cxi_ref.rst

pyrost CXI Protocol

Protocol

CXI protocol (:class:`pyrost.Protocol`) is helper class for a :class:`pyrost.STData` data container, which tells it where to look for the necessary data fields in a CXI file. The class is fully customizable so you can tailor it to your particular data structure of CXI file. The protocol consists of the following attributes for each data field (data, whitefield, etc.):

• datatypes : data type (float, int, or bool).
• default_paths : CXI file path.

Note

You can save protocol to an INI file with :func:`pyrost.Protocol.export_ini` and import protocol from INI file with :func:`pyrost.Protocol.import_ini`.

The default protocol can be accessed with :func:`pyrost.cxi_protocol`. The protocol is given by:

[config]
float_precision = float64

[datatypes]
basis_vectors = float
data = float
defocus = float
defocus_fs = float
defocus_ss = float
distance = float
energy = float
error_frame = float
good_frames = int
m0 = int
mask = bool
n0 = int
phase = float
pixel_aberrations = float
pixel_map = float
pixel_translations = float
reference_image = float
roi = int
translations = float
wavelength = float
whitefield = float
x_pixel_size = float
y_pixel_size = float

[default_paths]
basis_vectors = /entry_1/instrument_1/detector_1/basis_vectors
data = /entry_1/data_1/data
defocus = /speckle_tracking/defocus
defocus_fs = /speckle_tracking/dfs
defocus_ss = /speckle_tracking/dss
distance = /entry_1/instrument_1/detector_1/distance
energy = /entry_1/instrument_1/source_1/energy
error_frame = /speckle_tracking/error_frame
good_frames = /frame_selector/good_frames
m0 = /speckle_tracking/m0
mask = /speckle_tracking/mask
n0 = /speckle_tracking/n0
phase = /speckle_tracking/phase
pixel_aberrations = /speckle_tracking/pixel_aberrations
pixel_map = /speckle_tracking/pixel_map
pixel_translations = /speckle_tracking/pixel_translations
reference_image = /speckle_tracking/reference_image
roi = /speckle_tracking/roi
translations = /entry_1/sample_1/geometry/translations
wavelength = /entry_1/instrument_1/source_1/wavelength
whitefield = /speckle_tracking/whitefield
x_pixel_size = /entry_1/instrument_1/detector_1/x_pixel_size
y_pixel_size = /entry_1/instrument_1/detector_1/y_pixel_size

Loader

Speckle Tracking loader class (:class:`pyrost.STLoader`) uses a protocol to automatically load all the necessary data fields from a CXI file. Other than the information provided by a protocol, a loader class requires the following attributes:

• policy : loading policy for each attribute enlisted in protocol. If it's True, the corresponding attribute will be loaded.
• load_paths : list of extra CXI file paths, where the loader will look for the data field.

Note

You can save loader to an INI file with :func:`pyrost.STLoader.export_ini` and import protocol from INI file with :func:`pyrost.STLoader.import_ini`.

The default loader can be accessed with :func:`pyrost.loader`. The loader is given by:

[load_paths]
good_frames = [/speckle_tracking/good_frames, /frame_selector/good_frames, /process_3/good_frames]
mask = [/speckle_tracking/mask, /mask_maker/mask, /entry_1/instrument_1/detector_1/mask]
translations = [/entry_1/sample_1/geometry/translations, /entry_1/sample_1/geometry/translation, /pos_refine/translation, /entry_1/sample_3/geometry/translation]
whitefield = [/speckle_tracking/whitefield, /process_1/whitefield, /make_whitefield/whitefield, /process_2/whitefield, /process_3/whitefield]

[policy]
basis_vectors = True
data = True
defocus = True
defocus_fs = True
defocus_ss = True
distance = True
energy = False
error_frame = False
good_frames = True
m0 = False
mask = True
n0 = False
phase = False
pixel_aberrations = False
pixel_map = False
pixel_translations = False
reference_image = False
roi = True
translations = True
wavelength = True
whitefield = False
x_pixel_size = True
y_pixel_size = True