def save_log(self):
if self.display_length is None:
self.clear()
raise LookupError("Please display sequence first!")
if self.file_name is None:
self._get_file_name()
if self.keep_display == True:
self.file_name += '-complete'
elif self.keep_display == False:
self.file_name += '-incomplete'
# set up log object
directory = os.path.join(self.log_dir, 'visual_display_log')
if not (os.path.isdir(directory)):
os.makedirs(directory)
logFile = dict(self.seq_log)
displayLog = dict(self.__dict__)
displayLog.pop('seq_log')
displayLog.pop('sequence')
logFile.update({'presentation': displayLog})
file_name = self.file_name + ".pkl"
# generate full log dictionary
path = os.path.join(directory, file_name)
ft.saveFile(path, logFile)
print("\nLog file generated successfully. Log file path: ")
print('{}'.format(path))
if self.is_save_sequence:
tf.imsave(os.path.join(directory, self.file_name + '.tif'),
self.sequence.astype(np.float32))
print('\nSequence file generated successfully. File path: ')
print('{}'.format(os.path.join(directory,
self.file_name + '.tif')))
backupFileFolder = self._get_backup_folder()
if backupFileFolder is not None:
if not (os.path.isdir(backupFileFolder)):
os.makedirs(backupFileFolder)
backupFilePath = os.path.join(backupFileFolder, file_name)
ft.saveFile(backupFilePath, logFile)
if self.is_save_sequence:
tf.imsave(
os.path.join(backupFileFolder, self.file_name + '.tif'),
self.sequence.astype(np.float32))
print(
"\nBackup log file generated successfully. Backup log file path: "
)
print('{}'.format(backupFilePath))
else:
print("\nDid not find backup path, no backup was saved.")
def save_log(self):
if self.display_length is None:
self.clear()
raise LookupError("Please display sequence first!")
if self.file_name is None:
self._get_file_name()
if self.keep_display == True:
self.file_name += '-complete'
elif self.keep_display == False:
self.file_name += '-incomplete'
# set up log object
directory = os.path.join(self.log_dir, 'visual_display_log')
if not (os.path.isdir(directory)):
os.makedirs(directory)
logFile = dict(self.seq_log)
displayLog = dict(self.__dict__)
displayLog.pop('seq_log')
displayLog.pop('sequence')
logFile.update({'presentation': displayLog})
file_name = self.file_name + ".pkl"
# generate full log dictionary
path = os.path.join(directory, file_name)
ft.saveFile(path, logFile)
print("\nLog file generated successfully. Log file path: ")
print('{}'.format(path))
if self.is_save_sequence:
tf.imsave(os.path.join(directory, self.file_name + '.tif'),
self.sequence.astype(np.float32))
print('\nSequence file generated successfully. File path: ')
print('{}'.format(os.path.join(directory, self.file_name + '.tif')))
backupFileFolder = self._get_backup_folder()
if backupFileFolder is not None:
if not (os.path.isdir(backupFileFolder)):
os.makedirs(backupFileFolder)
backupFilePath = os.path.join(backupFileFolder, file_name)
ft.saveFile(backupFilePath, logFile)
if self.is_save_sequence:
tf.imsave(os.path.join(backupFileFolder, self.file_name + '.tif'),
self.sequence.astype(np.float32))
print("\nBackup log file generated successfully. Backup log file path: ")
print('{}'.format(backupFilePath))
else:
print("\nDid not find backup path, no backup was saved.")
def save_log(self):
if self.display_length is None:
self.clear()
raise LookupError, "Please display sequence first!"
if self.file_name is None:
self._get_file_name()
if self.keep_display == True:
self.file_name += '-complete'
elif self.keep_display == False:
self.file_name += '-incomplete'
#set up log object
directory = self.log_dir + '\sequence_display_log'
if not (os.path.isdir(directory)):
os.makedirs(directory)
logFile = dict(self.seq_log)
displayLog = dict(self.__dict__)
displayLog.pop('seq_log')
displayLog.pop('sequence')
logFile.update({'presentation': displayLog})
file_name = self.file_name + ".pkl"
#generate full log dictionary
path = os.path.join(directory, file_name)
ft.saveFile(path, logFile)
print ".pkl file generated successfully."
backupFileFolder = self._get_backup_folder()
if backupFileFolder is not None:
if not (os.path.isdir(backupFileFolder)):
os.makedirs(backupFileFolder)
backupFilePath = os.path.join(backupFileFolder, file_name)
ft.saveFile(backupFilePath, logFile)
print ".pkl backup file generate successfully"
else:
print "did not find backup path, no backup has been saved."
'signMapFilterSigma': 9.,
'signMapThr': 0.3,
'eccMapFilterSigma': 15.0,
'splitLocalMinCutStep': 10.,
'closeIter': 3,
'openIter': 3,
'dilationIter': 15,
'borderWidth': 1,
'smallPatchThr': 100,
'visualSpacePixelSize': 0.5,
'visualSpaceCloseIter': 15,
'splitOverlapThr': 1.1,
'mergeOverlapThr': 0.1
}
currFolder = os.path.dirname(os.path.realpath(__file__))
os.chdir(currFolder)
trial = rm.loadTrial(trialName)
trial.params = params
trial.processTrial(isPlot=True)
trialDict = trial.generateTrialDict()
trial.plotTrial(isSave=isSave, saveFolder=currFolder)
plt.show()
if isSave:
ft.saveFile(trial.getName() + '.pkl', trialDict)
'splitLocalMinCutStep': 10.,
'closeIter': 3,
'openIter': 3,
'dilationIter': 15,
'borderWidth': 1,
'smallPatchThr': 100,
'visualSpacePixelSize': 0.5,
'visualSpaceCloseIter': 15,
'splitOverlapThr': 1.1,
'mergeOverlapThr': 0.1
}
currFolder = os.path.dirname(os.path.realpath(__file__))
os.chdir(currFolder)
trial = rm.loadTrial(trialName)
trial.params=params
trial.processTrial(isPlot=True)
trialDict = trial.generateTrialDict()
trial.plotTrial(isSave=isSave,saveFolder=currFolder)
plt.show()
if isSave:
ft.saveFile(trial.getName()+'.pkl',trialDict)
# ['patch11', 'LLA'],
# ['patch12', 'MMP'],
# ['patch13', 'MMP']
# ['patch14', 'MMP']
]
currFolder = os.path.dirname(os.path.realpath(__file__))
os.chdir(currFolder)
trialPath = os.path.join(currFolder,trialName)
trialDict = ft.loadFile(trialPath)
finalPatches = dict(trialDict['finalPatches'])
for i, namePair in enumerate(names):
currPatch = finalPatches.pop(namePair[0])
newPatchDict = {namePair[1]:currPatch}
finalPatches.update(newPatchDict)
trialDict.update({'finalPatchesMarked':finalPatches})
ft.saveFile(trialPath,trialDict)
trial, _ = rm.loadTrial(trialPath)
f = plt.figure(figsize=(10,10))
ax = f.add_subplot(111)
trial.plotFinalPatchBorders(plotAxis = ax,borderWidth=4)
plt.show()
f.savefig(trialName[0:-4]+'_borders.pdf',dpi=600)
f.savefig(trialName[0:-4]+'_borders.png',dpi=300)