Tkakar/cat 1017 add 3d seg support (#146)

* Fixed mudata column names reading * Updated containers and versions * Changed sprm-json version * Updated input file in workflow * Minor comment move
hubmapconsortium · Feb 18, 2025 · 544f1f4 · 544f1f4
1 parent f97102a
commit 544f1f4
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Showing 9 changed files with 8 additions and 8 deletions.
diff --git a/containers/seg-mudata-to-zarr/VERSION b/containers/seg-mudata-to-zarr/VERSION
@@ -1 +1 @@
-0.0.4
+0.0.5
diff --git a/containers/seg-mudata-to-zarr/context/create_zarr_stores.py b/containers/seg-mudata-to-zarr/context/create_zarr_stores.py
@@ -69,6 +69,8 @@ def create_zarr_for_masks(mdata, output_path):
         None
     """
     try:
+        # to remove default: in the obs column-names
+        mdata.obs.columns = mdata.obs.columns.str.replace('default:', '')
         if mask_name_col not in mdata.obs.columns.str.lower():
             raise ValueError(f"Column '{mask_name_col}' not found in mdata.obs")
 

diff --git a/containers/seg-mudata-to-zarr/create-test-input.py b/containers/seg-mudata-to-zarr/create-test-input.py
@@ -42,8 +42,6 @@ def create_h5mu(h5mu_path):
     )
 
     mdata = MuData({'default': adata})
-    # to remove default: in the obs column-names
-    mdata.obs.columns = mdata.obs.columns.str.replace('default:', '')
     mdata.write(h5mu_path)
 
 

diff --git a/containers/seg-mudata-to-zarr/test-input/objects.h5mu b/containers/seg-mudata-to-zarr/test-input/objects.h5mu
diff --git a/containers/sprm-to-json/VERSION b/containers/sprm-to-json/VERSION
@@ -1 +1 @@
-0.0.5
+0.0.6
diff --git a/containers/sprm-to-json/context/main.py b/containers/sprm-to-json/context/main.py
@@ -83,7 +83,7 @@ def create_factors(tile_str, input_dir, output_dir):
         input_dir, tile_str, is_genes=False
     )
     for cluster_type in cluster_types:
-        cluster_names = sorted(df[cluster_type].unique().astype("uint8"))
+        cluster_names = sorted(df[cluster_type].unique())
         factors[cluster_type] = {
             "map": [str(cluster) for cluster in cluster_names],
             "cells": {k: v[cluster_type] for (k, v) in df_items},
@@ -106,7 +106,7 @@ def create_cell_sets(tile_str, input_dir, output_dir):
     )
 
     for cluster_type in cluster_types:
-        cluster_names = sorted(df[cluster_type].unique().astype("uint8"))
+        cluster_names = sorted(df[cluster_type].unique())
         cell_sets["tree"].append({
             "name": cluster_type,
             "children": [

diff --git a/seg-mudata-to-zarr.cwl b/seg-mudata-to-zarr.cwl
@@ -6,7 +6,7 @@ class: CommandLineTool
 baseCommand: ['python', '/main.py', '--output_dir', './seg-to-mudata-zarr', '--input_dir']
 hints:
   DockerRequirement:
-    dockerPull: hubmap/portal-container-seg-mudata-to-zarr:0.0.4
+    dockerPull: hubmap/portal-container-seg-mudata-to-zarr:0.0.5
 inputs:
   input_directory:
     type: Directory

diff --git a/sprm-to-json.cwl b/sprm-to-json.cwl
@@ -6,7 +6,7 @@ class: CommandLineTool
 baseCommand: ['python', '/main.py', '--output_dir', './output_json', '--input_dir']
 hints:
   DockerRequirement:
-    dockerPull: hubmap/portal-container-sprm-to-json:0.0.4
+    dockerPull: hubmap/portal-container-sprm-to-json:0.0.5
 inputs:
   input_directory:
     type: Directory

diff --git a/workflows/seg-mudata-to-zarr/test-input/objects.h5mu b/workflows/seg-mudata-to-zarr/test-input/objects.h5mu