Mercurial > repos > perssond > coreograph

annotate toolbox/PartitionOfImage.py @ 0:99308601eaa6 draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
author perssond
date Wed, 19 May 2021 21:34:38 +0000
parents
children
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99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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1 import numpy as np
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2 from toolbox.imtools import *
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3 # from toolbox.ftools import *
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4 # import sys
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5
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6 class PI2D:
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7 Image = None
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8 PaddedImage = None
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9 PatchSize = 128
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10 Margin = 14
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11 SubPatchSize = 100
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12 PC = None # patch coordinates
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13 NumPatches = 0
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14 Output = None
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15 Count = None
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16 NR = None
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17 NC = None
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18 NRPI = None
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19 NCPI = None
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20 Mode = None
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21 W = None
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22
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23 def setup(image,patchSize,margin,mode):
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24 PI2D.Image = image
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25 PI2D.PatchSize = patchSize
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26 PI2D.Margin = margin
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27 subPatchSize = patchSize-2*margin
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28 PI2D.SubPatchSize = subPatchSize
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29
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30 W = np.ones((patchSize,patchSize))
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31 W[[0,-1],:] = 0
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32 W[:,[0,-1]] = 0
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33 for i in range(1,2*margin):
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34 v = i/(2*margin)
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35 W[i,i:-i] = v
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36 W[-i-1,i:-i] = v
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37 W[i:-i,i] = v
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38 W[i:-i,-i-1] = v
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39 PI2D.W = W
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40
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41 if len(image.shape) == 2:
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42 nr,nc = image.shape
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43 elif len(image.shape) == 3: # multi-channel image
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44 nz,nr,nc = image.shape
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45
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46 PI2D.NR = nr
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47 PI2D.NC = nc
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48
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49 npr = int(np.ceil(nr/subPatchSize)) # number of patch rows
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50 npc = int(np.ceil(nc/subPatchSize)) # number of patch cols
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51
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52 nrpi = npr*subPatchSize+2*margin # number of rows in padded image
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53 ncpi = npc*subPatchSize+2*margin # number of cols in padded image
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54
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55 PI2D.NRPI = nrpi
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56 PI2D.NCPI = ncpi
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57
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58 if len(image.shape) == 2:
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59 PI2D.PaddedImage = np.zeros((nrpi,ncpi))
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60 PI2D.PaddedImage[margin:margin+nr,margin:margin+nc] = image
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61 elif len(image.shape) == 3:
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62 PI2D.PaddedImage = np.zeros((nz,nrpi,ncpi))
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63 PI2D.PaddedImage[:,margin:margin+nr,margin:margin+nc] = image
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64
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65 PI2D.PC = [] # patch coordinates [r0,r1,c0,c1]
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66 for i in range(npr):
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67 r0 = i*subPatchSize
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68 r1 = r0+patchSize
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69 for j in range(npc):
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70 c0 = j*subPatchSize
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71 c1 = c0+patchSize
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72 PI2D.PC.append([r0,r1,c0,c1])
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73
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74 PI2D.NumPatches = len(PI2D.PC)
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75 PI2D.Mode = mode # 'replace' or 'accumulate'
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76
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77 def getPatch(i):
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78 r0,r1,c0,c1 = PI2D.PC[i]
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79 if len(PI2D.PaddedImage.shape) == 2:
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80 return PI2D.PaddedImage[r0:r1,c0:c1]
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81 if len(PI2D.PaddedImage.shape) == 3:
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82 return PI2D.PaddedImage[:,r0:r1,c0:c1]
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83
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84 def createOutput(nChannels):
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85 if nChannels == 1:
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86 PI2D.Output = np.zeros((PI2D.NRPI,PI2D.NCPI),np.float16)
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87 else:
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88 PI2D.Output = np.zeros((nChannels,PI2D.NRPI,PI2D.NCPI),np.float16)
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89 if PI2D.Mode == 'accumulate':
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90 PI2D.Count = np.zeros((PI2D.NRPI,PI2D.NCPI),np.float16)
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91
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92 def patchOutput(i,P):
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93 r0,r1,c0,c1 = PI2D.PC[i]
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parents:
diff changeset
94 if PI2D.Mode == 'accumulate':
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parents:
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95 PI2D.Count[r0:r1,c0:c1] += PI2D.W
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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96 if len(P.shape) == 2:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
97 if PI2D.Mode == 'accumulate':
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parents:
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98 PI2D.Output[r0:r1,c0:c1] += np.multiply(P,PI2D.W)
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diff changeset
99 elif PI2D.Mode == 'replace':
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100 PI2D.Output[r0:r1,c0:c1] = P
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101 elif len(P.shape) == 3:
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102 if PI2D.Mode == 'accumulate':
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103 for i in range(P.shape[0]):
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104 PI2D.Output[i,r0:r1,c0:c1] += np.multiply(P[i,:,:],PI2D.W)
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diff changeset
