Merge origin/develop into feature/fmriprep_ingress

FCP-INDI · Oct 9, 2023 · 28c9b42 · 28c9b42
2 parents 68ee445 + 8ebbd4e
commit 28c9b42
Show file tree

Hide file tree

Showing 20 changed files with 513 additions and 113 deletions.
diff --git a/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile b/.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile
@@ -29,4 +29,5 @@ ENV PATH=$PATH:/home/c-pac_user/.local/bin \
     PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
 
 # set user
+WORKDIR /home/c-pac_user
 # USER c-pac_user
diff --git a/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile b/.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile
@@ -31,4 +31,5 @@ ENV PATH=$PATH:/home/c-pac_user/.local/bin \
     PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
 
 # set user
+WORKDIR /home/c-pac_user
 # USER c-pac_user
diff --git a/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-jammy.Dockerfile
@@ -48,4 +48,5 @@ ENV PATH=$PATH:/home/c-pac_user/.local/bin \
     PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
 
 # set user
+WORKDIR /home/c-pac_user
 # USER c-pac_user
diff --git a/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile b/.github/Dockerfiles/C-PAC.develop-lite-jammy.Dockerfile
@@ -49,4 +49,5 @@ ENV PATH=$PATH:/home/c-pac_user/.local/bin \
     PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
 
 # set user
+WORKDIR /home/c-pac_user
 # USER c-pac_user
diff --git a/.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile b/.github/Dockerfiles/Ubuntu.jammy-non-free.Dockerfile
@@ -56,6 +56,7 @@ RUN groupadd -r c-pac \
       graphviz-dev \
       locales \
       rdfind \
+      xvfb \
     && ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
     && echo $TZ > /etc/timezone \
     && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,6 +24,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## Fixed
 
 - Fixed a bug where some connectivity matrices wouldn't generate if anatomical and functional outputs were in different resolutions.
+- Handling of `3dECM` outputs for AFNI ≥ 21.1.1.
+- Fixed a bug where sparsity thresholds were not being scaled for network centrality.
 
 ### Changed
 
@@ -39,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - `click-aliases`
 - `dc`
+- `semver`
 
 ### Removed dependencies
 

diff --git a/CPAC/info.py b/CPAC/info.py
@@ -201,6 +201,7 @@ def get_cpac_gitversion():
     "scikit-learn",
     "scipy",
     "sdcflows",
+    "semver",
     "traits",
     "voluptuous>=0.12.0",
     "xvfbwrapper"

diff --git a/CPAC/network_centrality/__init__.py b/CPAC/network_centrality/__init__.py
@@ -1,3 +1,19 @@
-from .utils import convert_pvalue_to_r, merge_lists
+# Copyright (C) 2012-2023  C-PAC Developers
 
-__all__ = ['convert_pvalue_to_r', 'merge_lists']
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+from .utils import convert_pvalue_to_r, create_merge_node
+
+__all__ = ['convert_pvalue_to_r', 'create_merge_node']
diff --git a/CPAC/network_centrality/network_centrality.py b/CPAC/network_centrality/network_centrality.py
@@ -1,17 +1,48 @@
-from nipype.interfaces.afni.preprocess import DegreeCentrality, ECM, LFCD
+# Copyright (C) 2015-2023  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+from pathlib import Path
+from typing import Optional, Union
+from nipype.interfaces.afni.preprocess import DegreeCentrality, LFCD
+from nipype.pipeline.engine import Workflow
+from CPAC.network_centrality.utils import ThresholdOptionError
 from CPAC.pipeline.schema import valid_options
 from CPAC.utils.docs import docstring_parameter
+from CPAC.utils.interfaces.afni import AFNI_GTE_21_1_1, ECM
+from CPAC.utils.typing import LIST
 
 
 @docstring_parameter(m_options=valid_options['centrality']['method_options'],
                      t_options=valid_options['centrality'][
                         'threshold_options'],
                      w_options=valid_options['centrality']['weight_options'])
-def create_centrality_wf(wf_name, method_option, weight_options,
-                         threshold_option, threshold, num_threads=1,
-                         memory_gb=1.0):
+def create_centrality_wf(wf_name: str, method_option: str,
+                         weight_options: LIST[str], threshold_option: str,
+                         threshold: float, num_threads: Optional[int] = 1,
+                         memory_gb: Optional[float] = 1.0,
+                         base_dir: Optional[Union[Path, str]] = None
+                         ) -> Workflow:
     """
-    Function to create the afni-based centrality workflow
+    Function to create the afni-based centrality workflow.
+
+    .. seealso::
+
+        * :py:func:`~CPAC.network_centrality.pipeline.connect_centrality_workflow`
+        * :py:func:`~CPAC.network_centrality.utils.create_merge_node`
+        * :py:func:`~CPAC.network_centrality.utils.sep_nifti_subbriks`
 
