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- improve support for tiled czi's

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w.pomp
2026-03-30 11:35:25 +02:00
parent 6123eeee8b
commit 0ee456a064
2 changed files with 8 additions and 6 deletions
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12
ndbioimage/readers/cziread.py
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@@ -188,10 +188,12 @@ class Reader(AbstractReader, ABC):
if self.tiles != (1, 1): if self.tiles != (1, 1):
assert len({s for s, *_ in list(syx)}) == 1, "multiple tiled series not supported" assert len({s for s, *_ in list(syx)}) == 1, "multiple tiled series not supported"
x, y = np.array(list(syx))[:, 1:, 0].T x, y = np.array(list(syx))[:, 1:, 0].T
x = np.unique(x) a, b = np.min(x), np.max(x)
y = np.unique(y) n = self.tiles[0]
_, bx = np.histogram(x, self.tiles[0]) bx = np.linspace(a - (b - a) / (n - 1) / 2, b + (b - a) / (n - 1) / 2, n + 1)
_, by = np.histogram(y, self.tiles[1]) a, b = np.min(y), np.max(y)
n = self.tiles[1]
by = np.linspace(a - (b - a) / (n - 1) / 2, b + (b - a) / (n - 1) / 2, n + 1)
b = list(product([(i, j) for i, j in zip(by, by[1:])], [(i, j) for i, j in zip(bx, bx[1:])])) b = list(product([(i, j) for i, j in zip(by, by[1:])], [(i, j) for i, j in zip(bx, bx[1:])]))
if self.series < len(b): if self.series < len(b):
by, bx = b[self.series] by, bx = b[self.series]
@@ -199,7 +201,7 @@ class Reader(AbstractReader, ABC):
raise FileNotFoundError(f"Series {self.series} not found in {self.path}.") raise FileNotFoundError(f"Series {self.series} not found in {self.path}.")
for directory_entry in self.reader.filtered_subblock_directory: for directory_entry in self.reader.filtered_subblock_directory:
idx = self.get_index(directory_entry, self.reader.start) idx = self.get_index(directory_entry, self.reader.start)
if bx[0] <= idx[xi][0] <= bx[1] and by[0] <= idx[yi][0] <= by[1]: if bx[0] < idx[xi][0] < bx[1] and by[0] < idx[yi][0] < by[1]:
for cj in (0,) if ci is None else range(*idx[ci]): for cj in (0,) if ci is None else range(*idx[ci]):
for zj in (0,) if zi is None else range(*idx[zi]): for zj in (0,) if zi is None else range(*idx[zi]):
for tj in (0,) if ti is None else range(*idx[ti]): for tj in (0,) if ti is None else range(*idx[ti]):

2
pyproject.toml
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@@ -1,6 +1,6 @@
[project] [project]
name = "ndbioimage" name = "ndbioimage"
version = "2026.3.5" version = "2026.3.6"
description = "Bio image reading, metadata and some affine registration." description = "Bio image reading, metadata and some affine registration."
authors = [ authors = [
{ name = "W. Pomp", email = "w.pomp@nki.nl" } { name = "W. Pomp", email = "w.pomp@nki.nl" }