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This commit is contained in:
Martin Laasmaa
2025-12-16 13:24:20 +02:00
parent 0e0741d323
commit 6b995e7325
2 changed files with 31 additions and 10 deletions
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4
src/model/yolo_wrapper.py
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@@ -9,7 +9,7 @@ from typing import Optional, List, Dict, Callable, Any
import torch import torch
import tempfile import tempfile
import os import os
from src.utils.image import Image, convert_grayscale_to_rgb_preserve_range from src.utils.image import Image
from src.utils.logger import get_logger from src.utils.logger import get_logger
@@ -238,7 +238,7 @@ class YOLOWrapper:
img_obj = Image(source_path) img_obj = Image(source_path)
pil_img = img_obj.pil_image pil_img = img_obj.pil_image
if len(pil_img.getbands()) == 1: if len(pil_img.getbands()) == 1:
rgb_img = convert_grayscale_to_rgb_preserve_range(pil_img) rgb_img = img_obj.convert_grayscale_to_rgb_preserve_range()
else: else:
rgb_img = pil_img.convert("RGB") rgb_img = pil_img.convert("RGB")

37
src/utils/image_converters.py
View File

@@ -12,18 +12,27 @@ class UT:
Operetta files along with rois drawn in ImageJ Operetta files along with rois drawn in ImageJ
""" """
def __init__(self, roifile_fn: Path): def __init__(self, roifile_fn: Path, no_labels: bool):
self.roifile_fn = roifile_fn self.roifile_fn = roifile_fn
print("is file", self.roifile_fn.is_file()) print("is file", self.roifile_fn.is_file())
self.rois = ImagejRoi.fromfile(self.roifile_fn) self.rois = None
self.stem = self.roifile_fn.stem.split("Roi-")[1] if no_labels:
self.rois = ImagejRoi.fromfile(self.roifile_fn)
self.stem = self.roifile_fn.stem.split("Roi-")[1]
else:
self.roifile_fn = roifile_fn / roifile_fn.parts[-1]
self.stem = self.roifile_fn.stem
print(self.roifile_fn)
print(self.stem)
self.image, self.image_props = self._load_images() self.image, self.image_props = self._load_images()
def _load_images(self): def _load_images(self):
"""Loading sequence of tif files """Loading sequence of tif files
array sequence is CZYX array sequence is CZYX
""" """
print(self.roifile_fn.parent, self.stem) print("Loading images:", self.roifile_fn.parent, self.stem)
fns = list(self.roifile_fn.parent.glob(f"{self.stem.lower()}*.tif*")) fns = list(self.roifile_fn.parent.glob(f"{self.stem.lower()}*.tif*"))
stems = [fn.stem.split(self.stem)[-1] for fn in fns] stems = [fn.stem.split(self.stem)[-1] for fn in fns]
n_ch = len(set([stem.split("-ch")[-1].split("t")[0] for stem in stems])) n_ch = len(set([stem.split("-ch")[-1].split("t")[0] for stem in stems]))
@@ -116,6 +125,7 @@ class UT:
self.image = np.max(self.image[channel], axis=0) self.image = np.max(self.image[channel], axis=0)
print(self.image.shape) print(self.image.shape)
print(path / subfolder / f"{self.stem}.tif")
with TiffWriter(path / subfolder / f"{self.stem}.tif") as tif: with TiffWriter(path / subfolder / f"{self.stem}.tif") as tif:
tif.write(self.image) tif.write(self.image)
@@ -126,14 +136,25 @@ if __name__ == "__main__":
parser = argparse.ArgumentParser() parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input", nargs="*", type=Path) parser.add_argument("-i", "--input", nargs="*", type=Path)
parser.add_argument("-o", "--output", type=Path) parser.add_argument("-o", "--output", type=Path)
parser.add_argument(
"--no-labels",
action="store_false",
help="Source does not have labels, export only images",
)
args = parser.parse_args() args = parser.parse_args()
for path in args.input: for path in args.input:
print("Path:", path) print("Path:", path)
for rfn in Path(path).glob("*.zip"): if not args.no_labels:
print("Roi FN:", rfn) print("No labels")
ut = UT(rfn) ut = UT(path, args.no_labels)
ut.export_rois(args.output, class_index=0)
ut.export_image(args.output, plane_mode="max projection", channel=0) ut.export_image(args.output, plane_mode="max projection", channel=0)
else:
for rfn in Path(path).glob("*.zip"):
print("Roi FN:", rfn)
ut = UT(rfn, args.no_labels)
ut.export_rois(args.output, class_index=0)
ut.export_image(args.output, plane_mode="max projection", channel=0)
print() print()