From e6000962988de3406dfee8d9e3e82d28b961314c Mon Sep 17 00:00:00 2001
From: npinter <npinter@protonmail.com>
Date: Wed, 10 Apr 2024 21:38:17 +0200
Subject: [PATCH] Add --fill and --all argument

---
 .../qupath_roi_splitter.py                    | 157 ++++++++++--------
 .../qupath_roi_splitter.xml                   |  26 ++-
 2 files changed, 110 insertions(+), 73 deletions(-)

diff --git a/tools/qupath_roi_splitter/qupath_roi_splitter.py b/tools/qupath_roi_splitter/qupath_roi_splitter.py
index ba02875d2..93677d033 100644
--- a/tools/qupath_roi_splitter/qupath_roi_splitter.py
+++ b/tools/qupath_roi_splitter/qupath_roi_splitter.py
@@ -6,78 +6,97 @@
 import pandas as pd
 
 
-def draw_poly(input_df, input_img, col=(0, 0, 0)):
-    s = np.array(input_df)
-    output_img = cv2.fillPoly(input_img, pts=np.int32([s]), color=col)
-    return output_img
+def draw_poly(input_df, input_img, col=(0, 0, 0), fill=False):
+	s = np.array(input_df)
+	if fill:
+		output_img = cv2.fillPoly(input_img, pts=np.int32([s]), color=col)
+	else:
+		output_img = cv2.polylines(input_img, np.int32([s]), True, color=col, thickness=1)
+	return output_img
+
+
+def draw_roi(input_roi, input_img, fill):
+	if len(input_roi["geometry"]["coordinates"]) == 1:
+		# Polygon w/o holes
+		input_img = draw_poly(input_roi["geometry"]["coordinates"][0], input_img, fill=fill)
+	else:
+		first_roi = True
+		for sub_roi in input_roi["geometry"]["coordinates"]:
+			# Polygon with holes
+			if not isinstance(sub_roi[0][0], list):
+				if first_roi:
+					input_img = draw_poly(sub_roi, input_img, fill=fill)
+					first_roi = False
+				else:
+					# holes in ROI
+					input_img = draw_poly(sub_roi, input_img, col=(255, 255, 255), fill=fill)
+			else:
+				# MultiPolygon with holes
+				for sub_coord in sub_roi:
+					if first_roi:
+						input_img = draw_poly(sub_coord, input_img, fill=fill)
+						first_roi = False
+					else:
+						# holes in ROI
+						input_img = draw_poly(sub_coord, input_img, col=(255, 255, 255), fill=fill)
+
+	return input_img
 
 
 def split_qupath_roi(in_roi):
-    with open(in_roi) as file:
-        qupath_roi = geojson.load(file)
-
-    # HE dimensions
-    dim_plt = [qupath_roi["dim"]["width"], qupath_roi["dim"]["height"]]
-
-    tma_name = qupath_roi["name"]
-    cell_types = [ct.rsplit(" - ", 1)[-1] for ct in qupath_roi["featureNames"]]
-
-    for cell_type in cell_types:
-        # create numpy array with white background
-        img = np.zeros((dim_plt[1], dim_plt[0], 3), dtype="uint8")
-        img.fill(255)
-
-        for i, roi in enumerate(qupath_roi["features"]):
-            if roi["properties"]["classification"]["name"] == cell_type:
-                if len(roi["geometry"]["coordinates"]) == 1:
-                    # Polygon w/o holes
-                    img = draw_poly(roi["geometry"]["coordinates"][0], img)
-                else:
-                    first_roi = True
-                    for sub_roi in roi["geometry"]["coordinates"]:
-                        # Polygon with holes
-                        if not isinstance(sub_roi[0][0], list):
-                            if first_roi:
-                                img = draw_poly(sub_roi, img)
-                                first_roi = False
-                            else:
-                                # holes in ROI
-                                img = draw_poly(sub_roi, img, col=(255, 255, 255))
-                        else:
-                            # MultiPolygon with holes
-                            for sub_coord in sub_roi:
-                                if first_roi:
-                                    img = draw_poly(sub_coord, img)
-                                    first_roi = False
-                                else:
-                                    # holes in ROI
-                                    img = draw_poly(sub_coord, img, col=(255, 255, 255))
-
-        # get all black pixel
-        coords_arr = np.column_stack(np.where(img == (0, 0, 0)))
-
-        # remove duplicated rows
-        coords_arr_xy = coords_arr[coords_arr[:, 2] == 0]
-
-        # remove last column
-        coords_arr_xy = np.delete(coords_arr_xy, 2, axis=1)
-
-        # to pandas and rename columns to x and y
-        coords_df = pd.DataFrame(coords_arr_xy, columns=['x', 'y'])
-
-        # drop duplicates
-        coords_df = coords_df.drop_duplicates(
-            subset=['x', 'y'],
-            keep='last').reset_index(drop=True)
-
-        coords_df.to_csv("{}_{}.txt".format(tma_name, cell_type), sep='\t', index=False)
+	with open(in_roi) as file:
+		qupath_roi = geojson.load(file)
 
