large-image 1.23.4.dev18__tar.gz → 1.23.4.dev20__tar.gz

{large-image-1.23.4.dev18/large_image.egg-info → large-image-1.23.4.dev20}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image
-Version: 1.23.4.dev18
+Version: 1.23.4.dev20
 Summary: Python modules to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

{large-image-1.23.4.dev18 → large-image-1.23.4.dev20}/large_image/tilesource/base.py

@@ -1531,6 +1531,8 @@ class TileSource(IPyLeafletMixin):
                             sc.output[:sc.mask.shape[0], :sc.mask.shape[1], channel],
                             np.where(sc.mask, clrs, 0))
             sc.output = self._applyStyleFunction(sc.output, sc, 'postband')
+        if hasattr(sc, 'styleIndex'):
+            del sc.styleIndex
         sc.output = self._applyStyleFunction(sc.output, sc, 'main')
         if sc.dtype == 'uint16':
             sc.output = (sc.output * 65535 / 255).astype(np.uint16)

large-image-1.23.4.dev20/large_image/tilesource/stylefuncs.py

@@ -0,0 +1,94 @@
+# This module contains functions for use in styles
+
+import numpy as np
+
+from .utilities import _imageToNumpy, _imageToPIL
+
+
+def maskPixelValues(image, context, values=None, negative=None, positive=None):
+    """
+    This is a style utility function that returns a black-and-white 8-bit image
+    where the image is white if the pixel of the source image is in a list of
+    values and black otherwise.  The values is a list where each entry can
+    either be a tuple the same length as the band dimension of the output image
+    or a single value which is handled as 0xBBGGRR.
+
+    :param image: a numpy array of Y, X, Bands.
+    :param context: the style context.  context.image is the source image
+    :param values: an array of values, each of which is either an array of the
+        same number of bands as the source image or a single value of the form
+        0xBBGGRR assuming uint8 data.
+    :param negative: None to use [0, 0, 0, 255], or an RGBA uint8 value for
+        pixels not in the value list.
+    :param positive: None to use [255, 255, 255, 0], or an RGBA uint8 value for
+        pixels in the value list.
+    :returns: an RGBA numpy image which is exactly black or transparent white.
+    """
+    src = context.image
+    mask = np.full(src.shape[:2], False)
+    for val in values:
+        if not isinstance(val, (list, tuple)):
+            if src.shape[-1] == 1:
+                val = [val]
+            else:
+                val = [val % 256, val // 256 % 256, val // 65536 % 256]
+        val = (list(val) + [255] * src.shape[2])[:src.shape[2]]
+        match = np.array(val)
+        mask = mask | (src == match).all(axis=-1)
+    image[mask != True] = negative or [0, 0, 0, 255]  # noqa E712
+    image[mask] = positive or [255, 255, 255, 0]
+    image = image.astype(np.uint8)
+    return image
+
+
+def medianFilter(image, context=None, kernel=5, weight=1.0):
+    """
+    This is a style utility function that applies a median rank filter to the
+    image to sharpen it.
+
+    :param image: a numpy array of Y, X, Bands.
+    :param context: the style context.  context.image is the source image
+    :param kernel: the filter kernel size.
+    :param weight: the weight of the difference between the image and the
+        filtered image that is used to add into the image.  0 is no effect/
+    :returns: an numpy image which is the filtered version of the source.
+    """
+    import PIL.ImageFilter
+
+    filt = PIL.ImageFilter.MedianFilter(kernel)
+    if len(image.shape) != 3:
+        pimg = _imageToPIL(image)
+    elif image.shape[2] >= 3:
+        pimg = _imageToPIL(image[:, :, :3])
+    else:
+        pimg = _imageToPIL(image[:, :, :1])
+    fimg = _imageToNumpy(pimg.filter(filt))[0]
+    mul = 0
+    clip = 0
+    if image.dtype == np.uint8 or (
+            image.dtype.kind == 'f' and 1 < np.max(image) < 256 and np.min(image) >= 0):
+        mul = 1
+        clip = 255
+    elif image.dtype == np.uint16 or (
+            image.dtype.kind == 'f' and 1 < np.max(image) < 65536 and np.min(image) >= 0):
+        mul = 257
+        clip = 65535
+    elif image.dtype == np.uint32:
+        mul = (2 ** 32 - 1) / 255
+        clip = 2 ** 32 - 1
+    elif image.dtype.kind == 'f':
+        mul = 1
+    if mul:
+        pimg = image.astype(float)
+        if len(pimg.shape) == 2:
+            pimg = np.resize(pimg, (pimg.shape[0], pimg.shape[1], 1))
+        pimg = pimg[:, :, :fimg.shape[2]]
+        dimg = (pimg - fimg.astype(float) * mul) * weight
+        pimg = pimg[:, :, :fimg.shape[2]] + dimg
+        if clip:
+            pimg = pimg.clip(0, clip)
+        if len(image.shape) != 3:
+            image[:, :] = np.resize(pimg.astype(image.dtype), (pimg.shape[0], pimg.shape[1]))
+        else:
+            image[:, :, :fimg.shape[2]] = pimg.astype(image.dtype)
+    return image