105 elif PI2D.Mode == 'replace':
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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106 PI2D.Output[:,r0:r1,c0:c1] = P
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107
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108 def getValidOutput():
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109 margin = PI2D.Margin
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110 nr, nc = PI2D.NR, PI2D.NC
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111 if PI2D.Mode == 'accumulate':
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112 C = PI2D.Count[margin:margin+nr,margin:margin+nc]
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113 if len(PI2D.Output.shape) == 2:
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114 if PI2D.Mode == 'accumulate':
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115 return np.divide(PI2D.Output[margin:margin+nr,margin:margin+nc],C)
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116 if PI2D.Mode == 'replace':
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117 return PI2D.Output[margin:margin+nr,margin:margin+nc]
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118 if len(PI2D.Output.shape) == 3:
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119 if PI2D.Mode == 'accumulate':
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120 for i in range(PI2D.Output.shape[0]):
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121 PI2D.Output[i,margin:margin+nr,margin:margin+nc] = np.divide(PI2D.Output[i,margin:margin+nr,margin:margin+nc],C)
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122 return PI2D.Output[:,margin:margin+nr,margin:margin+nc]
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123
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124
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125 def demo():
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126 I = np.random.rand(128,128)
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127 # PI2D.setup(I,128,14)
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128 PI2D.setup(I,64,4,'replace')
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129
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130 nChannels = 2
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131 PI2D.createOutput(nChannels)
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132
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133 for i in range(PI2D.NumPatches):
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134 P = PI2D.getPatch(i)
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diff changeset
135 Q = np.zeros((nChannels,P.shape[0],P.shape[1]))
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136 for j in range(nChannels):
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137 Q[j,:,:] = P
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diff changeset
138 PI2D.patchOutput(i,Q)
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139
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diff changeset
140 J = PI2D.getValidOutput()
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141 J = J[0,:,:]
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142
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143 D = np.abs(I-J)
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144 print(np.max(D))
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145
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146 K = cat(1,cat(1,I,J),D)
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diff changeset
147 imshow(K)
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148
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149
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150 class PI3D:
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151 Image = None
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152 PaddedImage = None
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153 PatchSize = 128
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154 Margin = 14
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155 SubPatchSize = 100
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156 PC = None # patch coordinates
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157 NumPatches = 0
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158 Output = None
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159 Count = None
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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160 NR = None # rows
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161 NC = None # cols
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162 NZ = None # planes
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163 NRPI = None
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164 NCPI = None
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165 NZPI = None
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166 Mode = None
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167 W = None
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168
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diff changeset
169 def setup(image,patchSize,margin,mode):
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diff changeset
170 PI3D.Image = image
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171 PI3D.PatchSize = patchSize
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172 PI3D.Margin = margin
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173 subPatchSize = patchSize-2*margin
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diff changeset
174 PI3D.SubPatchSize = subPatchSize
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175
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176 W = np.ones((patchSize,patchSize,patchSize))
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177 W[[0,-1],:,:] = 0
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178 W[:,[0,-1],:] = 0
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179 W[:,:,[0,-1]] = 0
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diff changeset
180 for i in range(1,2*margin):
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diff changeset
181 v = i/(2*margin)
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diff changeset
182 W[[i,-i-1],i:-i,i:-i] = v
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diff changeset
183 W[i:-i,[i,-i-1],i:-i] = v
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parents:
diff changeset
184 W[i:-i,i:-i,[i,-i-1]] = v
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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diff changeset
185
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
186 PI3D.W = W
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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diff changeset
187
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
188 if len(image.shape) == 3:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
189 nz,nr,nc = image.shape
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
190 elif len(image.shape) == 4: # multi-channel image
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
191 nz,nw,nr,nc = image.shape
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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diff changeset
192
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
193 PI3D.NR = nr
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
194 PI3D.NC = nc
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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diff changeset
195 PI3D.NZ = nz
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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diff changeset
196
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
197 npr = int(np.ceil(nr/subPatchSize)) # number of patch rows
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
198 npc = int(np.ceil(nc/subPatchSize)) # number of patch cols
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
199 npz = int(np.ceil(nz/subPatchSize)) # number of patch planes
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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diff changeset
200
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
201 nrpi = npr*subPatchSize+2*margin # number of rows in padded image
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
202 ncpi = npc*subPatchSize+2*margin # number of cols in padded image
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
203 nzpi = npz*subPatchSize+2*margin # number of plns in padded image
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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diff changeset
204
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
205 PI3D.NRPI = nrpi
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
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206 PI3D.NCPI = ncpi
