Mercurial > repos > perssond > unmicst
annotate UnMicst.py @ 0:6bec4fef6b2e draft
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
author | perssond |
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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 numpy as np |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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2 from scipy import misc |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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3 import tensorflow.compat.v1 as tf |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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4 import shutil |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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5 import scipy.io as sio |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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6 import os, fnmatch, glob |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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7 import skimage.exposure as sk |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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8 import skimage.io |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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9 import argparse |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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10 import czifile |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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11 from nd2reader import ND2Reader |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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12 import tifffile |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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13 import sys |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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14 tf.disable_v2_behavior() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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15 #sys.path.insert(0, 'C:\\Users\\Public\\Documents\\ImageScience') |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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16 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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17 from toolbox.imtools import * |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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18 from toolbox.ftools import * |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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19 from toolbox.PartitionOfImage import PI2D |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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20 from toolbox import GPUselect |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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21 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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22 def concat3(lst): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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23 return tf.concat(lst, 3) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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24 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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25 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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26 class UNet2D: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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27 hp = None # hyper-parameters |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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28 nn = None # network |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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29 tfTraining = None # if training or not (to handle batch norm) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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30 tfData = None # data placeholder |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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31 Session = None |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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32 DatasetMean = 0 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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33 DatasetStDev = 0 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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34 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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35 def setupWithHP(hp): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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36 UNet2D.setup(hp['imSize'], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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37 hp['nChannels'], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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38 hp['nClasses'], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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39 hp['nOut0'], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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40 hp['featMapsFact'], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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41 hp['downSampFact'], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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42 hp['ks'], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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43 hp['nExtraConvs'], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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44 hp['stdDev0'], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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45 hp['nLayers'], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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46 hp['batchSize']) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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47 |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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48 def setup(imSize, nChannels, nClasses, nOut0, featMapsFact, downSampFact, kernelSize, nExtraConvs, stdDev0, |
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49 nDownSampLayers, batchSize): |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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50 UNet2D.hp = {'imSize': imSize, |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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51 'nClasses': nClasses, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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52 'nChannels': nChannels, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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53 'nExtraConvs': nExtraConvs, |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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54 'nLayers': nDownSampLayers, |
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55 'featMapsFact': featMapsFact, |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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56 'downSampFact': downSampFact, |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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57 'ks': kernelSize, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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58 'nOut0': nOut0, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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59 'stdDev0': stdDev0, |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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60 'batchSize': batchSize} |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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61 |
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62 nOutX = [UNet2D.hp['nChannels'], UNet2D.hp['nOut0']] |
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63 dsfX = [] |
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64 for i in range(UNet2D.hp['nLayers']): |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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65 nOutX.append(nOutX[-1] * UNet2D.hp['featMapsFact']) |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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66 dsfX.append(UNet2D.hp['downSampFact']) |
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67 |
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68 # -------------------------------------------------- |
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69 # downsampling layer |
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70 # -------------------------------------------------- |
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71 |
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72 with tf.name_scope('placeholders'): |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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73 UNet2D.tfTraining = tf.placeholder(tf.bool, name='training') |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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74 UNet2D.tfData = tf.placeholder("float", shape=[None, UNet2D.hp['imSize'], UNet2D.hp['imSize'], |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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75 UNet2D.hp['nChannels']], name='data') |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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76 |
