Commit ae89332a by simonabottani

Add abstract class to read tsv files for ML and ML workflwo

parent ab65d8f2
Pipeline #1045 passed with stages
in 2 minutes 25 seconds
......@@ -195,8 +195,8 @@ def t1_spm_pipeline(caps_dir, df, **kwargs):
Returns:
final_df: a DataFrame containing the information of the bids and the pipeline
"""
from ...pipelines.t1_spm_full_prep.t1_spm_full_prep_cli import T1SPMFullPrepCLI
instance = T1SPMFullPrepCLI()
from ...pipelines.t1_volume_new_template.t1_volume_new_template_cli import T1VolumeNewTemplateCLI
instance = T1VolumeNewTemplateCLI()
pipeline_name = instance.name
del instance
......
......@@ -483,7 +483,8 @@ class CAPSTSVBasedInput(CAPSInput):
"""
output_filename = path.join(output_dir, 'weights.nii.gz')
#output_filename = path.join(output_dir, 'weights.nii.gz')
rbio.weights_to_nifti(weights, self._atlas, output_filename)
#rbio.weights_to_nifti(weights, self._atlas, output_filename)
pass
\ No newline at end of file
......@@ -601,7 +601,7 @@ class TB_RepHoldOut_DualSVM(base.MLWorkflow):
self._algorithm.save_parameters(best_params, classifier_dir)
weights = self._algorithm.save_weights(classifier, x, classifier_dir)
self._input.save_weights_as_nifti(weights, classifier_dir)
#self._input.save_weights_as_nifti(weights, classifier_dir)
self._validation.save_results(self._output_dir)
......@@ -653,6 +653,6 @@ class TB_RepHoldOut_RandomForest(base.MLWorkflow):
self._algorithm.save_parameters(best_params, classifier_dir)
weights = self._algorithm.save_weights(classifier, classifier_dir)
self._input.save_weights_as_nifti(weights, classifier_dir)
#self._input.save_weights_as_nifti(weights, classifier_dir)
self._validation.save_results(self._output_dir)
#self._validation.save_results(self._output_dir)
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