Mercurial > repos > goeckslab > rename_tiff_channels

changeset 5:61fd94c7ce42 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
author goeckslab
date Thu, 11 Jul 2024 22:41:10 +0000
parents 55bc102d7709
children 4763362914f4
files macros.xml rename_tiff_channels.xml scale_cell_coordinates.py test-data/pixels.h5ad test-data/rename_channels.csv test-data/rename_test.ome.tiff test-data/rename_test.tiff test-data/test.xml
diffstat 8 files changed, 78 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Fri May 10 21:01:32 2024 +0000
+++ b/macros.xml	Thu Jul 11 22:41:10 2024 +0000
@@ -2,12 +2,12 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <container type="docker">quay.io/goeckslab/mti_utils:0.0.1</container>
+            <container type="docker">quay.io/goeckslab/mti_utils:@TOOL_VERSION@</container>
         </requirements>
     </xml>
 
     <xml name="version_cmd">
-        <version_command>echo @VERSION@</version_command>
+        <version_command>echo @TOOL_VERSION@</version_command>
     </xml>
     <xml name="citations">
         <citations>
@@ -15,7 +15,7 @@
         </citations>
     </xml>
     
-    <token name="@TOOL_VERSION@">0.0.1</token>
-    <token name="@VERSION_SUFFIX@">5</token>
+    <token name="@TOOL_VERSION@">0.0.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">19.01</token>
 </macros>
--- a/rename_tiff_channels.xml	Fri May 10 21:01:32 2024 +0000
+++ b/rename_tiff_channels.xml	Thu Jul 11 22:41:10 2024 +0000
@@ -33,11 +33,27 @@
 import os
 import sys 
 import argparse
+from itertools import cycle
 import pandas as pd
 import ome_types
-from ome_types.model import channel
+from ome_types.model import channel, Color
 from tifffile import tiffcomment
 
+# setting default colors to match avivator
+colors = [
+    (0,0,255,1.0),     # blue
+    (0,255,0,1.0),     # green
+    (255,0,255,1.0),   # magenta
+    (255,255,0,1.0),   # yellow
+    (255,127,0,1.0),   # orange
+    (0,255,255,1.0),   # cyan
+    (255,255,255,1.0), # white
+    (255,0,0,1.0)      # red
+]
+
+# convert to repeatable object of primitive int colors 
+color_cycle = cycle([Color(c).as_int32() for c in colors])
+
 cwd = os.getcwd()
 
 channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv'))
@@ -51,6 +67,7 @@
 
         new_name = channels_df.loc[c_idx, 'marker_name']
         channel.name = new_name
+        channel.color = next(color_cycle)
 
         if l_idx == 0:
 
@@ -72,11 +89,11 @@
     </outputs>
     <tests>
         <test>
-            <param name="image" value="rename_test.tiff" />
+            <param name="image" value="rename_test.ome.tiff" />
             <param name="channel_csv" value="rename_channels.csv" />
             <output name="renamed_image" ftype="ome.tiff">
                 <assert_contents>
-                    <has_size value="44000" delta="1000" />
+                    <has_size value="899000" delta="50000" />
                 </assert_contents>
             </output>
             <assert_stdout>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scale_cell_coordinates.py	Thu Jul 11 22:41:10 2024 +0000
@@ -0,0 +1,50 @@
+import argparse
+import json
+import warnings
+
+import anndata as ad
+
+
+def main(inputs, output):
+
+    """
+    inputs : str
+        File path to galaxy tool JSON inputs config file
+    output: str
+        File path to save the output h5ad file
+    """
+    warnings.simplefilter('ignore')
+
+    # read inputs JSON
+    with open(inputs, 'r') as param_handler:
+        params = json.load(param_handler)
+
+    # read input anndata file
+    adata = ad.read_h5ad(params['anndata'])
+
+    # scale coords
+    unit = params['unit']
+    new_col_names = []
+    for c in [params['x_coord'], params['y_coord']]:
+        scaled_col_name = f'{c}_{unit}'
+        adata.obs[scaled_col_name] = adata.obs[c] * params['resolution']
+        new_col_names.append(scaled_col_name)
+
+    # overwrite adata.obsm['spatial'] with scaled coordinates
+    adata.obsm['spatial'] = adata.obs[scaled_col_name].values
+
+    # write out anndata to h5ad file
+    adata.write_h5ad(output)
+
+
+if __name__ == '__main__':
+
+    aparser = argparse.ArgumentParser()
+    aparser.add_argument(
+        "-i", "--inputs", dest="inputs", required=True)
+    aparser.add_argument(
+        "-o", "--output", dest="output", required=False)
+
+    args = aparser.parse_args()
+
+    main(args.inputs, args.output)
Binary file test-data/pixels.h5ad has changed
--- a/test-data/rename_channels.csv	Fri May 10 21:01:32 2024 +0000
+++ b/test-data/rename_channels.csv	Thu Jul 11 22:41:10 2024 +0000
@@ -1,2 +1,3 @@
 channel_number,cycle_number,marker_name,Filter,excitation_wavelength,emission_wavelength
-0,6,DNA_6,DAPI,395,431
\ No newline at end of file
+0,6,DNA_6,DAPI,395,431
+0,6,DNA_7,DAPI,395,431
\ No newline at end of file
Binary file test-data/rename_test.ome.tiff has changed
Binary file test-data/rename_test.tiff has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.xml	Thu Jul 11 22:41:10 2024 +0000
@@ -0,0 +1,2 @@
+<?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>