Mercurial > repos > goeckslab > rename_tiff_channels
comparison rename_tiff_channels.xml @ 6:4763362914f4 draft default tip
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 5c324d06ad54dca76aa2b4c8118df5654f49da66
| author | goeckslab |
|---|---|
| date | Mon, 15 Jul 2024 21:37:39 +0000 |
| parents | 61fd94c7ce42 |
| children |
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| 5:61fd94c7ce42 | 6:4763362914f4 |
|---|---|
| 57 cwd = os.getcwd() | 57 cwd = os.getcwd() |
| 58 | 58 |
| 59 channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv')) | 59 channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv')) |
| 60 | 60 |
| 61 original_ome_xml = tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff')) | 61 original_ome_xml = tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff')) |
| 62 working_ome = ome_types.from_xml(original_ome_xml, parser = 'lxml') | 62 working_ome = ome_types.from_xml(original_ome_xml) |
| 63 | 63 |
| 64 for l_idx, level in enumerate(working_ome.images): | 64 for l_idx, level in enumerate(working_ome.images): |
| 65 | 65 |
| 66 for c_idx, channel in enumerate(level.pixels.channels): | 66 for c_idx, channel in enumerate(level.pixels.channels): |
| 67 | 67 |
| 71 | 71 |
| 72 if l_idx == 0: | 72 if l_idx == 0: |
| 73 | 73 |
| 74 print(f"Channel {c_idx} renamed to {new_name}") | 74 print(f"Channel {c_idx} renamed to {new_name}") |
| 75 | 75 |
| 76 updated_ome_xml = working_ome.to_xml() | 76 updated_ome_xml = working_ome.to_xml().encode() |
| 77 tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'), updated_ome_xml) | 77 tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'), updated_ome_xml) |
| 78 | 78 |
| 79 print("Updated OME-TIFF metadata:") | 79 print("Updated OME-TIFF metadata:") |
| 80 print(tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'))) | 80 print(tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'))) |
| 81 </configfile> | 81 </configfile> |
| 91 <test> | 91 <test> |
| 92 <param name="image" value="rename_test.ome.tiff" /> | 92 <param name="image" value="rename_test.ome.tiff" /> |
| 93 <param name="channel_csv" value="rename_channels.csv" /> | 93 <param name="channel_csv" value="rename_channels.csv" /> |
| 94 <output name="renamed_image" ftype="ome.tiff"> | 94 <output name="renamed_image" ftype="ome.tiff"> |
| 95 <assert_contents> | 95 <assert_contents> |
| 96 <has_size value="899000" delta="50000" /> | 96 <has_size value="900000" delta="50000" /> |
| 97 </assert_contents> | 97 </assert_contents> |
| 98 </output> | 98 </output> |
| 99 <assert_stdout> | 99 <assert_stdout> |
| 100 <has_text text="Channel 0 renamed to DNA_6" /> | 100 <has_text text="Channel 0 renamed to Hematoxylin" /> |
| 101 <has_text text="Updated OME-TIFF metadata" /> | 101 <has_text text="Updated OME-TIFF metadata" /> |
| 102 <has_text text="µm" /> | |
| 102 </assert_stdout> | 103 </assert_stdout> |
| 103 </test> | 104 </test> |
| 104 </tests> | 105 </tests> |
| 105 <help><![CDATA[ | 106 <help><![CDATA[ |
| 106 Given an OME.TIFF image and channel metadata CSV file, rename the image channels in the | 107 Given an OME.TIFF image and channel metadata CSV file, rename the image channels in the |