Merge pull request #107 from jhlegarreta/ref/clean-up-conf-params

REF: Remove unused parameters from PET confound workflow initialization

Author: mnoergaard

docs/workflows.rst

@@ -580,11 +580,6 @@ Confounds estimation
     wf = init_pet_confs_wf(
         name="discover_wf",
         mem_gb=1,
-        metadata={
-            "FrameTimesStart": [0, 2, 4, 6],
-            "FrameDuration": [2, 2, 2, 2],
-        },
-        regressors_all_comps=False,
         regressors_dvars_th=1.5,
         regressors_fd_th=0.5,
     )

petprep/workflows/pet/base.py

@@ -754,9 +754,7 @@ def init_pet_wf(
     if nvols > 2:  # run these only if PET has at least 3 frames
         pet_confounds_wf = init_pet_confs_wf(
             mem_gb=mem_gb['largemem'],
-            metadata=all_metadata[0],
             freesurfer=config.workflow.run_reconall,
-            regressors_all_comps=config.workflow.regressors_all_comps,
             regressors_fd_th=config.workflow.regressors_fd_th,
             regressors_dvars_th=config.workflow.regressors_dvars_th,
             name='pet_confounds_wf',

petprep/workflows/pet/confounds.py

@@ -47,8 +47,6 @@
 
 def init_pet_confs_wf(
     mem_gb: float,
-    metadata: dict,
-    regressors_all_comps: bool,
     regressors_dvars_th: float,
     regressors_fd_th: float,
     freesurfer: bool = False,
@@ -87,8 +85,6 @@ def init_pet_confs_wf(
             from petprep.workflows.pet.confounds import init_pet_confs_wf
             wf = init_pet_confs_wf(
                 mem_gb=1,
-                metadata={},
-                regressors_all_comps=False,
                 regressors_dvars_th=1.5,
                 regressors_fd_th=0.5,
             )
@@ -99,14 +95,8 @@ def init_pet_confs_wf(
         Size of PET file in GB - please note that this size
         should be calculated after resamplings that may extend
         the FoV
-    metadata : :obj:`dict`
-        BIDS metadata for PET file
     name : :obj:`str`
         Name of workflow (default: ``pet_confs_wf``)
-    regressors_all_comps : :obj:`bool`
-        Indicates whether CompCor decompositions should return all
-        components instead of the minimal number of components necessary
-        to explain 50 percent of the variance in the decomposition mask.
     regressors_dvars_th : :obj:`float`
         Criterion for flagging DVARS outliers
     regressors_fd_th : :obj:`float`

petprep/workflows/pet/tests/test_confounds.py

@@ -8,8 +8,6 @@ def test_dvars_connects_pet_mask(tmp_path):
     """Check dvars node connection and execution."""
     wf = init_pet_confs_wf(
         mem_gb=0.01,
-        metadata={},
-        regressors_all_comps=False,
         regressors_dvars_th=1.5,
         regressors_fd_th=0.5,
     )