large-image 1.27.5.dev99__tar.gz → 1.27.5.dev102__tar.gz

{large-image-1.27.5.dev99/large_image.egg-info → large-image-1.27.5.dev102}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image
-Version: 1.27.5.dev99
+Version: 1.27.5.dev102
 Summary: Python modules to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

{large-image-1.27.5.dev99 → large-image-1.27.5.dev102}/docs/example_usage.rst

@@ -244,6 +244,17 @@ Any of the frames of such an image are accessed by adding a ``frame=<integer>``
         format=large_image.constants.TILE_FORMAT_NUMPY)
     # nparray will contain data from the middle channel image
 
+Channels, Bands, Samples, and Axes
+----------------------------------
+
+Various large image formats refer to channels, bands, and samples.  This isn't consistent across different libraries.  In an attempt to harmonize the geospatial and medical image terminology, large_image uses ``bands`` or ``samples`` to refer to image plane components, such as red, green, blue, and alpha.  For geospatial data this can often have additional bands, such as near infrared or panchromatic.  ``channels`` are stored as separate frames and can be interpreted as different imaging modalities.  For example, a fluorescence microscopy image might have DAPI, CY5, and A594 channels.  A common color photograph file has 3 bands and 1 channel.
+
+At times, image ``axes`` are used to indicate the order of data, especially when interpreted as an n-dimensional array.  The ``x`` and ``y`` axes are the horizontal and vertical dimensions of the image.  The ``s`` axis is the ``bands`` or ``samples``, such as red, green, and blue.  The ``c`` axis is the ``channels`` with special support for channel names.  This corresponds to distinct frames.
+
+The ``z`` and ``t`` are common enough that they are sometimes considered as primary axes.  ``z`` corresponds to the direction orthogonal to ``x`` and ``y`` and is usually associated with altitude or microscope stage height.  ``t`` is time.
+
+Other axes are supported provided their names are case-insensitively unique.
+
 Styles - Changing colors, scales, and other properties
 ------------------------------------------------------
 
@@ -282,7 +293,7 @@ You can also composite a multi-frame image into a false-color output:
 Writing an Image
 ----------------
 
-If you wish to visualize numpy data, large_image can write a tiled tiff.  This requires a tile source that supports writing to be installed.  As of this writing, only the ``large-image-source-vips`` source supports this.
+If you wish to visualize numpy data, large_image can write a tiled tiff.  This requires a tile source that supports writing to be installed.  As of this writing, the ``large-image-source-zarr`` and ``large-image-source-vips`` sources supports this.  If both are installed, the ``large-image-source-zarr`` is the default.
 
 .. code-block:: python
 
@@ -292,3 +303,14 @@ If you wish to visualize numpy data, large_image can write a tiled tiff.  This r
         # We could optionally add a mask to limit the output
         source.addTile(nparray, x, y)
     source.write('/tmp/sample.tiff', lossy=False)
+
+The ``large-image-source-zarr`` can be used to store multiple frame data with arbitrary axes.
+
+.. code-block:: python
+
+    import large_image
+    source = large_image.new()
+    for nparray, x, y, time, param1 in fancy_algorithm():
+        source.addTile(nparray, x, y, time=time, p1=param1)
+    # The writer supports a variety of formats
+    source.write('/tmp/sample.zarr.zip', lossy=False)

{large-image-1.27.5.dev99 → large-image-1.27.5.dev102/large_image.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image
-Version: 1.27.5.dev99
+Version: 1.27.5.dev102
 Summary: Python modules to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