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77 def down_samp_layer(data, index): |
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78 with tf.name_scope('ld%d' % index): |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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79 ldXWeights1 = tf.Variable( |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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80 tf.truncated_normal([UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[index], nOutX[index + 1]], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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81 stddev=stdDev0), name='kernel1') |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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82 ldXWeightsExtra = [] |
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83 for i in range(nExtraConvs): |
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84 ldXWeightsExtra.append(tf.Variable( |
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85 tf.truncated_normal([UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[index + 1], nOutX[index + 1]], |
6bec4fef6b2e
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86 stddev=stdDev0), name='kernelExtra%d' % i)) |
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87 |
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88 c00 = tf.nn.conv2d(data, ldXWeights1, strides=[1, 1, 1, 1], padding='SAME') |
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89 for i in range(nExtraConvs): |
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90 c00 = tf.nn.conv2d(tf.nn.relu(c00), ldXWeightsExtra[i], strides=[1, 1, 1, 1], padding='SAME') |
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91 |
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92 ldXWeightsShortcut = tf.Variable( |
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93 tf.truncated_normal([1, 1, nOutX[index], nOutX[index + 1]], stddev=stdDev0), name='shortcutWeights') |
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94 shortcut = tf.nn.conv2d(data, ldXWeightsShortcut, strides=[1, 1, 1, 1], padding='SAME') |
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95 |
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96 bn = tf.layers.batch_normalization(tf.nn.relu(c00 + shortcut), training=UNet2D.tfTraining) |
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97 |
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98 return tf.nn.max_pool(bn, ksize=[1, dsfX[index], dsfX[index], 1], |
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99 strides=[1, dsfX[index], dsfX[index], 1], padding='SAME', name='maxpool') |
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100 |
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101 # -------------------------------------------------- |
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102 # bottom layer |
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103 # -------------------------------------------------- |
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104 |
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105 with tf.name_scope('lb'): |
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106 lbWeights1 = tf.Variable(tf.truncated_normal( |
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107 [UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[UNet2D.hp['nLayers']], nOutX[UNet2D.hp['nLayers'] + 1]], |
6bec4fef6b2e
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108 stddev=stdDev0), name='kernel1') |
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109 |
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110 def lb(hidden): |
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111 return tf.nn.relu(tf.nn.conv2d(hidden, lbWeights1, strides=[1, 1, 1, 1], padding='SAME'), name='conv') |
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112 |
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113 # -------------------------------------------------- |
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114 # downsampling |
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115 # -------------------------------------------------- |
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116 |
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117 with tf.name_scope('downsampling'): |
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118 dsX = [] |
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119 dsX.append(UNet2D.tfData) |
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120 |
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121 for i in range(UNet2D.hp['nLayers']): |
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122 dsX.append(down_samp_layer(dsX[i], i)) |
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123 |
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124 b = lb(dsX[UNet2D.hp['nLayers']]) |
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125 |
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126 # -------------------------------------------------- |
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127 # upsampling layer |
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128 # -------------------------------------------------- |
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129 |
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130 def up_samp_layer(data, index): |
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131 with tf.name_scope('lu%d' % index): |
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132 luXWeights1 = tf.Variable( |
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133 tf.truncated_normal([UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[index + 1], nOutX[index + 2]], |
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134 stddev=stdDev0), name='kernel1') |
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135 luXWeights2 = tf.Variable(tf.truncated_normal( |
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136 [UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[index] + nOutX[index + 1], nOutX[index + 1]], |
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137 stddev=stdDev0), name='kernel2') |
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138 luXWeightsExtra = [] |
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139 for i in range(nExtraConvs): |
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140 luXWeightsExtra.append(tf.Variable( |
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141 tf.truncated_normal([UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[index + 1], nOutX[index + 1]], |
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142 stddev=stdDev0), name='kernel2Extra%d' % i)) |
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143 |
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144 outSize = UNet2D.hp['imSize'] |
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145 for i in range(index): |
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146 outSize /= dsfX[i] |
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147 outSize = int(outSize) |
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148 |
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149 outputShape = [UNet2D.hp['batchSize'], outSize, outSize, nOutX[index + 1]] |
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150 us = tf.nn.relu( |
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151 tf.nn.conv2d_transpose(data, luXWeights1, outputShape, strides=[1, dsfX[index], dsfX[index], 1], |
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152 padding='SAME'), name='conv1') |
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153 cc = concat3([dsX[index], us]) |
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154 cv = tf.nn.relu(tf.nn.conv2d(cc, luXWeights2, strides=[1, 1, 1, 1], padding='SAME'), name='conv2') |
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155 for i in range(nExtraConvs): |
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156 cv = tf.nn.relu(tf.nn.conv2d(cv, luXWeightsExtra[i], strides=[1, 1, 1, 1], padding='SAME'), |
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157 name='conv2Extra%d' % i) |
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158 return cv |
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159 |
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160 # -------------------------------------------------- |
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161 # final (top) layer |
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162 # -------------------------------------------------- |
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163 |
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164 with tf.name_scope('lt'): |
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165 ltWeights1 = tf.Variable(tf.truncated_normal([1, 1, nOutX[1], nClasses], stddev=stdDev0), name='kernel') |
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166 |
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167 def lt(hidden): |
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168 return tf.nn.conv2d(hidden, ltWeights1, strides=[1, 1, 1, 1], padding='SAME', name='conv') |
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169 |
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170 # -------------------------------------------------- |
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171 # upsampling |
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172 # -------------------------------------------------- |
