pydfc 1.0.4__tar.gz

pydfc-1.0.4/.gitattributes

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+*.nii.gz filter=lfs diff=lfs merge=lfs -text

pydfc-1.0.4/.github/workflows/test.yml

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+name: Build and test
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "*"
+  pull_request:
+    branches:
+      - main
+  # Run weekly to avoid missing deprecations during low activity
+  schedule:
+    - cron: '0 0 * * 1'
+  # Allow job to be triggered manually from GitHub interface
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
+# Force tox and pytest to use color
+env:
+  FORCE_COLOR: true
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    # Check each OS, all supported Python, minimum versions and latest releases
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        include:
+          # Basic dependencies only
+          - os: ubuntu-latest
+            python-version: 3.8
+            dependencies: 'min'
+
+    env:
+      DEPENDS: ${{ matrix.dependencies }}
+      ARCH: ${{ !contains(fromJSON('["none", "min"]'), matrix.dependencies) && matrix.architecture }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: ${{ matrix.architecture }}
+          allow-prereleases: true
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install tox
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tox tox-gh-actions
+      - name: Show tox config
+        run: tox c
+      - name: Run tox
+        run: tox -v --exit-and-dump-after 1200
+
+  publish:
+    runs-on: ubuntu-latest
+    environment: "Package deployment"
+    needs: [test]
+    permissions:
+      # Required for trusted publishing
+      id-token: write
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - run: pipx run build
+      - uses: pypa/gh-action-pypi-publish@release/v1

pydfc-1.0.4/.github/workflows/validate_cff.yml

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+---
+name: validate CITATION.cff
+
+on:
+    push:
+        branches: ['*']
+        paths:
+        -   CITATION.cff
+        -   .github/workflows/validate_cff.yml
+    pull_request:
+        branches: ['*']
+        paths:
+        -   CITATION.cff
+        -   .github/workflows/validate_cff.yml
+
+jobs:
+    validate_cff:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   name: Check whether the citation metadata from CITATION.cff is valid
+            uses: citation-file-format/cffconvert-github-action@2.0.0
+            with:
+                args: --validate

pydfc-1.0.4/.gitignore

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+**/.DS_Store
+__pycache__
+*.pyc
+*.cpython
+sample_data/sub-0001_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
+sample_data/sub-0001_task-restingstate_acq-mb3_desc-confounds_regressors.tsv
+sample_data/sub-0002_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
+sample_data/sub-0002_task-restingstate_acq-mb3_desc-confounds_regressors.tsv
+sample_data/sub-0003_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
+sample_data/sub-0003_task-restingstate_acq-mb3_desc-confounds_regressors.tsv
+sample_data/sub-0004_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
+sample_data/sub-0004_task-restingstate_acq-mb3_desc-confounds_regressors.tsv
+sample_data/sub-0005_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
+sample_data/sub-0005_task-restingstate_acq-mb3_desc-confounds_regressors.tsv
+
+# build related
+pydfc.egg-info
+build
+dist/

pydfc-1.0.4/CITATION.cff

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+cff-version: 1.2.0
+
+title: "pydfc"
+
+version: 1.0.2
+
+abstract:
+  "An implementation of several well-known dynamic Functional Connectivity assessment methods."
+
+message: "If you use this software, please cite it as below."
+
+repository-code: "https://github.com/neurodatascience/dFC.git"
+
+
+contact:
+  - affiliation: "McGill University, Québec, Canada"
+    email: mohammad.torabi@mail.mcgill.ca
+    family-names: Torabi
+    given-names: Mohammad
+
+authors:
+  - family-names: "Torabi"
+    given-names: "Mohammad"
+    orcid: "https://orcid.org/0000-0002-4429-8481"
+    affiliation: Biological and Biomedical Engineering program, McGill University, Québec, Canada"
+
+license: MIT
+
+keywords:
+  - dynamic functional connectivity
+  - analytical flexibility
+  - neuroimaging
+  - reproducibility

