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: 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, iteration=False)[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.

  • iteration – the state, iterative or not, of the process.

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]

Bases: ProcessMIA

Non-local means for denoising 3D images

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

Note

  • Type ‘Denoise.help()’ for a full description of this process parameters.

  • Type ‘<Denoise>.get_input_spec()’ for a full description of this process input trait types.

  • Type ‘<Denoise>.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, iteration=False)[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.

  • iteration – the state, iterative or not, of the process.

Returns:

a dictionary with requirement, outputs and inheritance_dict.

run_process_mia()[source]

Dedicated to the process launch step of the brick.