fix bitdepth in rank.py

skimage/rank/rank.py

@@ -7,59 +7,23 @@ __docformat__ = 'restructuredtext en'
 
 import warnings
 from skimage import img_as_ubyte
+import numpy as np
 
-__all__ = ['mean','percentile_mean','bilateral_mean']
+import _crank16,_crank8
 
+__all__ = ['mean']
 
-def percentile_mean(image, selem, out=None, shift_x=False, shift_y=False, p0=.0, p1=1.):
-    """Return greyscale local mean of an image.
-
-    Mean is computed on the given structuring element. Only pixel values contained inside the
-    percentile interval [p0,p1] are taken into account.
-
-    Parameters
-    ----------
-    image : ndarray
-        Image array (uint8 array or uint16).
-    selem : ndarray
-        The neighborhood expressed as a 2-D array of 1's and 0's.
-    out : ndarray
-        The array to store the result of the morphology. If None is
-        passed, a new array will be allocated.
-    shift_x, shift_y : bool
-        shift structuring element about center point. This only affects
-        eccentric structuring elements (i.e. selem with even numbered sides).
-        Shift is bounded to the structuring element sizes.
-
-    Returns
-    -------
-    local mean : uint8 array or uint16 array depending on input image
-        The result of the local mean.
-
-    Examples
-    --------
-    to be updated
-    >>> # Erosion shrinks bright regions
-    >>> from skimage.morphology import square
-    >>> bright_square = np.array([[0, 0, 0, 0, 0],
-    ...                           [0, 1, 1, 1, 0],
-    ...                           [0, 1, 1, 1, 0],
-    ...                           [0, 1, 1, 1, 0],
-    ...                           [0, 0, 0, 0, 0]], dtype=np.uint8)
-    >>> erosion(bright_square, square(3))
-    array([[0, 0, 0, 0, 0],
-           [0, 0, 0, 0, 0],
-           [0, 0, 1, 0, 0],
-           [0, 0, 0, 0, 0],
-           [0, 0, 0, 0, 0]], dtype=uint8)
-
+def find_bitdepth(image):
+    """returns the max bith depth of a uint16 image
     """
-    pass
+    umax = np.max(image)
+    if umax>2:
+        return int(np.log2(umax))
+    else:
+        return 1
 
-def bilateral_mean(image, selem, out=None, shift_x=False, shift_y=False, s0=10, s1=10):
-    pass
 
-def mean(image, selem, out=None, shift_x=False, shift_y=False):
+def mean(image, selem, mask=None, out=None, shift_x=False, shift_y=False):
     """Return greyscale local mean of an image.
 
     Mean is computed on the given structuring element.
@@ -67,7 +31,11 @@ def mean(image, selem, out=None, shift_x=False, shift_y=False):
     Parameters
     ----------
     image : ndarray
-        Image array (uint8 array or uint16).
+        Image array (uint8 array or uint16). If image is uint16, as the algorithm uses max. 12bit histogram,
+        an exception will be raised if image has a value > 4095
+    mask : ndarray (uint8)
+        Mask array that defines (>0) area of the image included in the local neighborhood.
+        If None, the complete image is used (default).
     selem : ndarray
         The neighborhood expressed as a 2-D array of 1's and 0's.
     out : ndarray
@@ -101,12 +69,18 @@ def mean(image, selem, out=None, shift_x=False, shift_y=False):
            [0, 0, 0, 0, 0]], dtype=uint8)
 
     """
-    pass
-#    if image is out:
-#        raise NotImplementedError("In-place erosion not supported!")
-#    image = img_as_ubyte(image)
-#    selem = img_as_ubyte(selem)
-#    return cmorph.erode(image, selem, out=out,
-#        shift_x=shift_x, shift_y=shift_y)
-
+    if image is out:
+        raise NotImplementedError("In-place erosion not supported!")
+    selem = img_as_ubyte(selem)
+    if mask is not None:
+        mask = img_as_ubyte(mask)
+    if image.dtype == np.uint8:
+        return _crank8.mean(image,selem,shift_x=shift_x,shift_y=shift_y,mask=mask)
+    elif image.dtype == np.uint16:
+        bitdepth = find_bitdepth(image)
+        if bitdepth>11:
+            raise ValueError("only uint16 <4096 image are supported!")
+        return _crank16.mean(image,selem,shift_x=shift_x,shift_y=shift_y,mask=mask,bitdepth=bitdepth+1)
+    else:
+        raise TypeError("only uint8 and uint16 image supported!")
 

skimage/rank/tests/test_rank.py

@@ -2,9 +2,30 @@ import numpy as np
 import matplotlib.pyplot as plt
 
 from skimage import data
+from skimage.morphology.selem import disk
 import skimage.rank as rank
 
 print dir(rank)
 
+print rank.mean
+print rank.percentile_mean
+print rank.bilateral_mean
+
+a8 = data.camera()
+a16 = a8.astype('uint16')*16
+selem = disk(10)
+
+f8 = rank.mean(a8,selem)
+f16 = rank.mean(a16,selem)
+
+plt.figure()
+plt.imshow(np.hstack((a8,f8)))
+plt.colorbar()
+plt.figure()
+plt.imshow(np.hstack((a16,f16)))
+plt.colorbar()
+plt.show()
+
+