coreograph: UNetCoreograph.py annotate

annotate UNetCoreograph.py @ 0:99308601eaa6 draft

"planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty"

author	perssond
date	Wed, 19 May 2021 21:34:38 +0000
parents
children	57f1260ca94e

rev	line source
0 99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	1 import numpy as np
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	2 from scipy import misc as sm
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	3 import shutil
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	4 import scipy.io as sio
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	5 import os
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	6 import skimage.exposure as sk
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	7 import cv2
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	8 import argparse
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	9 import pytiff
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	10 import tifffile
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	11 import tensorflow as tf
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	12 from skimage.morphology import *
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	13 from skimage.exposure import rescale_intensity
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	14 from skimage.segmentation import chan_vese, find_boundaries, morphological_chan_vese
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	15 from skimage.measure import regionprops,label, find_contours
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	16 from skimage.transform import resize
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	17 from skimage.filters import gaussian
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	18 from skimage.feature import peak_local_max,blob_log
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	19 from skimage.color import label2rgb
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	20 import skimage.io as skio
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	21 from skimage import img_as_bool
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	22 from skimage.draw import circle_perimeter
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	23 from scipy.ndimage.filters import uniform_filter
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	24 from scipy.ndimage import gaussian_laplace
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	25 from os.path import *
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	26 from os import listdir, makedirs, remove
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	27
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	28
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	29
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	30 import sys
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	31 from typing import Any
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	32
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	33 #sys.path.insert(0, 'C:\\Users\\Public\\Documents\\ImageScience')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	34 from toolbox.imtools import *
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	35 from toolbox.ftools import *
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	36 from toolbox.PartitionOfImage import PI2D
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	37
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	38
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	39 def concat3(lst):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	40 return tf.concat(lst,3)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	41
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	42 class UNet2D:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	43 hp = None # hyper-parameters
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	44 nn = None # network
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	45 tfTraining = None # if training or not (to handle batch norm)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	46 tfData = None # data placeholder
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	47 Session = None
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	48 DatasetMean = 0
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	49 DatasetStDev = 0
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	50
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	51 def setupWithHP(hp):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	52 UNet2D.setup(hp['imSize'],
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	53 hp['nChannels'],
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	54 hp['nClasses'],
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	55 hp['nOut0'],
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	56 hp['featMapsFact'],
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	57 hp['downSampFact'],
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	58 hp['ks'],
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	59 hp['nExtraConvs'],
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	60 hp['stdDev0'],
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	61 hp['nLayers'],
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	62 hp['batchSize'])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	63
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	64 def setup(imSize,nChannels,nClasses,nOut0,featMapsFact,downSampFact,kernelSize,nExtraConvs,stdDev0,nDownSampLayers,batchSize):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	65 UNet2D.hp = {'imSize':imSize,
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	66 'nClasses':nClasses,
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	67 'nChannels':nChannels,
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	68 'nExtraConvs':nExtraConvs,
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	69 'nLayers':nDownSampLayers,
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	70 'featMapsFact':featMapsFact,
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	71 'downSampFact':downSampFact,
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	72 'ks':kernelSize,
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	73 'nOut0':nOut0,
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	74 'stdDev0':stdDev0,
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	75 'batchSize':batchSize}
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	76
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	77 nOutX = [UNet2D.hp['nChannels'],UNet2D.hp['nOut0']]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	78 dsfX = []
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	79 for i in range(UNet2D.hp['nLayers']):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	80 nOutX.append(nOutX[-1]*UNet2D.hp['featMapsFact'])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	81 dsfX.append(UNet2D.hp['downSampFact'])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	82
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	83
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	84 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	85 # downsampling layer
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	86 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	87
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	88 with tf.name_scope('placeholders'):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	89 UNet2D.tfTraining = tf.placeholder(tf.bool, name='training')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	90 UNet2D.tfData = tf.placeholder("float", shape=[None,UNet2D.hp['imSize'],UNet2D.hp['imSize'],UNet2D.hp['nChannels']],name='data')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	91
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	92 def down_samp_layer(data,index):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	93 with tf.name_scope('ld%d' % index):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	94 ldXWeights1 = tf.Variable(tf.truncated_normal([UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[index], nOutX[index+1]], stddev=stdDev0),name='kernel1')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	95 ldXWeightsExtra = []
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	96 for i in range(nExtraConvs):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	97 ldXWeightsExtra.append(tf.Variable(tf.truncated_normal([UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[index+1], nOutX[index+1]], stddev=stdDev0),name='kernelExtra%d' % i))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	98
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	99 c00 = tf.nn.conv2d(data, ldXWeights1, strides=[1, 1, 1, 1], padding='SAME')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	100 for i in range(nExtraConvs):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	101 c00 = tf.nn.conv2d(tf.nn.relu(c00), ldXWeightsExtra[i], strides=[1, 1, 1, 1], padding='SAME')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	102
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	103 ldXWeightsShortcut = tf.Variable(tf.truncated_normal([1, 1, nOutX[index], nOutX[index+1]], stddev=stdDev0),name='shortcutWeights')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	104 shortcut = tf.nn.conv2d(data, ldXWeightsShortcut, strides=[1, 1, 1, 1], padding='SAME')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	105
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	106 bn = tf.layers.batch_normalization(tf.nn.relu(c00+shortcut), training=UNet2D.tfTraining)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	107