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173 |
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174 with tf.name_scope('upsampling'): |
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175 usX = [] |
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176 usX.append(b) |
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177 |
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178 for i in range(UNet2D.hp['nLayers']): |
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179 usX.append(up_samp_layer(usX[i], UNet2D.hp['nLayers'] - 1 - i)) |
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180 |
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181 t = lt(usX[UNet2D.hp['nLayers']]) |
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182 |
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183 sm = tf.nn.softmax(t, -1) |
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184 UNet2D.nn = sm |
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185 |
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186 def train(imPath, logPath, modelPath, pmPath, nTrain, nValid, nTest, restoreVariables, nSteps, gpuIndex, |
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187 testPMIndex): |
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188 os.environ['CUDA_VISIBLE_DEVICES'] = '%d' % gpuIndex |
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189 |
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190 outLogPath = logPath |
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191 trainWriterPath = pathjoin(logPath, 'Train') |
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192 validWriterPath = pathjoin(logPath, 'Valid') |
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193 outModelPath = pathjoin(modelPath, 'model.ckpt') |
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194 outPMPath = pmPath |
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195 |
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196 batchSize = UNet2D.hp['batchSize'] |
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197 imSize = UNet2D.hp['imSize'] |
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198 nChannels = UNet2D.hp['nChannels'] |
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199 nClasses = UNet2D.hp['nClasses'] |
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200 |
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201 # -------------------------------------------------- |
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202 # data |
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203 # -------------------------------------------------- |
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204 |
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205 Train = np.zeros((nTrain, imSize, imSize, nChannels)) |
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206 Valid = np.zeros((nValid, imSize, imSize, nChannels)) |
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207 Test = np.zeros((nTest, imSize, imSize, nChannels)) |
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208 LTrain = np.zeros((nTrain, imSize, imSize, nClasses)) |
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209 LValid = np.zeros((nValid, imSize, imSize, nClasses)) |
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210 LTest = np.zeros((nTest, imSize, imSize, nClasses)) |
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211 |
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212 print('loading data, computing mean / st dev') |
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213 if not os.path.exists(modelPath): |
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214 os.makedirs(modelPath) |
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215 if restoreVariables: |
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216 datasetMean = loadData(pathjoin(modelPath, 'datasetMean.data')) |
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217 datasetStDev = loadData(pathjoin(modelPath, 'datasetStDev.data')) |
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218 else: |
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219 datasetMean = 0 |
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220 datasetStDev = 0 |
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221 for iSample in range(nTrain + nValid + nTest): |
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222 I = im2double(tifread('%s/I%05d_Img.tif' % (imPath, iSample))) |
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223 datasetMean += np.mean(I) |
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224 datasetStDev += np.std(I) |
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225 datasetMean /= (nTrain + nValid + nTest) |
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226 datasetStDev /= (nTrain + nValid + nTest) |
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227 saveData(datasetMean, pathjoin(modelPath, 'datasetMean.data')) |
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228 saveData(datasetStDev, pathjoin(modelPath, 'datasetStDev.data')) |
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229 |
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230 perm = np.arange(nTrain + nValid + nTest) |
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231 np.random.shuffle(perm) |
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232 |
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233 for iSample in range(0, nTrain): |
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234 path = '%s/I%05d_Img.tif' % (imPath, perm[iSample]) |
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235 im = im2double(tifread(path)) |
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236 Train[iSample, :, :, 0] = (im - datasetMean) / datasetStDev |
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237 path = '%s/I%05d_Ant.tif' % (imPath, perm[iSample]) |
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238 im = tifread(path) |
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239 for i in range(nClasses): |
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240 LTrain[iSample, :, :, i] = (im == i + 1) |
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241 |
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242 for iSample in range(0, nValid): |
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243 path = '%s/I%05d_Img.tif' % (imPath, perm[nTrain + iSample]) |
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244 im = im2double(tifread(path)) |
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245 Valid[iSample, :, :, 0] = (im - datasetMean) / datasetStDev |
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246 path = '%s/I%05d_Ant.tif' % (imPath, perm[nTrain + iSample]) |
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247 im = tifread(path) |
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248 for i in range(nClasses): |
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249 LValid[iSample, :, :, i] = (im == i + 1) |
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250 |
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251 for iSample in range(0, nTest): |
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252 path = '%s/I%05d_Img.tif' % (imPath, perm[nTrain + nValid + iSample]) |
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253 im = im2double(tifread(path)) |
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254 Test[iSample, :, :, 0] = (im - datasetMean) / datasetStDev |
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255 path = '%s/I%05d_Ant.tif' % (imPath, perm[nTrain + nValid + iSample]) |
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256 im = tifread(path) |
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257 for i in range(nClasses): |
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258 LTest[iSample, :, :, i] = (im == i + 1) |
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259 |
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260 # -------------------------------------------------- |
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261 # optimization |
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262 # -------------------------------------------------- |
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263 |
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264 tfLabels = tf.placeholder("float", shape=[None, imSize, imSize, nClasses], name='labels') |
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265 |
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266 globalStep = tf.Variable(0, trainable=False) |
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267 learningRate0 = 0.01 |
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268 decaySteps = 1000 |
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269 decayRate = 0.95 |
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270 learningRate = tf.train.exponential_decay(learningRate0, globalStep, decaySteps, decayRate, staircase=True) |
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271 |
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272 with tf.name_scope('optim'): |
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273 loss = tf.reduce_mean(-tf.reduce_sum(tf.multiply(tfLabels, tf.log(UNet2D.nn)), 3)) |
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274 updateOps = tf.get_collection(tf.GraphKeys.UPDATE_OPS) |
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275 # optimizer = tf.train.MomentumOptimizer(1e-3,0.9) |
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276 optimizer = tf.train.MomentumOptimizer(learningRate, 0.9) |
