Fix bug determining number of rows and cols #214
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ziw-liu
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commit fac2c13 Author: Ivan Ivanov <[email protected]> Date: Tue Apr 9 11:25:36 2024 -0700 Fix bug reading dragonfly acquisitions (#215) * fix bug reading dragonfly acquisitions * fix typo * style * bugfix commit 0c6984e Author: Ivan Ivanov <[email protected]> Date: Mon Mar 11 12:35:51 2024 -0700 Fix bug determining number of rows and cols (#214) * fix bug determining number of rows and cols * add another XY Stage variation * add docs and fix style commit 3ab89ba Author: Ziwen Liu <[email protected]> Date: Mon Mar 4 11:02:49 2024 -0800 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 <[email protected]>
ieivanov
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Apr 15, 2024
* 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 * sort metadata keys * Squashed commit of the following: commit fac2c13 Author: Ivan Ivanov <[email protected]> Date: Tue Apr 9 11:25:36 2024 -0700 Fix bug reading dragonfly acquisitions (#215) * fix bug reading dragonfly acquisitions * fix typo * style * bugfix commit 0c6984e Author: Ivan Ivanov <[email protected]> Date: Mon Mar 11 12:35:51 2024 -0700 Fix bug determining number of rows and cols (#214) * fix bug determining number of rows and cols * add another XY Stage variation * add docs and fix style commit 3ab89ba Author: Ziwen Liu <[email protected]> Date: Mon Mar 4 11:02:49 2024 -0800 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 <[email protected]> * black * bugfix --------- Co-authored-by: Ziwen Liu <[email protected]>
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In the case where you image all columns at row 35 (i.e. 1x38 FOVs) of a 38x38 grid you'd end up with incorrect determination of the number of rows and columns as (35, 38). This PR fixes this bug.