large-image 1.34.4.dev2__tar.gz → 1.34.4.dev6__tar.gz

{large_image-1.34.4.dev2/large_image.egg-info → large_image-1.34.4.dev6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: large-image
-Version: 1.34.4.dev2
+Version: 1.34.4.dev6
 Summary: Python modules to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -28,7 +28,7 @@ Requires-Dist: pylibmc>=1.5.1; platform_system != "Windows" and extra == "memcac
 Provides-Extra: redis
 Requires-Dist: redis>=4.5.5; extra == "redis"
 Provides-Extra: converter
-Requires-Dist: large-image-converter>=1.34.4.dev2; extra == "converter"
+Requires-Dist: large-image-converter>=1.34.4.dev6; extra == "converter"
 Provides-Extra: colormaps
 Requires-Dist: matplotlib; extra == "colormaps"
 Requires-Dist: tol-colors>=2.0.0; extra == "colormaps"
@@ -41,110 +41,115 @@ Requires-Dist: pyvips; extra == "tiledoutput"
 Provides-Extra: performance
 Requires-Dist: psutil>=4.2.0; extra == "performance"
 Requires-Dist: simplejpeg; extra == "performance"
+Provides-Extra: pykdtree
+Requires-Dist: pykdtree; extra == "pykdtree"
 Provides-Extra: bioformats
-Requires-Dist: large-image-source-bioformats>=1.34.4.dev2; extra == "bioformats"
+Requires-Dist: large-image-source-bioformats>=1.34.4.dev6; extra == "bioformats"
 Provides-Extra: deepzoom
-Requires-Dist: large-image-source-deepzoom>=1.34.4.dev2; extra == "deepzoom"
+Requires-Dist: large-image-source-deepzoom>=1.34.4.dev6; extra == "deepzoom"
 Provides-Extra: dicom
-Requires-Dist: large-image-source-dicom>=1.34.4.dev2; extra == "dicom"
+Requires-Dist: large-image-source-dicom>=1.34.4.dev6; extra == "dicom"
 Provides-Extra: dummy
-Requires-Dist: large-image-source-dummy>=1.34.4.dev2; extra == "dummy"
+Requires-Dist: large-image-source-dummy>=1.34.4.dev6; extra == "dummy"
 Provides-Extra: gdal
-Requires-Dist: large-image-source-gdal>=1.34.4.dev2; extra == "gdal"
+Requires-Dist: large-image-source-gdal>=1.34.4.dev6; extra == "gdal"
 Provides-Extra: mapnik
-Requires-Dist: large-image-source-mapnik>=1.34.4.dev2; extra == "mapnik"
+Requires-Dist: large-image-source-mapnik>=1.34.4.dev6; extra == "mapnik"
 Provides-Extra: multi
-Requires-Dist: large-image-source-multi>=1.34.4.dev2; extra == "multi"
+Requires-Dist: large-image-source-multi>=1.34.4.dev6; extra == "multi"
 Provides-Extra: nd2
-Requires-Dist: large-image-source-nd2>=1.34.4.dev2; extra == "nd2"
+Requires-Dist: large-image-source-nd2>=1.34.4.dev6; extra == "nd2"
 Provides-Extra: ometiff
-Requires-Dist: large-image-source-ometiff>=1.34.4.dev2; extra == "ometiff"
+Requires-Dist: large-image-source-ometiff>=1.34.4.dev6; extra == "ometiff"
 Provides-Extra: openjpeg
-Requires-Dist: large-image-source-openjpeg>=1.34.4.dev2; extra == "openjpeg"
+Requires-Dist: large-image-source-openjpeg>=1.34.4.dev6; extra == "openjpeg"
 Provides-Extra: openslide
-Requires-Dist: large-image-source-openslide>=1.34.4.dev2; extra == "openslide"
+Requires-Dist: large-image-source-openslide>=1.34.4.dev6; extra == "openslide"
 Provides-Extra: pil
-Requires-Dist: large-image-source-pil>=1.34.4.dev2; extra == "pil"
+Requires-Dist: large-image-source-pil>=1.34.4.dev6; extra == "pil"
 Provides-Extra: rasterio
-Requires-Dist: large-image-source-rasterio>=1.34.4.dev2; extra == "rasterio"
+Requires-Dist: large-image-source-rasterio>=1.34.4.dev6; extra == "rasterio"
 Provides-Extra: test
-Requires-Dist: large-image-source-test>=1.34.4.dev2; extra == "test"
+Requires-Dist: large-image-source-test>=1.34.4.dev6; extra == "test"
 Provides-Extra: tiff
-Requires-Dist: large-image-source-tiff>=1.34.4.dev2; extra == "tiff"
+Requires-Dist: large-image-source-tiff>=1.34.4.dev6; extra == "tiff"
 Provides-Extra: tifffile
-Requires-Dist: large-image-source-tifffile>=1.34.4.dev2; extra == "tifffile"
+Requires-Dist: large-image-source-tifffile>=1.34.4.dev6; extra == "tifffile"
 Provides-Extra: vips
-Requires-Dist: large-image-source-vips>=1.34.4.dev2; extra == "vips"
+Requires-Dist: large-image-source-vips>=1.34.4.dev6; extra == "vips"
 Provides-Extra: zarr
-Requires-Dist: large-image-source-zarr>=1.34.4.dev2; extra == "zarr"
