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Add --fill and --all argument
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@npinter
npinter committed Apr 10, 2024
1 parent 2cce57c commit e600096
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157 changes: 88 additions & 69 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 @@ -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)
26 changes: 22 additions & 4 deletions tools/qupath_roi_splitter/qupath_roi_splitter.xml
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Original file line number Diff line number Diff line change
@@ -1,20 +1,35 @@
<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>
<requirement type="package" version="1.24.2">numpy</requirement>
<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">
Expand All @@ -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>
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