{large-image-1.23.4.dev18 → large-image-1.23.4.dev20/large_image.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image
-Version: 1.23.4.dev18
+Version: 1.23.4.dev20
 Summary: Python modules to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

large-image-1.23.4.dev20/large_image.egg-info/requires.txt

@@ -0,0 +1,148 @@
+cachetools
+palettable
+Pillow
+numpy
+
+[:python_version < "3.8"]
+importlib-metadata<5
+
+[all]
+large-image-source-bioformats>=1.23.4.dev20
+matplotlib
+large-image-source-ometiff>=1.23.4.dev20
+large-image-source-pil[all]>=1.23.4.dev20
+large-image-source-openslide>=1.23.4.dev20
+large-image-source-gdal>=1.23.4.dev20
+large-image-source-test>=1.23.4.dev20
+large-image-source-openjpeg>=1.23.4.dev20
+large-image-source-tiff>=1.23.4.dev20
+large-image-source-mapnik>=1.23.4.dev20
+large-image-source-multi>=1.23.4.dev20
+psutil>=4.2.0
+large-image-source-pil>=1.23.4.dev20
+large-image-converter>=1.23.4.dev20
+pyvips
+large-image-source-deepzoom>=1.23.4.dev20
+large-image-source-dummy>=1.23.4.dev20
+large-image-source-vips>=1.23.4.dev20
+
+[all:platform_system != "Windows"]
+pylibmc>=1.5.1
+
+[all:python_version < "3.7"]
+simplejpeg<1.6.6
+
+[all:python_version >= "3.7"]
+simplejpeg
+large-image-source-nd2>=1.23.4.dev20
+large-image-source-tifffile>=1.23.4.dev20
+
+[all:python_version >= "3.8"]
+large-image-source-rasterio>=1.23.4.dev20
+large-image-source-rasterio[all]>=1.23.4.dev20
+large-image-source-dicom>=1.23.4.dev20
+
+[bioformats]
+large-image-source-bioformats>=1.23.4.dev20
+
+[colormaps]
+matplotlib
+
+[converter]
+large-image-converter>=1.23.4.dev20
+
+[deepzoom]
+large-image-source-deepzoom>=1.23.4.dev20
+
+[dicom]
+
+[dicom:python_version >= "3.8"]
+large-image-source-dicom>=1.23.4.dev20
+
+[dummy]
+large-image-source-dummy>=1.23.4.dev20
+
+[gdal]
+large-image-source-gdal>=1.23.4.dev20
+
+[mapnik]
+large-image-source-mapnik>=1.23.4.dev20
+
+[memcached]
+
+[memcached:platform_system != "Windows"]
+pylibmc>=1.5.1
+
+[multi]
+large-image-source-multi>=1.23.4.dev20
+
+[nd2]
+
+[nd2:python_version >= "3.7"]
+large-image-source-nd2>=1.23.4.dev20
+
+[ometiff]
+large-image-source-ometiff>=1.23.4.dev20
+
+[openjpeg]
+large-image-source-openjpeg>=1.23.4.dev20
+
+[openslide]
+large-image-source-openslide>=1.23.4.dev20
+
+[performance]
+psutil>=4.2.0
+
+[performance:python_version < "3.7"]
+simplejpeg<1.6.6
+
+[performance:python_version >= "3.7"]
+simplejpeg
+
+[pil]
+large-image-source-pil>=1.23.4.dev20
+
+[rasterio]
+
+[rasterio:python_version >= "3.8"]
+large-image-source-rasterio>=1.23.4.dev20
+
+[sources]
+large-image-source-bioformats>=1.23.4.dev20
+large-image-source-tiff>=1.23.4.dev20
+large-image-source-mapnik>=1.23.4.dev20
+large-image-source-multi>=1.23.4.dev20
+large-image-source-ometiff>=1.23.4.dev20
+large-image-source-pil>=1.23.4.dev20
+large-image-source-openslide>=1.23.4.dev20
+large-image-source-vips>=1.23.4.dev20
+large-image-source-test>=1.23.4.dev20
+large-image-source-gdal>=1.23.4.dev20
+large-image-source-deepzoom>=1.23.4.dev20
+large-image-source-dummy>=1.23.4.dev20
+large-image-source-openjpeg>=1.23.4.dev20
+
+[sources:python_version >= "3.7"]
+large-image-source-tifffile>=1.23.4.dev20
+large-image-source-nd2>=1.23.4.dev20
+
+[sources:python_version >= "3.8"]
+large-image-source-dicom>=1.23.4.dev20
+large-image-source-rasterio>=1.23.4.dev20
+
+[test]
+large-image-source-test>=1.23.4.dev20
+
+[tiff]
+large-image-source-tiff>=1.23.4.dev20
+
+[tifffile]
+
+[tifffile:python_version >= "3.7"]
+large-image-source-tifffile>=1.23.4.dev20
+
+[tiledoutput]
+pyvips
+
+[vips]
+large-image-source-vips>=1.23.4.dev20

