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Updating image converter and aading simple script to visulaize segmentation

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This commit is contained in:
Martin Laasmaa
2025-12-16 11:27:38 +02:00
parent 9c4c39fb39
commit dd99a0677c
2 changed files with 216 additions and 15 deletions
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47
src/utils/image_converters.py
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@@ -14,8 +14,9 @@ class UT:
def __init__(self, roifile_fn: Path):
self.roifile_fn = roifile_fn
print("is file", self.roifile_fn.is_file())
self.rois = ImagejRoi.fromfile(self.roifile_fn)
self.stem = self.roifile_fn.stem.strip("-RoiSet")
self.stem = self.roifile_fn.stem.split("Roi-")[1]
self.image, self.image_props = self._load_images()
def _load_images(self):
@@ -23,12 +24,11 @@ class UT:
array sequence is CZYX
"""
print(self.roifile_fn.parent, self.stem)
fns = list(self.roifile_fn.parent.glob(f"{self.stem}*.tif*"))
fns = list(self.roifile_fn.parent.glob(f"{self.stem.lower()}*.tif*"))
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_p = len(set([stem.split("-")[0] for stem in stems]))
n_t = len(set([stem.split("t")[1] for stem in stems]))
print(n_ch, n_p, n_t)
with TiffFile(fns[0]) as tif:
img = tif.asarray()
@@ -42,6 +42,7 @@ class UT:
"height": h,
"dtype": dtype,
}
print("Image props", self.image_props)
image_stack = np.zeros((n_ch, n_p, w, h), dtype=dtype)
for fn in fns:
@@ -49,7 +50,7 @@ class UT:
img = tif.asarray()
stem = fn.stem.split(self.stem)[-1]
ch = int(stem.split("-ch")[-1].split("t")[0])
p = int(stem.split("-")[0].lstrip("p"))
p = int(stem.split("-")[0].split("p")[1])
t = int(stem.split("t")[1])
print(fn.stem, "ch", ch, "p", p, "t", t)
image_stack[ch - 1, p - 1] = img
@@ -82,11 +83,22 @@ class UT:
):
"""Export rois to a file"""
with open(path / subfolder / f"{self.stem}.txt", "w") as f:
for roi in self.rois:
# TODO add image coordinates normalization
coords = ""
for x, y in roi.subpixel_coordinates:
coords += f"{x/self.width} {y/self.height}"
for i, roi in enumerate(self.rois):
rc = roi.subpixel_coordinates
if rc is None:
print(
f"No coordinates: {self.roifile_fn}, element {i}, out of {len(self.rois)}"
)
continue
xmn, ymn = rc.min(axis=0)
xmx, ymx = rc.max(axis=0)
xc = (xmn + xmx) / 2
yc = (ymn + ymx) / 2
bw = xmx - xmn
bh = ymx - ymn
coords = f"{xc/self.width} {yc/self.height} {bw/self.width} {bh/self.height} "
for x, y in rc:
coords += f"{x/self.width} {y/self.height} "
f.write(f"{class_index} {coords}\n")
return
@@ -112,11 +124,16 @@ if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("input", type=Path)
parser.add_argument("output", type=Path)
parser.add_argument("-i", "--input", nargs="*", type=Path)
parser.add_argument("-o", "--output", type=Path)
args = parser.parse_args()
for rfn in args.input.glob("*.zip"):
ut = UT(rfn)
ut.export_rois(args.output, class_index=0)
ut.export_image(args.output, plane_mode="max projection", channel=0)
for path in args.input:
print("Path:", path)
for rfn in Path(path).glob("*.zip"):
print("Roi FN:", rfn)
ut = UT(rfn)
ut.export_rois(args.output, class_index=0)
ut.export_image(args.output, plane_mode="max projection", channel=0)
print()