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Add task to pick ROIs

Merged Loic Huder requested to merge roi-task into main
3 unresolved threads

For #1

Edited by Loic Huder

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79 Scan.set_default_scan_path(scan_path)
80
81 above_list = [102, 106]
82 scan_above = Scan()
83 scan_above.load(above_list[0])
84 for ii in above_list[1::]:
85 _tmp = Scan()
86 _tmp.load(ii)
87 scan_above._det_images += _tmp._det_images
88 img = scan_above._det_images.sum(axis=0)
89 numpy.save(img_path, img)
90
91 app = qt.QApplication([])
92 window = RoiPicker(img)
93 window.show()
94 app.exec()
    • I am not able to install it. I have the following error:

      orangecontrib.ewoksixs.roi'.
      Traceback (most recent call last):
        File "/home/payno/dev/esrf/ewoks/venv/lib/python3.11/site-packages/orangecanvas/registry/discovery.py", line 309, in iter_widget_descriptions
          module = asmodule(name)
                   ^^^^^^^^^^^^^^
        File "/home/payno/dev/esrf/ewoks/venv/lib/python3.11/site-packages/orangecanvas/registry/discovery.py", line 552, in asmodule
          return __import__(module, fromlist=[""])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/payno/dev/esrf/ewoks/venv/lib/python3.11/site-packages/orangecontrib/ewoksixs/roi.py", line 3, in <module>
          from ewoksixs.gui.roi_picker import RoiPicker
        File "/home/payno/dev/esrf/ewoks/venv/lib/python3.11/site-packages/ewoksixs/gui/roi_picker.py", line 11, in <module>
          from ixstools.scan import Scan, SpecPath
      ModuleNotFoundError: No module named 'ixstools'
      2024-03-25 17:59:52,162:INFO:orangecanvas.main: Adding search path '/home/payno/dev/esrf/ewoks/venv/lib/python3.11/site-packages/orangecanvas/styles/orange' for prefix, 'canvas_icons'
      

      and couldn't find out how to install ixstools (no pypi wheel to install it)

    • It should be installed from the Git repo: https://gitlab.esrf.fr/ixstools/ixsscan

      I'll add it to the requirements

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  • Loic Huder added 2 commits

    added 2 commits

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  • Loic Huder added 1 commit

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    • ddcfce49 - Remove main section in roi_picker

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  • Please have a second look :grin:

    • Thanks for the update.

      1. First one more suggestion regarding the setup.cfg. Maybe it could help to have a full section - this way we make sure using pip install .[full] we can access to everything. Something like:
      full = 
          PyQt5

      Except this installation goes smoothly nice :muscle:

      1. I noticed that ixstools is an internal project. Does it make sense ? (simple question probably on beamline hand but if you want to have ewoksixs a bit open this will help)

      2. Then regarding the gui from a 'dummy user' perspective what I can be critic about is:

      3.1 the output of ROI picker and the input of collect results along axes have different names which is confusing

      3.2 maybe labels can be simplify. * Named of the HDF5 file to save the ROI -> output file ? HDF5 can be filtered from the FileDialog * scan numbers to sum for the ROI image: scan numbers

      3.3 maybe understanding can be improve

      • Params of the SPEC path: I have no clue what this can do and what are the valid / possible inputs
      • Regarding all the inputs I see sometime bliss and sometime spec can it read from both ?

      3.4 depending on the expected input of Scan number of sum for the ROI Image this can / should be improved.

      • once we know the possible valid scan numbers (if we know them) maybe it a dedicated interface can be proposed to select / unselect the scan number.
      1. on the collect results along axes (not part of the PR) I also noticed the following:
      • there is a lot of input which are not making much sense. Maybe some tooltips can help there.
      • I see that there is Axis names and Axis_choices. Why is there one with underscore and not the other ? Same for path_to_spec and spec_file_name.
      • For now I also see that there is some edf (spec) and hdf5 melt. What is the reason ? For now you expect all dataset to be stored unsed .edf and you save the processing to .hdf5 ?
      1. I cannot access /data/id21/inhouse/wout/ixstools/test_data so not able to process more test.

      2. icons could also help the users to understanding the meaning of each widget and find them more quickly.

      Edited by payno
      1. Good idea :thumbsup: (edfb833a)
      2. I'll have to check with Christoph

      3.1. Good point, I'll rename those (c17cb149)

      3.2 :thumbsup: (in next PR)

      3.3 My next PR will change Params of the SPEC path into more meaningful controls. For now, it only accepts SPEC but in the future (summer), it should accept BLISS paths.

      3.4. Perhaps. I'll discuss this specifically with Christoph

      1. Again, I hope that by discussing with Christoph, I'll be able to improve the controls. But you are right, there are a few typos to fix. As for the edf vs hdf5, I am merely following what ixstools is doing :shrug:

      2. You don't have a mounting of /data on your computer ?

      3. Good idea :thumbsup: (in a future PR)

      Edited by Loic Huder
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  • Loic Huder added 3 commits

    added 3 commits

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  • Loic Huder mentioned in commit bfff0d3f

    mentioned in commit bfff0d3f

  • merged

  • Loic Huder mentioned in merge request !5 (merged)

    mentioned in merge request !5 (merged)

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