pydfc-1.0.4/HCP_resting_state_analysis/FCS_estimate.py

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+from functions.dFC_funcs import *
+import numpy as np
+import time
+import hdf5storage
+import scipy.io as sio
+import os
+os.environ["MKL_NUM_THREADS"] = '64'
+os.environ["NUMEXPR_NUM_THREADS"] = '64'
+os.environ["OMP_NUM_THREADS"] = '64'
+
+print('################################# CODE started running ... #################################')
+
+################################# Parameters #################################
+
+###### DATA PARAMETERS ######
+
+output_root = './'
+
+# DATA_type is either 'sample' or 'Gordon' or 'simulated' or 'ICA'
+params_data_load = { 
+    'DATA_type': 'Gordon', 
+    'SESSIONs':['Rest1_LR' , 'Rest1_RL', 'Rest2_LR', 'Rest2_RL'], 
+    'networks2include':['Auditory', 'CinguloOperc', 'Default', 'DorsalAttn', 'FrontoParietal',
+        'MedialParietal', 'ParietoOccip', 'SMhand', 'SMmouth',
+        'Salience', 'VentralAttn', 'Visual'], 
+
+    'data_root_simul': './../../../../DATA/TVB data/', 
+    'data_root_sample': './sampleDATA/', 
+    'data_root_gordon': './../../../../DATA/HCP/HCP_Gordon/', 
+    'data_root_ica': './../../../../DATA/HCP/HCP_PTN1200/node_timeseries/3T_HCP1200_MSMAll_d50_ts2/'
+}
+
+###### MEASUREMENT PARAMETERS ######
+
+# W is in sec
+
+params_methods = { 
+    # Sliding Parameters
+    'W': 44, 'n_overlap': 0.5, 'sw_method':'pear_corr', 'tapered_window':True, 
+    # TIME_FREQ
+    'TF_method':'WTC', 
+    # CLUSTERING AND DHMM
+    'clstr_base_measure':'SlidingWindow', 
+    # HMM
+    'hmm_iter': 30, 'dhmm_obs_state_ratio': 16/24, 
+    # State Parameters
+    'n_states': 12, 'n_subj_clstrs': 20, 
+    # Parallelization Parameters
+    'n_jobs': 2, 'verbose': 0, 'backend': 'loky', 
+    # SESSION
+    'session': 'Rest1_LR', 
+    # Hyper Parameters
+    'normalization': True, 
+    'num_subj': 395, 
+    'num_select_nodes': 96, 
+    'num_time_point': 1200, 
+    'Fs_ratio': 1.00, 
+    'noise_ratio': 0.00, 
+    'num_realization': 1 
+}
+
+###### HYPER PARAMETERS ALTERNATIVE ######
+
+MEASURES_name_lst = [ 
+                'SlidingWindow', 
+                'Time-Freq', 
+                'CAP', 
+                'ContinuousHMM', 
+                'Windowless', 
+                'Clustering', 
+                'DiscreteHMM' 
+]
+
+alter_hparams = { \
+            'session': ['Rest1_RL', 'Rest2_LR', 'Rest2_RL'], 
+            # 'n_overlap': [0, 0.25, 0.75, 1], 
+            # 'n_states': [6, 16], 
+            # # 'normalization': [], 
+            # 'num_subj': [50, 100, 200], 
+            # 'num_select_nodes': [30, 50, 333], 
+            # 'num_time_point': [800, 1000], 
+            # 'Fs_ratio': [0.50, 0.75, 1.5], 
+            # 'noise_ratio': [1.00, 2.00, 3.00], 
+            # 'num_realization': [] 
+            }
+
+###### dFC ANALYZER PARAMETERS ######
+
+params_dFC_analyzer = { 
+    # Parallelization Parameters
+    'n_jobs': None, 'verbose': 0, 'backend': 'loky' 
+}
+
+
+################################# LOAD DATA #################################
+
+data_loader = DATA_LOADER(**params_data_load)
+BOLD = data_loader.load()
+
+################################# Visualize BOLD #################################
+
+# for session in BOLD:
+#     BOLD[session].visualize(start_time=0, end_time=50, nodes_lst=list(range(10)), \
+#         save_image=params_dFC_analyzer['save_image'], output_root=output_root+'BOLD_signal_'+session)
+
+################################# Measures of dFC #################################
+
+dFC_analyzer = DFC_ANALYZER( 
+    analysis_name='reproducibility assessment', 
+    **params_dFC_analyzer 
+)
+
+MEASURES_lst = dFC_analyzer.measures_initializer( 
+    MEASURES_name_lst, 
+    params_methods, 
+    alter_hparams 
+)
+
+tic = time.time()
+print('Measurement Started ...')
+
+################################# estimate FCS #################################
+
+task_id = int(os.getenv("SGE_TASK_ID"))
+MEASURE_id = task_id-1 # SGE_TASK_ID starts from 1 not 0
+
+
+if MEASURE_id >= len(MEASURES_lst):
+    print("MEASURE_id out of MEASURES_lst ")
+else:
+    measure = MEASURES_lst[MEASURE_id]
+
+    print("FCS estimation started...")
+
+    time_series = BOLD[measure.params['session']]
+    if measure.is_state_based:
+        measure.estimate_FCS(time_series=time_series)
+            
+    # dFC_analyzer.estimate_group_FCS(time_series_dict=BOLD)
+    print("FCS estimation done.")
+
+    print('Measurement required %0.3f seconds.' % (time.time() - tic, ))
+
+    # Save
+    np.save(output_root+'fitted_MEASURES/MEASURE_'+str(MEASURE_id)+'.npy', measure) 
+    np.save(output_root+'dFC_analyzer.npy', dFC_analyzer) 
+    np.save(output_root+'data_loader.npy', data_loader) 
+
+#################################################################################

