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FIX: Simplified deconvolution equations

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spotter
2013-02-28 17:31:52 +01:00
parent 74b37dbb05
commit b065580c0a
1 changed files with 9 additions and 13 deletions
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skimage/color/colorconv.py
+9 -13
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@@ -320,9 +320,9 @@ lab_ref_white = np.array([0.95047, 1., 1.08883])
# Analytical and quantitative cytology and histology / the International
# Academy of Cytology [and] American Society of Cytology, vol. 23, no. 4,
# pp. 291–9, Aug. 2001.
rgb_from_hed = np.array([[0.65, 0.70, 0.29],
[0.07, 0.99, 0.11],
[0.27, 0.57, 0.78]])
rgb_from_hed = np.array([[0.65, 0.70, 0.29],
[0.07, 0.99, 0.11],
[0.27, 0.57, 0.78]])
hed_from_rgb = linalg.inv(rgb_from_hed)
#-------------------------------------------------------------
@@ -769,13 +769,9 @@ def rgb2hed(rgb):
>>> ihc = data.ihc()
>>> ihc_hed = rgb2hed(ihc)
"""
rgb = dtype.img_as_ubyte(rgb)
arr = [1, 1, 1] - (np.log(rgb + [1, 1, 1]) / np.log(255))
row = np.reshape(arr, (-1,3))
scaled = np.dot(row, hed_from_rgb)
scaled[scaled < 0] = 0
scaled[scaled > 1] = 1
return np.reshape(scaled, rgb.shape)
rgb = rgb.astype(float) + 1
hed = np.dot(np.reshape(-np.log(rgb), (-1,3)), hed_from_rgb)
return np.reshape(hed, rgb.shape)
def hed2rgb(hed):
@@ -811,6 +807,6 @@ def hed2rgb(hed):
>>> ihc_hed = rgb2hed(ihc)
>>> ihc_rgb = hed2rgb(ihc_hed)
"""
hed = dtype.img_as_float(hed)
rgb = np.exp(-np.dot(np.reshape(hed * np.log(255), (-1,3)) , rgb_from_hed))
return np.reshape(rgb, hed.shape)
logrgb1 = np.dot(-np.reshape(hed, (-1,3)) , rgb_from_hed)
rgb1 = np.exp(logrgb1)
return np.reshape(rgb1 - 1, hed.shape)