- Slicing bugfix.

- Sort imports.
- Make sitk-elastix optional again.

README.md

@@ -77,4 +77,3 @@ for example: any file handles
 
 # TODO
 - more image formats
-- re-implement transforms 

ndbioimage/__init__.py

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

ndbioimage/jvm.py

@@ -36,9 +36,9 @@ try:
                 try:
                     import jpype.imports
                     from loci.common import DebugTools  # noqa
-                    from loci.formats import ImageReader  # noqa
                     from loci.formats import ChannelSeparator  # noqa
                     from loci.formats import FormatTools  # noqa
+                    from loci.formats import ImageReader  # noqa
                     from loci.formats import MetadataTools  # noqa
 
                     DebugTools.setRootLevel("ERROR")

ndbioimage/readers/__init__.py

@@ -1,3 +1,4 @@
 from pathlib import Path
+
 __all__ = [file.stem for file in Path(__file__).parent.iterdir()
            if file.suffix == ".py" and not file == Path(__file__) and not file.stem.startswith('.')]

ndbioimage/readers/bfread.py

@@ -1,10 +1,11 @@
 import multiprocessing
-import numpy as np
 from abc import ABC
 from multiprocessing import queues
 from traceback import print_exc
-from .. import AbstractReader, JVM
 
+import numpy as np
+
+from .. import JVM, AbstractReader
 
 jars = {'bioformats_package.jar':
             'https://downloads.openmicroscopy.org/bio-formats/latest/artifacts/bioformats_package.jar'}

ndbioimage/readers/cziread.py

@@ -1,12 +1,14 @@
-import czifile
-import numpy as np
 import re
-from lxml import etree
-from ome_types import model
 from abc import ABC
 from functools import cached_property
 from itertools import product
 from pathlib import Path
+
+import czifile
+import numpy as np
+from lxml import etree
+from ome_types import model
+
 from .. import AbstractReader
 
 

ndbioimage/readers/fijiread.py

@@ -1,12 +1,14 @@
 from abc import ABC
-from tifffile import TiffFile
 from functools import cached_property
 from itertools import product
-from ome_types import model
 from pathlib import Path
 from struct import unpack
 from warnings import warn
+
 import numpy as np
+from ome_types import model
+from tifffile import TiffFile
+
 from .. import AbstractReader
 
 

ndbioimage/readers/ndread.py

@@ -1,9 +1,11 @@
+from abc import ABC
+from functools import cached_property
+from itertools import product
+
 import numpy as np
 from ome_types import model
-from functools import cached_property
+
-from abc import ABC
 from .. import AbstractReader
-from itertools import product
 
 
 class Reader(AbstractReader, ABC):

ndbioimage/readers/seqread.py

@@ -1,13 +1,15 @@
+import re
+from abc import ABC
+from datetime import datetime
+from functools import cached_property
+from itertools import product
+from pathlib import Path
+
 import tifffile
 import yaml
-import re
-from pathlib import Path
-from functools import cached_property
 from ome_types import model
 from ome_types.units import _quantity_property  # noqa
-from itertools import product
+
-from datetime import datetime
-from abc import ABC
 from .. import AbstractReader
 
 

ndbioimage/readers/tifread.py

@@ -1,11 +1,13 @@
+from abc import ABC
+from functools import cached_property
+from itertools import product
+from pathlib import Path
+
 import numpy as np
 import tifffile
 import yaml
-from abc import ABC
-from functools import cached_property
 from ome_types import model
-from pathlib import Path
+
-from itertools import product
 from .. import AbstractReader
 
 

ndbioimage/transforms.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 import numpy as np
 import yaml
-from parfor import pmap, Chunks
+from parfor import Chunks, pmap
 from skimage import filters
 from tiffwrite import IJTiffFile
 from tqdm.auto import tqdm
@@ -255,9 +255,9 @@ class Transforms(dict):
 class Transform:
     def __init__(self):
         if sitk is None:
-            raise ImportError('SimpleElastix is not installed: '
+            self.transform = None
-                              'https://simpleelastix.readthedocs.io/GettingStarted.html')
+        else:
-        self.transform = sitk.ReadTransform(str(Path(__file__).parent / 'transform.txt'))
+            self.transform = sitk.ReadTransform(str(Path(__file__).parent / 'transform.txt'))
         self.dparameters = [0., 0., 0., 0., 0., 0.]
         self.shape = [512., 512.]
         self.origin = [255.5, 255.5]
@@ -275,6 +275,9 @@ class Transform:
     @classmethod
     def register(cls, fix, mov, kind=None):
         """ kind: 'affine', 'translation', 'rigid' """
+        if sitk is None:
+            raise ImportError('SimpleElastix is not installed: '
+                              'https://simpleelastix.readthedocs.io/GettingStarted.html')
         new = cls()
         kind = kind or 'affine'
         new.shape = fix.shape
@@ -342,7 +345,7 @@ class Transform:
 
