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Extend bitdepth from 12bit to full 16bit

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This commit is contained in:
Johannes Schönberger
2013-06-30 11:14:55 +02:00
parent c9e81053f7
commit ccd902fcb4
4 changed files with 38 additions and 98 deletions
Download Patch File Download Diff File Expand all files Collapse all files
skimage/filter/rank/bilateral.py
+5 -10
View File
@@ -3,8 +3,7 @@
The local histogram is computed using a sliding window similar to the method
described in [1]_.
Input image must be 16-bit with a value < 4096 (i.e. 12 bit),
the number of histogram bins is determined from the
Input image must be 16-bit, the number of histogram bins is determined from the
maximum value present in the image.
The pixel neighborhood is defined by:
@@ -61,8 +60,6 @@ def _apply(func8, func16, image, selem, out, mask, shift_x, shift_y, s0, s1):
if out is None:
out = np.zeros(image.shape, dtype=np.uint16)
bitdepth = find_bitdepth(image)
if bitdepth > 11:
raise ValueError("Only uint16 <4096 image (12bit) supported.")
func16(image, selem, shift_x=shift_x, shift_y=shift_y, mask=mask,
bitdepth=bitdepth + 1, out=out, s0=s0, s1=s1)
else:
@@ -88,9 +85,8 @@ def bilateral_mean(image, selem, out=None, mask=None, shift_x=False,
Parameters
----------
image : ndarray
Image array (uint16). As the algorithm uses max. 12bit histogram,
an exception will be raised if image has a value > 4095
image : ndarray (uint16)
Input image.
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -142,9 +138,8 @@ def bilateral_pop(image, selem, out=None, mask=None, shift_x=False,
Parameters
----------
image : ndarray
Image array (uint16). As the algorithm uses max. 12bit histogram,
an exception will be raised if image has a value > 4095
image : ndarray (uint16)
Input image.
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
skimage/filter/rank/core16_cy.pyx
+3 -3
View File
@@ -56,10 +56,10 @@ cdef void _core16(dtype_t kernel(Py_ssize_t*, float, dtype_t,
assert centre_c >= 0
assert centre_r < srows
assert centre_c < scols
assert bitdepth in range(2, 13)
maxbin_list = [0, 0, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096]
midbin_list = [0, 0, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048]
maxbin_list = [0, 0, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096,
8192, 16384, 32768, 65536]
midbin_list = [m / 2 for m in maxbin_list]
# set maxbin and midbin
cdef Py_ssize_t maxbin = maxbin_list[bitdepth]
skimage/filter/rank/generic.py
+20 -56
View File
@@ -1,11 +1,10 @@
"""The local histogram is computed using a sliding window similar to the method
described in [1]_.
Input image can be 8-bit or 16-bit with a value < 4096 (i.e. 12 bit), for 16-bit
input images, the number of histogram bins is determined from the maximum value
present in the image.
Input image can be 8-bit or 16-bit, for 16-bit input images, the number of
histogram bins is determined from the maximum value present in the image.
Result image is 8 or 16-bit with respect to the input image.
Result image is 8- or 16-bit with respect to the input image.
References
----------
@@ -61,9 +60,6 @@ def _apply(func8, func16, image, selem, out, mask, shift_x, shift_y):
if out is None:
out = np.zeros(image.shape, dtype=np.uint16)
bitdepth = find_bitdepth(image)
if bitdepth > 11:
image = image >> 4
bitdepth = find_bitdepth(image)
func16(image, selem, shift_x=shift_x, shift_y=shift_y, mask=mask,
bitdepth=bitdepth + 1, out=out)
@@ -85,9 +81,7 @@ def autolevel(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -127,9 +121,7 @@ def bottomhat(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -159,9 +151,7 @@ def equalize(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -203,9 +193,7 @@ def gradient(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -236,9 +224,7 @@ def maximum(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -278,9 +264,7 @@ def mean(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -321,9 +305,7 @@ def meansubtraction(image, selem, out=None, mask=None, shift_x=False,
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -354,9 +336,7 @@ def median(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -396,9 +376,7 @@ def minimum(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -438,9 +416,7 @@ def modal(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -473,9 +449,7 @@ def morph_contr_enh(image, selem, out=None, mask=None, shift_x=False,
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -517,9 +491,7 @@ def pop(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -566,9 +538,7 @@ def threshold(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -615,9 +585,7 @@ def tophat(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -648,9 +616,7 @@ def noise_filter(image, selem, out=None, mask=None, shift_x=False,
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -694,9 +660,7 @@ def entropy(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Parameters
----------
image : ndarray
Image array (uint8 array or uint16). If image is uint16, the algorithm
uses max. 12bit histogram, an exception will be raised if image has a
value > 4095.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -712,7 +676,7 @@ def entropy(image, selem, out=None, mask=None, shift_x=False, shift_y=False):
Returns
-------
out : uint8 array or uint16 array (same as input image)
entropy x10 (uint8 images) and entropy x1000 (uint16 images)
Entropy x10 (uint8 images) and entropy x1000 (uint16 images)
References
----------
skimage/filter/rank/percentile.py
+10 -29
View File
@@ -7,9 +7,8 @@ not produce halos.
The local histogram is computed using a sliding window similar to the method
described in [1]_.
Input image can be 8-bit or 16-bit with a value < 4096 (i.e. 12 bit), for 16-bit
input images, the number of histogram bins is determined from the maximum value
present in the image.
Input image can be 8-bit or 16-bit, for 16-bit input images, the number of
histogram bins is determined from the maximum value present in the image.
Result image is 8 or 16-bit with respect to the input image.
@@ -60,8 +59,6 @@ def _apply(func8, func16, image, selem, out, mask, shift_x, shift_y, p0, p1):
if out is None:
out = np.zeros(image.shape, dtype=np.uint16)
bitdepth = find_bitdepth(image)
if bitdepth > 11:
raise ValueError("Only uint16 <4096 image (12bit) supported.")
func16(image, selem, shift_x=shift_x, shift_y=shift_y, mask=mask,
bitdepth=bitdepth + 1, out=out, p0=p0, p1=p1)
else:
@@ -80,9 +77,7 @@ def percentile_autolevel(image, selem, out=None, mask=None, shift_x=False,
Parameters
----------
image : ndarray
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.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -121,9 +116,7 @@ def percentile_gradient(image, selem, out=None, mask=None, shift_x=False,
Parameters
----------
image : ndarray
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.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -161,9 +154,7 @@ def percentile_mean(image, selem, out=None, mask=None, shift_x=False,
Parameters
----------
image : ndarray
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.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -201,9 +192,7 @@ def percentile_mean_subtraction(image, selem, out=None, mask=None,
Parameters
----------
image : ndarray
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.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -243,9 +232,7 @@ def percentile_morph_contr_enh(
Parameters
----------
image : ndarray
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.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -284,9 +271,7 @@ def percentile(image, selem, out=None, mask=None, shift_x=False, shift_y=False,
Parameters
----------
image : ndarray
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.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -324,9 +309,7 @@ def percentile_pop(image, selem, out=None, mask=None, shift_x=False,
Parameters
----------
image : ndarray
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.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray
@@ -366,9 +349,7 @@ def percentile_threshold(image, selem, out=None, mask=None, shift_x=False,
Parameters
----------
image : ndarray
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.
Image array (uint8 array or uint16).
selem : ndarray
The neighborhood expressed as a 2-D array of 1's and 0's.
out : ndarray