def deepMedicTestMain(testConfigFilepath, absPathToSavedModelFromCmdLine):
print("Given Test-Configuration File: ", testConfigFilepath)
#Parse the config file in this naive fashion...
testConfig = TestConfig()
#configStruct = testConfig.configStruct
exec(open(testConfigFilepath).read(), testConfig.configStruct)
configGet = testConfig.get #Main interface
#Do checks.
#checkIfMainTestConfigIsCorrect(testConfig, testConfigFilepath, absPathToSavedModelFromCmdLine) #Checks REQUIRED fields are complete.
#checkIfFilesThatListFilesPerCaseAreCorrect(testConfig, testConfigFilepath) #Checks listing-files (whatever given).
#checkIfOptionalParametersAreGivenCorrectly(testConfig, testConfigFilepath)
#At this point it was checked that all parameters (that could be checked) and filepaths are correct, pointing to files/dirs and all files/dirs exist.
#Create Folders and Logger
mainOutputAbsFolder = getAbsPathEvenIfRelativeIsGiven(
configGet(testConfig.FOLDER_FOR_OUTPUT), testConfigFilepath)
sessionName = configGet(testConfig.SESSION_NAME) if configGet(
testConfig.SESSION_NAME
) else TestSessionParameters.getDefaultSessionName()
[folderForLogs, folderForPredictions, folderForFeatures
] = makeFoldersNeededForTestingSession(mainOutputAbsFolder, sessionName)
loggerFileName = folderForLogs + "/" + sessionName + ".txt"
sessionLogger = myLoggerModule.MyLogger(loggerFileName)
sessionLogger.print3(
"CONFIG: The configuration file for the testing session was loaded from: "
+ str(testConfigFilepath))
#Load the CNN Model!
sessionLogger.print3(
"=========== Loading the CNN model for testing... ===============")
#If CNN-Model was specified in command line, completely override the one in the config file.
filepathToCnnModelToLoad = None
if absPathToSavedModelFromCmdLine and configGet(
testConfig.CNN_MODEL_FILEPATH):
sessionLogger.print3(
"WARN: A CNN-Model to use was specified both in the command line input and in the test-config-file! The input by the command line will be used: "
+ str(absPathToSavedModelFromCmdLine))
filepathToCnnModelToLoad = absPathToSavedModelFromCmdLine
elif absPathToSavedModelFromCmdLine:
filepathToCnnModelToLoad = absPathToSavedModelFromCmdLine
else:
filepathToCnnModelToLoad = getAbsPathEvenIfRelativeIsGiven(
configGet(testConfig.CNN_MODEL_FILEPATH), testConfigFilepath)
sessionLogger.print3(
"...Loading the network can take a few minutes if the model is big...")
cnn3dInstance = load_object_from_gzip_file(filepathToCnnModelToLoad)
sessionLogger.print3("The CNN model was loaded successfully from: " +
str(filepathToCnnModelToLoad))
#Do final checks of the parameters. Check the ones that need check in comparison to the model's parameters! Such as: SAVE_PROBMAPS_PER_CLASS, INDICES_OF_FMS_TO_SAVE, Number of Channels!
#testConfig.checkIfConfigIsCorrectForParticularCnnModel(cnn3dInstance)
#Fill in the session's parameters.
#[[case1-ch1, ..., caseN-ch1], [case1-ch2,...,caseN-ch2]]
listOfAListPerChannelWithFilepathsOfAllCases = [
parseAbsFileLinesInList(
getAbsPathEvenIfRelativeIsGiven(channelConfPath,
testConfigFilepath))
for channelConfPath in configGet(testConfig.CHANNELS)
]
#[[case1-ch1, case1-ch2], ..., [caseN-ch1, caseN-ch2]]
listWithAListPerCaseWithFilepathPerChannel = [
list(item)
for item in zip(*tuple(listOfAListPerChannelWithFilepathsOfAllCases))
]
gtLabelsFilepaths = parseAbsFileLinesInList(
getAbsPathEvenIfRelativeIsGiven(configGet(testConfig.GT_LABELS),
testConfigFilepath)) if configGet(
testConfig.GT_LABELS) else None
roiMasksFilepaths = parseAbsFileLinesInList(
getAbsPathEvenIfRelativeIsGiven(configGet(testConfig.ROI_MASKS),
testConfigFilepath)) if configGet(
testConfig.ROI_MASKS) else None
namesToSavePredsAndFeats = parseFileLinesInList(
getAbsPathEvenIfRelativeIsGiven(
configGet(testConfig.NAMES_FOR_PRED_PER_CASE),
testConfigFilepath)) if configGet(
testConfig.NAMES_FOR_PRED_PER_CASE
) else None #CAREFUL: Here we use a different parsing function!
