add test

.circleci/config.yml

@@ -125,6 +125,30 @@ jobs:
           paths:
             - /src/qsirecon/.circleci/data/hsvs_data
 
+  Recon_SS3T_FOD_AutoTrack:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - restore_cache:
+          key: singleshell_output-01
+      - run: *runinstall
+      - run:
+          name: Test the SS3T AutoTrack workflow
+          no_output_timeout: 1h
+          command: |
+            pytest -rP -o log_cli=true -m "ss3t_fod_autotrack" --cov-config=/src/qsirecon/pyproject.toml --cov-append --cov-report term-missing --cov=qsirecon --data_dir=/src/qsirecon/.circleci/data --output_dir=/src/qsirecon/.circleci/out --working_dir=/src/qsirecon/.circleci/work qsirecon
+            mkdir /src/coverage
+            mv /src/qsirecon/.coverage /src/coverage/.coverage.ss3t_fod_autotrack
+            # remove nifti files before uploading artifacts
+            find /src/qsirecon/.circleci/out/ -name "*.nii.gz" -type f -delete
+            find /src/qsirecon/.circleci/out/ -name "*.fib.gz" -type f -delete
+      - persist_to_workspace:
+          root: /src/coverage/
+          paths:
+            - /src/coverage/.coverage.ss3t_fod_autotrack
+      - store_artifacts:
+          path: /src/qsirecon/.circleci/out/ss3t_fod_autotrack/
+
   Recon_3Tissue_Singleshell_ACT:
     <<: *dockersetup
     steps:
@@ -616,6 +640,13 @@ workflows:
             tags:
               only: /.*/
 
+      - Recon_SS3T_FOD_AutoTrack:
+          requires:
+            - download_singleshell_output
+          filters:
+            tags:
+              only: /.*/
+
       - Recon_msmt_Multishell_HSVS:
           requires:
             - download_hsvs_data
@@ -718,6 +749,7 @@ workflows:
           requires:
             - Recon_3Tissue_Singleshell_ACT
             - Recon_3Tissue_Singleshell_NoACT
+            - Recon_SS3T_FOD_AutoTrack
             - Recon_MRtrix3
             - Recon_Interfaces
             - Recon_AutoTrack
@@ -743,6 +775,7 @@ workflows:
           requires:
             - Recon_3Tissue_Singleshell_ACT
             - Recon_3Tissue_Singleshell_NoACT
+            - Recon_SS3T_FOD_AutoTrack
             - Recon_MRtrix3
             - Recon_Interfaces
             - Recon_msmt_Multishell_HSVS

qsirecon/tests/data/ss3t_fod_autotrack_outputs.txt

@@ -0,0 +1,41 @@
+atlases
+atlases/atlas-Gordon333Ext
+atlases/atlas-Gordon333Ext/atlas-Gordon333Ext_dseg.tsv
+atlases/atlas-Gordon333Ext/atlas-Gordon333Ext_space-MNI152NLin2009cAsym_res-01_dseg.json
+atlases/atlas-Gordon333Ext/atlas-Gordon333Ext_space-MNI152NLin2009cAsym_res-01_dseg.nii.gz
+atlases/dataset_description.json
+dataset_description.json
+derivatives
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/dataset_description.json
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/logs
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/logs/CITATION.bib
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/logs/CITATION.html
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/logs/CITATION.md
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/logs/CITATION.tex
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC.html
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_connectivity.mat
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_exemplarbundles.zip
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-mtnorm_param-inliermask_dwimap.nii.gz
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-mtnorm_param-norm_dwimap.nii.gz
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-sdstream_streamlines.tck.gz
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-sift2_mu.txt
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-sift2_streamlineweights.csv
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-CSF_dwimap.mif.gz
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-CSF_dwimap.txt
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-GM_dwimap.mif.gz
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-GM_dwimap.txt
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-WM_dwimap.mif.gz
+derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-WM_dwimap.txt
+logs
+logs/CITATION.bib
+logs/CITATION.html
+logs/CITATION.md
+logs/CITATION.tex
+sub-PNC
+sub-PNC/dwi
+sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_seg-Gordon333Ext_dseg.mif.gz
+sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_seg-Gordon333Ext_dseg.nii.gz
+sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_seg-Gordon333Ext_dseg.txt

qsirecon/tests/test_cli.py

@@ -26,6 +26,34 @@
 nipype_config.enable_debug_mode()
 
 
+@pytest.mark.integration
+@pytest.mark.ss3t_fod_autotrack
+def test_mrtrix_singleshell_ss3t_fod_autotrack(data_dir, output_dir, working_dir):
+    """Test the ss3t FOD-based autotrack workflow.
+
+    Inputs
+    ------
+    - qsirecon single shell results
+    """
+    TEST_NAME = "ss3t_fod_autotrack"
+
+    dataset_dir = download_test_data("singleshell_output", data_dir)
+    dataset_dir = os.path.join(dataset_dir, "qsiprep")
+    out_dir = os.path.join(output_dir, TEST_NAME)
+    work_dir = os.path.join(working_dir, TEST_NAME)
+
+    parameters = [
+        dataset_dir,
+        out_dir,
+        "participant",
+        f"-w={work_dir}",
+        "--sloppy",
+        "--recon-spec=ss3t_fod_autotrack",
+    ]
+
+    _run_and_generate(TEST_NAME, parameters, test_main=False)
+
+
 @pytest.mark.integration
 @pytest.mark.mrtrix_singleshell_ss3t_act
 def test_mrtrix_singleshell_ss3t_act(data_dir, output_dir, working_dir):

qsirecon/workflows/recon/build_workflow.py

@@ -1,7 +1,6 @@
 import nipype.pipeline.engine as pe
 from nipype.interfaces import utility as niu
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
-from scipy import special
 
 from ... import config
 from ...interfaces.interchange import default_input_set, recon_workflow_input_fields