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	108 return tf.nn.max_pool(bn, ksize=[1, dsfX[index], dsfX[index], 1], strides=[1, dsfX[index], dsfX[index], 1], padding='SAME',name='maxpool')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	109
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	110 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	111 # bottom layer
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	112 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	113
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	114 with tf.name_scope('lb'):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	115 lbWeights1 = tf.Variable(tf.truncated_normal([UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[UNet2D.hp['nLayers']], nOutX[UNet2D.hp['nLayers']+1]], stddev=stdDev0),name='kernel1')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	116 def lb(hidden):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	117 return tf.nn.relu(tf.nn.conv2d(hidden, lbWeights1, strides=[1, 1, 1, 1], padding='SAME'),name='conv')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	118
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	119 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	120 # downsampling
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	121 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	122
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	123 with tf.name_scope('downsampling'):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	124 dsX = []
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	125 dsX.append(UNet2D.tfData)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	126
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	127 for i in range(UNet2D.hp['nLayers']):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	128 dsX.append(down_samp_layer(dsX[i],i))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	129
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	130 b = lb(dsX[UNet2D.hp['nLayers']])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	131
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	132 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	133 # upsampling layer
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	134 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	135
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	136 def up_samp_layer(data,index):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	137 with tf.name_scope('lu%d' % index):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	138 luXWeights1 = tf.Variable(tf.truncated_normal([UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[index+1], nOutX[index+2]], stddev=stdDev0),name='kernel1')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	139 luXWeights2 = tf.Variable(tf.truncated_normal([UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[index]+nOutX[index+1], nOutX[index+1]], stddev=stdDev0),name='kernel2')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	140 luXWeightsExtra = []
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	141 for i in range(nExtraConvs):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	142 luXWeightsExtra.append(tf.Variable(tf.truncated_normal([UNet2D.hp['ks'], UNet2D.hp['ks'], nOutX[index+1], nOutX[index+1]], stddev=stdDev0),name='kernel2Extra%d' % i))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	143
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	144 outSize = UNet2D.hp['imSize']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	145 for i in range(index):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	146 outSize /= dsfX[i]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	147 outSize = int(outSize)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	148
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	149 outputShape = [UNet2D.hp['batchSize'],outSize,outSize,nOutX[index+1]]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	150 us = tf.nn.relu(tf.nn.conv2d_transpose(data, luXWeights1, outputShape, strides=[1, dsfX[index], dsfX[index], 1], padding='SAME'),name='conv1')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	151 cc = concat3([dsX[index],us])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	152 cv = tf.nn.relu(tf.nn.conv2d(cc, luXWeights2, strides=[1, 1, 1, 1], padding='SAME'),name='conv2')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	153 for i in range(nExtraConvs):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	154 cv = tf.nn.relu(tf.nn.conv2d(cv, luXWeightsExtra[i], strides=[1, 1, 1, 1], padding='SAME'),name='conv2Extra%d' % i)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	155 return cv
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	156
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	157 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	158 # final (top) layer
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	159 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	160
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	161 with tf.name_scope('lt'):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	162 ltWeights1 = tf.Variable(tf.truncated_normal([1, 1, nOutX[1], nClasses], stddev=stdDev0),name='kernel')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	163 def lt(hidden):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	164 return tf.nn.conv2d(hidden, ltWeights1, strides=[1, 1, 1, 1], padding='SAME',name='conv')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	165
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	166
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	167 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	168 # upsampling
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	169 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	170
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	171 with tf.name_scope('upsampling'):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	172 usX = []
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	173 usX.append(b)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	174
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	175 for i in range(UNet2D.hp['nLayers']):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	176 usX.append(up_samp_layer(usX[i],UNet2D.hp['nLayers']-1-i))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	177
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	178 t = lt(usX[UNet2D.hp['nLayers']])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	179
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	180
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	181 sm = tf.nn.softmax(t,-1)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	182 UNet2D.nn = sm
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	183
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	184
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	185 def train(imPath,logPath,modelPath,pmPath,nTrain,nValid,nTest,restoreVariables,nSteps,gpuIndex,testPMIndex):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	186 os.environ['CUDA_VISIBLE_DEVICES']= '%d' % gpuIndex
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	187
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	188 outLogPath = logPath
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	189 trainWriterPath = pathjoin(logPath,'Train')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	190 validWriterPath = pathjoin(logPath,'Valid')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	191 outModelPath = pathjoin(modelPath,'model.ckpt')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	192 outPMPath = pmPath
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	193
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	194 batchSize = UNet2D.hp['batchSize']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	195 imSize = UNet2D.hp['imSize']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	196 nChannels = UNet2D.hp['nChannels']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	197 nClasses = UNet2D.hp['nClasses']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	198
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	199 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	200 # data
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	201 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	202
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	203 Train = np.zeros((nTrain,imSize,imSize,nChannels))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	204 Valid = np.zeros((nValid,imSize,imSize,nChannels))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	205 Test = np.zeros((nTest,imSize,imSize,nChannels))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	206 LTrain = np.zeros((nTrain,imSize,imSize,nClasses))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	207 LValid = np.zeros((nValid,imSize,imSize,nClasses))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	208 LTest = np.zeros((nTest,imSize,imSize,nClasses))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	209
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	210 print('loading data, computing mean / st dev')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	211 if not os.path.exists(modelPath):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	212 os.makedirs(modelPath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	213 if restoreVariables:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	214 datasetMean = loadData(pathjoin(modelPath,'datasetMean.data'))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	215 datasetStDev = loadData(pathjoin(modelPath,'datasetStDev.data'))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	216 else:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	217 datasetMean = 0
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	218 datasetStDev = 0
