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Fix bugs from past refactoring that went unnoticed

Merged Philipp Schmidt requested to merge fix/refactor-bugs into master
All threads resolved!

Thanks to @danilo for spotting two bugs resulting from past refactoring that went unnoticed in the field. Using flake8 I found another one.

@danilo

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    • Resolved by Danilo Enoque Ferreira de Lima

      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
  • Philipp Schmidt mentioned in merge request !16 (merged)

    mentioned in merge request !16 (merged)

  • resolved all threads

  • mentioned in commit 584a2ffc

  • Philipp Schmidt mentioned in merge request !17 (merged)

    mentioned in merge request !17 (merged)

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