+Requires-Dist: large-image-source-zarr>=1.34.4.dev6; extra == "zarr"
 Provides-Extra: sources
-Requires-Dist: large-image-source-dummy>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-nd2>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-mapnik>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-tifffile>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-ometiff>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-dicom>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-gdal>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-tiff>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-vips>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-openslide>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-test>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-pil>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-deepzoom>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-bioformats>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-rasterio>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-openjpeg>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-multi>=1.34.4.dev2; extra == "sources"
-Requires-Dist: large-image-source-zarr>=1.34.4.dev2; extra == "sources"
+Requires-Dist: large-image-source-nd2>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-dummy>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-zarr>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-pil>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-openslide>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-test>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-multi>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-mapnik>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-deepzoom>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-rasterio>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-gdal>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-vips>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-tiff>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-ometiff>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-bioformats>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-openjpeg>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-tifffile>=1.34.4.dev6; extra == "sources"
+Requires-Dist: large-image-source-dicom>=1.34.4.dev6; extra == "sources"
 Provides-Extra: all
-Requires-Dist: large-image-converter>=1.34.4.dev2; extra == "all"
+Requires-Dist: large-image-source-nd2>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-dummy>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-tiff[all]>=1.34.4.dev6; extra == "all"
 Requires-Dist: ipyleaflet; extra == "all"
+Requires-Dist: large-image-source-pil>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-openslide>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-converter>=1.34.4.dev6; extra == "all"
+Requires-Dist: tol-colors>=2.0.0; extra == "all"
+Requires-Dist: large-image-source-deepzoom>=1.34.4.dev6; extra == "all"
 Requires-Dist: aiohttp; extra == "all"
-Requires-Dist: large-image-source-tiff>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-dicom>=1.34.4.dev2; extra == "all"
-Requires-Dist: pylibmc>=1.5.1; platform_system != "Windows" and extra == "all"
-Requires-Dist: large-image-source-tiff[all]>=1.34.4.dev2; extra == "all"
+Requires-Dist: large-image-source-gdal>=1.34.4.dev6; extra == "all"
+Requires-Dist: psutil>=4.2.0; extra == "all"
+Requires-Dist: large-image-source-tiff>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-rasterio>=1.34.4.dev6; extra == "all"
 Requires-Dist: ipyvue; extra == "all"
+Requires-Dist: pylibmc>=1.5.1; platform_system != "Windows" and extra == "all"
+Requires-Dist: large-image-source-bioformats>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-openjpeg>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-multi[all]>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-pil[all]>=1.34.4.dev6; extra == "all"
 Requires-Dist: redis>=4.5.5; extra == "all"
-Requires-Dist: large-image-source-deepzoom>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-bioformats>=1.34.4.dev2; extra == "all"