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	219 for iSample in range(nTrain+nValid+nTest):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	220 I = im2double(tifread('%s/I%05d_Img.tif' % (imPath,iSample)))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	221 datasetMean += np.mean(I)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	222 datasetStDev += np.std(I)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	223 datasetMean /= (nTrain+nValid+nTest)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	224 datasetStDev /= (nTrain+nValid+nTest)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	225 saveData(datasetMean, pathjoin(modelPath,'datasetMean.data'))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	226 saveData(datasetStDev, pathjoin(modelPath,'datasetStDev.data'))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	227
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	228 perm = np.arange(nTrain+nValid+nTest)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	229 np.random.shuffle(perm)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	230
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	231 for iSample in range(0, nTrain):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	232 path = '%s/I%05d_Img.tif' % (imPath,perm[iSample])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	233 im = im2double(tifread(path))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	234 Train[iSample,:,:,0] = (im-datasetMean)/datasetStDev
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	235 path = '%s/I%05d_Ant.tif' % (imPath,perm[iSample])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	236 im = tifread(path)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	237 for i in range(nClasses):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	238 LTrain[iSample,:,:,i] = (im == i+1)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	239
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	240 for iSample in range(0, nValid):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	241 path = '%s/I%05d_Img.tif' % (imPath,perm[nTrain+iSample])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	242 im = im2double(tifread(path))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	243 Valid[iSample,:,:,0] = (im-datasetMean)/datasetStDev
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	244 path = '%s/I%05d_Ant.tif' % (imPath,perm[nTrain+iSample])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	245 im = tifread(path)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	246 for i in range(nClasses):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	247 LValid[iSample,:,:,i] = (im == i+1)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	248
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	249 for iSample in range(0, nTest):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	250 path = '%s/I%05d_Img.tif' % (imPath,perm[nTrain+nValid+iSample])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	251 im = im2double(tifread(path))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	252 Test[iSample,:,:,0] = (im-datasetMean)/datasetStDev
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	253 path = '%s/I%05d_Ant.tif' % (imPath,perm[nTrain+nValid+iSample])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	254 im = tifread(path)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	255 for i in range(nClasses):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	256 LTest[iSample,:,:,i] = (im == i+1)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	257
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	258 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	259 # optimization
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	260 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	261
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	262 tfLabels = tf.placeholder("float", shape=[None,imSize,imSize,nClasses],name='labels')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	263
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	264 globalStep = tf.Variable(0,trainable=False)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	265 learningRate0 = 0.01
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	266 decaySteps = 1000
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	267 decayRate = 0.95
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	268 learningRate = tf.train.exponential_decay(learningRate0,globalStep,decaySteps,decayRate,staircase=True)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	269
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	270 with tf.name_scope('optim'):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	271 loss = tf.reduce_mean(-tf.reduce_sum(tf.multiply(tfLabels,tf.log(UNet2D.nn)),3))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	272 updateOps = tf.get_collection(tf.GraphKeys.UPDATE_OPS)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	273 # optimizer = tf.train.MomentumOptimizer(1e-3,0.9)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	274 optimizer = tf.train.MomentumOptimizer(learningRate,0.9)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	275 # optimizer = tf.train.GradientDescentOptimizer(learningRate)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	276 with tf.control_dependencies(updateOps):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	277 optOp = optimizer.minimize(loss,global_step=globalStep)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	278
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	279 with tf.name_scope('eval'):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	280 error = []
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	281 for iClass in range(nClasses):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	282 labels0 = tf.reshape(tf.to_int32(tf.slice(tfLabels,[0,0,0,iClass],[-1,-1,-1,1])),[batchSize,imSize,imSize])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	283 predict0 = tf.reshape(tf.to_int32(tf.equal(tf.argmax(UNet2D.nn,3),iClass)),[batchSize,imSize,imSize])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	284 correct = tf.multiply(labels0,predict0)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	285 nCorrect0 = tf.reduce_sum(correct)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	286 nLabels0 = tf.reduce_sum(labels0)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	287 error.append(1-tf.to_float(nCorrect0)/tf.to_float(nLabels0))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	288 errors = tf.tuple(error)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	289
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	290 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	291 # inspection
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	292 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	293
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	294 with tf.name_scope('scalars'):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	295 tf.summary.scalar('avg_cross_entropy', loss)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	296 for iClass in range(nClasses):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	297 tf.summary.scalar('avg_pixel_error_%d' % iClass, error[iClass])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	298 tf.summary.scalar('learning_rate', learningRate)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	299 with tf.name_scope('images'):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	300 split0 = tf.slice(UNet2D.nn,[0,0,0,0],[-1,-1,-1,1])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	301 split1 = tf.slice(UNet2D.nn,[0,0,0,1],[-1,-1,-1,1])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	302 if nClasses > 2:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	303 split2 = tf.slice(UNet2D.nn,[0,0,0,2],[-1,-1,-1,1])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	304 tf.summary.image('pm0',split0)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	305 tf.summary.image('pm1',split1)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	306 if nClasses > 2:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	307 tf.summary.image('pm2',split2)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	308 merged = tf.summary.merge_all()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	309
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	310
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	311 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	312 # session
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	313 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	314
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	315 saver = tf.train.Saver()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	316 sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True)) # config parameter needed to save variables when using GPU
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	317
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	318 if os.path.exists(outLogPath):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	319 shutil.rmtree(outLogPath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	320 trainWriter = tf.summary.FileWriter(trainWriterPath, sess.graph)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	321 validWriter = tf.summary.FileWriter(validWriterPath, sess.graph)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	322
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	323 if restoreVariables:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	324 saver.restore(sess, outModelPath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	325 print("Model restored.")
