FEAT: TensorStore + Zarr3 + Sharding

.gitignore

@@ -26,6 +26,8 @@ share/python-wheels/
 *.egg
 MANIFEST
 
+.idea/
+
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.

conda.yaml

@@ -2,13 +2,27 @@ name: linc-convert
 channels:
   - conda-forge
 dependencies:
-  - python
-  - ipython
-  - typer
-  - numpy
-  - glymur
-  - zarr
-  - nibabel
-  - tifffile
+  - python=3.12
+  - ipython=8.22.2
+  - typer=0.12.2
+  - numpy=1.26.4
+  - glymur=0.12.9.post2
+  - zarr=2.17.1
+  - nibabel=5.2.1
+  - tifffile=2024.4.18
+  - pandas=2.2.2
+  - scipy=1.13.0
+  - fsspec=2024.10.0
+  - pip
   - pip:
-    - cyclopts
+      - cyclopts==2.5.0
+      - rich==13.7.1
+      - universal_pathlib==0.2.5
+      - matplotlib==3.8.4
+      - dask==2024.4.2
+      - distributed==2024.4.2
+      - imagecodecs==2024.1.1
+      - pyarrow==15.0.2
+      - pyarrow-hotfix==0.6
+      - rich-rst==1.2.0
+      - tensorstore==0.1.68

linc_convert/modalities/df/__init__.py

@@ -1,5 +1,4 @@
 """Dark Field microscopy converters."""
 
 __all__ = ["cli", "multi_slice", "single_slice"]
-
 from . import cli, multi_slice, single_slice

linc_convert/modalities/df/multi_slice.py

@@ -20,7 +20,7 @@
 # internals
 from linc_convert.modalities.df.cli import df
 from linc_convert.utils.j2k import WrappedJ2K, get_pixelsize
-from linc_convert.utils.math import ceildiv, floordiv
+from linc_convert.utils.custom_math import ceildiv, floordiv
 from linc_convert.utils.orientation import center_affine, orientation_to_affine
 from linc_convert.utils.zarr import make_compressor
 

linc_convert/modalities/df/single_slice.py

@@ -19,7 +19,7 @@
 # internals
 from linc_convert.modalities.df.cli import df
 from linc_convert.utils.j2k import WrappedJ2K, get_pixelsize
-from linc_convert.utils.math import ceildiv
+from linc_convert.utils.custom_math import ceildiv
 from linc_convert.utils.orientation import center_affine, orientation_to_affine
 from linc_convert.utils.zarr import make_compressor
 

linc_convert/modalities/lsm/convert_tiff_to_zarr.py

@@ -0,0 +1 @@
+from linc_convert.modalities.lsm.mosaic import convert