Commit 1f9caade by simonabottani

Rename T1 Volume Pipelines

parent 80edbd21
Pipeline #818 failed with stages
in 14 seconds
......@@ -120,10 +120,10 @@ def execute():
from clinica.pipelines.t1_freesurfer_cross_sectional.t1_freesurfer_cross_sectional_cli import T1FreeSurferCrossSectionalCLI # noqa
from clinica.pipelines.t1_volume_segmentation.t1_volume_segmentation_cli import T1VolumeSegmentationCLI # noqa
from clinica.pipelines.t1_spm_dartel.t1_spm_dartel_cli import T1SPMDartelCLI # noqa
from clinica.pipelines.t1_spm_dartel2mni.t1_spm_dartel2mni_cli import T1SPMDartel2MNICLI # noqa
from clinica.pipelines.t1_spm_full_prep.t1_spm_full_prep_cli import T1SPMFullPrepCLI # noqa
from clinica.pipelines.t1_spm_dartel_existing_template.t1_spm_dartel_existing_template_cli import T1SPMDartelExistingTemplateCLI #noqa
from clinica.pipelines.t1_volume_create_dartel.t1_volume_create_dartel_cli import T1VolumeCreateDartelCLI # noqa
from clinica.pipelines.t1_volume_dartel2mni.t1_volume_dartel2mni_cli import T1VolumeDartel2MNICLI # noqa
from clinica.pipelines.t1_volume_new_template.t1_volume_new_template_cli import T1VolumeNewTemplate # noqa
from clinica.pipelines.t1_volume_existing_template.t1_volume_existing_template_cli import T1VolumeExistingTemplateCLI #noqa
from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_cli import DWIPreprocessingUsingT1CLI # noqa
from clinica.pipelines.dwi_preprocessing_using_phasediff_fieldmap.dwi_preprocessing_using_phasediff_fieldmap_cli import DWIPreprocessingUsingPhaseDiffFieldmapCLI # noqa
from clinica.pipelines.dwi_processing_dti.dwi_processing_dti_cli import DWIProcessingDTICLI # noqa
......@@ -137,10 +137,10 @@ def execute():
pipelines += [
T1FreeSurferCrossSectionalCLI(),
T1VolumeSegmentationCLI(),
T1SPMDartelCLI(),
T1SPMDartel2MNICLI(),
T1SPMFullPrepCLI(),
T1SPMDartelExistingTemplateCLI(),
T1VolumeCreateDartelCLI(),
T1VolumeDartel2MNICLI(),
T1VolumeNewTemplateCLI(),
T1VolumeExistingTemplateCLI(),
DWIPreprocessingUsingT1CLI(),
DWIPreprocessingUsingPhaseDiffFieldmapCLI(),
DWIProcessingDTICLI(),
......
{
"id": "aramislab/t1-spm-dartel",
"id": "aramislab/t1-volume-create-dartel",
"author": "SAMPER-GONZALEZ Jorge",
"version": "0.1",
"dependencies": [
......
......@@ -18,7 +18,7 @@ __email__ = "jorge.samper-gonzalez@inria.fr"
__status__ = "Development"
class T1SPMDartelCLI(ce.CmdParser):
class T1VolumeCreateDartelCLI(ce.CmdParser):
def define_name(self):
"""Define the sub-command name to run this pipelines.
......@@ -54,9 +54,9 @@ class T1SPMDartelCLI(ce.CmdParser):
"""
"""
from t1_spm_dartel_pipeline import T1SPMDartel
from t1_volume_create_dartel_pipeline import T1VolumeCreateDartel
pipeline = T1SPMDartel(bids_directory=self.absolute_path(args.bids_directory),
pipeline = T1VolumeCreateDartel(bids_directory=self.absolute_path(args.bids_directory),
caps_directory=self.absolute_path(args.caps_directory),
tsv_file=self.absolute_path(args.subjects_sessions_tsv),
group_id=args.group_id
......
......@@ -17,7 +17,7 @@ __email__ = "jorge.samper-gonzalez@inria.fr"
__status__ = "Development"
class T1SPMDartel(cpe.Pipeline):
class T1VolumeCreateDartel(cpe.Pipeline):
"""T1 SPM Dartel SHORT DESCRIPTION.