large-image-1.23.4.dev18/large_image/tilesource/stylefuncs.py

@@ -1,39 +0,0 @@
-# This module contains functions for use in styles
-
-import numpy as np
-
-
-def maskPixelValues(image, context, values=None, negative=None, positive=None):
-    """
-    This is a style utility function that returns a black-and-white 8-bit image
-    where the image is white if the pixel of the source image is in a list of
-    values and black otherwise.  The values is a list where each entry can
-    either be a tuple the same length as the band dimension of the output image
-    or a single value which is handled as 0xBBGGRR.
-
-    :param image: a numpy array of Y, X, Bands.
-    :param context: the style context.  context.image is the source image
-    :param values: an array of values, each of which is either an array of the
-        same number of bands as the source image or a single value of the form
-        0xBBGGRR assuming uint8 data.
-    :param negative: None to use [0, 0, 0, 255], or an RGBA uint8 value for
-        pixels not in the value list.
-    :param positive: None to use [255, 255, 255, 0], or an RGBA uint8 value for
-        pixels in the value list.
-    :returns: an RGBA numpy image which is exactly black or transparent white.
-    """
-    src = context.image
-    mask = np.full(src.shape[:2], False)
-    for val in values:
-        if not isinstance(val, (list, tuple)):
-            if src.shape[-1] == 1:
-                val = [val]
-            else:
-                val = [val % 256, val // 256 % 256, val // 65536 % 256]
-        val = (list(val) + [255] * src.shape[2])[:src.shape[2]]
-        match = np.array(val)
-        mask = mask | (src == match).all(axis=-1)
-    image[mask != True] = negative or [0, 0, 0, 255]  # noqa E712
-    image[mask] = positive or [255, 255, 255, 0]
-    image = image.astype(np.uint8)
-    return image