     Parameters
     ----------
@@ -25,38 +56,66 @@ def create_centrality_wf(wf_name, method_option, weight_options,
         one of {t_options}
     threshold : float
         the threshold value for thresholding the similarity matrix
-    num_threads : integer (optional); default=1
-        the number of threads to utilize for centrality computation
-    memory_gb : float (optional); default=1.0
-        the amount of memory the centrality calculation will take (GB)
+    num_threads : integer, optional
+        the number of threads to utilize for centrality computation; default=1
+    memory_gb : float,optional
+        the amount of memory the centrality calculation will take (GB);
+        default=1.0
+    base_dir : path or str, optional
+        the base directory for the workflow; default=None
 
     Returns
     -------
     centrality_wf : nipype Workflow
         the initialized nipype workflow for the afni centrality command
-    """
 
+    Notes
+    -----
+    Workflow Inputs::
+
+        inputspec.in_file : string
+            path to input functional data NIfTI file
+
+        inputspec.template : string
+            path to input mask template NIfTI file
+
+        inputspec.threshold : float
+            threshold value for thresholding the similarity matrix
+
+    Workflow Outputs::
+
+        outputspec.outfile_list : list of strings
+            list of paths to output files (binarized and weighted)
+    """  # pylint: disable=line-too-long
     from CPAC.pipeline import nipype_pipeline_engine as pe
-    import nipype.interfaces.utility as util
-    import CPAC.network_centrality.utils as utils
+    from nipype.interfaces import utility as util
+    from CPAC.network_centrality import utils
+    from CPAC.utils.interfaces.function import Function
 
     test_thresh = threshold
 
-    if threshold_option == 'sparsity':
+    if threshold_option == 'Sparsity threshold':
         test_thresh = threshold / 100.0
 
     method_option, threshold_option = \
         utils.check_centrality_params(method_option, threshold_option,
                                       test_thresh)
-
-    centrality_wf = pe.Workflow(name=wf_name)
+    # Eigenvector centrality and AFNI ≥ 21.1.1?
+    ecm_gte_21_1_01 = ((method_option == 'eigenvector_centrality') and
+                       AFNI_GTE_21_1_1)
+    out_names = tuple(f'{method_option}_{x}' for x in weight_options)
+    if base_dir is None:
+        centrality_wf = pe.Workflow(name=wf_name)
+    else:
+        centrality_wf = pe.Workflow(name=wf_name, base_dir=base_dir)
 
     input_node = pe.Node(util.IdentityInterface(fields=['in_file',
                                                         'template',
                                                         'threshold']),
                          name='inputspec')
-
     input_node.inputs.threshold = threshold
+    output_node = pe.Node(util.IdentityInterface(fields=['outfile_list']),
+                          name='outputspec')
 
     # Degree centrality
     if method_option == 'degree_centrality':
@@ -68,11 +127,24 @@ def create_centrality_wf(wf_name, method_option, weight_options,
 
     # Eigenvector centrality
     elif method_option == 'eigenvector_centrality':
-        afni_centrality_node = pe.Node(ECM(environ={
-            'OMP_NUM_THREADS': str(num_threads)
-        }), name='afni_centrality', mem_gb=memory_gb)
-        afni_centrality_node.inputs.out_file = \
-            'eigenvector_centrality_merged.nii.gz'
+        if ecm_gte_21_1_01:
+            afni_centrality_node = pe.MapNode(ECM(environ={
+                'OMP_NUM_THREADS': str(num_threads)
+            }), name='afni_centrality', mem_gb=memory_gb,
+                iterfield=['do_binary', 'out_file'])
+            afni_centrality_node.inputs.out_file = [
+                f'eigenvector_centrality_{w_option}.nii.gz' for
+                w_option in weight_options]
+            afni_centrality_node.inputs.do_binary = [
+                w_option == 'Binarized' for w_option in weight_options]
+            centrality_wf.connect(afni_centrality_node, 'out_file',
+                                  output_node, 'outfile_list')
+        else:
+            afni_centrality_node = pe.Node(ECM(environ={
+                'OMP_NUM_THREADS': str(num_threads)
+            }), name='afni_centrality', mem_gb=memory_gb)
+            afni_centrality_node.inputs.out_file = \
+                'eigenvector_centrality_merged.nii.gz'
         afni_centrality_node.inputs.memory = memory_gb  # 3dECM input only
 
