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iohub info fails on MM datasets without xy_pixel_size #180

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talonchandler opened this issue Aug 24, 2023 · 0 comments · Fixed by #222
Closed

iohub info fails on MM datasets without xy_pixel_size #180

talonchandler opened this issue Aug 24, 2023 · 0 comments · Fixed by #222
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bug Something isn't working μManager Micro-Manager files and metadata
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@talonchandler
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...and xy_pixel_size is absent in our 1.3.0 zenodo datasets (and oftentimes from the microscopes if the pixel size isn't calibrated).

For example:

$ iohub info 2022_08_04_recOrder_pytest_20x_04NA/2T_3P_16Z_128Y_256X_Kazansky_1/
Reading file:	 /Users/talon.chandler/Desktop/0.4.0-release/misc/recOrder_test_data/2022_08_04_recOrder_pytest_20x_04NA/2T_3P_16Z_128Y_256X_Kazansky_1
Traceback (most recent call last):
  File "/opt/anaconda3/envs/recorder-dev/bin/iohub", line 8, in <module>
    sys.exit(cli())
  File "/opt/anaconda3/envs/recorder-dev/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/opt/anaconda3/envs/recorder-dev/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/opt/anaconda3/envs/recorder-dev/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/anaconda3/envs/recorder-dev/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/anaconda3/envs/recorder-dev/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/Users/talon.chandler/iohub/iohub/cli/cli.py", line 43, in info
    print_info(file, verbose=verbose)
  File "/Users/talon.chandler/iohub/iohub/reader.py", line 267, in print_info
    reader.xy_pixel_size,
  File "/Users/talon.chandler/iohub/iohub/multipagetiff.py", line 309, in xy_pixel_size
    raise AttributeError("XY pixel size cannot be determined.")
AttributeError: XY pixel size cannot be determined.. Did you mean: '_xy_pixel_size'?
@ziw-liu ziw-liu added this to the 0.2.0 milestone Mar 4, 2024
@ziw-liu ziw-liu linked a pull request Jun 12, 2024 that will close this issue
@ziw-liu ziw-liu added bug Something isn't working μManager Micro-Manager files and metadata labels Jun 13, 2024
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