large-image-1.27.5.dev102/large_image.egg-info/requires.txt

@@ -0,0 +1,145 @@
+cachetools
+palettable
+Pillow
+numpy
+typing-extensions
+
+[all]
+large-image-source-zarr>=1.27.5.dev102
+large-image-source-multi>=1.27.5.dev102
+psutil>=4.2.0
+large-image-source-pil>=1.27.5.dev102
+large-image-source-rasterio>=1.27.5.dev102
+large-image-source-deepzoom>=1.27.5.dev102
+large-image-source-dicom>=1.27.5.dev102
+large-image-source-pil[all]>=1.27.5.dev102
+large-image-source-gdal>=1.27.5.dev102
+large-image-source-rasterio[all]>=1.27.5.dev102
+large-image-source-dummy>=1.27.5.dev102
+large-image-source-openslide>=1.27.5.dev102
+simplejpeg
+large-image-source-tifffile>=1.27.5.dev102
+large-image-source-ometiff>=1.27.5.dev102
+pyvips
+matplotlib
+large-image-source-mapnik>=1.27.5.dev102
+large-image-source-vips>=1.27.5.dev102
+large-image-source-tiff>=1.27.5.dev102
+large-image-source-test>=1.27.5.dev102
+large-image-converter>=1.27.5.dev102
+large-image-source-multi[all]>=1.27.5.dev102
+large-image-source-openjpeg>=1.27.5.dev102
+large-image-source-bioformats>=1.27.5.dev102
+large-image-source-nd2>=1.27.5.dev102
+
+[all:platform_system != "Windows"]
+pylibmc>=1.5.1
+
+[bioformats]
+large-image-source-bioformats>=1.27.5.dev102
+
+[colormaps]
+matplotlib
+
+[common]
+large-image-source-zarr>=1.27.5.dev102
+simplejpeg
+large-image-source-multi>=1.27.5.dev102
+large-image-source-tifffile>=1.27.5.dev102
+matplotlib
+psutil>=4.2.0
+large-image-source-pil[all]>=1.27.5.dev102
+large-image-source-test>=1.27.5.dev102
+large-image-source-dicom>=1.27.5.dev102
+large-image-source-deepzoom>=1.27.5.dev102
+large-image-source-rasterio[all]>=1.27.5.dev102
+large-image-source-nd2>=1.27.5.dev102
+
+[common:platform_system != "Windows"]
+pylibmc>=1.5.1
+
+[converter]
+large-image-converter>=1.27.5.dev102
+
+[deepzoom]
+large-image-source-deepzoom>=1.27.5.dev102
+
+[dicom]
+large-image-source-dicom>=1.27.5.dev102
+
+[dummy]
+large-image-source-dummy>=1.27.5.dev102
+
+[gdal]
+large-image-source-gdal>=1.27.5.dev102
+
+[mapnik]
+large-image-source-mapnik>=1.27.5.dev102
+
+[memcached]
+
+[memcached:platform_system != "Windows"]
+pylibmc>=1.5.1
+
+[multi]
+large-image-source-multi>=1.27.5.dev102
+
+[nd2]
+large-image-source-nd2>=1.27.5.dev102
+
+[ometiff]
+large-image-source-ometiff>=1.27.5.dev102
+
+[openjpeg]
+large-image-source-openjpeg>=1.27.5.dev102
+
+[openslide]
+large-image-source-openslide>=1.27.5.dev102
+
+[performance]
+psutil>=4.2.0
+simplejpeg
+
+[pil]
+large-image-source-pil>=1.27.5.dev102
+
+[rasterio]
+large-image-source-rasterio>=1.27.5.dev102
+
+[sources]
+large-image-source-zarr>=1.27.5.dev102
+large-image-source-openslide>=1.27.5.dev102
+large-image-source-multi>=1.27.5.dev102
+large-image-source-tifffile>=1.27.5.dev102
+large-image-source-ometiff>=1.27.5.dev102
+large-image-source-mapnik>=1.27.5.dev102
+large-image-source-tiff>=1.27.5.dev102
+large-image-source-vips>=1.27.5.dev102
+large-image-source-pil>=1.27.5.dev102
+large-image-source-rasterio>=1.27.5.dev102
+large-image-source-deepzoom>=1.27.5.dev102
+large-image-source-dicom>=1.27.5.dev102
+large-image-source-test>=1.27.5.dev102
+large-image-source-nd2>=1.27.5.dev102
+large-image-source-openjpeg>=1.27.5.dev102
+large-image-source-gdal>=1.27.5.dev102
+large-image-source-bioformats>=1.27.5.dev102
+large-image-source-dummy>=1.27.5.dev102
+
+[test]
+large-image-source-test>=1.27.5.dev102
+
+[tiff]
+large-image-source-tiff>=1.27.5.dev102
+
+[tifffile]
+large-image-source-tifffile>=1.27.5.dev102
+
+[tiledoutput]
+pyvips
+
+[vips]
+large-image-source-vips>=1.27.5.dev102
+
+[zarr]
+large-image-source-zarr>=1.27.5.dev102

