Working at the Sigray laboratory#
LogProtocol#
Log protocol (pyrost.LogProtocol) is a helper class to
retrieve the data from the log files generated at the Sigray laboratory,
which contain the readouts from the motors and other instruments
during the speckle tracking scan. The data extracted from the log
files is used to generate CXI datasets by pyrost.KamzikConverter
(look KamzikConverter). The protocol consists of
the log keys of the attributes that are required to extract from the
header part of a log file and their corresponding data types:
datatypes : Data type of the attributes (float, int, str, or bool).
log_keys : Log key to find the attribute in the log file.
part_keys : The name of the part where the attribute is stored in the log log file.
Note
You can save protocol to an INI file with pyrost.LogProtocol.to_ini()
and import protocol from INI file with pyrost.LogProtocol.import_ini().
The default protocol can be accessed with pyrost.LogProtocol.import_default().
The protocol is given by:
[datatypes]
lens_down_dist = float
lens_up_dist = float
exposure = float
n_points = int
n_steps = int
scan_type = str
step_size = float
x_sample = float
y_sample = float
z_sample = float
[log_keys]
lens_down_dist = [Z-LENSE-DOWN_det_dist]
lens_up_dist = [Z-LENSE-UP_det_dist]
exposure = [Exposure]
n_points = [Points count]
n_steps = [Steps count]
scan_type = [Device]
step_size = [Step size]
x_sample = [X-SAM, SAM-X, SCAN-X]
y_sample = [Y-SAM, SAM-Y, SCAN-Y]
z_sample = [Z-SAM, SAM-Z, SCAN-Z]
[part_keys]
lens_down_dist = Session logged attributes
lens_up_dist = Session logged attributes
exposure = Type: Method
n_points = Type: Scan
n_steps = Type: Scan
scan_type = Type: Scan
step_size = Type: Scan
x_sample = Session logged attributes
y_sample = Session logged attributes
z_sample = Session logged attributes
KamzikConverter#
Log data converter class provides an interface to read Kamzik log files
(pyrost.KamzikConverter.read_logs()), and convert data to CXI attributes,
that can be parsed to pyrost.STData container. A converter object
needs a log protocol (pyrost.LogProtocol), a fast scan detector axis, and
a slow scan detector axis. One can obtain a list of CXI datasets available to
generate with pyrost.KamzikConverter.cxi_keys(), and generate a dictionary of
CXI datasets with pyrost.KamzikConverter.cxi_get().
The following attributes can be extracted from log files:
basis_vectors : A set of detector axes defined for each image.
dist_down : down-lens-to-detector distance in meters.
dist_up : up-lens-to-detector distance in meters.
sim_translations : A set of sample translations simulated from the log attributes.
log_translations : A set of sample translations read from the log file.
x_pixel_size : Detector pixel size along the x-axis in meters.
y_pixel_size : Detector pixel size along the y-axis in meters.