Warnings:
......@@ -39,8 +39,8 @@ class T1SPMDartel(cpe.Pipeline):
Example:
>>> from t1_spm_dartel import T1SPMDartel
>>> pipelines = T1SPMDartel('myGroup', '~/MYDATASET_BIDS', '~/MYDATASET_CAPS')
>>> from t1_volume_create_dartel import T1VolumeCreateDartel
>>> pipelines = T1VolumeCreateDartel('myGroup', '~/MYDATASET_BIDS', '~/MYDATASET_CAPS')
>>> pipelines.parameters.update({
>>> # ...
>>> })
......@@ -51,7 +51,7 @@ class T1SPMDartel(cpe.Pipeline):
def __init__(self, bids_directory=None, caps_directory=None, tsv_file=None, name=None, group_id='default'):
import os
super(T1SPMDartel, self).__init__(bids_directory, caps_directory, tsv_file, name)
super(T1VolumeCreateDartel, self).__init__(bids_directory, caps_directory, tsv_file, name)
if not group_id.isalnum():
raise ValueError('Not valid group_id value. It must be composed only by letters and/or numbers')
......
{
"id": "aramislab/t1-spm-dartel2mni",
"id": "aramislab/t1-volume-dartel2mni",
"author": "SAMPER-GONZALEZ Jorge; BOTTANI, Simona",
"version": "0.1.0",
"dependencies": [
......
......@@ -18,7 +18,7 @@ __email__ = "jorge.samper-gonzalez@inria.fr"
__status__ = "Development"
class T1SPMDartel2MNICLI(ce.CmdParser):
class T1VolumeDartel2MNICLI(ce.CmdParser):
def define_name(self):
"""Define the sub-command name to run this pipelines.
......@@ -65,9 +65,9 @@ class T1SPMDartel2MNICLI(ce.CmdParser):
"""
"""
from t1_spm_dartel2mni_pipeline import T1SPMDartel2MNI
from t1_volume_dartel2mni_pipeline import T1VolumeDartel2MNI
pipeline = T1SPMDartel2MNI(bids_directory=self.absolute_path(args.bids_directory),
pipeline = T1VolumeDartel2MNI(bids_directory=self.absolute_path(args.bids_directory),
caps_directory=self.absolute_path(args.caps_directory),
tsv_file=self.absolute_path(args.subjects_sessions_tsv),
group_id=args.group_id
......
......@@ -17,7 +17,7 @@ __email__ = "jorge.samper-gonzalez@inria.fr"
__status__ = "Development"
class T1SPMDartel2MNI(cpe.Pipeline):
class T1VolumeDartel2MNI(cpe.Pipeline):
"""T1 SPM Dartel2MNI SHORT DESCRIPTION.
Warnings:
......@@ -39,8 +39,8 @@ class T1SPMDartel2MNI(cpe.Pipeline):
Example:
>>> from t1_spm_dartel2mni import T1SPMDartel2MNI
>>> pipelines = T1SPMDartel2MNI('myGroup', '~/MYDATASET_BIDS', '~/MYDATASET_CAPS')
>>> from t1_volume_dartel2mni import T1VolumeDartel2MNI
>>> pipelines = T1VolumeDartel2MNI('myGroup', '~/MYDATASET_BIDS', '~/MYDATASET_CAPS')
>>> pipelines.parameters.update({
>>> # ...
>>> })
......@@ -50,7 +50,7 @@ class T1SPMDartel2MNI(cpe.Pipeline):
def __init__(self, bids_directory=None, caps_directory=None, tsv_file=None, name=None, group_id='default'):
import os
super(T1SPMDartel2MNI, self).__init__(bids_directory, caps_directory, tsv_file, name)
super(T1VolumeDartel2MNI, self).__init__(bids_directory, caps_directory, tsv_file, name)
if not group_id.isalnum():
raise ValueError('Not valid group_id value. It must be composed only by letters and/or numbers')
......@@ -234,7 +234,7 @@ class T1SPMDartel2MNI(cpe.Pipeline):
import nipype.pipeline.engine as npe
import nipype.interfaces.utility as nutil
from clinica.utils.io import unzip_nii
from t1_spm_dartel2mni_utils import prepare_flowfields, join_smoothed_files, atlas_statistics, select_gm_images
from t1_volume_dartel2mni_utils import prepare_flowfields, join_smoothed_files, atlas_statistics, select_gm_images
spm_home = os.getenv("SPM_HOME")
mlab_home = os.getenv("MATLABCMD")
......
