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)