- Can pycharm please stop adding wrong imports please?
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@@ -8,7 +8,6 @@ from pathlib import Path
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import numpy as np
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import numpy as np
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import tifffile
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import tifffile
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import yaml
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import yaml
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from lfdfiles import TiffFile
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from ome_types import from_xml, model
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from ome_types import from_xml, model
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from .. import AbstractReader, try_default
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from .. import AbstractReader, try_default
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@@ -36,12 +35,12 @@ class Reader(AbstractReader, ABC):
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match = re.match(r'^(.*)(pos.*)$', self.path.stem, flags=re.IGNORECASE)
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match = re.match(r'^(.*)(pos.*)$', self.path.stem, flags=re.IGNORECASE)
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if match is not None and len(match.groups()) == 2:
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if match is not None and len(match.groups()) == 2:
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a, b = match.groups()
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a, b = match.groups()
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file0 = TiffFile(self.path.with_stem(a + re.sub(r'\d', '0', b)))
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with tifffile.TiffFile(self.path.with_stem(a + re.sub(r'\d', '0', b))) as file0:
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with warnings.catch_warnings():
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with warnings.catch_warnings():
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warnings.simplefilter('ignore', category=UserWarning)
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warnings.simplefilter('ignore', category=UserWarning)
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ome = from_xml(file0.ome_metadata)
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ome = from_xml(file0.ome_metadata)
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ome.images = [image for image in ome.images if self.path.stem[:len(image.name)] == image.name]
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ome.images = [image for image in ome.images if self.path.stem[:len(image.name)] == image.name]
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return ome
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return ome
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page = self.reader.pages[0]
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page = self.reader.pages[0]
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size_y = page.imagelength
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size_y = page.imagelength
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@@ -1,6 +1,6 @@
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[project]
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[project]
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name = "ndbioimage"
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name = "ndbioimage"
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version = "2025.3.1"
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version = "2025.3.2"
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description = "Bio image reading, metadata and some affine registration."
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description = "Bio image reading, metadata and some affine registration."
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authors = [
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authors = [
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{ name = "W. Pomp", email = "w.pomp@nki.nl" }
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{ name = "W. Pomp", email = "w.pomp@nki.nl" }
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