+	# HE dimensions
+	dim_plt = [qupath_roi["dim"]["width"], qupath_roi["dim"]["height"]]
 
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="Split ROI coordinates of QuPath TMA annotation by cell type (classfication)")
-    parser.add_argument("--qupath_roi", default=False, help="Input QuPath annotation (GeoJSON file)")
-    parser.add_argument('--version', action='version', version='%(prog)s 0.1.0')
-    args = parser.parse_args()
+	tma_name = qupath_roi["name"]
+	cell_types = [ct.rsplit(" - ", 1)[-1] for ct in qupath_roi["featureNames"]]
+
+	for cell_type in cell_types:
+		# create numpy array with white background
+		img = np.zeros((dim_plt[1], dim_plt[0], 3), dtype="uint8")
+		img.fill(255)
+
+		for i, roi in enumerate(qupath_roi["features"]):
+			if not args.all:
+				if "classification" not in roi["properties"]:
+					continue
+				if roi["properties"]["classification"]["name"] == cell_type:
+					img = draw_roi(roi, img, args.fill)
+			else:
+				img = draw_roi(roi, img, args.fill)
+
+		# get all black pixel
+		coords_arr = np.column_stack(np.where(img == (0, 0, 0)))
+
+		# remove duplicated rows
+		coords_arr_xy = coords_arr[coords_arr[:, 2] == 0]
+
+		# remove last column
+		coords_arr_xy = np.delete(coords_arr_xy, 2, axis=1)
 
-    if args.qupath_roi:
-        split_qupath_roi(args.qupath_roi)
+		# to pandas and rename columns to x and y
+		coords_df = pd.DataFrame(coords_arr_xy, columns=['y', 'x'])
+
+		# reorder columns
+		coords_df = coords_df[['x', 'y']]
+
+		# drop duplicates
+		coords_df = coords_df.drop_duplicates(
+			subset=['x', 'y'],
+			keep='last').reset_index(drop=True)
+
+		coords_df.to_csv("{}_{}.txt".format(tma_name, cell_type), sep='\t', index=False)
+
+
+if __name__ == "__main__":
+	parser = argparse.ArgumentParser(description="Split ROI coordinates of QuPath TMA annotation by cell type (classfication)")
+	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")
+	parser.add_argument('--version', action='version', version='%(prog)s 0.1.0')
+	parser.add_argument("--all", action="store_true", required=False, help="Extracts all ROIs")
+	args = parser.parse_args()
+
+	if args.qupath_roi:
+		split_qupath_roi(args.qupath_roi)
diff --git a/tools/qupath_roi_splitter/qupath_roi_splitter.xml b/tools/qupath_roi_splitter/qupath_roi_splitter.xml
index 7dc186569..077409632 100644
--- a/tools/qupath_roi_splitter/qupath_roi_splitter.xml
+++ b/tools/qupath_roi_splitter/qupath_roi_splitter.xml
@@ -1,4 +1,4 @@
-<tool id="qupath_roi_splitter" name="QuPath ROI Splitter" version="0.1.0+galaxy1">
+<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>
     <requirements>
         <requirement type="package" version="3.0.1">geojson</requirement>
@@ -6,15 +6,30 @@
         <requirement type="package" version="4.7.0">opencv</requirement>
         <requirement type="package" version="2.0.0">pandas</requirement>        
     </requirements>
+    <macros>
+        <token name="@VERSION@">0.2.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
      <command detect_errors="exit_code"><![CDATA[
         #for $input in $input_collection
-            python3 '$__tool_directory__/qupath_roi_splitter.py' --qupath_roi '$input' &&
+            python3 '$__tool_directory__/qupath_roi_splitter.py'
+                    --qupath_roi '$input'
+                    #if $optional.fill
+                        --fill
+                    #end if
+                    #if $optional.all
+                        --all
+                    #end if
         #end for
-        mkdir out &&
-        mv *.txt out/
+        && mkdir out
+        && mv *.txt out/
     ]]></command>
     <inputs>
         <param name="input_collection" type="data_collection" format="geojson" label="Input QuPath annotation" help="Collection containing GeoJSON files"/>
+        <section name="optional" title="Optional">
+            <param name="fill" type="boolean" truevalue="--fill" falsevalue="" checked="false" label="Fill ROIs" help="Fill pixels in ROIs"/>
+            <param name="all" type="boolean" truevalue="--all" falsevalue="" checked="false" label="Extract all" help="Extracts all ROIs"/>
+        </section>
     </inputs>
     <outputs>
         <collection name="output_txts" type="list" label="${tool.name} on ${on_string}: ROI data">
@@ -29,6 +44,9 @@
                     <element name="annotations_TMA_F-5.geojson" value="annotations_TMA_F-5.geojson" />
                 </collection>
             </param>
+            <section name="optional">
+                <param name="fill" value="true"/>
+            </section>
             <output_collection name="output_txts" type="list" count="4">
                 <element name="F-5_Stroma">
                     <assert_contents>