Mercurial > repos > perssond > unmicst

annotate toolbox/imtools.py @ 0:6bec4fef6b2e draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
author perssond
date Fri, 12 Mar 2021 00:17:29 +0000
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6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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1 import matplotlib.pyplot as plt
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2 import tifffile
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3 import os
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4 import numpy as np
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5 from skimage import io as skio
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6 from scipy.ndimage import *
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7 from skimage.morphology import *
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8 from skimage.transform import resize
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9
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10 def tifread(path):
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11 return tifffile.imread(path)
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12
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13 def tifwrite(I,path):
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14 tifffile.imsave(path, I)
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15
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16 def imshow(I,**kwargs):
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17 if not kwargs:
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18 plt.imshow(I,cmap='gray')
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19 else:
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20 plt.imshow(I,**kwargs)
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21
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22 plt.axis('off')
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23 plt.show()
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24
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25 def imshowlist(L,**kwargs):
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26 n = len(L)
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27 for i in range(n):
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28 plt.subplot(1, n, i+1)
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29 if not kwargs:
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30 plt.imshow(L[i],cmap='gray')
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31 else:
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32 plt.imshow(L[i],**kwargs)
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33 plt.axis('off')
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34 plt.show()
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35
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36 def imread(path):
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37 return skio.imread(path)
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38
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39 def imwrite(I,path):
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40 skio.imsave(path,I)
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41
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42 def im2double(I):
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43 if I.dtype == 'uint16':
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44 return I.astype('float64')/65535
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45 elif I.dtype == 'uint8':
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46 return I.astype('float64')/255
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47 elif I.dtype == 'float32':
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48 return I.astype('float64')
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49 elif I.dtype == 'float64':
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50 return I
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51 else:
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52 print('returned original image type: ', I.dtype)
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53 return I
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54
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55 def size(I):
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56 return list(I.shape)
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57
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58 def imresizeDouble(I,sizeOut): # input and output are double
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59 return resize(I,(sizeOut[0],sizeOut[1]),mode='reflect')
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60
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61 def imresize3Double(I,sizeOut): # input and output are double
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62 return resize(I,(sizeOut[0],sizeOut[1],sizeOut[2]),mode='reflect')
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63
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64 def imresizeUInt8(I,sizeOut): # input and output are UInt8
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65 return np.uint8(resize(I.astype(float),(sizeOut[0],sizeOut[1]),mode='reflect',order=0))
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66
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67 def imresize3UInt8(I,sizeOut): # input and output are UInt8
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68 return np.uint8(resize(I.astype(float),(sizeOut[0],sizeOut[1],sizeOut[2]),mode='reflect',order=0))
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69
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70 def normalize(I):
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71 m = np.min(I)
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72 M = np.max(I)
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73 if M > m:
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74 return (I-m)/(M-m)
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75 else:
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76 return I
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77
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78 def snormalize(I):
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79 m = np.mean(I)
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80 s = np.std(I)
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81 if s > 0:
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82 return (I-m)/s
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83 else:
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84 return I
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85
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86 def cat(a,I,J):
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87 return np.concatenate((I,J),axis=a)
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88
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89 def imerode(I,r):
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90 return binary_erosion(I, disk(r))
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91
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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92 def imdilate(I,r):
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93 return binary_dilation(I, disk(r))
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94
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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95 def imerode3(I,r):
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96 return morphology.binary_erosion(I, ball(r))
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97
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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98 def imdilate3(I,r):
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99 return morphology.binary_dilation(I, ball(r))
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100
