def motor_position_at_zero(self):
""" Motor position (x, y and z in microns) corresponding to the scan's (0, 0, 0)
point. For non-multiroi scans, (x=0, y=0) marks the center of the FOV."""
match = re.search(r'hMotors\.motorPosition = (?P<motor_position>.*)',
self.header)
motor_position = matlabstr2py(
match.group('motor_position'))[:3] if match else None
return motor_position
def requested_scanning_depths(self):
match = re.search(r'hStackManager\.zs = (?P<zs>.*)', self.header)
if match:
zs = matlabstr2py(match.group('zs'))
scanning_depths = zs if isinstance(zs, list) else [zs]
else:
scanning_depths = None
return scanning_depths
def num_channels(self):
match = re.search(r'hChannels\.channelSave = (?P<channels>.*)',
self.header)
if match:
channels = matlabstr2py(match.group('channels'))
num_channels = len(channels) if isinstance(channels, list) else 1
else:
num_channels = None
return num_channels
def image_width_in_microns(self):
match = re.search(r'hRoiManager\.imagingFovUm = (?P<fov_corners>.*)',
self.header)
if match:
fov_corners = matlabstr2py(match.group('fov_corners'))
image_width_in_microns = fov_corners[1][0] - fov_corners[0][
0] # x1-x0
else:
image_width_in_microns = None
return image_width_in_microns
def initial_secondary_z(self):
""" Initial position in z (microns) of the secondary motor (if any)."""
match = re.search(r'hMotors\.motorPosition = (?P<motor_position>.*)',
self.header)
if match:
motor_position = matlabstr2py(match.group('motor_position'))
secondary_z = motor_position[3] if len(
motor_position) > 3 else None
else:
secondary_z = None
return secondary_z
def MINI2P_scope(self):
'''
MINI 2P scope name
'''
match = re.search(r'SI.*.MINI2P_scope\s*?=\s*?(?P<scope>.*)',
self.header)
if match:
mini2p_scope = matlabstr2py(match.group('scope').strip())
return mini2p_scope
else:
return None
def MINI2P_objective(self):
'''
MINI 2P objective name
'''
match = re.search(r'SI.*.MINI2P_objective\s*?=\s*?(?P<obj>.*)',
self.header)
if match:
mini2p_objective = matlabstr2py(match.group('obj').strip())
return mini2p_objective
else:
return None
def MINI2P_system(self):
'''
MINI 2P setup (system) name
'''
match = re.search(r'SI.*.MINI2P_system\s*?=\s*?(?P<system>.*)',
self.header)
if match:
mini2p_system = matlabstr2py(match.group('system').strip())
return mini2p_system
else:
return None
def MINI2P_transform_matrix_path(self):
'''
Path of transform matrix object (.mat file)
that was used for unwarping (correcting) raw scanimage data
SI.Custom.MINI2P.tf_path | str | transformMatrixDirectory
'''
match = re.search(r'SI.*.tf_path\s*?=\s*?(?P<tf_path>.*)', self.header)
if match:
path = matlabstr2py(match.group('tf_path').strip())
return path
else:
return None
def requested_scanning_depths_relative(self):
match = re.search(r'hStackManager\.zsRelative = (?P<zs_relative>.*)',
self.header)
if match:
zs = matlabstr2py(match.group('zs_relative'))
if isinstance(zs, list):
scanning_depths_relative = [z[0] for z in zs]
else:
scanning_depths_relative = [zs]
else:
scanning_depths_relative = None
return scanning_depths_relative
def MINI2P_corrected(self):
'''
Was MINI2P unwarping applied to the data?
SI.Custom.MINI2P.MINI2P_Corrected | 'true' or '1'
'''
match = re.search(r'SI.*.MINI2P_Corrected\s*?=\s*?(?P<corrected>.*)',
self.header)
if match:
corrected = matlabstr2py(match.group('corrected').strip())
return corrected in [1, True]
else:
return False
def MINI2P_transform_matrix_index(self):
'''
Returns index in (matlab) transform matrix object
(see transform_matrix_path() above)
that was used to correct the data.
WARNING! 1-indexing
'''
match = re.search(r'SI.*.tfused\s*?=\s*?(?P<tfused>.*)', self.header)
if match:
tfused = matlabstr2py(match.group('tfused').strip())
return int(tfused)
else:
return None
