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Universal API implementations for Micro-Manager OME-TIFF and NDTiff (#185)
* wip: draft mmstack ome-tiff fov * MM FOV base class * tests * bump tifffile * comment * fix indent after rebase * use get default * test pixel indexing * set MM metadata * style * update dependencies * add xarray * move old readers to the `_deprecated` namespace * uapi for ndtiff * refactor test setup to parametrize by dataset use globals instead of fixtures since parametrization happens before fixture evaluation * convert mmstack * fix and test chunking * fix metadata conversion and test ndtiff * update cli * fix scaling * test 1.4 and incomplete ome-tiffs * move reader tests * deprecate reader tests * update deprecated tests * update ngff tests * isort * update black target to 3.10 * lint * fix download paths * update docs references and theme * untrack autogenerated file * ignore execution time file * add github icon * update docstring * update docstring * show channel names and chunk size in info * print plate chunk size if verbose * fallback for pixel size * remove log level setting * do not filter logs and warnings in reader * avoid root logger * isort * set default logging level to INFO * format docstring * improve conversion messages * black * fix ome-tiff channel name indexing * fix ndtiff channel name indexing * update converter test * remove use of os.path in `reader` * expand _check_ndtiff checks * fix iteration * fix python 3.10 using `Path.glob(*/)` to get subdirs was added in 3.11 * bump zarr version to include resizing fix zarr-developers/zarr-python#1540 * fix cli default * set log level with an environment variable * fix unset * catch non-existent page * implement fallback for incomplete channel names workaround for the Dragonfly microscope where the multi-camera setup only has one channel name written * add debug logs * handle virtual frames * try reading pages from TiffFile directly * filter error logs about ImageJ metadata being broken this is a known MM limitation when writing OME-TIFFs * fix regex * remove use of os.path in `convert.py` * better channel indexing in `_get_summary_metadata` * style * safer NoneType check * private default axis names for NDTiff * update documentation to reflect new entry point * add repr to MM FOV and dataset types * rename mm_meta and expose summary metadata * add MicroManagerFOVMapping.root * add MicroManagerFOVMapping.zyx_scale * add warning log for failed position grid * fix grid layout * suppress hypothesis flakiness * different health check suppression --------- Co-authored-by: Ivan Ivanov <ivan.ivanov@czbiohub.org>
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‎.github/workflows/pr.yml‎

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pip install black
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- name: Check code styling with Black
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run: |
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black --diff -S -t py39 iohub
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black --check -S -t py39 iohub
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black --diff -S -t py310 iohub
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black --check -S -t py310 iohub
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lint:
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name: Lint Check

‎.gitignore‎

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# Sphinx documentation
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docs/_build/
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docs/source/auto_examples/
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docs/source/sg_execution_times.rst
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# PyBuilder
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target/

‎README.md‎

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Read a directory containing a TIFF dataset:
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```py
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from iohub import read_micromanager
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from iohub import read_images
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reader = read_micromanager("/path/to/data/")
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reader = read_images("/path/to/data/")
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print(reader.shape)
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```
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‎docs/source/api/mm_converter.rst‎

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.. autoclass:: TIFFConverter
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:members:
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:special-members: __call__

‎docs/source/api/mm_ometiff_reader.rst‎

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Read MMStack OME-TIFF
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=====================
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.. currentmodule:: iohub.multipagetiff
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.. currentmodule:: iohub.mmstack
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.. autoclass:: MicromanagerOmeTiffReader
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.. autoclass:: MMStack
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:members:
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:inherited-members:
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.. autoclass:: MMOmeTiffFOV
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:members:
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:inherited-members:

‎docs/source/api/mm_reader.rst‎

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Read Micro-Manager datasets
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===========================
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Read multi-FOV datasets
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=======================
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.. currentmodule:: iohub
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.. autofunction:: read_micromanager
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.. autofunction:: read_images

‎docs/source/api/mm_sequence_reader.rst‎

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Read MM TIFF sequence
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=====================
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.. currentmodule:: iohub.singlepagetiff
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.. currentmodule:: iohub._deprecated.singlepagetiff
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.. autoclass:: MicromanagerSequenceReader
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‎docs/source/api/ndtiff.rst‎

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.. currentmodule:: iohub.ndtiff
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.. autoclass:: NDTiffReader
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.. autoclass:: NDTiffDataset
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:inherited-members:
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.. autoclass:: NDTiffFOV
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:inherited-members:

‎docs/source/api/ngff.rst‎

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Convenience
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-----------
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`open_ome_zarr`
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^^^^^^^^^^^^^^^
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.. autofunction:: open_ome_zarr
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.. currentmodule:: iohub.ngff
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`NGFFNode`
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^^^^^^^^^^
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:members:
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`Position`
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^^^^^^^^^^
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.. autoclass:: Position
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`TiledPosition`
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`Plate`
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‎docs/source/api/upti.rst‎

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Read PTI TIFF
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=============
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.. currentmodule:: iohub.upti
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.. currentmodule:: iohub._deprecated.upti
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.. autoclass:: UPTIReader
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