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fix: autoload _cp_masks and escape glob metacharacters in paths #1421

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fix: autoload _cp_masks and escape glob metacharacters in paths #1421

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17 changes: 12 additions & 5 deletions cellpose/gui/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -124,11 +124,18 @@ def _load_image(parent, filename=None, load_seg=True, load_3D=False):
load_3D=load_3D)
return
elif parent.autoloadMasks.isChecked():
mask_file = os.path.splitext(filename)[0] + "_masks" + os.path.splitext(
filename)[-1]
mask_file = os.path.splitext(filename)[
0] + "_masks.tif" if not os.path.isfile(mask_file) else mask_file
load_mask = True if os.path.isfile(mask_file) else False
base = os.path.splitext(filename)[0]
ext = os.path.splitext(filename)[-1]
candidates = list(dict.fromkeys([
base + "_cp_masks.png",
base + "_cp_masks.tif",
base + "_cp_masks" + ext,
base + "_masks" + ext,
base + "_masks.tif",
base + "_masks.png",
]))
mask_file = next((f for f in candidates if os.path.isfile(f)), None)
load_mask = mask_file is not None
try:
print(f"GUI_INFO: loading image: {filename}")
if not load_3D:
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9 changes: 5 additions & 4 deletions cellpose/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -410,17 +410,18 @@ def get_image_files(folder, mask_filter, imf=None, look_one_level_down=False):

folders = []
if look_one_level_down:
folders = natsorted(glob.glob(os.path.join(folder, "*/")))
folders = natsorted(glob.glob(os.path.join(glob.escape(folder), "*/")))
folders.append(folder)
exts = [".png", ".jpg", ".jpeg", ".tif", ".tiff", ".flex", ".dax", ".nd2", ".nrrd"]
l0 = 0
al = 0
for folder in folders:
all_files = glob.glob(folder + "/*")
escaped = glob.escape(folder)
all_files = glob.glob(escaped + "/*")
al += len(all_files)
for ext in exts:
image_names.extend(glob.glob(folder + f"/*{imf}{ext}"))
image_names.extend(glob.glob(folder + f"/*{imf}{ext.upper()}"))
image_names.extend(glob.glob(escaped + f"/*{imf}{ext}"))
image_names.extend(glob.glob(escaped + f"/*{imf}{ext.upper()}"))
l0 += len(image_names)

# return error if no files found
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