{
"id": "aramislab/t1-spm-dartel-existing-template",
"id": "aramislab/t1-volume-existing-template",
"author": "Jorge SAMPER-GONZALEZ",
"version": "0.1.0",
"dependencies": [
......
......@@ -17,12 +17,12 @@ __maintainer__ = "Jorge Samper Gonzalez"
__email__ = "jorge.samper-gonzalez@inria.fr"
__status__ = "Development"
class T1SPMDartelExistingTemplateCLI(ce.CmdParser):
class T1VolumeExistingTemplateCLI(ce.CmdParser):
def define_name(self):
"""Define the sub-command name to run this pipelines.
"""
self._name = 't1-volume-existing-dartel'
self._name = 't1-volume-existing-template'
def define_description(self):
"""Define a description of this pipeline.
......@@ -52,9 +52,9 @@ class T1SPMDartelExistingTemplateCLI(ce.CmdParser):
def run_command(self, args):
"""
"""
from t1_spm_dartel_existing_template_pipeline import T1SPMDartelExistingTemplate
from t1_volume_existing_template_pipeline import T1VolumeExistingTemplate
pipeline = T1SPMDartelExistingTemplate(bids_directory=self.absolute_path(args.bids_directory),
pipeline = T1VolumeExistingTemplate(bids_directory=self.absolute_path(args.bids_directory),
caps_directory=self.absolute_path(args.caps_directory),
tsv_file=self.absolute_path(args.subjects_sessions_tsv),
group_id=args.group_id
......
......@@ -17,7 +17,7 @@ __email__ = "jorge.samper-gonzalez@inria.fr"
__status__ = "Development"
class T1SPMDartelExistingTemplate(cpe.Pipeline):
class T1VolumeExistingTemplate(cpe.Pipeline):
"""T1 SPM Dartel Existing Template SHORT DESCRIPTION.
Warnings:
......@@ -39,8 +39,8 @@ class T1SPMDartelExistingTemplate(cpe.Pipeline):
Example:
>>> from t1_spm_dartel_existing_template import T1SPMDartelExistingTemplate
>>> pipelines = T1SPMDartelExistingTemplate('~/MYDATASET_BIDS', '~/MYDATASET_CAPS')
>>> from t1_volume_existing_template import T1VolumeExistingTemplate
>>> pipelines = T1VolumeExistingTemplate('~/MYDATASET_BIDS', '~/MYDATASET_CAPS')
>>> pipelines.parameters = {
>>> # ...
>>> }
......@@ -49,7 +49,7 @@ class T1SPMDartelExistingTemplate(cpe.Pipeline):
"""
def __init__(self, bids_directory=None, caps_directory=None, tsv_file=None, name=None, group_id='default'):
super(T1SPMDartelExistingTemplate, self).__init__(bids_directory, caps_directory, tsv_file, name)
super(T1VolumeExistingTemplate, self).__init__(bids_directory, caps_directory, tsv_file, name)
if not group_id.isalnum():
raise ValueError('Not valid group_id value. It must be composed only by letters and/or numbers')
......@@ -181,7 +181,7 @@ class T1SPMDartelExistingTemplate(cpe.Pipeline):
import nipype.pipeline.engine as npe
import nipype.interfaces.utility as nutil
from clinica.utils.io import unzip_nii
import t1_spm_dartel_existing_template_utils as utils
import t1_volume_existing_template_utils as utils
# Unzipping
# =========
......
{
"id": "aramislab/t1-spm-full-prep",
"id": "aramislab/t1-volume-new-template",
"author": "SAMPER-GONZALEZ Jorge; BOTTANI, Simona",
"version": "0.1.0",
"dependencies": [
......
