🔀 Merge develop into func_switches

FCP-INDI · Jul 17, 2023 · 2f84dd3 · 2f84dd3
2 parents ed0152f + 95271e2
commit 2f84dd3
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diff --git a/.github/Dockerfiles/C-PAC.develop-lite-bionic.Dockerfile b/.github/Dockerfiles/C-PAC.develop-lite-bionic.Dockerfile
@@ -1,3 +1,19 @@
+# Copyright (C) 2022-2023  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 ghcr.io/fcp-indi/c-pac/stage-base:lite-v1.8.6.dev1
 LABEL org.opencontainers.image.description "Full C-PAC image without FreeSurfer"
 LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,9 +21,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Updates develop version numbers to adhere to [PEP440](https://peps.python.org/pep-0440) by changing `{major}.{minor}.{patch}.{SHA}-{dev}` to `{major}.{minor}.{patch}.dev{integer}+{SHA}`
 - Adds checksum steps to `curl`d steps in Docker build process (for standard and `lite` images)
 - Makes in-container root directory writable by all
+- Updates multiword CLI commands and options to accept either standard `-`s or backwards-compatible `_`s interchangeably
+- Removes `torch` from preinstalled dependencies and only installs if we're running `unet`
 
-### Added dependency
+### Added dependencies
 
+- `click-aliases`
 - `dc`
 
 ### Removed dependencies

diff --git a/CPAC/__main__.py b/CPAC/__main__.py
@@ -18,6 +18,7 @@
 import os
 import pkg_resources as p
 import click
+from click_aliases import ClickAliasedGroup
 from CPAC.utils.docs import version_report
 
 # CLI tree
@@ -61,9 +62,9 @@ def version():
 
 @main.command()
 @click.argument('data_config')
-@click.option('--pipe_config')
-@click.option('--num_cores')
-@click.option('--ndmg_mode', is_flag=True)
+@click.option('--pipe-config', '--pipe_config')
+@click.option('--num-cores', '--num_cores')
+@click.option('--ndmg-mode', '--ndmg_mode', is_flag=True)
 @click.option('--debug', is_flag=True)
 def run(data_config, pipe_config=None, num_cores=None, ndmg_mode=False,
         debug=False):
@@ -146,7 +147,7 @@ def group():
 
 
 # Group analysis - FSL FEAT
-@group.group()
+@group.group(cls=ClickAliasedGroup)
 def feat():
     pass
 
@@ -172,17 +173,17 @@ def randomise(group_config):
     cgr.run_feat(group_config, feat=False)
 
 
-@feat.group()
+@feat.group(aliases=['load_preset'], cls=ClickAliasedGroup)
 def load_preset():
     pass
 
-@load_preset.command()
+@load_preset.command(aliases=['single_grp_avg'])
 @click.argument('pipeline_dir')
 @click.argument('z_thresh')
 @click.argument('p_thresh')
 @click.argument('model_name')
-@click.option('--output_dir', default=None)
-@click.option('--group_participants', default=None)
+@click.option('--output-dir', '--output_dir', default=None)
+@click.option('--group-participants', '--group_participants', default=None)
 def single_grp_avg(pipeline_dir, z_thresh, p_thresh, model_name,
                    output_dir=None, group_participants=None):
     from CPAC.utils import create_fsl_flame_preset
@@ -193,16 +194,16 @@ def single_grp_avg(pipeline_dir, z_thresh, p_thresh, model_name,
                                 output_dir=output_dir,
                                 model_name=model_name)
 
-@load_preset.command()
+@load_preset.command(aliases=['single_grp_cov'])
 @click.argument('pipeline_dir')
 @click.argument('z_thresh')
 @click.argument('p_thresh')
 @click.argument('pheno_file')
 @click.argument('pheno_sub')
 @click.argument('covariate')
 @click.argument('model_name')
-@click.option('--output_dir', default=None)
-@click.option('--group_participants', default=None)
+@click.option('--output-dir', '--output_dir', default=None)
+@click.option('--group-participants', '--group_participants', default=None)
 def single_grp_cov(pipeline_dir, z_thresh, p_thresh, pheno_file,
                    pheno_sub, covariate, model_name, output_dir=None,
                    group_participants=None):
@@ -216,16 +217,16 @@ def single_grp_cov(pipeline_dir, z_thresh, p_thresh, pheno_file,
                                 covariate=covariate, output_dir=output_dir,
                                 model_name=model_name)
 
-@load_preset.command()
+@load_preset.command(aliases=['unpaired_two'])
 @click.argument('pipeline_dir')
 @click.argument('z_thresh')
 @click.argument('p_thresh')
 @click.argument('pheno_file')
 @click.argument('pheno_sub')
 @click.argument('covariate')
 @click.argument('model_name')
-@click.option('--output_dir', default=None)
-@click.option('--group_participants', default=None)
+@click.option('--output-dir', '--output_dir', default=None)
+@click.option('--group-participants', '--group_participants', default=None)
 def unpaired_two(pipeline_dir, z_thresh, p_thresh, pheno_file,
                  pheno_sub, covariate, model_name, output_dir=None,
                  group_participants=None):
@@ -239,15 +240,15 @@ def unpaired_two(pipeline_dir, z_thresh, p_thresh, pheno_file,
                                 covariate=covariate, output_dir=output_dir,
                                 model_name=model_name)
 