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	326 else:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	327 sess.run(tf.global_variables_initializer())
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	328
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	329 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	330 # train
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	331 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	332
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	333 batchData = np.zeros((batchSize,imSize,imSize,nChannels))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	334 batchLabels = np.zeros((batchSize,imSize,imSize,nClasses))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	335 for i in range(nSteps):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	336 # train
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	337
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	338 perm = np.arange(nTrain)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	339 np.random.shuffle(perm)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	340
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	341 for j in range(batchSize):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	342 batchData[j,:,:,:] = Train[perm[j],:,:,:]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	343 batchLabels[j,:,:,:] = LTrain[perm[j],:,:,:]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	344
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	345 summary,_ = sess.run([merged,optOp],feed_dict={UNet2D.tfData: batchData, tfLabels: batchLabels, UNet2D.tfTraining: 1})
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	346 trainWriter.add_summary(summary, i)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	347
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	348 # validation
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	349
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	350 perm = np.arange(nValid)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	351 np.random.shuffle(perm)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	352
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	353 for j in range(batchSize):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	354 batchData[j,:,:,:] = Valid[perm[j],:,:,:]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	355 batchLabels[j,:,:,:] = LValid[perm[j],:,:,:]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	356
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	357 summary, es = sess.run([merged, errors],feed_dict={UNet2D.tfData: batchData, tfLabels: batchLabels, UNet2D.tfTraining: 0})
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	358 validWriter.add_summary(summary, i)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	359
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	360 e = np.mean(es)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	361 print('step %05d, e: %f' % (i,e))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	362
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	363 if i == 0:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	364 if restoreVariables:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	365 lowestError = e
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	366 else:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	367 lowestError = np.inf
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	368
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	369 if np.mod(i,100) == 0 and e < lowestError:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	370 lowestError = e
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	371 print("Model saved in file: %s" % saver.save(sess, outModelPath))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	372
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	373
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	374 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	375 # test
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	376 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	377
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	378 if not os.path.exists(outPMPath):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	379 os.makedirs(outPMPath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	380
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	381 for i in range(nTest):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	382 j = np.mod(i,batchSize)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	383
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	384 batchData[j,:,:,:] = Test[i,:,:,:]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	385 batchLabels[j,:,:,:] = LTest[i,:,:,:]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	386
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	387 if j == batchSize-1 or i == nTest-1:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	388
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	389 output = sess.run(UNet2D.nn,feed_dict={UNet2D.tfData: batchData, tfLabels: batchLabels, UNet2D.tfTraining: 0})
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	390
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	391 for k in range(j+1):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	392 pm = output[k,:,:,testPMIndex]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	393 gt = batchLabels[k,:,:,testPMIndex]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	394 im = np.sqrt(normalize(batchData[k,:,:,0]))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	395 imwrite(np.uint8(255*np.concatenate((im,np.concatenate((pm,gt),axis=1)),axis=1)),'%s/I%05d.png' % (outPMPath,i-j+k+1))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	396
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	397
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	398 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	399 # save hyper-parameters, clean-up
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	400 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	401
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	402 saveData(UNet2D.hp,pathjoin(modelPath,'hp.data'))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	403
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	404 trainWriter.close()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	405 validWriter.close()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	406 sess.close()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	407
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	408 def deploy(imPath,nImages,modelPath,pmPath,gpuIndex,pmIndex):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	409 os.environ['CUDA_VISIBLE_DEVICES']= '%d' % gpuIndex
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	410 variablesPath = pathjoin(modelPath,'model.ckpt')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	411 outPMPath = pmPath
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	412
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	413 hp = loadData(pathjoin(modelPath,'hp.data'))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	414 UNet2D.setupWithHP(hp)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	415
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	416 batchSize = UNet2D.hp['batchSize']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	417 imSize = UNet2D.hp['imSize']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	418 nChannels = UNet2D.hp['nChannels']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	419 nClasses = UNet2D.hp['nClasses']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	420
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	421 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	422 # data
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	423 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	424
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	425 Data = np.zeros((nImages,imSize,imSize,nChannels))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	426
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	427 datasetMean = loadData(pathjoin(modelPath,'datasetMean.data'))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	428 datasetStDev = loadData(pathjoin(modelPath,'datasetStDev.data'))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	429
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	430 for iSample in range(0, nImages):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	431 path = '%s/I%05d_Img.tif' % (imPath,iSample)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	432 im = im2double(tifread(path))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	433 Data[iSample,:,:,0] = (im-datasetMean)/datasetStDev
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	434
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	435 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	436 # session
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	437 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	438
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	439 saver = tf.train.Saver()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	440 sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True)) # config parameter needed to save variables when using GPU
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	441
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	442 saver.restore(sess, variablesPath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	443 print("Model restored.")