+Requires-Dist: pykdtree; extra == "all"
+Requires-Dist: matplotlib; extra == "all"
+Requires-Dist: large-image-source-zarr>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-test>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-multi>=1.34.4.dev6; extra == "all"
 Requires-Dist: simplejpeg; extra == "all"
-Requires-Dist: large-image-source-zarr>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-dummy>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-nd2>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-rasterio[all]>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-mapnik>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-tifffile>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-ometiff>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-vips>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-gdal>=1.34.4.dev2; extra == "all"
-Requires-Dist: psutil>=4.2.0; extra == "all"
-Requires-Dist: large-image-source-openslide>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-test>=1.34.4.dev2; extra == "all"
-Requires-Dist: tol-colors>=2.0.0; extra == "all"
-Requires-Dist: large-image-source-multi[all]>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-pil>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-rasterio>=1.34.4.dev2; extra == "all"
+Requires-Dist: large-image-source-mapnik>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-rasterio[all]>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-vips>=1.34.4.dev6; extra == "all"
 Requires-Dist: pyvips; extra == "all"
-Requires-Dist: large-image-source-pil[all]>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-openjpeg>=1.34.4.dev2; extra == "all"
-Requires-Dist: large-image-source-multi>=1.34.4.dev2; extra == "all"
-Requires-Dist: matplotlib; extra == "all"
+Requires-Dist: large-image-source-tifffile>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-ometiff>=1.34.4.dev6; extra == "all"
+Requires-Dist: large-image-source-dicom>=1.34.4.dev6; extra == "all"
 Provides-Extra: common
-Requires-Dist: large-image-source-pil[common]>=1.34.4.dev2; extra == "common"
-Requires-Dist: large-image-source-zarr>=1.34.4.dev2; extra == "common"
-Requires-Dist: large-image-source-rasterio[all]>=1.34.4.dev2; extra == "common"
-Requires-Dist: large-image-source-tifffile>=1.34.4.dev2; extra == "common"
-Requires-Dist: large-image-source-dicom>=1.34.4.dev2; extra == "common"
-Requires-Dist: psutil>=4.2.0; extra == "common"
-Requires-Dist: large-image-source-openslide>=1.34.4.dev2; extra == "common"
-Requires-Dist: large-image-source-test>=1.34.4.dev2; extra == "common"
-Requires-Dist: tol-colors>=2.0.0; extra == "common"
-Requires-Dist: large-image-source-deepzoom>=1.34.4.dev2; extra == "common"
-Requires-Dist: large-image-source-nd2>=1.34.4.dev2; extra == "common"
-Requires-Dist: simplejpeg; extra == "common"
-Requires-Dist: large-image-source-multi>=1.34.4.dev2; extra == "common"
 Requires-Dist: matplotlib; extra == "common"
+Requires-Dist: large-image-source-zarr>=1.34.4.dev6; extra == "common"
+Requires-Dist: large-image-source-openslide>=1.34.4.dev6; extra == "common"
+Requires-Dist: large-image-source-test>=1.34.4.dev6; extra == "common"
+Requires-Dist: large-image-source-multi>=1.34.4.dev6; extra == "common"
+Requires-Dist: simplejpeg; extra == "common"
+Requires-Dist: large-image-source-rasterio[all]>=1.34.4.dev6; extra == "common"
+Requires-Dist: tol-colors>=2.0.0; extra == "common"
+Requires-Dist: large-image-source-deepzoom>=1.34.4.dev6; extra == "common"
+Requires-Dist: large-image-source-pil[common]>=1.34.4.dev6; extra == "common"
+Requires-Dist: psutil>=4.2.0; extra == "common"
+Requires-Dist: large-image-source-tifffile>=1.34.4.dev6; extra == "common"
+Requires-Dist: large-image-source-nd2>=1.34.4.dev6; extra == "common"
+Requires-Dist: large-image-source-dicom>=1.34.4.dev6; extra == "common"
+Provides-Extra: eager
+Requires-Dist: pykdtree; extra == "eager"
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{large_image-1.34.4.dev2 → large_image-1.34.4.dev6}/docs/conf.py