-@load_preset.command()
+@load_preset.command(aliases=['paired_two'])
 @click.argument('pipeline_dir')
 @click.argument('z_thresh')
 @click.argument('p_thresh')
 @click.argument('conditions')
 @click.argument('condition_type')
 @click.argument('model_name')
-@click.option('--output_dir', default=None)
-@click.option('--group_participants', default=None)
+@click.option('--output-dir', '--output_dir', default=None)
+@click.option('--group-participants', '--group_participants', default=None)
 def paired_two(pipeline_dir, z_thresh, p_thresh, conditions,
                condition_type, model_name, output_dir=None,
                group_participants=None):
@@ -261,15 +262,15 @@ def paired_two(pipeline_dir, z_thresh, p_thresh, conditions,
                                 output_dir=output_dir, model_name=model_name)
 
 
-@load_preset.command()
+@load_preset.command(aliases=['tripled_two'])
 @click.argument('pipeline_dir')
 @click.argument('z_thresh')
 @click.argument('p_thresh')
 @click.argument('conditions')
 @click.argument('condition_type')
 @click.argument('model_name')
-@click.option('--output_dir', default=None)
-@click.option('--group_participants', default=None)
+@click.option('--output-dir', '--output_dir', default=None)
+@click.option('--group-participants', '--group_participants', default=None)
 def tripled_two(pipeline_dir, z_thresh, p_thresh, conditions,
                 condition_type, model_name, output_dir=None,
                 group_participants=None):
@@ -313,7 +314,7 @@ def qpp(group_config):
 
 
 # Utilities
-@main.group()
+@main.group(cls=ClickAliasedGroup)
 def utils():
     pass
 
@@ -332,8 +333,8 @@ def accept_all(object, name, value):
         display_crash_file(crash_file, False, False, None)
 
 
-@utils.group()
-@click.option('--tracking_opt-out', is_flag=True,
+@utils.group(aliases=['data_config'], cls=ClickAliasedGroup)
+@click.option('--tracking-opt-out', '--tracking_opt-out', is_flag=True,
               help='Disable usage tracking.')
 def data_config(tracking_opt_out):
     if not tracking_opt_out:
@@ -342,7 +343,7 @@ def data_config(tracking_opt_out):
         track_config('cli')
 
 
-@data_config.command()
+@data_config.command(aliases=['new_settings_template'])
 def new_settings_template():
     from CPAC.utils.build_data_config import util_copy_template
     util_copy_template('data_settings')
@@ -355,8 +356,8 @@ def build(data_settings_file):
     run(data_settings_file)
 
 
-@utils.group()
-@click.option('--tracking_opt-out', is_flag=True,
+@utils.group(aliases=['pipe_config'], cls=ClickAliasedGroup)
+@click.option('--tracking-opt-out', '--tracking_opt-out', is_flag=True,
               help='Disable usage tracking.')
 def pipe_config(tracking_opt_out):
     if not tracking_opt_out:
@@ -365,14 +366,14 @@ def pipe_config(tracking_opt_out):
         track_config('cli')
 
 
-@pipe_config.command(name='new_template')
+@pipe_config.command(name='new-template', aliases=['new_template'])
 def new_pipeline_template():
     from CPAC.utils.build_data_config import util_copy_template
     util_copy_template('pipeline_config')
 
 
-@utils.group()
-@click.option('--tracking_opt-out', is_flag=True,
+@utils.group(aliases=['group_config'], cls=ClickAliasedGroup)
+@click.option('--tracking-opt-out', '--tracking_opt-out', is_flag=True,
               help='Disable usage tracking.')
 def group_config(tracking_opt_out):
     if not tracking_opt_out:
@@ -381,25 +382,25 @@ def group_config(tracking_opt_out):
         track_config('cli')
 
 
-@group_config.command(name='new_template')
+@group_config.command(name='new-template', aliases=['new_template'])
 def new_group_template():
     from CPAC.utils.build_data_config import util_copy_template
     util_copy_template('group_config')
 
 
-@utils.group()
+@utils.group(cls=ClickAliasedGroup)
 def tools():
     pass
 
 
-@tools.command()
+@tools.command(aliases=['ants_apply_warp'])
 @click.argument('moving_image')
 @click.argument('reference')
 @click.option('--initial', default=None)
 @click.option('--rigid', default=None)
 @click.option('--affine', default=None)
 @click.option('--nonlinear', default=None)
-@click.option('--func_to_anat', default=None)
+@click.option('--func-to-anat', '--func_to_anat', default=None)
 @click.option('--dim', default=3)
 @click.option('--interp', default='Linear')
 @click.option('--inverse', default=False)
@@ -424,12 +425,12 @@ def repickle(directory):
         repickle_util(directory)
 