......@@ -18,7 +18,7 @@ __email__ = "jorge.samper-gonzalez@inria.fr"
__status__ = "Development"
class T1SPMFullPrepCLI(ce.CmdParser):
class T1VolumeNewTemplateCLI(ce.CmdParser):
def define_name(self):
"""Define the sub-command name to run this pipelines.
......@@ -98,9 +98,9 @@ class T1SPMFullPrepCLI(ce.CmdParser):
def run_command(self, args):
"""
"""
from t1_spm_full_prep_pipeline import T1SPMFullPrep
from t1_volume_new_template_pipeline import T1VolumeNewTemplate
pipeline = T1SPMFullPrep(bids_directory=self.absolute_path(args.bids_directory),
pipeline = T1VolumeNewTemplate (bids_directory=self.absolute_path(args.bids_directory),
caps_directory=self.absolute_path(args.caps_directory),
tsv_file=self.absolute_path(args.subjects_sessions_tsv),
group_id=args.group_id
......
......@@ -18,7 +18,7 @@ __email__ = "jorge.samper-gonzalez@inria.fr"
__status__ = "Development"
class T1SPMFullPrep(cpe.Pipeline):
class T1VolumeNewTemplate(cpe.Pipeline):
"""T1 SPM Full Prep SHORT DESCRIPTION.
Warnings:
......@@ -40,8 +40,8 @@ class T1SPMFullPrep(cpe.Pipeline):
Example:
>>> from clinica.pipelines.t1_spm_full_prep import T1SPMFullPrep
>>> pipelines = T1SPMFullPrep('~/MYDATASET_BIDS', '~/MYDATASET_CAPS')
>>> from clinica.pipelines.t1_volume_new_template import T1VolumeNewTemplate
>>> pipelines = T1VolumeNewTemplate('~/MYDATASET_BIDS', '~/MYDATASET_CAPS')
>>> pipelines.parameters = {
>>> # ...
>>> }
......@@ -52,7 +52,7 @@ class T1SPMFullPrep(cpe.Pipeline):
def __init__(self, bids_directory=None, caps_directory=None, tsv_file=None, name=None, group_id='default'):
import os
super(T1SPMFullPrep, self).__init__(bids_directory, caps_directory, tsv_file, name)
super(T1VolumeNewTemplate, self).__init__(bids_directory, caps_directory, tsv_file, name)
if not group_id.isalnum():
raise ValueError('Not valid group_id value. It must be composed only by letters and/or numbers')
......@@ -141,7 +141,7 @@ class T1SPMFullPrep(cpe.Pipeline):
import nipype.pipeline.engine as npe
import nipype.interfaces.utility as nutil
import clinica.pipelines.t1_spm_segmentation.t1_spm_segmentation_utils as seg_utils
import clinica.pipelines.t1_volume_segmentation.t1_volume_segmentation_utils as seg_utils
# Reading BIDS
# ============
......@@ -160,7 +160,7 @@ class T1SPMFullPrep(cpe.Pipeline):
import nipype.pipeline.engine as npe
import nipype.interfaces.io as nio
import clinica.pipelines.t1_spm_segmentation.t1_spm_segmentation_utils as seg_utils
import clinica.pipelines.t1_volume_segmentation.t1_volume_segmentation_utils as seg_utils
from clinica.utils.io import zip_nii
import os.path as op
import re
......@@ -324,9 +324,9 @@ class T1SPMFullPrep(cpe.Pipeline):
import nipype.interfaces.matlab as mlab
import nipype.pipeline.engine as npe
import nipype.interfaces.utility as nutil
import clinica.pipelines.t1_spm_segmentation.t1_spm_segmentation_utils as seg_utils
import clinica.pipelines.t1_spm_dartel.t1_spm_dartel_utils as dartel_utils
import clinica.pipelines.t1_spm_dartel2mni.t1_spm_dartel2mni_utils as dartel2mni_utils
import clinica.pipelines.t1_volume_segmentation.t1_volume_segmentation_utils as seg_utils
import clinica.pipelines.t1_volume_create_dartel.t1_volume_create_darte_utils as dartel_utils
import clinica.pipelines.t1_volume_dartel2mni.t1_volume_dartel2mni_utils as dartel2mni_utils
from clinica.utils.io import unzip_nii
spm_home = os.getenv("SPM_HOME")
......
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