large-image-1.23.4.dev18/large_image.egg-info/requires.txt

@@ -1,148 +0,0 @@
-cachetools
-palettable
-Pillow
-numpy
-
-[:python_version < "3.8"]
-importlib-metadata<5
-
-[all]
-large-image-source-openjpeg>=1.23.4.dev18
-large-image-source-pil[all]>=1.23.4.dev18
-large-image-source-dummy>=1.23.4.dev18
-large-image-converter>=1.23.4.dev18
-large-image-source-test>=1.23.4.dev18
-large-image-source-bioformats>=1.23.4.dev18
-matplotlib
-psutil>=4.2.0
-large-image-source-vips>=1.23.4.dev18
-large-image-source-pil>=1.23.4.dev18
-large-image-source-openslide>=1.23.4.dev18
-large-image-source-gdal>=1.23.4.dev18
-large-image-source-ometiff>=1.23.4.dev18
-pyvips
-large-image-source-mapnik>=1.23.4.dev18
-large-image-source-tiff>=1.23.4.dev18
-large-image-source-deepzoom>=1.23.4.dev18
-large-image-source-multi>=1.23.4.dev18
-
-[all:platform_system != "Windows"]
-pylibmc>=1.5.1
-
-[all:python_version < "3.7"]
-simplejpeg<1.6.6
-
-[all:python_version >= "3.7"]
-large-image-source-tifffile>=1.23.4.dev18
-large-image-source-nd2>=1.23.4.dev18
-simplejpeg
-
-[all:python_version >= "3.8"]
-large-image-source-dicom>=1.23.4.dev18
-large-image-source-rasterio>=1.23.4.dev18
-large-image-source-rasterio[all]>=1.23.4.dev18
-
-[bioformats]
-large-image-source-bioformats>=1.23.4.dev18
-
-[colormaps]
-matplotlib
-
-[converter]
-large-image-converter>=1.23.4.dev18
-
-[deepzoom]
-large-image-source-deepzoom>=1.23.4.dev18
-
-[dicom]
-
-[dicom:python_version >= "3.8"]
-large-image-source-dicom>=1.23.4.dev18
-
-[dummy]
-large-image-source-dummy>=1.23.4.dev18
-
-[gdal]
-large-image-source-gdal>=1.23.4.dev18
-
-[mapnik]
-large-image-source-mapnik>=1.23.4.dev18
-
-[memcached]
-
-[memcached:platform_system != "Windows"]
-pylibmc>=1.5.1
-
-[multi]
-large-image-source-multi>=1.23.4.dev18
-
-[nd2]
-
-[nd2:python_version >= "3.7"]
-large-image-source-nd2>=1.23.4.dev18
-
-[ometiff]
-large-image-source-ometiff>=1.23.4.dev18
-
-[openjpeg]
-large-image-source-openjpeg>=1.23.4.dev18
-
-[openslide]
-large-image-source-openslide>=1.23.4.dev18
-
-[performance]
-psutil>=4.2.0
-
-[performance:python_version < "3.7"]
-simplejpeg<1.6.6
-
-[performance:python_version >= "3.7"]
-simplejpeg
-
-[pil]
-large-image-source-pil>=1.23.4.dev18
-
-[rasterio]
-
-[rasterio:python_version >= "3.8"]
-large-image-source-rasterio>=1.23.4.dev18
-
-[sources]
-large-image-source-openslide>=1.23.4.dev18
-large-image-source-gdal>=1.23.4.dev18
-large-image-source-ometiff>=1.23.4.dev18
-large-image-source-openjpeg>=1.23.4.dev18
-large-image-source-dummy>=1.23.4.dev18
-large-image-source-mapnik>=1.23.4.dev18
-large-image-source-pil>=1.23.4.dev18
-large-image-source-deepzoom>=1.23.4.dev18
-large-image-source-test>=1.23.4.dev18
-large-image-source-bioformats>=1.23.4.dev18
-large-image-source-tiff>=1.23.4.dev18
-large-image-source-vips>=1.23.4.dev18
-large-image-source-multi>=1.23.4.dev18
-
-[sources:python_version >= "3.7"]
-large-image-source-nd2>=1.23.4.dev18
-large-image-source-tifffile>=1.23.4.dev18
-
-[sources:python_version >= "3.8"]
-large-image-source-dicom>=1.23.4.dev18
-large-image-source-rasterio>=1.23.4.dev18
-
-[test]
-large-image-source-test>=1.23.4.dev18
-
-[tiff]
-large-image-source-tiff>=1.23.4.dev18
-
-[tifffile]
-
-[tifffile:python_version >= "3.7"]
-large-image-source-tifffile>=1.23.4.dev18
-
-[tiledoutput]
-pyvips
-
-[vips]
-large-image-source-vips>=1.23.4.dev18