def __init__(self, filename):
self.filename = filename
self.dt = DictTools()
ft = FileTools()
self.file = ft.processFile(filename)
self.transition_matrix = {}
self.first_words = {}
self.second_words = {}
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(self, data, fullname='../data/temp/temp.npy', log=True):
fullname = FT.newname(fullname)
np.save(fullname, data)
self._temp_list.append(fullname)
if log:
with open(self._log, 'a') as f:
f.write(time.strftime('%X') + " <> SAVED: " + fullname + '\n')
def __init__(self, log_path):
self.log_dict = ft.loadFile(log_path)
if not self.log_dict['presentation']['is_by_index']:
raise NotImplementedError('The visual stimuli display should be indexed.')
self.check_integrity()
def __init__(self, log_path):
self.log_dict = ft.loadFile(log_path)
if not self.log_dict['presentation']['is_by_index']:
raise NotImplementedError('The visual stimuli display should be indexed.')
self.check_integrity()
def start(chano,
stc,
name='test',
path='../data/',
exposures=[10, 100, 1000, 10000],
mov={'shift': [0, 1, 2, 3, 4, 5]}):
normalized_name = os.path.normpath(path + '/' + name)
path, name, extension = FileTools.splitname(normalized_name)
base_name = os.path.normpath(path + "/" + name)
mask = 'Exposure: {:6d} Theta: {:6.2f} Shift: {:6.2f} Phi: {:6.2f}'
time.sleep(5)
print("\n\n")
try:
for motor, sweep in mov.items():
for x in sweep:
setattr(chano, motor, x)
for exposure in exposures:
stc.exposure = exposure
image = stc.capture()
newname = FileTools.newname(base_name + '.npz')
np.savez(newname,
image=image,
exposure=exposure,
chanosat_pos=chano.pos)
print(
mask.format(exposure, chano.theta, chano.shift,
chano.phi))
time_now = time.gmtime(time.time())
print("\n" + time.strftime("%X", time_now), end='')
print(' - Saved as: {}'.format(os.path.relpath(newname)))
time.sleep(1)
except:
print('\n\nUnexpected error.'
' Trying to reset chanosat to zero position\n\n')
chano.pos = [0, 0, 0]
time.sleep(1)
raise
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)
def load(self, fullname='temp.npy'):
fullname = FT.file_exist(fullname, default_path=self._path_data)
return np.load(fullname)
def save(self, data, fullname='temp.npy'):
fullname = FT.newname(fullname, default=self._path_data)
np.save(fullname, data)
self._temp_list.append(fullname)
return fullname
'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)
import time
parser = argparse.ArgumentParser()
parser.add_argument('-name', type=str, default='dark')
parser.add_argument('-path', type=str, default='../data/')
parser.add_argument('-stc', type=str, default='/dev/video1')
parser.add_argument('-captures', type=str, default=10)
params = parser.parse_args()
stc = Device(dev_name=params.stc)
exposures = [1, 10, 50, 100, 200, 500, 1000, 2000, 5000, 10000]
normalized_name = os.path.normpath(params.path + '/' + params.name)
path, name, extension = FileTools.splitname(normalized_name)
base_name = os.path.normpath(path + "/" + name)
mask = 'Exposure: {:6d}'
time.sleep(5)
print("\n\n")
for exposure in exposures:
stc.exposure = exposure
print(mask.format(exposure))
for i in range(params.captures):
image = stc.capture()
filename = base_name + '{:02d}_exp_{:06}.npz'.format(i, exposure)
np.savez(filename, image=image)
time_now = time.gmtime(time.time())
['patch07', 'MMA'],
['patch08', 'MMP'],
['patch09', 'LLA'],
# ['patch10', 'AM'],
# ['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)