mia_processes.bricks.preprocess.dipy package¶

The atomic calculations from dipy.

Submodules¶

mia_processes.bricks.preprocess.dipy.processes module¶

The dipy preprocess library of the mia_processes package.

The purpose of this module is to customise the main dipy preprocessing bricks provided by nipype and to correct some things that do not work directly in populse_mia.

Contains

Class

Denoise
ComputeDKI

class mia_processes.bricks.preprocess.dipy.processes.ComputeDKI[source]¶

Bases: populse_mia.user_interface.pipeline_manager.process_mia.ProcessMIA

Compute DKI

Please, see the complete documentation for the ComputeDKI brick in the mia_processes website

Note

Type ‘ComputeDKI.help()’ for a full description of this process parameters.
Type ‘<ComputeDKI>.get_input_spec()’ for a full description of this process input trait types.
Type ‘<ComputeDKI>.get_output_spec()’ for a full description of this process output trait types.

__init__()[source]¶

Dedicated to the attributes initialisation/instantiation.

The input and output plugs are defined here. The special ‘self.requirement’ attribute (optional) is used to define the third-party products necessary for the running of the brick.

list_outputs(is_plugged=None)[source]¶

Dedicated to the initialisation step of the brick.

The main objective of this method is to produce the outputs of the bricks (self.outputs) and the associated tags (self.inheritance_dic), if defined here. In order not to include an output in the database, this output must be a value of the optional key ‘notInDb’ of the self.outputs dictionary. To work properly this method must return self.make_initResult() object.

Parameters: is_plugged – the state, linked or not, of the plugs.
Returns: a dictionary with requirement, outputs and inheritance_dict.

run_process_mia()[source]¶: Dedicated to the process launch step of the brick.

class mia_processes.bricks.preprocess.dipy.processes.Denoise[source]¶