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.
- 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.