large-image-1.27.5.dev99/large_image.egg-info/requires.txt

@@ -1,145 +0,0 @@
-cachetools
-palettable
-Pillow
-numpy
-typing-extensions
-
-[all]
-large-image-source-mapnik>=1.27.5.dev99
-large-image-source-rasterio>=1.27.5.dev99
-large-image-source-deepzoom>=1.27.5.dev99
-psutil>=4.2.0
-matplotlib
-large-image-source-multi[all]>=1.27.5.dev99
-large-image-source-dummy>=1.27.5.dev99
-large-image-source-vips>=1.27.5.dev99
-large-image-source-gdal>=1.27.5.dev99
-simplejpeg
-large-image-converter>=1.27.5.dev99
-pyvips
-large-image-source-test>=1.27.5.dev99
-large-image-source-multi>=1.27.5.dev99
-large-image-source-openslide>=1.27.5.dev99
-large-image-source-tifffile>=1.27.5.dev99
-large-image-source-ometiff>=1.27.5.dev99
-large-image-source-pil[all]>=1.27.5.dev99
-large-image-source-rasterio[all]>=1.27.5.dev99
-large-image-source-bioformats>=1.27.5.dev99
-large-image-source-zarr>=1.27.5.dev99
-large-image-source-nd2>=1.27.5.dev99
-large-image-source-dicom>=1.27.5.dev99
-large-image-source-openjpeg>=1.27.5.dev99
-large-image-source-tiff>=1.27.5.dev99
-large-image-source-pil>=1.27.5.dev99
-
-[all:platform_system != "Windows"]
-pylibmc>=1.5.1
-
-[bioformats]
-large-image-source-bioformats>=1.27.5.dev99
-
-[colormaps]
-matplotlib
-
-[common]
-large-image-source-test>=1.27.5.dev99
-large-image-source-multi>=1.27.5.dev99
-large-image-source-pil[all]>=1.27.5.dev99
-large-image-source-tifffile>=1.27.5.dev99
-large-image-source-rasterio[all]>=1.27.5.dev99
-large-image-source-zarr>=1.27.5.dev99
-large-image-source-nd2>=1.27.5.dev99
-large-image-source-dicom>=1.27.5.dev99
-large-image-source-deepzoom>=1.27.5.dev99
-psutil>=4.2.0
-matplotlib
-simplejpeg
-
-[common:platform_system != "Windows"]
-pylibmc>=1.5.1
-
-[converter]
-large-image-converter>=1.27.5.dev99
-
-[deepzoom]
-large-image-source-deepzoom>=1.27.5.dev99
-
-[dicom]
-large-image-source-dicom>=1.27.5.dev99
-
-[dummy]
-large-image-source-dummy>=1.27.5.dev99
-
-[gdal]
-large-image-source-gdal>=1.27.5.dev99
-
-[mapnik]
-large-image-source-mapnik>=1.27.5.dev99
-
-[memcached]
-
-[memcached:platform_system != "Windows"]
-pylibmc>=1.5.1
-
-[multi]
-large-image-source-multi>=1.27.5.dev99
-
-[nd2]
-large-image-source-nd2>=1.27.5.dev99
-
-[ometiff]
-large-image-source-ometiff>=1.27.5.dev99
-
-[openjpeg]
-large-image-source-openjpeg>=1.27.5.dev99
-
-[openslide]
-large-image-source-openslide>=1.27.5.dev99
-
-[performance]
-psutil>=4.2.0
-simplejpeg
-
-[pil]
-large-image-source-pil>=1.27.5.dev99
-
-[rasterio]
-large-image-source-rasterio>=1.27.5.dev99
-
-[sources]
-large-image-source-openjpeg>=1.27.5.dev99
-large-image-source-vips>=1.27.5.dev99
-large-image-source-test>=1.27.5.dev99
-large-image-source-mapnik>=1.27.5.dev99
-large-image-source-multi>=1.27.5.dev99
-large-image-source-ometiff>=1.27.5.dev99
-large-image-source-openslide>=1.27.5.dev99
-large-image-source-tiff>=1.27.5.dev99
-large-image-source-tifffile>=1.27.5.dev99
-large-image-source-bioformats>=1.27.5.dev99
-large-image-source-zarr>=1.27.5.dev99
-large-image-source-rasterio>=1.27.5.dev99
-large-image-source-deepzoom>=1.27.5.dev99
-large-image-source-dicom>=1.27.5.dev99
-large-image-source-nd2>=1.27.5.dev99
-large-image-source-dummy>=1.27.5.dev99
-large-image-source-gdal>=1.27.5.dev99
-large-image-source-pil>=1.27.5.dev99
-
-[test]
-large-image-source-test>=1.27.5.dev99
-
-[tiff]
-large-image-source-tiff>=1.27.5.dev99
-
-[tifffile]
-large-image-source-tifffile>=1.27.5.dev99
-
-[tiledoutput]
-pyvips
-
-[vips]
-large-image-source-vips>=1.27.5.dev99
-
-[zarr]
-large-image-source-zarr>=1.27.5.dev99