ngio 0.1.5__py3-none-any.whl → 0.1.6__py3-none-any.whl

ngio/core/ngff_image.py

@@ -152,7 +152,7 @@ class NgffImage:
 
         if meta.omero is None:
             raise NotImplementedError(
-                "OMERO metadata not found. " " Please add OMERO metadata to the image."
+                "OMERO metadata not found.  Please add OMERO metadata to the image."
             )
 
         channel_list = meta.omero.channels
@@ -269,7 +269,7 @@ class NgffImage:
 
         if meta.omero is None:
             raise NotImplementedError(
-                "OMERO metadata not found. " " Please add OMERO metadata to the image."
+                "OMERO metadata not found.  Please add OMERO metadata to the image."
             )
 
         channel_list = meta.omero.channels

ngio/core/utils.py

@@ -67,17 +67,17 @@ def _build_empty_pyramid(
 
     if chunks is not None and len(on_disk_shape) != len(chunks):
         raise ValueError(
-            "The shape and chunks must have the same number " "of dimensions."
+            "The shape and chunks must have the same number of dimensions."
         )
 
     if len(on_disk_shape) != len(scaling_factor):
         raise ValueError(
-            "The shape and scaling factor must have the same number " "of dimensions."
+            "The shape and scaling factor must have the same number of dimensions."
         )
 
     if len(on_disk_shape) != len(on_disk_axis):
         raise ValueError(
-            "The shape and on-disk axis must have the same number " "of dimensions."
+            "The shape and on-disk axis must have the same number of dimensions."
         )
 
     for dataset in image_meta.datasets:

ngio/io/_zarr_group_utils.py

@@ -50,8 +50,7 @@ def open_group_wrapper(
     if isinstance(store, zarr.Group):
         _group = _pass_through_group(store, mode=mode, zarr_format=zarr_format)
         ngio_logger.debug(
-            f"Passing through group: {_group}, "
-            f"located in store: {_group.store.path}"
+            f"Passing through group: {_group}, located in store: {_group.store.path}"
         )
         return _group
 

ngio/pipes/_zoom_utils.py

@@ -4,7 +4,48 @@ from typing import Literal
 import dask.array as da
 import numpy as np
 import zarr
-from scipy.ndimage import zoom
+from scipy.ndimage import zoom as scipy_zoom
+
+
+def _stacked_zoom(x, zoom_y, zoom_x, order=1, mode="grid-constant", grid_mode=True):
+    *rest, yshape, xshape = x.shape
+    x = x.reshape(-1, yshape, xshape)
+    scale_xy = (zoom_y, zoom_x)
+    x_out = np.stack(
+        [
+            scipy_zoom(x[i], scale_xy, order=order, mode=mode, grid_mode=True)
+            for i in range(x.shape[0])
+        ]
+    )
+    return x_out.reshape(*rest, *x_out.shape[1:])
+
+
+def fast_zoom(x, zoom, order=1, mode="grid-constant", grid_mode=True, auto_stack=True):
+    """Fast zoom function.
+
+    Scipy zoom function that can handle singleton dimensions
+    but the performance degrades with the number of dimensions.
+
+    This function has two small optimizations:
+     - it removes singleton dimensions before calling zoom
+     - if it detects that the zoom is only on the last two dimensions
+         it stacks the first dimensions to call zoom only on the last two.
+    """
+    mask = np.isclose(x.shape, 1)
+    zoom = np.array(zoom)
+    singletons = tuple(np.where(mask)[0])
+    xs = np.squeeze(x, axis=singletons)
+    new_zoom = zoom[~mask]
+
+    *zoom_rest, zoom_y, zoom_x = new_zoom
+    if auto_stack and np.allclose(zoom_rest, 1):
+        xs = _stacked_zoom(
+            xs, zoom_y, zoom_x, order=order, mode=mode, grid_mode=grid_mode
+        )
+    else:
+        xs = scipy_zoom(xs, new_zoom, order=order, mode=mode, grid_mode=grid_mode)
+    x = np.expand_dims(xs, axis=singletons)
+    return x
 
 
 def _zoom_inputs_check(
@@ -73,7 +114,7 @@ def _dask_zoom(
     block_output_shape = tuple(np.ceil(better_source_chunks * _scale).astype(int))
 
     zoom_wrapper = partial(
-        zoom, zoom=_scale, order=order, mode="grid-constant", grid_mode=True
+        fast_zoom, zoom=_scale, order=order, mode="grid-constant", grid_mode=True
     )
 
     out_array = da.map_blocks(
@@ -109,7 +150,7 @@ def _numpy_zoom(
         source_array=source_array, scale=scale, target_shape=target_shape
     )
 
-    out_array = zoom(
+    out_array = fast_zoom(
         source_array, zoom=_scale, order=order, mode="grid-constant", grid_mode=True
     )
     assert isinstance(out_array, np.ndarray)
@@ -149,6 +190,7 @@ def on_disk_zoom(
     target_array = _dask_zoom(source_array, target_shape=target.shape, order=order)
 
     target_array = target_array.rechunk(target.chunks)
+    target_array.compute_chunk_sizes()
     target_array.to_zarr(target)
 
 
@@ -180,7 +222,7 @@ def on_disk_coarsen(
             coarsening_setup[i] = int(factor)
         else:
             raise ValueError(
-                "Coarsening factor must be an integer, got " f"{factor} on axis {i}"
+                f"Coarsening factor must be an integer, got {factor} on axis {i}"
             )
 
     out_target = da.coarsen(

{ngio-0.1.5.dist-info → ngio-0.1.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.1.5
+Version: 0.1.6
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio
@@ -13,6 +13,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
 Requires-Python: >=3.10
 Requires-Dist: aiohttp

