| Previous changeset 1:9340cbc7796c (2020-03-24) Next changeset 3:381f248febba (2020-04-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85" |
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modified:
idr_download_by_ids.py idr_download_by_ids.xml test-data/test1.tiff |
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| diff -r 9340cbc7796c -r 17b1cd0f4812 idr_download_by_ids.py --- a/idr_download_by_ids.py Tue Mar 24 13:48:46 2020 -0400 +++ b/idr_download_by_ids.py Tue Apr 14 10:27:25 2020 -0400 |
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| @@ -2,7 +2,7 @@ import os import sys -from matplotlib import pyplot as plt +from libtiff import TIFF from omero.gateway import BlitzGateway # noqa from omero.constants.namespaces import NSBULKANNOTATIONS # noqa @@ -17,8 +17,8 @@ def find_channel_index(image, channel_name): channel_name = channel_name.lower() - for n, channel in enumerate(image.getChannels()): - if channel_name == channel.getLabel().lower(): + for n, channel in enumerate(image.getChannelLabels()): + if channel_name == channel.lower(): return n # Check map annotation for information (this is necessary for some images) for ann in image.listAnnotations(NSBULKANNOTATIONS): @@ -82,11 +82,21 @@ def download_plane_as_tiff(image, tile, z, c, t, fname): pixels = image.getPrimaryPixels() - selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile) + try: + selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile) + except Exception: + warning = '{0} (ID: {1})'.format(image.getName(), + image.getId()) + warn('Could not download the requested region', warning) + return if fname[-5:] != '.tiff': fname += '.tiff' - plt.imsave(fname, selection) + try: + tiff = TIFF.open(fname, mode='w') + tiff.write_image(selection) + finally: + tiff.close() def download_image_data( @@ -182,7 +192,7 @@ ) else: channel_index = find_channel_index(image, channel) - if channel_index == -1: + if channel_index == -1 or channel_index >= image.getSizeC(): raise ValueError( '"{0}" is not a known channel name for image {1}' .format(channel, image.getName()) |
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| diff -r 9340cbc7796c -r 17b1cd0f4812 idr_download_by_ids.xml --- a/idr_download_by_ids.xml Tue Mar 24 13:48:46 2020 -0400 +++ b/idr_download_by_ids.xml Tue Apr 14 10:27:25 2020 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="idr_download_by_ids" name="IDR Download" version="0.10" profile="18.09"> +<tool id="idr_download_by_ids" name="IDR Download" version="0.20" profile="18.09"> <description>- download images from the Image Data Resource using image IDs</description> <macros> <xml name="region_spec" token_pos="upper-left corner"> @@ -17,7 +17,7 @@ </macros> <requirements> <requirement type="package" version="5.6.0">python-omero</requirement> - <requirement type="package" version="3.1.3">matplotlib</requirement> + <requirement type="package" version="0.4.2">pylibtiff</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ mkdir downloads && cd downloads && @@ -154,7 +154,7 @@ <output_collection name="output_file" type="list" count="3"> <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024"> <assert_contents> - <has_size value="4194510" /> + <has_size value="2097286" /> </assert_contents> </element> </output_collection> @@ -191,7 +191,7 @@ <output_collection name="output_file" type="list" count="2"> <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024"> <assert_contents> - <has_size value="4194510" /> + <has_size value="2097286" /> </assert_contents> </element> </output_collection> |
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| diff -r 9340cbc7796c -r 17b1cd0f4812 test-data/test1.tiff |
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| Binary file test-data/test1.tiff has changed |