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
207 PI3D.NZPI = nzpi
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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diff changeset
208
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
209 if len(image.shape) == 3:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
210 PI3D.PaddedImage = np.zeros((nzpi,nrpi,ncpi))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
211 PI3D.PaddedImage[margin:margin+nz,margin:margin+nr,margin:margin+nc] = image
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
212 elif len(image.shape) == 4:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
213 PI3D.PaddedImage = np.zeros((nzpi,nw,nrpi,ncpi))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
214 PI3D.PaddedImage[margin:margin+nz,:,margin:margin+nr,margin:margin+nc] = image
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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diff changeset
215
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
216 PI3D.PC = [] # patch coordinates [z0,z1,r0,r1,c0,c1]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
217 for iZ in range(npz):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
218 z0 = iZ*subPatchSize
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
219 z1 = z0+patchSize
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
220 for i in range(npr):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
221 r0 = i*subPatchSize
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
222 r1 = r0+patchSize
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
223 for j in range(npc):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
224 c0 = j*subPatchSize
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
225 c1 = c0+patchSize
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
226 PI3D.PC.append([z0,z1,r0,r1,c0,c1])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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diff changeset
227
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
228 PI3D.NumPatches = len(PI3D.PC)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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parents:
diff changeset
229 PI3D.Mode = mode # 'replace' or 'accumulate'
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
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diff changeset
230
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
231 def getPatch(i):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
232 z0,z1,r0,r1,c0,c1 = PI3D.PC[i]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
233 if len(PI3D.PaddedImage.shape) == 3:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
234 return PI3D.PaddedImage[z0:z1,r0:r1,c0:c1]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
235 if len(PI3D.PaddedImage.shape) == 4:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
236 return PI3D.PaddedImage[z0:z1,:,r0:r1,c0:c1]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
237
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
238 def createOutput(nChannels):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
239 if nChannels == 1:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
240 PI3D.Output = np.zeros((PI3D.NZPI,PI3D.NRPI,PI3D.NCPI))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
241 else:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
242 PI3D.Output = np.zeros((PI3D.NZPI,nChannels,PI3D.NRPI,PI3D.NCPI))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
243 if PI3D.Mode == 'accumulate':
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
244 PI3D.Count = np.zeros((PI3D.NZPI,PI3D.NRPI,PI3D.NCPI))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
245
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
246 def patchOutput(i,P):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
247 z0,z1,r0,r1,c0,c1 = PI3D.PC[i]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
248 if PI3D.Mode == 'accumulate':
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
249 PI3D.Count[z0:z1,r0:r1,c0:c1] += PI3D.W
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
250 if len(P.shape) == 3:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
251 if PI3D.Mode == 'accumulate':
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
252 PI3D.Output[z0:z1,r0:r1,c0:c1] += np.multiply(P,PI3D.W)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
253 elif PI3D.Mode == 'replace':
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
254 PI3D.Output[z0:z1,r0:r1,c0:c1] = P
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
255 elif len(P.shape) == 4:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
256 if PI3D.Mode == 'accumulate':
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
257 for i in range(P.shape[1]):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
258 PI3D.Output[z0:z1,i,r0:r1,c0:c1] += np.multiply(P[:,i,:,:],PI3D.W)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
259 elif PI3D.Mode == 'replace':
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
260 PI3D.Output[z0:z1,:,r0:r1,c0:c1] = P
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
261
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
262 def getValidOutput():
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
263 margin = PI3D.Margin
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
264 nz, nr, nc = PI3D.NZ, PI3D.NR, PI3D.NC
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
265 if PI3D.Mode == 'accumulate':
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
266 C = PI3D.Count[margin:margin+nz,margin:margin+nr,margin:margin+nc]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
267 if len(PI3D.Output.shape) == 3:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
268 if PI3D.Mode == 'accumulate':
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
269 return np.divide(PI3D.Output[margin:margin+nz,margin:margin+nr,margin:margin+nc],C)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
270 if PI3D.Mode == 'replace':
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
diff changeset
271 return PI3D.Output[margin:margin+nz,margin:margin+nr,margin:margin+nc]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"
perssond
parents:
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272 if len(PI3D.Output.shape) == 4:
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273 if PI3D.Mode == 'accumulate':
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274 for i in range(PI3D.Output.shape[1]):
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275 PI3D.Output[margin:margin+nz,i,margin:margin+nr,margin:margin+nc] = np.divide(PI3D.Output[margin:margin+nz,i,margin:margin+nr,margin:margin+nc],C)
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276 return PI3D.Output[margin:margin+nz,:,margin:margin+nr,margin:margin+nc]
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277
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278
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279 def demo():
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280 I = np.random.rand(128,128,128)
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281 PI3D.setup(I,64,4,'accumulate')
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282
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283 nChannels = 2
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284 PI3D.createOutput(nChannels)
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285
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286 for i in range(PI3D.NumPatches):
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287 P = PI3D.getPatch(i)
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288 Q = np.zeros((P.shape[0],nChannels,P.shape[1],P.shape[2]))
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289 for j in range(nChannels):
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290 Q[:,j,:,:] = P
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291 PI3D.patchOutput(i,Q)
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292
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293 J = PI3D.getValidOutput()
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294 J = J[:,0,:,:]
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295
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296 D = np.abs(I-J)
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297 print(np.max(D))
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298
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299 pI = I[64,:,:]
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300 pJ = J[64,:,:]
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301 pD = D[64,:,:]
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302
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303 K = cat(1,cat(1,pI,pJ),pD)
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304 imshow(K)
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305