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	444
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	445 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	446 # deploy
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	447 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	448
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	449 batchData = np.zeros((batchSize,imSize,imSize,nChannels))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	450
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	451 if not os.path.exists(outPMPath):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	452 os.makedirs(outPMPath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	453
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	454 for i in range(nImages):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	455 print(i,nImages)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	456
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	457 j = np.mod(i,batchSize)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	458
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	459 batchData[j,:,:,:] = Data[i,:,:,:]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	460
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	461 if j == batchSize-1 or i == nImages-1:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	462
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	463 output = sess.run(UNet2D.nn,feed_dict={UNet2D.tfData: batchData, UNet2D.tfTraining: 0})
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	464
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	465 for k in range(j+1):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	466 pm = output[k,:,:,pmIndex]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	467 im = np.sqrt(normalize(batchData[k,:,:,0]))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	468 # imwrite(np.uint8(255*np.concatenate((im,pm),axis=1)),'%s/I%05d.png' % (outPMPath,i-j+k+1))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	469 imwrite(np.uint8(255*im),'%s/I%05d_Im.png' % (outPMPath,i-j+k+1))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	470 imwrite(np.uint8(255*pm),'%s/I%05d_PM.png' % (outPMPath,i-j+k+1))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	471
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	472
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	473 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	474 # clean-up
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	475 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	476
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	477 sess.close()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	478
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	479 def singleImageInferenceSetup(modelPath,gpuIndex):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	480 os.environ['CUDA_VISIBLE_DEVICES']= '%d' % gpuIndex
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	481 variablesPath = pathjoin(modelPath,'model.ckpt')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	482 hp = loadData(pathjoin(modelPath,'hp.data'))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	483 UNet2D.setupWithHP(hp)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	484
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	485 UNet2D.DatasetMean =loadData(pathjoin(modelPath,'datasetMean.data'))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	486 UNet2D.DatasetStDev = loadData(pathjoin(modelPath,'datasetStDev.data'))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	487 print(UNet2D.DatasetMean)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	488 print(UNet2D.DatasetStDev)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	489
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	490 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	491 # session
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	492 # --------------------------------------------------
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	493
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	494 saver = tf.train.Saver()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	495 UNet2D.Session = tf.Session(config=tf.ConfigProto(allow_soft_placement=True)) # config parameter needed to save variables when using GPU
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	496 #UNet2D.Session = tf.Session(config=tf.ConfigProto(device_count={'GPU': 0}))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	497 saver.restore(UNet2D.Session, variablesPath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	498 print("Model restored.")
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	499
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	500 def singleImageInferenceCleanup():
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	501 UNet2D.Session.close()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	502
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	503 def singleImageInference(image,mode,pmIndex):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	504 print('Inference...')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	505
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	506 batchSize = UNet2D.hp['batchSize']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	507 imSize = UNet2D.hp['imSize']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	508 nChannels = UNet2D.hp['nChannels']
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	509
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	510 PI2D.setup(image,imSize,int(imSize/8),mode)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	511 PI2D.createOutput(nChannels)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	512
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	513 batchData = np.zeros((batchSize,imSize,imSize,nChannels))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	514 for i in range(PI2D.NumPatches):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	515 j = np.mod(i,batchSize)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	516 batchData[j,:,:,0] = (PI2D.getPatch(i)-UNet2D.DatasetMean)/UNet2D.DatasetStDev
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	517 if j == batchSize-1 or i == PI2D.NumPatches-1:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	518 output = UNet2D.Session.run(UNet2D.nn,feed_dict={UNet2D.tfData: batchData, UNet2D.tfTraining: 0})
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	519 for k in range(j+1):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	520 pm = output[k,:,:,pmIndex]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	521 PI2D.patchOutput(i-j+k,pm)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	522 # PI2D.patchOutput(i-j+k,normalize(imgradmag(PI2D.getPatch(i-j+k),1)))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	523
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	524 return PI2D.getValidOutput()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	525
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	526
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	527 def identifyNumChan(path):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	528 tiff = tifffile.TiffFile(path)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	529 shape = tiff.pages[0].shape
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	530 numChan=None
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	531 for i, page in enumerate(tiff.pages):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	532 if page.shape != shape:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	533 numChan = i
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	534 return numChan
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	535 break
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	536 # else:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	537 # raise Exception("Did not find any pyramid subresolutions")
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	538
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	539 if not numChan:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	540 numChan = len(tiff.pages)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	541 return numChan
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	542