{ngio-0.1.5.dist-info → ngio-0.1.6.dist-info}/RECORD

@@ -4,13 +4,13 @@ ngio/core/dimensions.py,sha256=AyiXXwgfwe1LiJ7cNhefUVTG2GQqVzDiO0ge_KePf8Q,3722
 ngio/core/image_handler.py,sha256=2eiklMWCSZD9ajZHEwYJHB1WoQE92YTVOy7qslrtSaw,7569
 ngio/core/image_like_handler.py,sha256=_k1xs3Uct_FXKoyUDTfQwG755SmiMGlztGhsQW-OtOA,18821
 ngio/core/label_handler.py,sha256=yBWMQbhme0j4XhXcoWuNY0x3Kt_MH3aYTu6peOfWyTc,14102
-ngio/core/ngff_image.py,sha256=3C4FE9Q-wtKwLn0Cdy7sCGIvFstgZbRWbUq-pUReOG4,13757
+ngio/core/ngff_image.py,sha256=F3TOWzL2SuQmnkilWuKjYRcpnCS67LW4z7ayCj9pfYs,13751
 ngio/core/roi.py,sha256=Vn9aKNxRvJs77ZfVFMAdjOzhy2I2ctpikLcbFP5aj74,2884
-ngio/core/utils.py,sha256=Z3_nI7nLtMZT2gHFgEFtAox6fcENiFuQA5n6UuK2uDo,10170
+ngio/core/utils.py,sha256=GsujsKwOJDeFhcj3DgkZO99wG_Dm0wO7nTNL-uiD78c,10161
 ngio/io/__init__.py,sha256=g7KmkgRcVBTZbVkqstl_FldUFzz66R-b__HV9hsLvtc,400
 ngio/io/_zarr.py,sha256=4AM8p7ENDPAqSuR99HaP0uosPqwY80h86GZch3l7C20,2605
 ngio/io/_zarr_array_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ngio/io/_zarr_group_utils.py,sha256=-cqgxQBvSqPhy5m7iXADOCji3IiEmCgc7zOLeJW5fYw,1754
+ngio/io/_zarr_group_utils.py,sha256=ZvVQ7Z0UvLNepNyU_NmKgjKKuVXACOLPi8-OkaI6H30,1738
 ngio/iterators/__init__.py,sha256=-jQ5h6oNftLKtiHDru8nPOrR3x8H1rMo85hzvqkhxmw,29
 ngio/ngff_meta/__init__.py,sha256=HhtHzjjk55gaHYbjiHoHRyYmOs1QZgBdWeCBb7O19Vo,560
 ngio/ngff_meta/fractal_image_meta.py,sha256=yc97iEGj5VjaCWv0Md94b5I2p9qzx94DMu_HlyKmrmg,43353
@@ -22,7 +22,7 @@ ngio/ngff_meta/v04/zarr_utils.py,sha256=02ISrsAGIXB1iLfcXPpqDljDlp0vC8Y_MyL5c016
 ngio/pipes/__init__.py,sha256=Ypt9bCqrk0qSg81GTBNqH5oljMg2rQPwyOWVZRKzaYg,299
 ngio/pipes/_slicer_transforms.py,sha256=UyN_aeAg-mtO9wsbqcvUIvnV5PJFTbj8AUmegMsF05k,5812
 ngio/pipes/_transforms.py,sha256=S7PqIwyf10i1cjQ-lKcJLr7YLfW2zKJKGf6DKKP3bTA,1067
-ngio/pipes/_zoom_utils.py,sha256=mDH2llMcoG01tnGRXXFu8UUVBu7KRsOEkNAE8wFQXeQ,6460
+ngio/pipes/_zoom_utils.py,sha256=omkaJFNeqS09qdIsBmEQaSc_xKjP8hoHwOpsx_yd5B4,7957
 ngio/pipes/data_pipe.py,sha256=SBe-3kTgbHyvFC2lVYyVZj12JazmHCx9QaTDZW1PNxU,1907
 ngio/tables/__init__.py,sha256=kedgmeeFVxBAJACoZ1yxfoyTmlmI1HCBWFhgyprbNWI,260
 ngio/tables/_ad_reader.py,sha256=OQJ3ZwS0wMedlSjz-wQuovIDBojnHRk2Qhq6FL29248,2677
@@ -38,7 +38,7 @@ ngio/utils/_common_types.py,sha256=ylo6RfCyKVyXPx1Mz7WAwFfz8F85R9yd2_TPlRGRUyo,1
 ngio/utils/_errors.py,sha256=rLy9LOFkaEmsSD0-nToKUrXY1ZuPfcpcGpmeHVSnTNg,583
 ngio/utils/_logger.py,sha256=zvFG-Ta3ZIJxTyY93zYoPGp2A6TTUf7mSO0zr_uFy4A,837
 ngio/utils/_pydantic_utils.py,sha256=uN5-76cjE3bvV8GvLX62fpxoRi8GOsZu6K5aynGH1bY,1711
-ngio-0.1.5.dist-info/METADATA,sha256=foHqb5q_WPlk8-fJ2fnwBcirrAY_rbcT0NYPATqy7us,5705
-ngio-0.1.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.1.5.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.1.5.dist-info/RECORD,,
+ngio-0.1.6.dist-info/METADATA,sha256=w4iV12bvnoiCfP6AAWMpqH0ORoh0kZxA8WeqQjKzhBI,5756
+ngio-0.1.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.1.6.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.1.6.dist-info/RECORD,,