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Fix for QuPath ROI Splitter (v0.3.1) #772

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merged 3 commits into from
Jul 30, 2024
Merged

Fix for QuPath ROI Splitter (v0.3.1) #772

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d359412
Fix for LMD data
npinter Jul 30, 2024
ccb87f9
Fix png output
npinter Jul 30, 2024
8c14af3
Fix test
npinter Jul 30, 2024
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23 changes: 14 additions & 9 deletions tools/qupath_roi_splitter/qupath_roi_splitter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,15 +22,20 @@ def collect_roi_coords(input_roi, feature_index):
else:
coord_index = 0
for sub_roi in input_roi["geometry"]["coordinates"]:
# Polygon with holes or MultiPolygon
if not isinstance(sub_roi[0][0], list):
all_coords.extend(collect_coords(sub_roi, feature_index, coord_index))
coord_index += len(sub_roi)
if len(sub_roi) == 2:
# Special case: LMD data
all_coords.extend(collect_coords([sub_roi], feature_index, coord_index))
coord_index += 1
else:
# MultiPolygon with holes
for sub_coord in sub_roi:
all_coords.extend(collect_coords(sub_coord, feature_index, coord_index))
coord_index += len(sub_coord)
# Polygon with holes or MultiPolygon
if not isinstance(sub_roi[0][0], list):
all_coords.extend(collect_coords(sub_roi, feature_index, coord_index))
coord_index += len(sub_roi)
else:
# MultiPolygon with holes
for sub_coord in sub_roi:
all_coords.extend(collect_coords(sub_coord, feature_index, coord_index))
coord_index += len(sub_coord)
return all_coords


Expand Down Expand Up @@ -103,7 +108,7 @@ def split_qupath_roi(in_roi):
parser = argparse.ArgumentParser(description="Split ROI coordinates of QuPath TMA annotation by cell type (classification)")
parser.add_argument("--qupath_roi", default=False, help="Input QuPath annotation (GeoJSON file)")
parser.add_argument("--fill", action="store_true", required=False, help="Fill pixels in ROIs (order of coordinates will be lost)")
parser.add_argument('--version', action='version', version='%(prog)s 0.3.0')
parser.add_argument('--version', action='version', version='%(prog)s 0.3.1')
parser.add_argument("--all", action="store_true", required=False, help="Extracts all ROIs")
parser.add_argument("--img", action="store_true", required=False, help="Generates image of ROIs")
args = parser.parse_args()
Expand Down
9 changes: 6 additions & 3 deletions tools/qupath_roi_splitter/qupath_roi_splitter.xml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<tool id="qupath_roi_splitter" name="QuPath ROI Splitter" version="@VERSION@+galaxy@VERSION_SUFFIX@">
<description>Split ROI coordinates of QuPath TMA annotation by cell type (classification)</description>
<macros>
<token name="@VERSION@">0.3.0</token>
<token name="@VERSION@">0.3.1</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<requirements>
Expand All @@ -21,7 +21,9 @@
#end for
mkdir out
&& mv *.txt out/
#if $optional.img
&& mv *.png out/
#end if
]]></command>
<inputs>
<param name="input_collection" type="data_collection" format="geojson" label="Input QuPath annotation" help="Collection containing GeoJSON files"/>
Expand All @@ -33,14 +35,15 @@
</inputs>
<outputs>
<collection name="output_txts" type="list" label="${tool.name} on ${on_string}: ROI data">
<discover_datasets pattern="(?P&lt;name&gt;.*\.txt)" directory="out" visible="false" ext="txt"/>
<discover_datasets pattern="(?P&lt;name&gt;.*\.txt)" directory="out" visible="false" ext="tabular"/>
</collection>
<collection name="output_imgs" type="list" label="${tool.name} on ${on_string}: Images of ROIs">
<filter>optional['img']</filter>
<discover_datasets pattern="(?P&lt;name&gt;.*\.png)" directory="out" visible="false" ext="png"/>
</collection>
</outputs>
<tests>
<test>
<test expect_num_outputs="2">
<param name="input_collection">
<collection type="list">
<element name="annotations_TMA_E-5.geojson" value="annotations_TMA_E-5.geojson" />
Expand Down