added mandatory dtatgrabber field

chrisgorgo · chrisgorgo · commit f34ab50a576d · 2013-10-15T15:48:44.000+02:00
diff --git a/examples/dmri_camino_dti.py b/examples/dmri_camino_dti.py
@@ -102,6 +102,7 @@ def get_affine(volume):
 
 datasource.inputs.field_template = dict(dwi='%s/%s.nii.gz')
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 """
 An inputnode is used to pass the data obtained by the data grabber to the actual processing functions
diff --git a/examples/dmri_connectivity.py b/examples/dmri_connectivity.py
@@ -154,6 +154,7 @@ def select_aparc_annot(list_of_files):
 datasource.inputs.field_template = dict(dwi='%s/%s.nii.gz')
 datasource.inputs.template_args = info
 datasource.inputs.base_directory = data_dir
+datasource.inputs.sort_filelist = True
 
 """
 FreeSurferSource nodes are used to retrieve a number of image
diff --git a/examples/dmri_connectivity_advanced.py b/examples/dmri_connectivity_advanced.py
@@ -121,6 +121,7 @@
 datasource.inputs.base_directory = data_dir
 datasource.inputs.field_template = dict(dwi='%s/%s.nii.gz')
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 """
 The input node and Freesurfer sources declared here will be the main
diff --git a/examples/dmri_dtk_dti.py b/examples/dmri_dtk_dti.py
@@ -109,6 +109,7 @@
 
 datasource.inputs.field_template = dict(dwi='%s/%s.nii.gz')
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 
 """
diff --git a/examples/dmri_dtk_odf.py b/examples/dmri_dtk_odf.py
@@ -109,6 +109,7 @@
 
 datasource.inputs.field_template = dict(dwi='%s/%s.nii')
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 
 """
diff --git a/examples/dmri_fsl_dti.py b/examples/dmri_fsl_dti.py
@@ -120,7 +120,7 @@
                                         seed_file="%s.bedpostX/%s.nii.gz",
                                         target_masks="%s.bedpostX/%s.nii.gz")
 datasource.inputs.template_args = info
-
+datasource.inputs.sort_filelist = True
 
 """
 Setup for Diffusion Tensor Computation
diff --git a/examples/dmri_mrtrix_dti.py b/examples/dmri_mrtrix_dti.py
@@ -64,6 +64,7 @@
 datasource.inputs.base_directory = data_dir
 datasource.inputs.field_template = dict(dwi='%s/%s.nii.gz')
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 """
 An inputnode is used to pass the data obtained by the data grabber to the actual processing functions
diff --git a/examples/dmri_tbss_nki.py b/examples/dmri_tbss_nki.py
@@ -51,6 +51,7 @@
 datasource.inputs.template_args = dict(dwi=[['subject_id', 'nii.gz']],
                                        bvec=[['subject_id', 'bvec']],
                                        bval=[['subject_id', 'bval']])
+datasource.inputs.sort_filelist = True
 gen_fa.connect(subject_id_infosource, 'subject_id', datasource, 'subject_id')
 
 eddy_correct = create_eddy_correct_pipeline()
@@ -92,6 +93,7 @@
 tbss_source.inputs.template = '%s/%s_%s.nii'
 tbss_source.inputs.template_args = dict(fa_list=[['FA', subjects_list, 'FA']],
                                         md_list=[['MD', subjects_list, 'MD']])
+tbss_source.inputs.sort_filelist = True
 
 """
 TBSS analysis
diff --git a/examples/fmri_freesurfer_smooth.py b/examples/fmri_freesurfer_smooth.py
@@ -418,6 +418,7 @@
 datasource.inputs.base_directory = data_dir
 datasource.inputs.template = '%s/%s.nii'
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 
 """
@@ -588,6 +589,7 @@ def getsubs(subject_id):
 l2source.inputs.field_template = dict(con='*/contrasts/con_%04d.img',
                                       reg='*/registrations/*.dat')
 l2source.inputs.template_args = dict(con=[['con_id']],reg=[[]])
+l2source.inputs.sort_filelist = True
 
 l2flow.connect(l2inputnode, 'contrasts', l2source, 'con_id')
 
diff --git a/examples/fmri_fsl.py b/examples/fmri_fsl.py
@@ -539,6 +539,7 @@ def num_copes(files):
 datasource.inputs.base_directory = data_dir
 datasource.inputs.template = '%s/%s.nii'
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 """
 Use the get_node function to retrieve an internal node by name. Then set the
diff --git a/examples/fmri_fsl_feeds.py b/examples/fmri_fsl_feeds.py
@@ -474,6 +474,7 @@ def num_copes(files):
 datasource.inputs.base_directory = feeds_data_dir
 datasource.inputs.template = '%s.nii.gz'
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 firstlevel.inputs.preproc.smooth.fwhm = 5
 