testSessionParameters = TestSessionParameters(
sessionName = sessionName,
sessionLogger = sessionLogger,
mainOutputAbsFolder = mainOutputAbsFolder,
cnn3dInstance = cnn3dInstance,
cnnModelFilepath = filepathToCnnModelToLoad,
#Input:
listWithAListPerCaseWithFilepathPerChannel = listWithAListPerCaseWithFilepathPerChannel,
gtLabelsFilepaths = gtLabelsFilepaths,
roiMasksFilepaths = roiMasksFilepaths,
#Output
namesToSavePredictionsAndFeatures = namesToSavePredsAndFeats,
#predictions
saveSegmentation = configGet(testConfig.SAVE_SEGM),
saveProbMapsBoolPerClass = configGet(testConfig.SAVE_PROBMAPS_PER_CLASS),
folderForPredictions = folderForPredictions,
#features:
saveIndividualFmImages = configGet(testConfig.SAVE_INDIV_FMS),
saveMultidimensionalImageWithAllFms = configGet(testConfig.SAVE_4DIM_FMS),
indicesOfFmsToVisualisePerPathwayAndLayer = [configGet(testConfig.INDICES_OF_FMS_TO_SAVE_NORMAL)] +\
[configGet(testConfig.INDICES_OF_FMS_TO_SAVE_SUBSAMPLED)] +\
[configGet(testConfig.INDICES_OF_FMS_TO_SAVE_FC)
],
folderForFeatures = folderForFeatures,
padInputImagesBool = configGet(testConfig.PAD_INPUT),
)
testSessionParameters.sessionLogger.print3(
"\n=========== NEW TESTING SESSION ===============")
testSessionParameters.printParametersOfThisSession()
testSessionParameters.sessionLogger.print3(
"\n=======================================================")
testSessionParameters.sessionLogger.print3(
"=========== Compiling the Testing Function ============")
testSessionParameters.sessionLogger.print3(
"=======================================================")
cnn3dInstance.compileTestAndVisualisationFunction(
*testSessionParameters.getTupleForCompilationOfTestFunc())
testSessionParameters.sessionLogger.print3(
"\n======================================================")
testSessionParameters.sessionLogger.print3(
"=========== Testing with the CNN model ===============")
testSessionParameters.sessionLogger.print3(
"======================================================")
performInferenceForTestingOnWholeVolumes(
*testSessionParameters.getTupleForCnnTesting())
testSessionParameters.sessionLogger.print3(
"\n======================================================")
testSessionParameters.sessionLogger.print3(
"=========== Testing session finished =================")
testSessionParameters.sessionLogger.print3(
"======================================================")
def deepMedicTestMain(testConfigFilepath, absPathToSavedModelFromCmdLine) :
print "Given Test-Configuration File: ", testConfigFilepath
#Parse the config file in this naive fashion...
testConfig = TestConfig()
#configStruct = testConfig.configStruct
execfile(testConfigFilepath, testConfig.configStruct)
configGet = testConfig.get #Main interface
#Do checks.
#checkIfMainTestConfigIsCorrect(testConfig, testConfigFilepath, absPathToSavedModelFromCmdLine) #Checks REQUIRED fields are complete.
#checkIfFilesThatListFilesPerCaseAreCorrect(testConfig, testConfigFilepath) #Checks listing-files (whatever given).
#checkIfOptionalParametersAreGivenCorrectly(testConfig, testConfigFilepath)
#At this point it was checked that all parameters (that could be checked) and filepaths are correct, pointing to files/dirs and all files/dirs exist.
#Create Folders and Logger
mainOutputAbsFolder = getAbsPathEvenIfRelativeIsGiven(configGet(testConfig.FOLDER_FOR_OUTPUT), testConfigFilepath)
sessionName = configGet(testConfig.SESSION_NAME) if configGet(testConfig.SESSION_NAME) else TestSessionParameters.getDefaultSessionName()
[folderForLogs,
folderForPredictions,
folderForFeatures] = makeFoldersNeededForTestingSession(mainOutputAbsFolder, sessionName)
loggerFileName = folderForLogs + "/" + sessionName + ".txt"
sessionLogger = myLoggerModule.MyLogger(loggerFileName)
sessionLogger.print3("CONFIG: The configuration file for the testing session was loaded from: " + str(testConfigFilepath))
#Load the CNN Model!
sessionLogger.print3("=========== Loading the CNN model for testing... ===============")
#If CNN-Model was specified in command line, completely override the one in the config file.