 
-@utils.group()
+@utils.group(cls=ClickAliasedGroup)
 def test():
     pass
 
 
-@test.command()
+@test.command(aliases=['run_suite'])
 @click.option('--list', '-l', 'show_list', is_flag=True)
 @click.option('--filter', '-f', 'pipeline_filter', default='')
 def run_suite(show_list=False, pipeline_filter=''):
@@ -489,12 +490,12 @@ def run_suite(show_list=False, pipeline_filter=''):
         print("")
 
 
-@test.group()
+@test.group(cls=ClickAliasedGroup)
 def functions():
     pass
 
 
-@functions.command()
+@functions.command(aliases=['gather_outputs_func'])
 @click.argument('pipe_config')
 def gather_outputs_func(pipe_config):
     #from CPAC.pipeline.

diff --git a/CPAC/anat_preproc/anat_preproc.py b/CPAC/anat_preproc/anat_preproc.py
@@ -1,8 +1,23 @@
 # -*- coding: utf-8 -*-
-from copy import deepcopy
+# Copyright (C) 2012-2023  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 copy import deepcopy
 import os
 from CPAC.pipeline.nodeblock import nodeblock
-from nipype import logging
 from nipype.interfaces import afni
 from nipype.interfaces import ants
 from nipype.interfaces import fsl
@@ -20,7 +35,6 @@
     VolumeRemoveIslands, \
     normalize_wmparc
 from CPAC.utils.interfaces.fsl import Merge as fslMerge
-from CPAC.unet.function import predict_volumes
 
 
 def acpc_alignment(config=None, acpc_target='whole-head', mask=False,
@@ -719,7 +733,7 @@ def unet_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
     kernel_root: 16
     rescale_dim: 256
     """
-
+    from CPAC.unet.function import predict_volumes
     unet_mask = pe.Node(util.Function(input_names=['model_path', 'cimg_in'],
                                       output_names=['out_path'],
                                       function=predict_volumes),

diff --git a/CPAC/info.py b/CPAC/info.py
@@ -171,6 +171,7 @@ def get_cpac_gitversion():
 REQUIREMENTS = [
     "boto3",
     "click",
+    "click-aliases",
     "configparser",
     "cython",
     "future",

diff --git a/CPAC/pipeline/cpac_pipeline.py b/CPAC/pipeline/cpac_pipeline.py
@@ -425,15 +425,16 @@ def run_workflow(sub_dict, c, run, pipeline_timing_info=None, p_name=None,
                                     'local_functional_connectivity_density'][
                                     'weight_options']) != 0
 
-    # Check system dependencies
-    check_ica_aroma = c.nuisance_corrections['1-ICA-AROMA']['run']
-    if isinstance(check_ica_aroma, list):
-        check_ica_aroma = True in check_ica_aroma
-    check_system_deps(check_ants='ANTS' in c.registration_workflows[
-        'anatomical_registration']['registration']['using'],
-                      check_ica_aroma=check_ica_aroma,
-                      check_centrality_degree=check_centrality_degree,
-                      check_centrality_lfcd=check_centrality_lfcd)
+    if not test_config:
+        # Check system dependencies
+        check_ica_aroma = c.nuisance_corrections['1-ICA-AROMA']['run']
+        if isinstance(check_ica_aroma, list):
+            check_ica_aroma = True in check_ica_aroma
+        check_system_deps(check_ants='ANTS' in c.registration_workflows[
+            'anatomical_registration']['registration']['using'],
+                        check_ica_aroma=check_ica_aroma,
+                        check_centrality_degree=check_centrality_degree,
+                        check_centrality_lfcd=check_centrality_lfcd)
 
     # absolute paths of the dirs
     c.pipeline_setup['working_directory']['path'] = os.path.join(

diff --git a/CPAC/pipeline/engine.py b/CPAC/pipeline/engine.py
@@ -1261,19 +1261,6 @@ def __init__(self, node_block_functions, debug=False):
                     {'logging': {'workflow_level': 'INFO'}})
                 logging.update_logging(config)
 
-            logger.info('Connecting %s...', name)
-            if debug:
-                config.update_config(
-                    {'logging': {'workflow_level': 'DEBUG'}})
-                logging.update_logging(config)
-                logger.debug('"inputs": %s\n\t "outputs": %s%s',
-                             init_dct["inputs"], list(self.outputs.keys()),
-                             f'\n\t"options": {self.options}'
-                             if self.options != ['base'] else '')
-                config.update_config(
-                    {'logging': {'workflow_level': 'INFO'}})
-                logging.update_logging(config)
-
     def get_name(self):
         return self.name
 

diff --git a/CPAC/resources/configs/data_settings_template.yml b/CPAC/resources/configs/data_settings_template.yml
@@ -99,6 +99,16 @@ scanParametersCSV: None
 brain_mask_template: None
 
 
+# File Path for Freesurfer Directory.
+# This should be the directory for the `recon-all` output
+# Each participant should contain subdirectories: label, mri, scripts, stats, surf, tmp, touch, trash
+#
+# Examples:
+# /recon-all_path/{participant}
+# 
+freesurfer_dir: None
+
+
 # File Path Template for Field Map Phase files
 # For field-map based distortion correction.
 # Custom Data Format only.