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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101 def sphericalStructuralElement(imShape,fRadius):
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102 if len(imShape) == 2:
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103 return disk(fRadius,dtype=float)
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104 if len(imShape) == 3:
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105 return ball(fRadius,dtype=float)
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106
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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107 def medfilt(I,filterRadius):
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108 return median_filter(I,footprint=sphericalStructuralElement(I.shape,filterRadius))
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109
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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110 def maxfilt(I,filterRadius):
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111 return maximum_filter(I,footprint=sphericalStructuralElement(I.shape,filterRadius))
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112
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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113 def minfilt(I,filterRadius):
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114 return minimum_filter(I,footprint=sphericalStructuralElement(I.shape,filterRadius))
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115
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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116 def ptlfilt(I,percentile,filterRadius):
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117 return percentile_filter(I,percentile,footprint=sphericalStructuralElement(I.shape,filterRadius))
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118
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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119 def imgaussfilt(I,sigma,**kwargs):
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120 return gaussian_filter(I,sigma,**kwargs)
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121
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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122 def imlogfilt(I,sigma,**kwargs):
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123 return -gaussian_laplace(I,sigma,**kwargs)
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124
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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125 def imgradmag(I,sigma):
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126 if len(I.shape) == 2:
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127 dx = imgaussfilt(I,sigma,order=[0,1])
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128 dy = imgaussfilt(I,sigma,order=[1,0])
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129 return np.sqrt(dx**2+dy**2)
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130 if len(I.shape) == 3:
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131 dx = imgaussfilt(I,sigma,order=[0,0,1])
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132 dy = imgaussfilt(I,sigma,order=[0,1,0])
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133 dz = imgaussfilt(I,sigma,order=[1,0,0])
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134 return np.sqrt(dx**2+dy**2+dz**2)
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135
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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136 def localstats(I,radius,justfeatnames=False):
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137 ptls = [10,30,50,70,90]
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138 featNames = []
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139 for i in range(len(ptls)):
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140 featNames.append('locPtl%d' % ptls[i])
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141 if justfeatnames == True:
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142 return featNames
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143 sI = size(I)
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144 nFeats = len(ptls)
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145 F = np.zeros((sI[0],sI[1],nFeats))
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146 for i in range(nFeats):
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147 F[:,:,i] = ptlfilt(I,ptls[i],radius)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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148 return F
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149
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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150 def localstats3(I,radius,justfeatnames=False):
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151 ptls = [10,30,50,70,90]
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152 featNames = []
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153 for i in range(len(ptls)):
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154 featNames.append('locPtl%d' % ptls[i])
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155 if justfeatnames == True:
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156 return featNames
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157 sI = size(I)
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158 nFeats = len(ptls)
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159 F = np.zeros((sI[0],sI[1],sI[2],nFeats))
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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160 for i in range(nFeats):
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161 F[:,:,:,i] = ptlfilt(I,ptls[i],radius)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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162 return F
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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163
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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164 def imderivatives(I,sigmas,justfeatnames=False):
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165 if type(sigmas) is not list:
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166 sigmas = [sigmas]
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167 derivPerSigmaFeatNames = ['d0','dx','dy','dxx','dxy','dyy','normGrad','normHessDiag']
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168 if justfeatnames == True:
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169 featNames = [];
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170 for i in range(len(sigmas)):
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171 for j in range(len(derivPerSigmaFeatNames)):
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172 featNames.append('derivSigma%d%s' % (sigmas[i],derivPerSigmaFeatNames[j]))
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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173 return featNames
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174 nDerivativesPerSigma = len(derivPerSigmaFeatNames)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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175 nDerivatives = len(sigmas)*nDerivativesPerSigma
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176 sI = size(I)
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177 D = np.zeros((sI[0],sI[1],nDerivatives))
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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178 for i in range(len(sigmas)):
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diff changeset
179 sigma = sigmas[i]
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180 dx = imgaussfilt(I,sigma,order=[0,1])
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181 dy = imgaussfilt(I,sigma,order=[1,0])
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182 dxx = imgaussfilt(I,sigma,order=[0,2])