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277 # optimizer = tf.train.GradientDescentOptimizer(learningRate) |
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278 with tf.control_dependencies(updateOps): |
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279 optOp = optimizer.minimize(loss, global_step=globalStep) |
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280 |
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281 with tf.name_scope('eval'): |
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282 error = [] |
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283 for iClass in range(nClasses): |
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284 labels0 = tf.reshape(tf.to_int32(tf.slice(tfLabels, [0, 0, 0, iClass], [-1, -1, -1, 1])), |
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285 [batchSize, imSize, imSize]) |
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286 predict0 = tf.reshape(tf.to_int32(tf.equal(tf.argmax(UNet2D.nn, 3), iClass)), |
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287 [batchSize, imSize, imSize]) |
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288 correct = tf.multiply(labels0, predict0) |
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289 nCorrect0 = tf.reduce_sum(correct) |
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290 nLabels0 = tf.reduce_sum(labels0) |
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291 error.append(1 - tf.to_float(nCorrect0) / tf.to_float(nLabels0)) |
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292 errors = tf.tuple(error) |
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293 |
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294 # -------------------------------------------------- |
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295 # inspection |
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296 # -------------------------------------------------- |
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297 |
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298 with tf.name_scope('scalars'): |
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299 tf.summary.scalar('avg_cross_entropy', loss) |
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300 for iClass in range(nClasses): |
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301 tf.summary.scalar('avg_pixel_error_%d' % iClass, error[iClass]) |
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302 tf.summary.scalar('learning_rate', learningRate) |
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303 with tf.name_scope('images'): |
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304 split0 = tf.slice(UNet2D.nn, [0, 0, 0, 0], [-1, -1, -1, 1]) |
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305 split1 = tf.slice(UNet2D.nn, [0, 0, 0, 1], [-1, -1, -1, 1]) |
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306 if nClasses > 2: |
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307 split2 = tf.slice(UNet2D.nn, [0, 0, 0, 2], [-1, -1, -1, 1]) |
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308 tf.summary.image('pm0', split0) |
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309 tf.summary.image('pm1', split1) |
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310 if nClasses > 2: |
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311 tf.summary.image('pm2', split2) |
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312 merged = tf.summary.merge_all() |
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313 |
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314 # -------------------------------------------------- |
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315 # session |
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316 # -------------------------------------------------- |
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317 |
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318 saver = tf.train.Saver() |
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319 sess = tf.Session(config=tf.ConfigProto( |
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320 allow_soft_placement=True)) # config parameter needed to save variables when using GPU |
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321 |
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322 if os.path.exists(outLogPath): |
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323 shutil.rmtree(outLogPath) |
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"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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324 trainWriter = tf.summary.FileWriter(trainWriterPath, sess.graph) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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325 validWriter = tf.summary.FileWriter(validWriterPath, sess.graph) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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326 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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327 if restoreVariables: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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328 saver.restore(sess, outModelPath) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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329 print("Model restored.") |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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330 else: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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331 sess.run(tf.global_variables_initializer()) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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332 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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333 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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334 # train |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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335 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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336 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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337 batchData = np.zeros((batchSize, imSize, imSize, nChannels)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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338 batchLabels = np.zeros((batchSize, imSize, imSize, nClasses)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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339 for i in range(nSteps): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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340 # train |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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341 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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342 perm = np.arange(nTrain) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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343 np.random.shuffle(perm) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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344 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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345 for j in range(batchSize): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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346 batchData[j, :, :, :] = Train[perm[j], :, :, :] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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347 batchLabels[j, :, :, :] = LTrain[perm[j], :, :, :] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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348 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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349 summary, _ = sess.run([merged, optOp], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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350 feed_dict={UNet2D.tfData: batchData, tfLabels: batchLabels, UNet2D.tfTraining: 1}) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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351 trainWriter.add_summary(summary, i) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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352 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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353 # validation |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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354 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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355 perm = np.arange(nValid) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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356 np.random.shuffle(perm) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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357 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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358 for j in range(batchSize): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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359 batchData[j, :, :, :] = Valid[perm[j], :, :, :] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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360 batchLabels[j, :, :, :] = LValid[perm[j], :, :, :] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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361 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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362 