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Batch export ROIs from screen #156

Merged
merged 5 commits into from
Feb 21, 2020
Merged

Batch export ROIs from screen #156

merged 5 commits into from
Feb 21, 2020

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will-moore
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I found this useful recently, exporting big CSV from many images in a Screen or Plate.

To test:

  • Create lots of ROIs on many images in a Screen or Project.
  • Try to Export ROIs via this script from Screen, Plate, Project.

@will-moore
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Travis failed with

oving network scripts_default
The command ".omero/docker scripts" exited with 1.

Re-running...

@will-moore will-moore mentioned this pull request Feb 10, 2020
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@will-moore will-moore changed the title Batch_ROI_Export.py supports Screen, Plate, Project Batch export ROIs from screen Feb 10, 2020
jburel
jburel reviewed Feb 11, 2020
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omero/export_scripts/Batch_ROI_Export.py
@@ -247,15 +247,36 @@ def link_annotation(objects, file_ann):
o.linkAnnotation(file_ann)


def get_images_from_plate(plate):
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Note for self
This is the kind of method to add to "omero-py-toolbox"

jburel
jburel reviewed Feb 11, 2020
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omero/export_scripts/Batch_ROI_Export.py
message = "Exported %s shapes" % len(export_data)
return file_ann, message


def run_script():
"""The main entry point of the script, as called by the client."""
data_types = [rstring('Dataset'), rstring('Image')]
data_types = [rstring(s) for s in
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@jburel jburel Feb 11, 2020 •
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This is much more than Screen as indicated in the PR title.
All types of containers need to be reviewed

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Yes, that is in the description. Not space in the title for all testing instructions.

@will-moore will-moore closed this Feb 17, 2020
@will-moore will-moore reopened this Feb 17, 2020
@pwalczysko
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  • run it on Project, Dataset, Plate, Screen, aslo in multiples
  • All works as expected, but couple of RFEs see below.

RFEs:

  • For plates, have a well (row, column, e.g. A1) as a parameter in the csv
  • For plates, the activities do not suggest "navigate to the plate where I just attached the csv" icon (unlike for P/Ds)
  • For multi-selections (select several Datasets or several Plates or several Projects or Screens, then run the script) or single Projects and Screens with multiple Datasets and Plates respectively, the parameter missing is the originating P/D/S/P

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jburel commented Feb 21, 2020

RFE #172

@jburel jburel merged commit cd74e00 into ome:develop Feb 21, 2020
@will-moore will-moore mentioned this pull request Mar 13, 2020
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3 participants
@will-moore @pwalczysko @jburel