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	543 def getProbMaps(I,dsFactor,modelPath):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	544 hsize = int((float(I.shape[0]) * float(0.5)))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	545 vsize = int((float(I.shape[1]) * float(0.5)))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	546 imagesub = cv2.resize(I,(vsize,hsize),cv2.INTER_NEAREST)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	547
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	548 UNet2D.singleImageInferenceSetup(modelPath, 1)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	549
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	550 for iSize in range(dsFactor):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	551 hsize = int((float(I.shape[0]) * float(0.5)))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	552 vsize = int((float(I.shape[1]) * float(0.5)))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	553 I = cv2.resize(I,(vsize,hsize),cv2.INTER_NEAREST)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	554 I = im2double(I)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	555 I = im2double(sk.rescale_intensity(I, in_range=(np.min(I), np.max(I)), out_range=(0, 0.983)))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	556 probMaps = UNet2D.singleImageInference(I,'accumulate',1)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	557 UNet2D.singleImageInferenceCleanup()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	558 return probMaps
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	559
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	560 def coreSegmenterOutput(I,probMap,initialmask,preBlur,findCenter):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	561 hsize = int((float(I.shape[0]) * float(0.1)))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	562 vsize = int((float(I.shape[1]) * float(0.1)))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	563 nucGF = cv2.resize(I,(vsize,hsize),cv2.INTER_CUBIC)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	564 # Irs = cv2.resize(I,(vsize,hsize),cv2.INTER_CUBIC)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	565 # I=I.astype(np.float)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	566 # r,c = I.shape
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	567 # I+=np.random.rand(r,c)*1e-6
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	568 # c1 = uniform_filter(I, 3, mode='reflect')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	569 # c2 = uniform_filter(I*I, 3, mode='reflect')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	570 # nucGF = np.sqrt(c2 - c1c1)np.sqrt(9./8)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	571 # nucGF[np.isnan(nucGF)]=0
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	572 #active contours
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	573 hsize = int(float(nucGF.shape[0]))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	574 vsize = int(float(nucGF.shape[1]))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	575 initialmask = cv2.resize(initialmask,(vsize,hsize),cv2.INTER_NEAREST)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	576 initialmask = dilation(initialmask,disk(15)) >0
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	577
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	578 # init=np.argwhere(eroded>0)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	579 nucGF = gaussian(nucGF,0.7)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	580 nucGF=nucGF/np.amax(nucGF)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	581
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	582
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	583 # initialmask = nucGF>0
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	584 nuclearMask = morphological_chan_vese(nucGF, 100, init_level_set=initialmask, smoothing=10,lambda1=1.001, lambda2=1)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	585
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	586 # nuclearMask = chan_vese(nucGF, mu=1.5, lambda1=6, lambda2=1, tol=0.0005, max_iter=2000, dt=15, init_level_set=initialmask, extended_output=True)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	587 # nuclearMask = nuclearMask[0]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	588
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	589
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	590 TMAmask = nuclearMask
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	591 # nMaskDist =distance_transform_edt(nuclearMask)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	592 # fgm = peak_local_max(h_maxima(nMaskDist, 2*preBlur),indices =False)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	593 # markers= np.logical_or(erosion(1-nuclearMask,disk(3)),fgm)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	594 # TMAmask=watershed(-nMaskDist,label(markers),watershed_line=True)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	595 # TMAmask = nuclearMask*(TMAmask>0)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	596 TMAmask = remove_small_objects(TMAmask>0,round(TMAmask.shape[0])round(TMAmask.shape[1])0.005)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	597 TMAlabel = label(TMAmask)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	598 # find object closest to center
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	599 if findCenter==True:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	600
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	601 stats= regionprops(TMAlabel)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	602 counter=1
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	603 minDistance =-1
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	604 index =[]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	605 for props in stats:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	606 centroid = props.centroid
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	607 distanceFromCenter = np.sqrt((centroid[0]-nucGF.shape[0]/2)2+(centroid[1]-nucGF.shape[1]/2)2)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	608 # if distanceFromCenter<0.6/2np.sqrt(TMAlabel.shape[0]TMAlabel.shape[1]):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	609 if distanceFromCenter<minDistance or minDistance==-1 :
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	610 minDistance =distanceFromCenter
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	611 index = counter
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	612 counter=counter+1
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	613 # dist = 0.6/2np.sqrt(TMAlabel.shape[0]TMAlabel.shape[1])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	614 TMAmask = morphology.binary_closing(TMAlabel==index,disk(3))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	615
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	616 return TMAmask
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	617
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	618 def overlayOutline(outline,img):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	619 img2 = img.copy()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	620 stacked_img = np.stack((img2,)*3, axis=-1)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	621 stacked_img[outline > 0] = [1, 0, 0]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	622 imshowpair(img2,stacked_img)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	623
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	624 def imshowpair(A,B):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	625 plt.imshow(A,cmap='Purples')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	626 plt.imshow(B,cmap='Greens',alpha=0.5)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	627 plt.show()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	628
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	629
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	630 if __name__ == '__main__':
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	631 parser=argparse.ArgumentParser()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	632 parser.add_argument("--imagePath")
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	633 parser.add_argument("--outputPath")
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	634 parser.add_argument("--maskPath")