summary, es = sess.run([merged, errors], |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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363 feed_dict={UNet2D.tfData: batchData, tfLabels: batchLabels, UNet2D.tfTraining: 0}) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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364 validWriter.add_summary(summary, i) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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365 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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366 e = np.mean(es) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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367 print('step %05d, e: %f' % (i, e)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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368 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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369 if i == 0: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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370 if restoreVariables: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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371 lowestError = e |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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372 else: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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373 lowestError = np.inf |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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374 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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375 if np.mod(i, 100) == 0 and e < lowestError: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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376 lowestError = e |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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377 print("Model saved in file: %s" % saver.save(sess, outModelPath)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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378 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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379 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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380 # test |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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381 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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382 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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383 if not os.path.exists(outPMPath): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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384 os.makedirs(outPMPath) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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385 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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386 for i in range(nTest): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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387 j = np.mod(i, batchSize) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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388 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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389 batchData[j, :, :, :] = Test[i, :, :, :] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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390 batchLabels[j, :, :, :] = LTest[i, :, :, :] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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391 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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392 if j == batchSize - 1 or i == nTest - 1: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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|
393 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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394 output = sess.run(UNet2D.nn, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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395 feed_dict={UNet2D.tfData: batchData, tfLabels: batchLabels, UNet2D.tfTraining: 0}) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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396 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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397 for k in range(j + 1): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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398 pm = output[k, :, :, testPMIndex] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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399 gt = batchLabels[k, :, :, testPMIndex] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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400 im = np.sqrt(normalize(batchData[k, :, :, 0])) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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401 imwrite(np.uint8(255 * np.concatenate((im, np.concatenate((pm, gt), axis=1)), axis=1)), |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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402 '%s/I%05d.png' % (outPMPath, i - j + k + 1)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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|
403 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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|
404 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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|
405 # save hyper-parameters, clean-up |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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406 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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407 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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408 saveData(UNet2D.hp, pathjoin(modelPath, 'hp.data')) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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409 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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410 trainWriter.close() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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411 validWriter.close() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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412 sess.close() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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413 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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414 def deploy(imPath, nImages, modelPath, pmPath, gpuIndex, pmIndex): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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415 os.environ['CUDA_VISIBLE_DEVICES'] = '%d' % gpuIndex |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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416 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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417 variablesPath = pathjoin(modelPath, 'model.ckpt') |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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418 outPMPath = pmPath |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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419 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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420 hp = loadData(pathjoin(modelPath, 'hp.data')) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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421 UNet2D.setupWithHP(hp) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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422 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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423 batchSize = UNet2D.hp['batchSize'] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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424 imSize = UNet2D.hp['imSize'] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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425 nChannels = UNet2D.hp['nChannels'] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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426 nClasses = UNet2D.hp['nClasses'] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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427 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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428 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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429 # data |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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430 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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431 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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432 Data = np.zeros((nImages, imSize, imSize, nChannels)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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433 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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434 datasetMean = loadData(pathjoin(modelPath, 'datasetMean.data')) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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435 datasetStDev = loadData(pathjoin(modelPath, 'datasetStDev.data')) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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436 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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437 for iSample in range(0, nImages): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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438 path = '%s/I%05d_Img.tif' % (imPath, iSample) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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439 im = im2double(tifread(path)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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440 Data[iSample, :, :, 0] = (im - datasetMean) / datasetStDev |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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441 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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442 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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443 # session |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