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183 dyy = imgaussfilt(I,sigma,order=[2,0])
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184 D[:,:,nDerivativesPerSigma*i ] = imgaussfilt(I,sigma)
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185 D[:,:,nDerivativesPerSigma*i+1] = dx
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186 D[:,:,nDerivativesPerSigma*i+2] = dy
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187 D[:,:,nDerivativesPerSigma*i+3] = dxx
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188 D[:,:,nDerivativesPerSigma*i+4] = imgaussfilt(I,sigma,order=[1,1])
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189 D[:,:,nDerivativesPerSigma*i+5] = dyy
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190 D[:,:,nDerivativesPerSigma*i+6] = np.sqrt(dx**2+dy**2)
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191 D[:,:,nDerivativesPerSigma*i+7] = np.sqrt(dxx**2+dyy**2)
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192 return D
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193 # derivatives are indexed by the last dimension, which is good for ML features but not for visualization,
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194 # in which case the expected dimensions are [plane,channel,y(row),x(col)]; to obtain that ordering, do
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195 # D = np.moveaxis(D,[0,3,1,2],[0,1,2,3])
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196
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197 def imderivatives3(I,sigmas,justfeatnames=False):
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198 if type(sigmas) is not list:
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199 sigmas = [sigmas]
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200
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201 derivPerSigmaFeatNames = ['d0','dx','dy','dz','dxx','dxy','dxz','dyy','dyz','dzz','normGrad','normHessDiag']
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202
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203 # derivPerSigmaFeatNames = ['d0','normGrad','normHessDiag']
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204
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205 if justfeatnames == True:
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206 featNames = [];
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207 for i in range(len(sigmas)):
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208 for j in range(len(derivPerSigmaFeatNames)):
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209 featNames.append('derivSigma%d%s' % (sigmas[i],derivPerSigmaFeatNames[j]))
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210 return featNames
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211 nDerivativesPerSigma = len(derivPerSigmaFeatNames)
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212 nDerivatives = len(sigmas)*nDerivativesPerSigma
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213 sI = size(I)
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214 D = np.zeros((sI[0],sI[1],sI[2],nDerivatives)) # plane, channel, y, x
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215 for i in range(len(sigmas)):
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216 sigma = sigmas[i]
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217 dx = imgaussfilt(I,sigma,order=[0,0,1]) # z, y, x
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218 dy = imgaussfilt(I,sigma,order=[0,1,0])
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219 dz = imgaussfilt(I,sigma,order=[1,0,0])
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220 dxx = imgaussfilt(I,sigma,order=[0,0,2])
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221 dyy = imgaussfilt(I,sigma,order=[0,2,0])
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222 dzz = imgaussfilt(I,sigma,order=[2,0,0])
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223
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224 D[:,:,:,nDerivativesPerSigma*i ] = imgaussfilt(I,sigma)
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225 D[:,:,:,nDerivativesPerSigma*i+1 ] = dx
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226 D[:,:,:,nDerivativesPerSigma*i+2 ] = dy
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227 D[:,:,:,nDerivativesPerSigma*i+3 ] = dz
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228 D[:,:,:,nDerivativesPerSigma*i+4 ] = dxx
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229 D[:,:,:,nDerivativesPerSigma*i+5 ] = imgaussfilt(I,sigma,order=[0,1,1])
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230 D[:,:,:,nDerivativesPerSigma*i+6 ] = imgaussfilt(I,sigma,order=[1,0,1])
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231 D[:,:,:,nDerivativesPerSigma*i+7 ] = dyy
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232 D[:,:,:,nDerivativesPerSigma*i+8 ] = imgaussfilt(I,sigma,order=[1,1,0])
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233 D[:,:,:,nDerivativesPerSigma*i+9 ] = dzz
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234 D[:,:,:,nDerivativesPerSigma*i+10] = np.sqrt(dx**2+dy**2+dz**2)
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235 D[:,:,:,nDerivativesPerSigma*i+11] = np.sqrt(dxx**2+dyy**2+dzz**2)
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diff changeset
236
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237 # D[:,:,:,nDerivativesPerSigma*i ] = imgaussfilt(I,sigma)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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238 # D[:,:,:,nDerivativesPerSigma*i+1 ] = np.sqrt(dx**2+dy**2+dz**2)
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239 # D[:,:,:,nDerivativesPerSigma*i+2 ] = np.sqrt(dxx**2+dyy**2+dzz**2)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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diff changeset
240 return D
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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diff changeset
241 # derivatives are indexed by the last dimension, which is good for ML features but not for visualization,
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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parents:
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242 # in which case the expected dimensions are [plane,y(row),x(col)]; to obtain that ordering, do
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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243 # D = np.moveaxis(D,[2,0,1],[0,1,2])
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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244
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parents:
diff changeset
245 def imfeatures(I=[],sigmaDeriv=1,sigmaLoG=1,locStatsRad=0,justfeatnames=False):
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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diff changeset
246 if type(sigmaDeriv) is not list:
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247 sigmaDeriv = [sigmaDeriv]
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parents:
diff changeset
248 if type(sigmaLoG) is not list:
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249 sigmaLoG = [sigmaLoG]
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parents:
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250 derivFeatNames = imderivatives([],sigmaDeriv,justfeatnames=True)
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251 nLoGFeats = len(sigmaLoG)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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252 locStatsFeatNames = []
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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diff changeset
253 if locStatsRad > 1:
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254 locStatsFeatNames = localstats([],locStatsRad,justfeatnames=True)
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255 nLocStatsFeats = len(locStatsFeatNames)
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256 if justfeatnames == True:
