.9/site-packages/exdf/data_reduction/red_writer.py", line 242, in write_collection
    self.write_item(
  File "/gpfs/exfel/data/scratch/danilo/envs/pes_to_spec/lib/python3.9/site-packages/exdf/data_reduction/red_writer.py", line 315, in write_item
    self.write_sequence(seq_path, seq_sources, seq_no)
  File "/gpfs/exfel/data/scratch/danilo/envs/pes_to_spec/lib/python3.9/site-packages/exdf/write/sd_writer.py", line 118, in write_sequence
    self.write_base(f, sources, sequence)
  File "/gpfs/exfel/data/scratch/danilo/envs/pes_to_spec/lib/python3.9/site-packages/exdf/data_reduction/red_writer.py", line 320, in write_base
    super().write_base(f, sources, sequence)
  File "/gpfs/exfel/data/scratch/danilo/envs/pes_to_spec/lib/python3.9/site-packages/exdf/write/sd_writer.py", line 151, in write_base
    train_ids, *index_dsets = get_index_root_data(sources)
  File "/gpfs/exfel/data/scratch/danilo/envs/pes_to_spec/lib/python3.9/site-packages/exdf/write/sd_writer.py", line 378, in get_index_root_data
    sel_timestamps = np.array(fa.file['INDEX/timestamp'][sel_rows])
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/gpfs/exfel/data/scratch/danilo/envs/pes_to_spec/lib/python3.9/site-packages/h5py/_hl/dataset.py", line 841, in __getitem__
    selection = sel.select(self.shape, args, dataset=self)
  File "/gpfs/exfel/data/scratch/danilo/envs/pes_to_spec/lib/python3.9/site-packages/h5py/_hl/selections.py", line 82, in select
    return selector.make_selection(args)
  File "h5py/_selector.pyx", line 282, in h5py._selector.Selector.make_selection
  File "h5py/_selector.pyx", line 215, in h5py._selector.Selector.apply_args
TypeError: Indexing elements must be in increasing order

mentioned in merge request !16 (merged)

resolved all threads

LGTM

merged

mentioned in commit 584a2ffc

mentioned in merge request !17 (merged)

Fix bugs from past refactoring that went unnoticed

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