     # lFCD
@@ -82,39 +154,48 @@ def create_centrality_wf(wf_name, method_option, weight_options,
             }), name='afni_centrality', mem_gb=memory_gb)
         afni_centrality_node.inputs.out_file = 'lfcd_merged.nii.gz'
 
-    out_names = tuple(f'{method_option}_{x}' for x in weight_options)
+    if not ecm_gte_21_1_01:
+        # Need to separate sub-briks except for 3dECM if AFNI > 21.1.01
+        sep_subbriks_node = \
+            pe.Node(Function(input_names=['nifti_file', 'out_names'],
+                             output_names=['output_niftis'],
+                             function=utils.sep_nifti_subbriks),
+                    name='sep_nifti_subbriks')
+        sep_subbriks_node.inputs.out_names = out_names
+        centrality_wf.connect([(afni_centrality_node, sep_subbriks_node,
+                                [('out_file', 'nifti_file')]),
+                               (sep_subbriks_node, output_node,
+                                [('output_niftis', 'outfile_list')])])
 
     afni_centrality_node.interface.num_threads = num_threads
 
-    # Connect input image and mask tempalte
-    centrality_wf.connect(input_node, 'in_file',
-                          afni_centrality_node, 'in_file')
-    centrality_wf.connect(input_node, 'template',
-                          afni_centrality_node, 'mask')
+    # Connect input image and mask template
+    centrality_wf.connect([(input_node, afni_centrality_node,
+                            [('in_file', 'in_file'),
+                             ('template', 'mask')])])
 
-    # If we're doing significan thresholding, convert to correlation
+    # If we're doing significance thresholding, convert to correlation
     if threshold_option == 'Significance threshold':
         # Check and (possibly) conver threshold
         convert_thr_node = pe.Node(
-            util.Function(input_names=['datafile',
-                                       'p_value',
-                                       'two_tailed'],
-                          output_names=['rvalue_threshold'],
-                          function=utils.convert_pvalue_to_r),
+            Function(input_names=['datafile',
+                                  'p_value',
+                                  'two_tailed'],
+                     output_names=['rvalue_threshold'],
+                     function=utils.convert_pvalue_to_r),
             name='convert_threshold')
         # Wire workflow to connect in conversion node
-        centrality_wf.connect(input_node, 'in_file',
-                              convert_thr_node, 'datafile')
-        centrality_wf.connect(input_node, 'threshold',
-                              convert_thr_node, 'p_value')
-        centrality_wf.connect(convert_thr_node, 'rvalue_threshold',
-                              afni_centrality_node, 'thresh')
+        centrality_wf.connect([(input_node, convert_thr_node,
+                                [('in_file', 'datafile'),
+                                 ('threshold', 'p_value')]),
+                               (convert_thr_node, afni_centrality_node,
+                                [('rvalue_threshold', 'thresh')])])
 
     # Sparsity thresholding
     elif threshold_option == 'Sparsity threshold':
         # Check to make sure it's not lFCD
         if method_option == 'local_functional_connectivity_density':
-            raise Exception('Sparsity thresholding is not supported for lFCD')
+            raise ThresholdOptionError(threshold_option, method_option)
 
         # Otherwise, connect threshold to sparsity input
         centrality_wf.connect(input_node, 'threshold',
@@ -125,27 +206,4 @@ def create_centrality_wf(wf_name, method_option, weight_options,
         centrality_wf.connect(input_node, 'threshold',
                               afni_centrality_node, 'thresh')
 
-    # Need to separate sub-briks
-    sep_nifti_imports = ["import os", "import nibabel as nib",
-                         "from CPAC.pipeline.schema import valid_options",
-                         "from CPAC.utils.docs import docstring_parameter"]
-    sep_subbriks_node = \
-        pe.Node(util.Function(input_names=['nifti_file', 'out_names'],
-                              output_names=['output_niftis'],
-                              function=utils.sep_nifti_subbriks,
-                              imports=sep_nifti_imports),
-                name='sep_nifti_subbriks')
-
-    sep_subbriks_node.inputs.out_names = out_names
-
-    centrality_wf.connect(afni_centrality_node, 'out_file',
-                          sep_subbriks_node, 'nifti_file')
-
-    output_node = pe.Node(util.IdentityInterface(fields=['outfile_list',
-                                                         'oned_output']),
-                          name='outputspec')
-
-    centrality_wf.connect(sep_subbriks_node, 'output_niftis',
-                          output_node, 'outfile_list')
-
     return centrality_wf