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	635 parser.add_argument("--downsampleFactor",type = int, default = 5)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	636 parser.add_argument("--channel",type = int, default = 0)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	637 parser.add_argument("--buffer",type = float, default = 2)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	638 parser.add_argument("--outputChan", type=int, nargs = '+', default=[-1])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	639 parser.add_argument("--sensitivity",type = float, default=0.3)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	640 parser.add_argument("--useGrid",action='store_true')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	641 parser.add_argument("--cluster",action='store_true')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	642 args = parser.parse_args()
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	643
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	644 outputPath = args.outputPath
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	645 imagePath = args.imagePath
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	646 sensitivity = args.sensitivity
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	647 #scriptPath = os.path.dirname(os.path.realpath(__file__))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	648 #modelPath = os.path.join(scriptPath, 'TFModel - 3class 16 kernels 5ks 2 layers')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	649 #modelPath = 'D:\\LSP\\Coreograph\\model-4layersMaskAug20'
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	650 scriptPath = os.path.dirname(os.path.realpath(__file__))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	651 modelPath = os.path.join(scriptPath, 'model')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	652 # outputPath = 'D:\\LSP\\cycif\\testsets\\exemplar-002\\dearrayPython' ############
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	653 maskOutputPath = os.path.join(outputPath, 'masks')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	654 # imagePath = 'D:\\LSP\\cycif\\testsets\\exemplar-002\\registration\\exemplar-002.ome.tif'###########
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	655 # imagePath = 'Y:\\sorger\\data\\RareCyte\\Connor\\TMAs\\CAJ_TMA11_13\\original_data\\TMA11\\registration\\TMA11.ome.tif'
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	656 # imagePath = 'Y:\\sorger\\data\\RareCyte\\Connor\\TMAs\\Z124_TMA20_22\\TMA22\\registration\\TMA22.ome.tif'
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	657 # classProbsPath = 'D:\\unetcoreograph.tif'
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	658 # imagePath = 'Y:\\sorger\\data\\RareCyte\\Connor\\Z155_PTCL\\TMA_552\\registration\\TMA_552.ome.tif'
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	659 # classProbsPath = 'Y:\\sorger\\data\\RareCyte\\Connor\\Z155_PTCL\\TMA_552\\probMapCore\\TMA_552_CorePM_1.tif'
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	660 # imagePath = 'Y:\\sorger\\data\\RareCyte\\Zoltan\\Z112_TMA17_19\\190403_ashlar\\TMA17_1092.ome.tif'
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	661 # classProbsPath = 'Z:\\IDAC\\Clarence\\LSP\\CyCIF\\TMA\\probMapCore\\1new_CorePM_1.tif'
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	662 # imagePath = 'Y:\\sorger\\data\\RareCyte\\ANNIINA\\Julia\\2018\\TMA6\\julia_tma6.ome.tif'
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	663 # classProbsPath = 'Z:\\IDAC\\Clarence\\LSP\\CyCIF\\TMA\\probMapCore\\3new_CorePM_1.tif'
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	664
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	665
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	666 # if not os.path.exists(outputPath):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	667 # os.makedirs(outputPath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	668 # else:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	669 # shutil.rmtree(outputPath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	670 if not os.path.exists(maskOutputPath):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	671 os.makedirs(maskOutputPath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	672
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	673
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	674 channel = args.channel
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	675 dsFactor = 1/(2**args.downsampleFactor)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	676 # I = tifffile.imread(imagePath, key=channel)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	677 I = skio.imread(imagePath, img_num=channel)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	678
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	679 imagesub = resize(I,(int((float(I.shape[0]) * dsFactor)),int((float(I.shape[1]) * dsFactor))))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	680 numChan = identifyNumChan(imagePath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	681
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	682 outputChan = args.outputChan
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	683 if len(outputChan)==1:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	684 if outputChan[0]==-1:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	685 outputChan = [0, numChan-1]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	686 else:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	687 outputChan.append(outputChan[0])
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	688
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	689 classProbs = getProbMaps(I,args.downsampleFactor,modelPath)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	690 # classProbs = tifffile.imread(classProbsPath,key=0)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	691 preMask = gaussian(np.uint8(classProbs*255),1)>0.8
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	692
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	693 P = regionprops(label(preMask),cache=False)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	694 area = [ele.area for ele in P]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	695 print(str(len(P)) + ' cores detected!')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	696 if len(P) <3:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	697 medArea = np.median(area)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	698 maxArea = np.percentile(area,99)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	699 else:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	700 count=0
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	701 labelpreMask = np.zeros(preMask.shape,dtype=np.uint32)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	702 for props in P:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	703 count += 1
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	704 yi = props.coords[:, 0]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	705 xi = props.coords[:, 1]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	706 labelpreMask[yi, xi] = count
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	707 P=regionprops(labelpreMask)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	708 area = [ele.area for ele in P]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	709 medArea = np.median(area)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	710 maxArea = np.percentile(area,99)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	711 preMask = remove_small_objects(preMask,0.2*medArea)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	712 coreRad = round(np.sqrt(medArea/np.pi))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	713 estCoreDiam = round(np.sqrt(maxArea/np.pi)1.2args.buffer)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	714
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	715 #preprocessing
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	716 fgFiltered = blob_log(preMask,coreRad*0.6,threshold=sensitivity)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	717 Imax = np.zeros(preMask.shape,dtype=np.uint8)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	718 for iSpot in range(fgFiltered.shape[0]):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	719 yi = np.uint32(round(fgFiltered[iSpot, 0]))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	720 xi = np.uint32(round(fgFiltered[iSpot, 1]))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	721 Imax[yi, xi] = 1