diff --git a/examples/fmri_fsl_reuse.py b/examples/fmri_fsl_reuse.py
@@ -169,6 +169,7 @@ def num_copes(files):
 datasource.inputs.base_directory = data_dir
 datasource.inputs.template = '%s/%s.nii'
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 """
 Use the get_node function to retrieve an internal node by name. Then set the
diff --git a/examples/fmri_nipy_glm.py b/examples/fmri_nipy_glm.py
@@ -102,7 +102,7 @@
 datasource.inputs.base_directory = data_dir
 datasource.inputs.template = '%s/%s.nii'
 datasource.inputs.template_args = info
-
+datasource.inputs.sort_filelist = True
 
 """Use :class:`nipype.interfaces.spm.Realign` for motion correction
 and register all images to the mean image.
diff --git a/examples/fmri_slicer_coregistration.py b/examples/fmri_slicer_coregistration.py
@@ -96,6 +96,7 @@
 datasource.inputs.base_directory = data_dir
 datasource.inputs.template = '%s/%s.nii'
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 coregister = pe.Node(interface=BRAINSFit(), name="coregister")
 coregister.inputs.outputTransform = True
diff --git a/examples/fmri_spm.py b/examples/fmri_spm.py
@@ -345,6 +345,7 @@ def getstripdir(subject_id):
 # iterate over all contrast images
 l2source.iterables = [('fwhm',fwhmlist),
                       ('con',contrast_ids)]
+l2source.inputs.sort_filelist = True
 
 
 """Use :class:`nipype.interfaces.spm.OneSampleTTestDesign` to perform a
diff --git a/examples/fmri_spm_auditory.py b/examples/fmri_spm_auditory.py
@@ -265,7 +265,7 @@ def makelist(item):
 datasource.inputs.base_directory = data_dir
 datasource.inputs.template = '%s%s/%s%s_%03d.img'
 datasource.inputs.template_args = info
-
+datasource.inputs.sort_filelist = True
 
 
 """
diff --git a/examples/fmri_spm_dartel.py b/examples/fmri_spm_dartel.py
@@ -263,6 +263,7 @@
 datasource.inputs.base_directory = data_dir
 datasource.inputs.template = '%s/%s.nii'
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 """We need to create a separate workflow to make the DARTEL template
 """
@@ -274,7 +275,7 @@
 datasource_dartel.inputs.base_directory = data_dir
 datasource_dartel.inputs.template = '%s/%s.nii'
 datasource_dartel.inputs.template_args = dict(struct=[['subject_id','struct']])
-
+datasource_dartel.inputs.sort_filelist = True
 datasource_dartel.inputs.subject_id = subject_list
 
 """Here we make sure that struct files have names corresponding to the subject ids.
@@ -484,6 +485,7 @@ def getstripdir(subject_id):
 # iterate over all contrast images
 l2source.iterables = [('fwhm',fwhmlist),
                       ('con',contrast_ids)]
+l2source.inputs.sort_filelist = True
 
 
 """Use :class:`nipype.interfaces.spm.OneSampleTTestDesign` to perform a
diff --git a/examples/fmri_spm_face.py b/examples/fmri_spm_face.py
@@ -254,7 +254,7 @@ def makelist(item):
 datasource.inputs.base_directory = data_dir
 datasource.inputs.template = '%s/s%s_%04d%s.img'
 datasource.inputs.template_args = info
-
+datasource.inputs.sort_filelist = True
 
 
 """
diff --git a/examples/fmri_spm_nested.py b/examples/fmri_spm_nested.py
@@ -269,7 +269,7 @@
 datasource.inputs.base_directory = data_dir
 datasource.inputs.template = '%s/%s.nii'
 datasource.inputs.template_args = info
-
+datasource.inputs.sort_filelist = True
 
 
 """
@@ -439,6 +439,7 @@ def getstripdir(subject_id):
 # iterate over all contrast images
 l2source.iterables = [('fwhm',fwhmlist),
                       ('con',contrast_ids)]
+l2source.inputs.sort_filelist = True
 