filepathToCnnModelToLoad = None
if absPathToSavedModelFromCmdLine and configGet(testConfig.CNN_MODEL_FILEPATH) :
sessionLogger.print3("WARN: A CNN-Model to use was specified both in the command line input and in the test-config-file! The input by the command line will be used: " + str(absPathToSavedModelFromCmdLine) )
filepathToCnnModelToLoad = absPathToSavedModelFromCmdLine
elif absPathToSavedModelFromCmdLine :
filepathToCnnModelToLoad = absPathToSavedModelFromCmdLine
else :
filepathToCnnModelToLoad = getAbsPathEvenIfRelativeIsGiven(configGet(testConfig.CNN_MODEL_FILEPATH), testConfigFilepath)
sessionLogger.print3("...Loading the network can take a few minutes if the model is big...")
cnn3dInstance = load_object_from_gzip_file(filepathToCnnModelToLoad)
sessionLogger.print3("The CNN model was loaded successfully from: " + str(filepathToCnnModelToLoad))
#Do final checks of the parameters. Check the ones that need check in comparison to the model's parameters! Such as: SAVE_PROBMAPS_PER_CLASS, INDICES_OF_FMS_TO_SAVE, Number of Channels!
#testConfig.checkIfConfigIsCorrectForParticularCnnModel(cnn3dInstance)
#Fill in the session's parameters.
#[[case1-ch1, ..., caseN-ch1], [case1-ch2,...,caseN-ch2]]
listOfAListPerChannelWithFilepathsOfAllCases = [parseAbsFileLinesInList(getAbsPathEvenIfRelativeIsGiven(channelConfPath, testConfigFilepath)) for channelConfPath in configGet(testConfig.CHANNELS)]
#[[case1-ch1, case1-ch2], ..., [caseN-ch1, caseN-ch2]]
listWithAListPerCaseWithFilepathPerChannel = [ list(item) for item in zip(*tuple(listOfAListPerChannelWithFilepathsOfAllCases)) ]
gtLabelsFilepaths = parseAbsFileLinesInList( getAbsPathEvenIfRelativeIsGiven(configGet(testConfig.GT_LABELS), testConfigFilepath) ) if configGet(testConfig.GT_LABELS) else None
roiMasksFilepaths = parseAbsFileLinesInList( getAbsPathEvenIfRelativeIsGiven(configGet(testConfig.ROI_MASKS), testConfigFilepath) ) if configGet(testConfig.ROI_MASKS) else None
namesToSavePredsAndFeats = parseFileLinesInList( getAbsPathEvenIfRelativeIsGiven(configGet(testConfig.NAMES_FOR_PRED_PER_CASE), testConfigFilepath) ) if configGet(testConfig.NAMES_FOR_PRED_PER_CASE) else None #CAREFUL: Here we use a different parsing function!
testSessionParameters = TestSessionParameters(
sessionName = sessionName,
sessionLogger = sessionLogger,
mainOutputAbsFolder = mainOutputAbsFolder,
cnn3dInstance = cnn3dInstance,
cnnModelFilepath = filepathToCnnModelToLoad,
#Input:
listWithAListPerCaseWithFilepathPerChannel = listWithAListPerCaseWithFilepathPerChannel,
gtLabelsFilepaths = gtLabelsFilepaths,
roiMasksFilepaths = roiMasksFilepaths,
#Output
namesToSavePredictionsAndFeatures = namesToSavePredsAndFeats,
#predictions
saveSegmentation = configGet(testConfig.SAVE_SEGM),
saveProbMapsBoolPerClass = configGet(testConfig.SAVE_PROBMAPS_PER_CLASS),
folderForPredictions = folderForPredictions,
#features:
saveIndividualFmImages = configGet(testConfig.SAVE_INDIV_FMS),
saveMultidimensionalImageWithAllFms = configGet(testConfig.SAVE_4DIM_FMS),
indicesOfFmsToVisualisePerPathwayAndLayer = [ configGet(testConfig.INDICES_OF_FMS_TO_SAVE_NORMAL),
configGet(testConfig.INDICES_OF_FMS_TO_SAVE_SUBSAMPLED),
configGet(testConfig.INDICES_OF_FMS_TO_SAVE_FC)
],
folderForFeatures = folderForFeatures,
padInputImagesBool = configGet(testConfig.PAD_INPUT),
)
testSessionParameters.sessionLogger.print3("=========== NEW TESTING SESSION ===============")
testSessionParameters.printParametersOfThisSession()
testSessionParameters.sessionLogger.print3("======================================================")
testSessionParameters.sessionLogger.print3("=========== Testing with the CNN model ===============")
testSessionParameters.sessionLogger.print3("======================================================")
performInferenceForTestingOnWholeVolumes(*testSessionParameters.getTupleForCnnTesting())
testSessionParameters.sessionLogger.print3("======================================================")
testSessionParameters.sessionLogger.print3("=========== Testing session finished =================")
testSessionParameters.sessionLogger.print3("======================================================")