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	722 Imax = Imax*preMask
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	723 Idist = distance_transform_edt(1-Imax)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	724 markers = label(Imax)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	725 coreLabel = watershed(Idist,markers,watershed_line=True,mask = preMask)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	726 P = regionprops(coreLabel)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	727 centroids = np.array([ele.centroid for ele in P])/dsFactor
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	728 numCores = len(centroids)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	729 estCoreDiamX = np.ones(numCores)*estCoreDiam/dsFactor
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	730 estCoreDiamY = np.ones(numCores)*estCoreDiam/dsFactor
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	731
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	732 if numCores ==0 & args.cluster:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	733 print('No cores detected. Try adjusting the downsample factor')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	734 sys.exit(255)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	735
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	736 singleMaskTMA = np.zeros(imagesub.shape)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	737 maskTMA = np.zeros(imagesub.shape)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	738 bbox = [None] * numCores
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	739
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	740
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	741 x=np.zeros(numCores)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	742 xLim=np.zeros(numCores)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	743 y=np.zeros(numCores)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	744 yLim=np.zeros(numCores)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	745
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	746 # segmenting each core
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	747 #######################
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	748 for iCore in range(numCores):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	749 x[iCore] = centroids[iCore,1] - estCoreDiamX[iCore]/2
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	750 xLim[iCore] = x[iCore]+estCoreDiamX[iCore]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	751 if xLim[iCore] > I.shape[1]:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	752 xLim[iCore] = I.shape[1]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	753 if x[iCore]<1:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	754 x[iCore]=1
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	755
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	756 y[iCore] = centroids[iCore,0] - estCoreDiamY[iCore]/2
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	757 yLim[iCore] = y[iCore] + estCoreDiamY[iCore]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	758 if yLim[iCore] > I.shape[0]:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	759 yLim[iCore] = I.shape[0]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	760 if y[iCore]<1:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	761 y[iCore]=1
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	762
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	763 bbox[iCore] = [round(x[iCore]), round(y[iCore]), round(xLim[iCore]), round(yLim[iCore])]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	764
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	765 for iChan in range(outputChan[0],outputChan[1]+1):
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	766 with pytiff.Tiff(imagePath, "r", encoding='utf-8') as handle:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	767 handle.set_page(iChan)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	768 coreStack= handle[np.uint32(bbox[iCore][1]):np.uint32(bbox[iCore][3]-1), np.uint32(bbox[iCore][0]):np.uint32(bbox[iCore][2]-1)]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	769 skio.imsave(outputPath + os.path.sep + str(iCore+1) + '.tif',coreStack,append=True)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	770
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	771 with pytiff.Tiff(imagePath, "r", encoding='utf-8') as handle:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	772 handle.set_page(args.channel)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	773 coreSlice= handle[np.uint32(bbox[iCore][1]):np.uint32(bbox[iCore][3]-1), np.uint32(bbox[iCore][0]):np.uint32(bbox[iCore][2]-1)]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	774
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	775 core = (coreLabel ==(iCore+1))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	776 initialmask = core[np.uint32(y[iCore]dsFactor):np.uint32(yLim[iCore]dsFactor),np.uint32(x[iCore]dsFactor):np.uint32(xLim[iCore]dsFactor)]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	777 initialmask = resize(initialmask,size(coreSlice),cv2.INTER_NEAREST)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	778
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	779 singleProbMap = classProbs[np.uint32(y[iCore]dsFactor):np.uint32(yLim[iCore]dsFactor),np.uint32(x[iCore]dsFactor):np.uint32(xLim[iCore]dsFactor)]
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	780 singleProbMap = resize(np.uint8(255*singleProbMap),size(coreSlice),cv2.INTER_NEAREST)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	781 TMAmask = coreSegmenterOutput(coreSlice,singleProbMap,initialmask,coreRad/20,False)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	782 if np.sum(TMAmask)==0:
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	783 TMAmask = np.ones(TMAmask.shape)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	784 vsize = int(float(coreSlice.shape[0]))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	785 hsize = int(float(coreSlice.shape[1]))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	786 masksub = resize(resize(TMAmask,(vsize,hsize),cv2.INTER_NEAREST),(int((float(coreSlice.shape[0])dsFactor)),int((float(coreSlice.shape[1])dsFactor))),cv2.INTER_NEAREST)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	787 singleMaskTMA[int(y[iCore]dsFactor):int(y[iCore]dsFactor)+masksub.shape[0],int(x[iCore]dsFactor):int(x[iCore]dsFactor)+masksub.shape[1]]=masksub
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	788 maskTMA = maskTMA + resize(singleMaskTMA,maskTMA.shape,cv2.INTER_NEAREST)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	789 cv2.putText(imagesub, str(iCore+1), (int(P[iCore].centroid[1]),int(P[iCore].centroid[0])), 0, 0.5, (np.amax(imagesub), np.amax(imagesub), np.amax(imagesub)), 1, cv2.LINE_AA)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	790
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	791 skio.imsave(maskOutputPath + os.path.sep + str(iCore+1) + '_mask.tif',np.uint8(TMAmask))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	792 print('Segmented core ' + str(iCore+1))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	793
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	794 boundaries = find_boundaries(maskTMA)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	795 imagesub = imagesub/np.percentile(imagesub,99.9)
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	796 imagesub[boundaries==1] = 1
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	797 skio.imsave(outputPath + os.path.sep + 'TMA_MAP.tif' ,np.uint8(imagesub*255))
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	798 print('Segmented all cores!')
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	799
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	800
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	801 #restore GPU to 0
99308601eaa6 "planemo upload for repository https://github.com/ohsu-comp-bio/UNetCoreograph commit fb90660a1805b3f68fcff80d525b5459c3f7dfd6-dirty" perssond parents: diff changeset	802 #image load using tifffile

Mercurial > repos > perssond > coreograph

annotate UNetCoreograph.py @ 0:99308601eaa6 draft