     @staticmethod
     def cast_image(im):
-        if not isinstance(im, sitk.Image):
+        if isinstance(im, sitk.Image):
             im = sitk.GetImageFromArray(im)
         return im
 
@@ -376,24 +379,30 @@ class Transform:
 
     @property
     def parameters(self):
-        return list(self.transform.GetParameters())
+        if self.transform is not None:
+            return list(self.transform.GetParameters())
 
     @parameters.setter
     def parameters(self, value):
-        value = np.asarray(value)
+        if self.transform is not None:
-        self.transform.SetParameters(value.tolist())
+            value = np.asarray(value)
+            self.transform.SetParameters(value.tolist())
 
     @property
     def origin(self):
-        return self.transform.GetFixedParameters()
+        if self.transform is not None:
+            return self.transform.GetFixedParameters()
 
     @origin.setter
     def origin(self, value):
-        value = np.asarray(value)
+        if self.transform is not None:
-        self.transform.SetFixedParameters(value.tolist())
+            value = np.asarray(value)
+            self.transform.SetFixedParameters(value.tolist())
 
     @property
     def inverse(self):
+        if self.is_unity():
+            return self
         if self._last is None or self._last != self.asdict():
             self._last = self.asdict()
             self._inverse = Transform.from_dict(self.asdict())
@@ -414,6 +423,9 @@ class Transform:
         if self.is_unity():
             return im
         else:
+            if sitk is None:
+                raise ImportError('SimpleElastix is not installed: '
+                                  'https://simpleelastix.readthedocs.io/GettingStarted.html')
             dtype = im.dtype
             im = im.astype('float')
             intp = sitk.sitkBSpline if np.issubdtype(dtype, np.floating) else sitk.sitkNearestNeighbor

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ndbioimage"
-version = "2023.10.3"
+version = "2023.11.0"
 description = "Bio image reading, metadata and some affine registration."
 authors = ["W. Pomp <w.pomp@nki.nl>"]
 license = "GPLv3"
@@ -34,6 +34,9 @@ test = ["pytest-xdist"]
 [tool.poetry.scripts]
 ndbioimage = "ndbioimage:main"
 
+[tool.pytest.ini_options]
+filterwarnings = ["ignore:::(colorcet)"]
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

tests/test_open.py

@@ -1,7 +1,8 @@
 import pickle
-import pytest
-from pathlib import Path
 from multiprocessing import active_children
+from pathlib import Path
+
+import pytest
 from ndbioimage import Imread, ReaderNotFoundError
 
 

tests/test_slicing.py

@@ -0,0 +1,23 @@
+from itertools import combinations_with_replacement
+from numbers import Number
+
+import numpy as np
+import pytest
+from ndbioimage import Imread
+
+r = np.random.randint(0, 255, (64, 64, 2, 3, 4))
+im = Imread(r)
+a = np.array(im)
+
+
+@pytest.mark.parametrize('s', combinations_with_replacement(
+    (0, -1, 1, slice(None), slice(0, 1), slice(-1, 0), slice(1, 1)), 5))
+def test_slicing(s):
+    s_im, s_a = im[s], a[s]
+    if isinstance(s_a, Number):
+        assert isinstance(s_im, Number)
+        assert s_im == s_a
+    else:
+        assert isinstance(s_im, Imread)
+        assert s_im.shape == s_a.shape
+        assert np.all(s_im == s_a)

tests/test_ufuncs.py

@@ -1,8 +1,8 @@
-import pytest
-import numpy as np
-from ndbioimage import Imread
 from itertools import product
 
+import numpy as np
+import pytest
+from ndbioimage import Imread
 
 r = np.random.randint(0, 255, (64, 64, 2, 3, 4))
 im = Imread(r)