configuration: Used by the interpreter to know about reconstructions to run

configuration used to run freeart reconstruction. The interpreter will have an instance of _ReconsConfig which can either be a TxConfig or a FluoConfig

Those classes can saved and read to configuration files. freeart is using a silx.io.dictdump.DictDump object. So those configuration can be saved into (.ini, .cfg, .h5) files. To save them you simply have to call save() and read() to load them.

Transmission configuration

This is an example of a configuration file (.cfg) and what are the main parameters.

[general_settings]
date  = 14/11/2017
reconstruction_type = Transmission
freeart_version = 3.0.0
precision = simple

[normalization]
i0 = 1.0
i0_index = 
rotation_center = 327
computeminuslog = True
normalizationi0fromafile = False

[reconstruction_properties]
include_last_angle = False
solid_angle_is_off = False
voxel_size = 1.0
oversampling = 2
relaxation_factor = 0.00311526479751
bean_calculation_method = 0

[reduction_data]
definition_reducted_by = 1
projection_number_reducted_by = 1

[projection_information]
projections_sel = 0:321
acqui_inv = False
min_angle = 0.0
max_angle = 6.28318530718

[data_source_tx]
sino_file = /users/toto/sinogram.edf
sino_file_index = 0

Fluorescence configuration

This is an example of a configuration file (.cfg) and what are the main parameters.

[general_settings]
date  = 14/11/2017
reconstruction_type = Fluorescence
freeart_version = 3.0.0
precision = double

[normalization]
i0 = 1.0
i0_index = 
rotation_center = 
normalizationi0fromafile = False

[reconstruction_properties]
include_last_angle = False
solid_angle_is_off = False
voxel_size = 1.0
oversampling = 2
relaxation_factor = 0.00311526479751
bean_calculation_method = 0
e0 = 1.0
outgoing_bean_calculation_method = 0

[reduction_data]
definition_reducted_by = 1
projection_number_reducted_by = 1

[projection_information]
projections_sel = :
acqui_inv = False
min_angle = 0.0
max_angle = 6.28318530718

[detector_setup]
det_pos_x = 1000.0
det_pos_y = 1000.0
det_pos_z = 0.0
det_width = 1.0

[data_source_fluo]
materials_file = 
absorption_file = absorptionMatrix.edf
samp_composition_file = 
absorption_file_is_a_sinogram = False
samp_composition_file_index = 
absorption_file_index = 0
materials_file_index = 

[fluo_sino_file_0]
self_absorption_file_0 = absorptionFile.edf
data_set_index_0 = 0
data_name_0 = 
data_physical_element_0 = H
ef_0 = 1.0
file_path = fluoSinogram.edf

Note

In order to generate for configuration file you can use tomogui (http://gitlab.esrf.fr/tomoTools/tomogui)

freeart.configuration.read(filePath)

Read the configuration stored in the given file path

Parameters:filePath – file to read Returns:the object containing the information for the reconstruction Return type:_ReconsConfig instance

freeart.configuration.save(configuration, filePath)

save the given configuration into the given filePath

Parameters:

• configuration – the configuration to write
• filePath – storage location

• config: define classes containing needed information to run reconstructions
• fileInfo: classes to know where to save / load data
• structs: IPython console widgets