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- Slicing bugfix.

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Wim Pomp
2023-11-21 16:08:57 +01:00
parent 5a34adef7b
commit a6457ea497
3 changed files with 7 additions and 7 deletions
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9
README.md
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@@ -4,11 +4,12 @@
Exposes (bio) images as a numpy ndarray-like object, but without loading the whole Exposes (bio) images as a numpy ndarray-like object, but without loading the whole
image into memory, reading from the file only when needed. Some metadata is read image into memory, reading from the file only when needed. Some metadata is read
and stored in an ome structure. Additionally, it can automatically calculate an affine and stored in an [ome](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47) structure.
transform that corrects for chromatic aberrations etc. and apply it on the fly to the image. Additionally, it can automatically calculate an affine transform that corrects for chromatic aberrations etc. and apply
it on the fly to the image.
Currently, supports imagej tif files, czi files, micromanager tif sequences and anything Currently, it supports imagej tif files, czi files, micromanager tif sequences and anything
bioformats can handle. [bioformats](https://www.openmicroscopy.org/bio-formats/) can handle.
## Installation ## Installation

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ndbioimage/__init__.py
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@@ -277,8 +277,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
new_slice.append(s[e]) new_slice.append(s[e])
# TODO: check output dimensionality when requested shape in some dimension is 1 # TODO: check output dimensionality when requested shape in some dimension is 1
if (all([isinstance(s, Number) for s in new_slice[:len(self.axes)]]) if all([isinstance(s, Number) or a < 0 and s.size == 1 for s, a in zip(new_slice, axes_idx)]):
and all([isinstance(s, Number) or s.size == 1 for s in new_slice[len(self.axes):]])):
return self.block(*new_slice).item() return self.block(*new_slice).item()
else: else:
new = View(self) new = View(self)

2
pyproject.toml
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@@ -1,6 +1,6 @@
[tool.poetry] [tool.poetry]
name = "ndbioimage" name = "ndbioimage"
version = "2023.11.0" version = "2023.11.1"
description = "Bio image reading, metadata and some affine registration." description = "Bio image reading, metadata and some affine registration."
authors = ["W. Pomp <w.pomp@nki.nl>"] authors = ["W. Pomp <w.pomp@nki.nl>"]
license = "GPLv3" license = "GPLv3"