 
 """Use :class:`nipype.interfaces.spm.OneSampleTTestDesign` to perform a
diff --git a/examples/frontiers_paper/smoothing_comparison.py b/examples/frontiers_paper/smoothing_comparison.py
@@ -152,6 +152,7 @@ def chooseindex(roi):
                                                      ['f3','f5','f7','f10']]],
                                               struct=[['subject_id','struct']])
 datasource.inputs.subject_id = 's1'
+datasource.inputs.sort_filelist = True
 
 main_workflow.connect(datasource, 'func', preprocessing, 'realign.in_files')
 main_workflow.connect(datasource, 'struct', preprocessing,
diff --git a/examples/frontiers_paper/workflow_from_scratch.py b/examples/frontiers_paper/workflow_from_scratch.py
@@ -123,6 +123,7 @@
 datasource.inputs.template_args = dict(func=[['subject_id',
                                               ['f3','f5','f7','f10']]])
 datasource.inputs.subject_id = 's1'
+datasource.inputs.sort_filelist = True
 
 main_workflow.connect(datasource, 'func', preprocessing, 'realign.in_files')
 
diff --git a/examples/rsfmri_fsl.py b/examples/rsfmri_fsl.py
@@ -220,6 +220,7 @@ def pickfirst(files):
 datasource.inputs.base_directory = data_dir
 datasource.inputs.template = '%s/%s.nii'
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 
 """
diff --git a/examples/rsfmri_fsl_compcorr.py b/examples/rsfmri_fsl_compcorr.py
@@ -64,6 +64,7 @@
 info = dict(func=[['subject_id', ['f3',]]])
 
 datasource.inputs.template_args = info
+datasource.inputs.sort_filelist = True
 
 """
 Store significant result-files in a special directory
diff --git a/examples/smri_ants_build_template.py b/examples/smri_ants_build_template.py
@@ -82,6 +82,7 @@
                     name='InputImages' )
 datasource.inputs.imageList=input_images
 datasource.inputs.passiveImagesDictionariesList=input_passive_images
+datasource.inputs.sort_filelist = True
 
 """
 5. Template is initialized by a simple average
diff --git a/examples/smri_antsregistration_build_template.py b/examples/smri_antsregistration_build_template.py
@@ -110,6 +110,7 @@
 datasource.inputs.ListOfImagesDictionaries=ListOfImagesDictionaries
 datasource.inputs.registrationImageTypes=registrationImageTypes
 datasource.inputs.interpolationMapping=interpolationMapping
+datasource.inputs.sort_filelist = True
 
 """
 5. Template is initialized by a simple average in this simple example,
diff --git a/examples/smri_freesurfer.py b/examples/smri_freesurfer.py
@@ -39,7 +39,7 @@
 datasource.inputs.template = '%s/%s.nii'
 datasource.inputs.template_args = dict(struct=[['subject_id', 'struct']])
 datasource.inputs.subject_id = subject_list
-
+datasource.inputs.sort_filelist = True
 """
 Run recon-all
 """
diff --git a/examples/workshop_dartmouth_2010.py b/examples/workshop_dartmouth_2010.py
@@ -229,22 +229,26 @@
 
 datasource1 = nio.DataGrabber()
 datasource1.inputs.template = 'data/s1/f3.nii'
+datasource1.inputs.sort_filelist = True
 results = datasource1.run()
 print results.outputs
 
 datasource2 = nio.DataGrabber()
 datasource2.inputs.template = 'data/s*/f*.nii'
+datasource2.inputs.sort_filelist = True
 results = datasource2.run()
 print results.outputs
 
 datasource3 = nio.DataGrabber(infields=['run'])
 datasource3.inputs.template = 'data/s1/f%d.nii'
+datasource3.inputs.sort_filelist = True
 datasource3.inputs.run = [3, 7]
 results = datasource3.run()
 print results.outputs
 
 datasource4 = nio.DataGrabber(infields=['subject_id', 'run'])
 datasource4.inputs.template = 'data/%s/f%d.nii'
+datasource4.inputs.sort_filelist = True
 datasource4.inputs.run = [3, 7]
 datasource4.inputs.subject_id = ['s1', 's3']
 results = datasource4.run()
@@ -267,6 +271,7 @@
 datasource.inputs.template = '%s/%s.nii'
 datasource.inputs.base_directory = os.path.abspath('data')
 datasource.inputs.template_args = dict(func=[['subject_id','f3']], struct=[['subject_id','struct']])
+datasource.inputs.sort_filelist = True
 
 my_workflow = pe.Workflow(name="my_workflow")
 my_workflow.base_dir = os.path.abspath('.')
diff --git a/nipype/workflows/dmri/camino/group_connectivity.py b/nipype/workflows/dmri/camino/group_connectivity.py
@@ -62,6 +62,7 @@ def create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_
     datasource.inputs.base_directory = data_dir
     datasource.inputs.field_template = dict(dwi='%s/%s.nii')
     datasource.inputs.template_args = info
+    datasource.inputs.sort_filelist = True
 