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444 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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445 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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446 saver = tf.train.Saver() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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447 sess = tf.Session(config=tf.ConfigProto( |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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448 allow_soft_placement=True)) # config parameter needed to save variables when using GPU |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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449 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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450 saver.restore(sess, variablesPath) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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451 print("Model restored.") |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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452 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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453 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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454 # deploy |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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455 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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456 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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457 batchData = np.zeros((batchSize, imSize, imSize, nChannels)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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458 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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459 if not os.path.exists(outPMPath): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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460 os.makedirs(outPMPath) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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461 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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462 for i in range(nImages): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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463 print(i, nImages) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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464 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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465 j = np.mod(i, batchSize) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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466 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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467 batchData[j, :, :, :] = Data[i, :, :, :] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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468 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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469 if j == batchSize - 1 or i == nImages - 1: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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470 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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471 output = sess.run(UNet2D.nn, feed_dict={UNet2D.tfData: batchData, UNet2D.tfTraining: 0}) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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472 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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473 for k in range(j + 1): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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474 pm = output[k, :, :, pmIndex] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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475 im = np.sqrt(normalize(batchData[k, :, :, 0])) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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476 # imwrite(np.uint8(255*np.concatenate((im,pm),axis=1)),'%s/I%05d.png' % (outPMPath,i-j+k+1)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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477 imwrite(np.uint8(255 * im), '%s/I%05d_Im.png' % (outPMPath, i - j + k + 1)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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478 imwrite(np.uint8(255 * pm), '%s/I%05d_PM.png' % (outPMPath, i - j + k + 1)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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479 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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480 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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481 # clean-up |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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482 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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483 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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484 sess.close() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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485 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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486 def singleImageInferenceSetup(modelPath, gpuIndex,mean,std): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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487 variablesPath = pathjoin(modelPath, 'model.ckpt') |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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488 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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489 hp = loadData(pathjoin(modelPath, 'hp.data')) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
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490 UNet2D.setupWithHP(hp) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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491 if mean ==-1: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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492 UNet2D.DatasetMean = loadData(pathjoin(modelPath, 'datasetMean.data')) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
493 else: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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494 UNet2D.DatasetMean = mean |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
495 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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496 if std == -1: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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497 UNet2D.DatasetStDev = loadData(pathjoin(modelPath, 'datasetStDev.data')) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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498 else: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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499 UNet2D.DatasetStDev = std |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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500 print(UNet2D.DatasetMean) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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501 print(UNet2D.DatasetStDev) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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502 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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503 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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504 # session |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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505 # -------------------------------------------------- |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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506 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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parents:
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507 saver = tf.train.Saver() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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508 UNet2D.Session = tf.Session(config=tf.ConfigProto()) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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509 # allow_soft_placement=True)) # config parameter needed to save variables when using GPU |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
510 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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511 saver.restore(UNet2D.Session, variablesPath) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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parents:
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512 print("Model restored.") |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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513 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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514 def singleImageInferenceCleanup(): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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515 UNet2D.Session.close() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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parents:
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516 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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517 def singleImageInference(image, mode, pmIndex): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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parents:
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518 print('Inference...') |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
519 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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520 batchSize = UNet2D.hp['batchSize'] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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521 imSize = UNet2D.hp['imSize'] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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522 nChannels = UNet2D.hp['nChannels'] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
523 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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524 PI2D.setup(image, imSize, int(imSize / 8), mode) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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525 PI2D.createOutput(nChannels) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
526 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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527 batchData = np.zeros((batchSize, imSize, imSize, nChannels)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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528 for i in range(PI2D.NumPatches): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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529 j = np.mod(i, batchSize) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
530 batchData[j, :, :, 0] = (PI2D.getPatch(i) - UNet2D.DatasetMean) / UNet2D.DatasetStDev |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
531 if j == batchSize - 1 or i == PI2D.NumPatches - 1: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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532 output = UNet2D.Session.run(UNet2D.nn, feed_dict={UNet2D.tfData: batchData, UNet2D.tfTraining: 0}) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
533 for k in range(j + 1): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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534 pm = output[k, :, :, pmIndex] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
535 PI2D.patchOutput(i - j + k, pm) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
536 # PI2D.patchOutput(i-j+k,normalize(imgradmag(PI2D.getPatch(i-j+k),1))) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
537 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
538 return PI2D.getValidOutput() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
539 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
540 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
541 if __name__ == '__main__': |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
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542 parser = argparse.ArgumentParser() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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543 parser.add_argument("imagePath", help="path to the .tif file") |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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544 parser.add_argument("--model", help="type of model. For example, nuclei vs cytoplasm",default = 'nucleiDAPI') |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
545 parser.add_argument("--outputPath", help="output path of probability map") |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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|
546 parser.add_argument("--channel", help="channel to perform inference on", type=int, default=0) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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547 parser.add_argument("--classOrder", help="background, contours, foreground", type = int, nargs = '+', default=-1) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
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changeset
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548 parser.add_argument("--mean", help="mean intensity of input image. Use -1 to use model", type=float, default=-1) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
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549 parser.add_argument("--std", help="mean standard deviation of input image. Use -1 to use model", type=float, default=-1) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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550 parser.add_argument("--scalingFactor", help="factor by which to increase/decrease image size by", type=float, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
551 default=1) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
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552 parser.add_argument("--stackOutput", help="save probability maps as separate files", action='store_true') |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
553 parser.add_argument("--GPU", help="explicitly select GPU", type=int, default = -1) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
554 parser.add_argument("--outlier", |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
555 help="map percentile intensity to max when rescaling intensity values. Max intensity as default", |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
556 type=float, default=-1) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
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557 args = parser.parse_args() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
558 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
559 logPath = '' |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
560 scriptPath = os.path.dirname(os.path.realpath(__file__)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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561 modelPath = os.path.join(scriptPath, 'models', args.model) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
562 # modelPath = os.path.join(scriptPath, 'models/cytoplasmINcell') |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
563 # modelPath = os.path.join(scriptPath, 'cytoplasmZeissNikon') |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
564 pmPath = '' |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
565 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
566 if os.system('nvidia-smi') == 0: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
567 if args.GPU == -1: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
568 print("automatically choosing GPU") |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
569 GPU = GPUselect.pick_gpu_lowest_memory() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
570 else: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
571 GPU = args.GPU |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
572 print('Using GPU ' + str(GPU)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
573 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
574 else: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
575 if sys.platform == 'win32': # only 1 gpu on windows |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
576 if args.GPU==-1: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
577 GPU = 0 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
578 else: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
579 GPU = args.GPU |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
580 print('Using GPU ' + str(GPU)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
581 else: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
582 GPU=0 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
583 print('Using CPU') |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
584 os.environ['CUDA_VISIBLE_DEVICES'] = '%d' % GPU |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
585 UNet2D.singleImageInferenceSetup(modelPath, GPU,args.mean,args.std) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
586 nClass = UNet2D.hp['nClasses'] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
587 imagePath = args.imagePath |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
588 dapiChannel = args.channel |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
589 dsFactor = args.scalingFactor |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