pydfc-1.0.4/HCP_resting_state_analysis/dFC_assessment.py

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+from functions.dFC_funcs import *
+import numpy as np
+import time
+import hdf5storage
+import scipy.io as sio
+import os
+os.environ["MKL_NUM_THREADS"] = '64'
+os.environ["NUMEXPR_NUM_THREADS"] = '64'
+os.environ["OMP_NUM_THREADS"] = '64'
+
+print('################################# subject-level dFC assessment CODE started running ... #################################')
+
+################################# Parameters #################################
+###### DATA PARAMETERS ######
+
+input_root = './'
+output_root = './'
+
+################################# LOAD #################################
+
+dFC_analyzer = np.load(input_root+'dFC_analyzer.npy',allow_pickle='TRUE').item()
+data_loader = np.load(input_root+'data_loader.npy',allow_pickle='TRUE').item()
+
+################################# LOAD FIT MEASURES #################################
+
+if dFC_analyzer.MEASURES_fit_lst==[]:
+    ALL_RECORDS = os.listdir(input_root+'fitted_MEASURES/')
+    ALL_RECORDS = [i for i in ALL_RECORDS if 'MEASURE' in i]
+    ALL_RECORDS.sort()
+    MEASURES_fit_lst = list()
+    for s in ALL_RECORDS:
+        fit_measure = np.load(input_root+'fitted_MEASURES/'+s, allow_pickle='TRUE').item()
+        MEASURES_fit_lst.append(fit_measure)
+    dFC_analyzer.set_MEASURES_fit_lst(MEASURES_fit_lst)
+    print('fitted MEASURES loaded ...')
+    # np.save('./dFC_analyzer.npy', dFC_analyzer) 
+
+################################# LOAD DATA #################################
+
+task_id = int(os.getenv("SGE_TASK_ID"))
+subj_id = data_loader.SUBJECTS[task_id-1] # SGE_TASK_ID starts from 1 not 0
+
+BOLD = data_loader.load(subj_id2load=subj_id)
+
+################################# dFC ASSESSMENT #################################
+
+tic = time.time()
+print('Measurement Started ...')
+
+print("dFCM estimation started...")
+dFCM_dict = dFC_analyzer.subj_lvl_dFC_assess(time_series_dict=BOLD)
+print("dFCM estimation done.")
+
+print('Measurement required %0.3f seconds.' % (time.time() - tic, ))
+
+################################# SAVE DATA #################################
+
+# folder = output_root+'dFC_assessed/SUBJ_'+str(subj_id)
+# if not os.path.exists(folder):
+#     os.makedirs(folder)
+
+# for dFCM_id, dFCM in enumerate(dFCM_dict['dFCM_lst']):
+#     np.save(folder+'/dFCM_'+str(dFCM_id)+'.npy', dFCM) 
+
+################################# SIMILARITY MEASUREMENT #################################
+
+similarity_assessment = SIMILARITY_ASSESSMENT(dFCM_lst=dFCM_dict['dFCM_lst'])
+
+tic = time.time()
+print('Measurement Started ...')
+
+print("Similarity measurement started...")
+SUBJ_output = similarity_assessment.run(FILTERS=dFC_analyzer.hyper_param_info, downsampling_method='default')
+print("Similarity measurement done.")
+
+print('Measurement required %0.3f seconds.' % (time.time() - tic, ))
+
+# Save
+folder = output_root+'similarity_measured'
+if not os.path.exists(folder):
+    os.makedirs(folder)
+
+np.save(folder+'/SUBJ_'+str(subj_id)+'_output.npy', SUBJ_output) 
+
+#################################################################################