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c64aca9
Initital glob reader
jrussell25 Aug 11, 2021
d031a0f
test glob reader on single frame tiffs
jrussell25 Aug 30, 2021
3050f24
correct file this time
jrussell25 Aug 30, 2021
6b3b1dd
guess glob reader for list of str or str with wildcard
jrussell25 Sep 1, 2021
8ca9c36
add list of str as valid image type
jrussell25 Sep 1, 2021
fa18e6c
use pathlib for filename in default indexer
jrussell25 Sep 1, 2021
8983f70
handle stacking along dimensions included in single files
jrussell25 Sep 2, 2021
42c8aed
stopping for now. still working out all the cases of stacking multidi…
jrussell25 Sep 2, 2021
5f81288
refactor to support globbing along dimenions contained in single files
jrussell25 Sep 2, 2021
5625774
more fixes toward supporting multidim images
jrussell25 Sep 2, 2021
0e51b14
Implement tests for multidimensionsal image files.
jrussell25 Sep 2, 2021
a030ec0
fix reshaping of chunks to handle multidimensional single files
jrussell25 Sep 8, 2021
e0bc6f4
process metadata from single file for each scene
jrussell25 Sep 8, 2021
3ca0218
Update aicsimageio/readers/glob_reader.py
jrussell25 Sep 8, 2021
f75cf06
Implement changes from discussion.
jrussell25 Sep 8, 2021
28aba42
add self
jrussell25 Sep 8, 2021
1158562
get rid of chunkmode kwarg in imread
jrussell25 Sep 8, 2021
ca37b7e
more cleanup including formatting. more comments
jrussell25 Sep 9, 2021
0f53cd1
formatting
jrussell25 Sep 9, 2021
b468101
finish renaming some variables
jrussell25 Sep 9, 2021
c59985e
Change name to TiffGlobReader and add some comments
jrussell25 Oct 7, 2021
b9192b8
add examples to tiff glob reader docstring
jrussell25 Oct 7, 2021
53d34b4
formatting
jrussell25 Oct 7, 2021
8e1711b
bump tifffile version to 2021.8.30
jrussell25 Oct 8, 2021
d73b12e
Add typing
jrussell25 Oct 12, 2021
372945a
flake8 fixes
jrussell25 Oct 12, 2021
f98357f
pre-commit fixes
jrussell25 Oct 13, 2021
ad45de4
Add test for AICSimage
jrussell25 Oct 15, 2021
8b9c47c
remove other tests
ianhi Oct 18, 2021
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10 changes: 10 additions & 0 deletions aicsimageio/aics_image.py
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
from . import dimensions, exceptions, transforms, types
from .formats import FORMAT_IMPLEMENTATIONS, READER_TO_INSTALL
from .metadata import utils as metadata_utils
from .readers import TiffGlobReader
from .readers.reader import Reader
from .types import PhysicalPixelSizes

Expand Down Expand Up @@ -148,8 +149,17 @@ def determine_reader(image: types.ImageLike, **kwargs: Any) -> Type[Reader]:
exceptions.UnsupportedFileFormatError
No reader could be found that supports the provided image.
"""

if isinstance(image, list) and isinstance(image[0], str):
return TiffGlobReader
elif isinstance(image, str) and "*" in image:
return TiffGlobReader
elif isinstance(image, Path) and "*" in str(image):
return TiffGlobReader

# Try reader detection based off of file path extension
if isinstance(image, (str, Path)):

path = str(image)

# Check for extension in FORMAT_IMPLEMENTATIONS
Expand Down
2 changes: 2 additions & 0 deletions aicsimageio/readers/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
from .nd2_reader import ND2Reader # noqa: F401
from .ome_tiff_reader import OmeTiffReader # noqa: F401
from .reader import Reader
from .tiff_glob_reader import TiffGlobReader # noqa: F401
from .tiff_reader import TiffReader # noqa: F401


Expand All @@ -27,6 +28,7 @@
".nd2_reader.ND2Reader",
".ome_tiff_reader.OmeTiffReader",
".tiff_reader.TiffReader",
".tiff_glob_reader.TiffGlobReader",
)
_LOOKUP = {k.rsplit(".", 1)[-1]: k for k in _READERS}
__all__ = list(_LOOKUP)
Expand Down
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