590 parentFolder = os.path.dirname(os.path.dirname(imagePath)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
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|
591 fileName = os.path.basename(imagePath) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
592 fileNamePrefix = fileName.split(os.extsep, 1) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
593 print(fileName) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
594 fileType = fileNamePrefix[1] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
595 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
596 if fileType=='ome.tif' or fileType == 'btf' : |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
597 I = skio.imread(imagePath, img_num=dapiChannel,plugin='tifffile') |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
598 elif fileType == 'tif' : |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
599 I = tifffile.imread(imagePath, key=dapiChannel) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
600 elif fileType == 'czi': |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
601 with czifile.CziFile(imagePath) as czi: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
602 image = czi.asarray() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
603 I = image[0, 0, dapiChannel, 0, 0, :, :, 0] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
604 elif fileType == 'nd2': |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
605 with ND2Reader(imagePath) as fullStack: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
606 I = fullStack[dapiChannel] |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
607 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
608 if args.classOrder == -1: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
609 args.classOrder = range(nClass) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
610 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
611 rawI = I |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
612 print(type(I)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
613 hsize = int((float(I.shape[0]) * float(dsFactor))) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
614 vsize = int((float(I.shape[1]) * float(dsFactor))) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
615 I = resize(I, (hsize, vsize)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
616 if args.outlier == -1: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
617 maxLimit = np.max(I) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
618 else: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
619 maxLimit = np.percentile(I, args.outlier) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
620 I = im2double(sk.rescale_intensity(I, in_range=(np.min(I), maxLimit), out_range=(0, 0.983))) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
621 rawI = im2double(rawI) / np.max(im2double(rawI)) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
622 if not args.outputPath: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
623 args.outputPath = parentFolder + '//probability_maps' |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
624 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
625 if not os.path.exists(args.outputPath): |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
626 os.makedirs(args.outputPath) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
627 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
628 append_kwargs = { |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
629 'bigtiff': True, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
630 'metadata': None, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
631 'append': True, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
632 } |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
633 save_kwargs = { |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
634 'bigtiff': True, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
635 'metadata': None, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
636 'append': False, |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
637 } |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
638 if args.stackOutput: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
639 slice=0 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
640 for iClass in args.classOrder[::-1]: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
641 PM = np.uint8(255*UNet2D.singleImageInference(I, 'accumulate', iClass)) # backwards in order to align with ilastik... |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
642 PM = resize(PM, (rawI.shape[0], rawI.shape[1])) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
643 if slice==0: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
644 skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Probabilities_' + str(dapiChannel) + '.tif', np.uint8(255 * PM),**save_kwargs) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
645 else: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
646 skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Probabilities_' + str(dapiChannel) + '.tif',np.uint8(255 * PM),**append_kwargs) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
647 if slice==1: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
648 save_kwargs['append'] = False |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
|
649 skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif', np.uint8(255 * PM), **save_kwargs) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
perssond
parents:
diff
changeset
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650 skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif', np.uint8(255 * rawI), **append_kwargs) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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651 slice = slice + 1 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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652 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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653 else: |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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654 contours = np.uint8(255*UNet2D.singleImageInference(I, 'accumulate', args.classOrder[1])) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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655 hsize = int((float(I.shape[0]) * float(1 / dsFactor))) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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656 vsize = int((float(I.shape[1]) * float(1 / dsFactor))) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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657 contours = resize(contours, (rawI.shape[0], rawI.shape[1])) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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658 skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_ContoursPM_' + str(dapiChannel) + '.tif',np.uint8(255 * contours),**save_kwargs) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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659 skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_ContoursPM_' + str(dapiChannel) + '.tif',np.uint8(255 * rawI), **append_kwargs) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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660 del contours |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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661 nuclei = np.uint8(255*UNet2D.singleImageInference(I, 'accumulate', args.classOrder[2])) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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662 nuclei = resize(nuclei, (rawI.shape[0], rawI.shape[1])) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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663 skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_NucleiPM_' + str(dapiChannel) + '.tif',np.uint8(255 * nuclei), **save_kwargs) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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664 del nuclei |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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665 UNet2D.singleImageInferenceCleanup() |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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666 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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667 #aligned output files to reflect ilastik |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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668 #outputting all classes as single file |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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669 #handles multiple formats including tif, ome.tif, nd2, czi |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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670 #selectable models (human nuclei, mouse nuclei, cytoplasm) |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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671 |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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672 #added legacy function to save output files |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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673 #append save function to reduce memory footprint |
6bec4fef6b2e
"planemo upload for repository https://github.com/ohsu-comp-bio/unmicst commit 73e4cae15f2d7cdc86719e77470eb00af4b6ebb7-dirty"
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674 #added --classOrder parameter to specify which class is background, contours, and nuclei respectively |