@@ -16,6 +16,14 @@ import sys
 docs_dir = os.path.dirname(__file__)
 sys.path.insert(0, os.path.abspath(os.path.join(docs_dir, '..', '..')))
 
+try:
+    import pypandoc
+except ImportError:
+    pass
+else:
+    pandoc_dir = os.path.dirname(pypandoc.get_pandoc_path())
+    os.environ['PATH'] = pandoc_dir + os.pathsep + os.environ.get('PATH', '')
+
 # -- Project information -----------------------------------------------------
 
 project = 'large_image'
@@ -76,6 +84,10 @@ html_permalinks_icon = '&#128279'
 
 autoclass_content = 'both'
 
+autodoc_type_aliases = {
+    'TileSource': 'large_image.tilesource.base.TileSource',
+}
+
 mermaid_version = '10.6.0'
 mermaid_init_js = 'mermaid.initialize({startOnLoad:true});'
 mermaid_width = '50%'

{large_image-1.34.4.dev2 → large_image-1.34.4.dev6}/large_image/tilesource/base.py

@@ -28,6 +28,7 @@ from ..constants import (TILE_FORMAT_IMAGE, TILE_FORMAT_NUMPY, TILE_FORMAT_PIL,
                          TileInputUnits, TileOutputMimeTypes,
                          TileOutputPILFormat)
 from . import utilities
+from .eageriterator import EagerIterator
 from .jupyter import IPyLeafletMixin
 from .tiledict import LazyTileDict
 from .tileiterator import TileIterator
@@ -2372,6 +2373,26 @@ class TileSource(IPyLeafletMixin):
             level = max(0, min(mag['level'] or 0, level))
         return level
 
+    def eagerIterator(self, **kwargs) -> EagerIterator:
+        """Create an eager iterator for batched tile or region reads.
+
+        The eager iterator is intended for AI and machine-learning workflows that need
+        prefetched numpy or torch batches from a Large Image tile source. It supports tile
+        mode and explicit region mode, optional masking, scaling, padding, transforms,
+        and dynamic transform-scale callbacks.
+
+        :param kwargs: EagerIterator options such as output_mode, tile_overlap, mask,
+            region, scale, tile_size, region_size, source_scale, dtype, chunk_mult,
+            edge, pad_mode, pad_fill_mode, nchw, batch, prefetch, workers, tiles,
+            regions, transform, randomize_chunks, seed, area_threshold, threshold_mask,
+            transform_save_mode, and transform_scale.
+        :returns: An EagerIterator. Each iteration returns a dictionary with 'tile' as a
+            SharedArray plus tile metadata including format, gx, gy, level_x, level_y,
+            tile_position, width, height, level, magnification, mm_x, mm_y, gwidth, and
+            gheight.
+        """
+        return EagerIterator(self, **kwargs)
+
     def tileIterator(
             self, format: str | tuple[str] = (TILE_FORMAT_NUMPY, ),
             resample: bool = True, **kwargs) -> Iterator[LazyTileDict]:

large_image-1.34.4.dev6/large_image/tilesource/eager_utils/__init__.py

@@ -0,0 +1,5 @@
+"""Utilities used by the eager tile iterator."""
+
+from . import eager_fn as eager_fn
+
+__all__ = ['eager_fn']

large_image-1.34.4.dev6/large_image/tilesource/eager_utils/eager_fn.py

@@ -0,0 +1,53 @@
+"""Share eager iterator callables with worker processes."""
+
+from collections.abc import Callable
+
+_eager_fns: dict[str, Callable | None] = {
+    'transform': None,
+    'transform_scale': None,
+}
+
+
+def set_transform(fn: Callable) -> None:
+    """Store the process-local eager transform callable.
+
+    :param fn: A callable function with either one or three arguments that takes
+        in a numpy array containing image data and returns a numpy array containing
+        the transformed image data. If the function has three arguments, the first
+        argument is the image data, the second argument is the x coordinate of the
+        tile, and the third argument is the y coordinate of the tile as tile number
+        (transform save mode: tile_x_y) or base pixel coordinates
+        (transform save mode: region_x_y).
+    :returns: None.
+    """
+    _eager_fns['transform'] = fn
+
+
+def get_transform() -> Callable | None:
+    """Return the process-local eager transform callable.
+
+    :returns: The callable set by set_transform, or None if unset.
+    """
+    return _eager_fns['transform']
+
+
+def set_transform_scale(fn: Callable) -> None:
+    """Store the process-local eager transform-scale callable.
+
+    :param fn: a callable function that takes in a numpy array of read_kwargs,
+        a slide_dimensions dictionary, and returns a tuple containing the read coordinates,
+        tile size, and target scale metadata in the following order: xlt, ytt,
+        xrt, ybt, mm_x, mm_y, tile_size, target_scale, conv_mm_x, conv_mm_y.
+        See default_region_coords_and_target_scale_from_read_args in
+        eager_read_args.py for more details.
+    :returns: None.
+    """
+    _eager_fns['transform_scale'] = fn
+
+
+def get_transform_scale() -> Callable | None:
+    """Return the process-local eager transform-scale callable.
+
+    :returns: The callable set by set_transform_scale, or None if unset.
+    """
+    return _eager_fns['transform_scale']