from CommonUtil.FileReaders import *
from CommonUtil.FileDataManager import *
from CommonUtil.PlotsManager import *
from CommonUtil.WorkDirsManager import *
from Networks.Metrics import *
from Networks.Networks import *
import numpy as np
BATCH_SIZE = 1
FORMATOUTIMAGES = 'nifti'
IMODEL = 'Unet3D'
#MAIN
workDirsManager = WorkDirsManager(BASEDIR)
RawMasksDataPath= workDirsManager.getNameNewPath(workDirsManager.getNameTestingDataPath(), 'RawMasks')
TestingDataPath = workDirsManager.getNameNewPath(workDirsManager.getNameTestingDataPath(), 'ProcVolsData')
PredictMasksPath= workDirsManager.getNameNewPath(BASEDIR, 'Predictions')
ModelsPath = workDirsManager.getNameModelsPath()
print('-' * 30)
print('Loading saved weights...')
print('-' * 30)
model = DICTAVAILNETWORKS3D[IMODEL].getModel(IMAGES_DEPTHZ, IMAGES_HEIGHT, IMAGES_WIDTH)
model.summary()
weightsPath = ModelsPath + '/bestModel.hdf5'
model.load_weights(weightsPath)
# Last update: 09/02/2018
########################################################################################
from CommonUtil.Constants import *
from CommonUtil.FileReaders import *
from CommonUtil.FileDataManager import *
from CommonUtil.PlotsManager import *
from CommonUtil.WorkDirsManager import *
from Networks.Metrics import *
from Networks.Networks import *
from glob import glob
import numpy as np
import os
#MAIN
workDirsManager = WorkDirsManager(BASEDIR)
InputDICOMfilesPath = workDirsManager.getNameNewPath(
workDirsManager.getNameTestingDataPath(), 'RawMasks')
OutputDICOMfilesPath = workDirsManager.getNameNewPath(
workDirsManager.getNameTestingDataPath(), 'RawMasks')
ModelsPath = workDirsManager.getNameModelsPath()
# LOADING DATA
# ----------------------------------------------
print('-' * 30)
print('Loading data...')
print('-' * 30)
listInputDICOMFiles = sorted(glob(InputDICOMfilesPath + '/av*.dcm'))
for inputDICOMfile in listInputDICOMFiles:
# Medical Informatics
#
# created on 09/02/2018
# Last update: 09/02/2018
########################################################################################
from CommonUtil.Constants import *
from CommonUtil.WorkDirsManager import *
from CommonUtil.PlotsManager import *
from CommonUtil.ErrorMessages import *
import sys
TYPEDATA = 'training'
# MAIN
workDirsManager = WorkDirsManager(BASEDIR)
DataPath = workDirsManager.getNameNewPath(
workDirsManager.getNameTrainingDataPath(), 'ProcSlicesData')
# Get the file list:
listImagesFiles = sorted(glob(DataPath + '/slicesImages*.npy'))
listMasksFiles = sorted(glob(DataPath + '/slicesMasks*.npy'))
for imageFile, maskFile in zip(listImagesFiles, listMasksFiles):
images_array = np.load(imageFile).astype(FORMATIMAGEDATA)
masks_array = np.load(maskFile).astype(FORMATMASKDATA)
print('Number training images: %s' % (images_array.shape[0]))
PlotsManager.plot_image_mask_2D(images_array, masks_array)
from keras.preprocessing import image as Kpreprocessing
import time
NBEPOCHS = 500
BATCH_SIZE = 1
LEARN_RATE = 1.0e-05
IMODEL = 'Unet3D'
IOPTIMIZER = 'Adam'
USE_DATAAUGMENTATION = False
USE_RESTARTMODEL = False
#MAIN
workDirsManager = WorkDirsManager(BASEDIR)
TrainingDataPath = workDirsManager.getNameNewPath(
workDirsManager.getNameTrainingDataPath(), 'ProcVolsData')
ValidationDataPath = workDirsManager.getNameNewPath(
workDirsManager.getNameValidationDataPath(), 'ProcVolsData')
TestingDataPath = workDirsManager.getNameNewPath(
workDirsManager.getNameTestingDataPath(), 'ProcVolsData')
ModelsPath = workDirsManager.getNameModelsPath()
# LOADING DATA
# ----------------------------------------------
print('-' * 30)
print('Loading data...')
print('-' * 30)
listTrainImagesFiles = sorted(glob(TrainingDataPath + '/volsImages*.npy'))
# Last update: 09/02/2018
########################################################################################
from CommonUtil.Constants import *
from CommonUtil.FileDataManager import *
from CommonUtil.PlotsManager import *
from CommonUtil.WorkDirsManager import *
from Networks.Metrics import *
from Networks.Networks import *
BATCH_SIZE = 12
IMODEL = 'Unet2D'
#MAIN
workDirsManager = WorkDirsManager(BASEDIR)
TestingDataPath = workDirsManager.getNameTestingDataPath()
ModelsPath = workDirsManager.getNameModelsPath()
# LOADING DATA
# ----------------------------------------------
print('-' * 30)
print('Loading data...')
print('-' * 30)
listTestImagesFiles = sorted(glob(TestingDataPath + 'images*.npy'))
listTestMasksFiles = sorted(glob(TestingDataPath + 'masks*.npy' ))
(xTest, yTest) = FileDataManager.loadDataListFiles2D(listTestImagesFiles, listTestMasksFiles)
# Medical Informatics
#
# created on 09/02/2018
# Last update: 09/02/2018
########################################################################################
from CommonUtil.Constants import *
from CommonUtil.WorkDirsManager import *
from CommonUtil.PlotsManager import *
from CommonUtil.ErrorMessages import *
import sys
TYPEDATA = 'testing'
# MAIN
workDirsManager = WorkDirsManager(BASEDIR)
DataPath = workDirsManager.getNameNewPath(
workDirsManager.getNameDataPath(TYPEDATA), 'ProcVolsData')
OutFilesPath = workDirsManager.getNameNewPath(
workDirsManager.getNameDataPath(TYPEDATA), 'VisualCases')
# Get the file list:
listImagesFiles = sorted(glob(DataPath + '/volsImages*.npy'))
listMasksFiles = sorted(glob(DataPath + '/volsMasks*.npy'))
for imageFile, maskFile in zip(listImagesFiles, listMasksFiles):
images_array = np.load(imageFile).astype(FORMATIMAGEDATA)
masks_array = np.load(maskFile).astype(FORMATMASKDATA)
print('Number training images: %s' % (images_array.shape[0]))