Mercurial > repos > goeckslab > rename_tiff_channels

changeset 6:4763362914f4 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
files macros.xml rename_tiff_channels.xml test-data/rename_channels.csv test-data/rename_test.ome.tiff test-data/test.xml
diffstat 5 files changed, 26 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Jul 11 22:41:10 2024 +0000
+++ b/macros.xml	Mon Jul 15 21:37:39 2024 +0000
@@ -16,6 +16,6 @@
     </xml>
     
     <token name="@TOOL_VERSION@">0.0.2</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">19.01</token>
 </macros>
--- a/rename_tiff_channels.xml	Thu Jul 11 22:41:10 2024 +0000
+++ b/rename_tiff_channels.xml	Mon Jul 15 21:37:39 2024 +0000
@@ -59,7 +59,7 @@
 channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv'))
 
 original_ome_xml = tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'))
-working_ome = ome_types.from_xml(original_ome_xml, parser = 'lxml')
+working_ome = ome_types.from_xml(original_ome_xml)
 
 for l_idx, level in enumerate(working_ome.images):
 
@@ -73,7 +73,7 @@
 
             print(f"Channel {c_idx} renamed to {new_name}")
 
-updated_ome_xml = working_ome.to_xml()
+updated_ome_xml = working_ome.to_xml().encode()
 tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'), updated_ome_xml)
 
 print("Updated OME-TIFF metadata:")
@@ -93,12 +93,13 @@
             <param name="channel_csv" value="rename_channels.csv" />
             <output name="renamed_image" ftype="ome.tiff">
                 <assert_contents>
-                    <has_size value="899000" delta="50000" />
+                    <has_size value="900000" delta="50000" />
                 </assert_contents>
             </output>
             <assert_stdout>
-                <has_text text="Channel 0 renamed to DNA_6" />
+                <has_text text="Channel 0 renamed to Hematoxylin" />
                 <has_text text="Updated OME-TIFF metadata" />
+                <has_text text="µm" />
             </assert_stdout>
         </test>
     </tests>
--- a/test-data/rename_channels.csv	Thu Jul 11 22:41:10 2024 +0000
+++ b/test-data/rename_channels.csv	Mon Jul 15 21:37:39 2024 +0000
@@ -1,3 +1,20 @@
-channel_number,cycle_number,marker_name,Filter,excitation_wavelength,emission_wavelength
-0,6,DNA_6,DAPI,395,431
-0,6,DNA_7,DAPI,395,431
\ No newline at end of file
+channel_number,marker_name
+1,Hematoxylin
+2,HLA_DRDPDQ
+3,DCLAMP
+4,CD3
+5,CD45
+6,CD8
+7,GRZB
+8,CD20
+9,CD11b
+10,CD66b
+11,CD11c
+12,CD163
+13,HLA-ClassI
+14,EOMES
+15,FOXP3
+16,Ki67
+17,panCK
+18,PD-1
+19,PD-L1
Binary file test-data/rename_test.ome.tiff has changed
--- a/test-data/test.xml	Thu Jul 11 22:41:10 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:be7b96c1-399b-41a1-a9f8-ab50da05159b" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0"><Pixels BigEndian="false" DimensionOrder="XYZCT" ID="Pixels:0" PhysicalSizeX="0.6499999761581421" PhysicalSizeXUnit="µm" PhysicalSizeY="0.6499999761581421" PhysicalSizeYUnit="µm" SizeC="32" SizeT="1" SizeX="13720" SizeY="9420" SizeZ="1" Type="uint16"><Channel ID="Channel:0:0" Name="DNA" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:1" Name="Control-488nm" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:2" Name="Control-555nm" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:3" Name="Control-647nm" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:4" Name="DNA (2)" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:5" Name="ERK-1 (pT202; pY204)" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:6" Name="ERK-1 (pT202; pY204) (2)" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:7" Name="hRAD51" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:8" Name="DNA (3)" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:9" Name="G1/S-specific cyclin-D1" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:10" Name="Vimentin" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:11" Name="Aortic smooth muscle actin" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:12" Name="DNA (4)" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:13" Name="E-cadherin" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:14" Name="ER" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:15" Name="PR" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:16" Name="DNA (5)" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:17" Name="Epidermal growth factor receptor" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:18" Name="Rb (pS807; pS811)" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:19" Name="CD45" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:20" Name="DNA (6)" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:21" Name="Antigen Ki67" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:22" Name="CK-19" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:23" Name="p21" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:24" Name="DNA (7)" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:25" Name="CK-14" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:26" Name="Androgen Receptor" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:27" Name="Cleaved PARP-1" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:28" Name="DNA (8)" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:29" Name="CK-17" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:30" Name="CK-7" SamplesPerPixel="1"><LightPath /></Channel><Channel ID="Channel:0:31" Name="HER2" SamplesPerPixel="1"><LightPath /></Channel><TiffData IFD="0" PlaneCount="32" /><Plane TheC="0" TheT="0" TheZ="0" /><Plane TheC="1" TheT="0" TheZ="0" /><Plane TheC="2" TheT="0" TheZ="0" /><Plane TheC="3" TheT="0" TheZ="0" /><Plane TheC="4" TheT="0" TheZ="0" /><Plane TheC="5" TheT="0" TheZ="0" /><Plane TheC="6" TheT="0" TheZ="0" /><Plane TheC="7" TheT="0" TheZ="0" /><Plane TheC="8" TheT="0" TheZ="0" /><Plane TheC="9" TheT="0" TheZ="0" /><Plane TheC="10" TheT="0" TheZ="0" /><Plane TheC="11" TheT="0" TheZ="0" /><Plane TheC="12" TheT="0" TheZ="0" /><Plane TheC="13" TheT="0" TheZ="0" /><Plane TheC="14" TheT="0" TheZ="0" /><Plane TheC="15" TheT="0" TheZ="0" /><Plane TheC="16" TheT="0" TheZ="0" /><Plane TheC="17" TheT="0" TheZ="0" /><Plane TheC="18" TheT="0" TheZ="0" /><Plane TheC="19" TheT="0" TheZ="0" /><Plane TheC="20" TheT="0" TheZ="0" /><Plane TheC="21" TheT="0" TheZ="0" /><Plane TheC="22" TheT="0" TheZ="0" /><Plane TheC="23" TheT="0" TheZ="0" /><Plane TheC="24" TheT="0" TheZ="0" /><Plane TheC="25" TheT="0" TheZ="0" /><Plane TheC="26" TheT="0" TheZ="0" /><Plane TheC="27" TheT="0" TheZ="0" /><Plane TheC="28" TheT="0" TheZ="0" /><Plane TheC="29" TheT="0" TheZ="0" /><Plane TheC="30" TheT="0" TheZ="0" /><Plane TheC="31" TheT="0" TheZ="0" /></Pixels></Image></OME>