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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257 featNames = derivFeatNames
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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parents:
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258 for i in range(nLoGFeats):
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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259 featNames.append('logSigma%d' % sigmaLoG[i])
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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parents:
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260 for i in range(nLocStatsFeats):
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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261 featNames.append(locStatsFeatNames[i])
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262 return featNames
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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263 nDerivFeats = len(derivFeatNames)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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264 nFeatures = nDerivFeats+nLoGFeats+nLocStatsFeats
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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265 sI = size(I)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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266 F = np.zeros((sI[0],sI[1],nFeatures))
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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267 F[:,:,:nDerivFeats] = imderivatives(I,sigmaDeriv)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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268 for i in range(nLoGFeats):
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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269 F[:,:,nDerivFeats+i] = imlogfilt(I,sigmaLoG[i])
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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270 if locStatsRad > 1:
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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271 F[:,:,nDerivFeats+nLoGFeats:] = localstats(I,locStatsRad)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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272 return F
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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273
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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274 def imfeatures3(I=[],sigmaDeriv=2,sigmaLoG=2,locStatsRad=0,justfeatnames=False):
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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275 if type(sigmaDeriv) is not list:
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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276 sigmaDeriv = [sigmaDeriv]
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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277 if type(sigmaLoG) is not list:
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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278 sigmaLoG = [sigmaLoG]
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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279 derivFeatNames = imderivatives3([],sigmaDeriv,justfeatnames=True)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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280 nLoGFeats = len(sigmaLoG)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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281 locStatsFeatNames = []
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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282 if locStatsRad > 1:
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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283 locStatsFeatNames = localstats3([],locStatsRad,justfeatnames=True)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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284 nLocStatsFeats = len(locStatsFeatNames)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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285 if justfeatnames == True:
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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286 featNames = derivFeatNames
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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287 for i in range(nLoGFeats):
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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288 featNames.append('logSigma%d' % sigmaLoG[i])
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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289 for i in range(nLocStatsFeats):
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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290 featNames.append(locStatsFeatNames[i])
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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291 return featNames
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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292 nDerivFeats = len(derivFeatNames)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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293 nFeatures = nDerivFeats+nLoGFeats+nLocStatsFeats
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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294 sI = size(I)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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295 F = np.zeros((sI[0],sI[1],sI[2],nFeatures))
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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296 F[:,:,:,:nDerivFeats] = imderivatives3(I,sigmaDeriv)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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297 for i in range(nLoGFeats):
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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298 F[:,:,:,nDerivFeats+i] = imlogfilt(I,sigmaLoG[i])
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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diff changeset
299 if locStatsRad > 1:
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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300 F[:,:,:,nDerivFeats+nLoGFeats:] = localstats3(I,locStatsRad)
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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301 return F
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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302
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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303 def stack2list(S):
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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304 L = []
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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305 for i in range(size(S)[2]):
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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306 L.append(S[:,:,i])
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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parents:
diff changeset
307 return L
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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parents:
diff changeset
308
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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309 def thrsegment(I,wsBlr,wsThr): # basic threshold segmentation
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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310 G = imgaussfilt(I,sigma=(1-wsBlr)+wsBlr*5) # min 1, max 5
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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diff changeset
311 M = G > wsThr
6bec4fef6b2e "planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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diff changeset
312 return M