     """
     Create a connectivity mapping workflow
diff --git a/nipype/workflows/dmri/connectivity/group_connectivity.py b/nipype/workflows/dmri/connectivity/group_connectivity.py
@@ -104,6 +104,7 @@ def create_merge_networks_by_group_workflow(group_list, group_id, data_dir, subj
     l2source.inputs.template_args = dict(CFFfiles=[['group_id']])
     l2source.inputs.template=op.join(output_dir,'%s/cff/*/connectome.cff')
     l2source.inputs.base_directory = data_dir
+    l2source.inputs.sort_filelist = True
 
     l2inputnode = pe.Node(interface=util.IdentityInterface(fields=['CFFfiles']), name='l2inputnode')
     MergeCNetworks = pe.Node(interface=cmtk.MergeCNetworks(), name="MergeCNetworks")
@@ -171,6 +172,7 @@ def create_merge_network_results_by_group_workflow(group_list, group_id, data_di
     l2source.inputs.field_template=dict(CFFfiles=op.join(output_dir,'%s/cff/*/connectome.cff'),
      CSVmatrices=op.join(output_dir,'%s/cmatrices_csv/*/*.csv'), CSVnodal=op.join(output_dir,'%s/nxcsv/*/*nodal*.csv'),
      CSVglobal=op.join(output_dir,'%s/nxcsv/*/*global*.csv'), CSVfibers=op.join(output_dir,'%s/fiber_csv/*/*fibers*.csv'))
+    l2source.inputs.sort_filelist = True
 
     l2inputnode = pe.Node(interface=util.IdentityInterface(fields=['CFFfiles',
     'CSVfibers', 'CSVmatrices', 'CSVnodal', 'CSVglobal', 'network_file']), name='l2inputnode')
@@ -268,6 +270,7 @@ def create_merge_group_networks_workflow(group_list, data_dir, subjects_dir, out
     l3source = pe.Node(nio.DataGrabber(infields=['group_id'], outfields=['CFFfiles']), name='l3source')
     l3source.inputs.template_args = dict(CFFfiles=[['group_id','group_id']])
     l3source.inputs.template=op.join(output_dir,'%s/%s.cff')
+    l3source.inputs.sort_filelist = True
 
     l3inputnode = pe.Node(interface=util.IdentityInterface(fields=['Group_CFFs']), name='l3inputnode')
 
@@ -326,6 +329,7 @@ def create_merge_group_network_results_workflow(group_list, data_dir, subjects_d
 
 	l3source.inputs.field_template=dict(CFFfiles=op.join(output_dir,'%s/*.cff'), CSVnodemetrics=op.join(output_dir,'%s/node_csv/*.csv'),
 	CSVglobalmetrics=op.join(output_dir,'%s/global_csv/*.csv'), CSVmatrices=op.join(output_dir,'%s/cmatrices_csv/*/*.csv'))
+    l3source.inputs.sort_filelist = True
 
 	l3inputnode = pe.Node(interface=util.IdentityInterface(fields=['Group_CFFs', 'Group_CSVnodemetrics', 'Group_CSVglobalmetrics', 'Group_CSVmatrices']), name='l3inputnode')
 
@@ -410,6 +414,7 @@ def create_average_networks_by_group_workflow(group_list, data_dir, subjects_dir
         fibmean=op.join(output_dir,'%s/mean_fiber_length/*/*%s*.mat'), fibdev=op.join(output_dir,'%s/fiber_length_std/*/*%s*.mat'))
     l4source_grp1.inputs.base_directory = output_dir
     l4source_grp1.inputs.template_args = l4info
+    l4source_grp1.inputs.sort_filelist = True
 
     l4source_grp2 = l4source_grp1.clone(name='l4source_grp2')
 
diff --git a/nipype/workflows/dmri/mrtrix/group_connectivity.py b/nipype/workflows/dmri/mrtrix/group_connectivity.py
@@ -78,6 +78,7 @@ def create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_
     datasource.inputs.base_directory = data_dir
     datasource.inputs.field_template = dict(dwi='%s/%s.nii')
     datasource.inputs.template_args = info
+    datasource.inputs.sort_filelist = True
 
     """
     Create a connectivity mapping workflow
