Rf/smoothing (#412)

Add analysis-level option to XCP

.circleci/RunPyTests.sh

@@ -39,7 +39,7 @@ run_pytest_cmd () {
     cwd_mount="-v ${PWD}/tests:/rundir:rw"
     PYTEST_RUN="docker run --rm -ti -u $(id -u) -w /rundir --entrypoint pytest "
     PYTEST_RUN+="${workdir_mount} ${patch_mount} ${cwd_mount} ${cfg_arg} ${bids_mount} ${output_mount} ${IMAGE} "
-    PYTEST_RUN+="--data_dir=/bids-input --output_dir=/out --working_dir=/work /rundir"
+    PYTEST_RUN+="--data_dir=/bids-input --output_dir=/out participant --working_dir=/work /rundir"
 
   fi
 

.circleci/get_data.sh

@@ -5,7 +5,7 @@ fi
 
 # Edit these for project-wide testing
 WGET="wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q"
-LOCAL_PATCH=~/projects/xcp_d/xcp_d
+LOCAL_PATCH=/Users/kahinim/Desktop/Repos/xcp_d/xcp_d
 IMAGE=pennlinc/xcp_d:unstable
 
 # Determine if we're in a CI test
@@ -32,7 +32,7 @@ run_xcpd_cmd () {
   # test that uses 
   if [[ "${CIRCLECI}" = "true" ]]; then
     # In circleci we're running from inside the container. call directly
-    XCPD_RUN="/usr/local/miniconda/bin/xcp_d ${bids_dir} ${output_dir} -w ${workdir}"
+    XCPD_RUN="/usr/local/miniconda/bin/xcp_d ${bids_dir} ${output_dir} participant -w ${workdir}"
   else
     patch_mount=""
     if [[ -n "${LOCAL_PATCH}" ]]; then
@@ -50,7 +50,7 @@ run_xcpd_cmd () {
     bids_mount="-v ${bids_dir}:/bids-input:ro"
     output_mount="-v ${output_dir}:/out:rw"
     workdir_mount="-v ${workdir}:/work:rw"
-    XCPD_RUN="docker run --rm -u $(id -u) ${workdir_mount} ${patch_mount} ${cfg_arg} ${bids_mount} ${output_mount} ${IMAGE} /bids-input /out -w /work"
+    XCPD_RUN="docker run --rm -u $(id -u) ${workdir_mount} ${patch_mount} ${cfg_arg} ${bids_mount} ${output_mount} ${IMAGE} /bids-input /out participant -w /work"
 
   fi
   echo "${XCPD_RUN} --nthreads ${NTHREADS} --omp-nthreads ${OMP_NTHREADS}"

setup.cfg

@@ -28,6 +28,7 @@ install_requires =
     brainsprite ~= 0.14.2
     psutil >= 5.4
     pybids >= 0.14.0
+    matplotlib ~= 3.3.4 
     pyyaml
     templateflow ~= 0.6.1
     sentry-sdk ~= 1.4.3

xcp_d/cli/run.py

@@ -60,6 +60,10 @@ def get_parser():
                         action='store',
                         type=Path,
                         help='the output path for xcp_d')
+    parser.add_argument('analysis_level',
+                        action='store',
+                        type=Path,
+                        help='the output path for xcp_d')
 
     # optional arguments
     parser.add_argument('--version', action='version', version=verstr)
@@ -482,6 +486,12 @@ def build_workflow(opts, retval):
             'derivatives' / ('xcp_d-%s' % __version__.split('+')[0]))
         retval['return_code'] = 1
         return retval
+    if str(opts.analysis_level) != 'participant':
+        print (opts.analysis_level)
+        build_log.error(
+            'Please select analysis level "participant"')
+        retval['return_code'] = 1
+        return retval
 
     # First check that fmriprep_dir looks like a BIDS folder
     if opts.input_type == 'dcan':
@@ -623,6 +633,7 @@ def build_workflow(opts, retval):
         smoothing=opts.smoothing,
         params=opts.nuissance_regressors,
         cifti=opts.cifti,
+        analysis_level=opts.analysis_level,
         output_dir=str(output_dir),
         head_radius=opts.head_radius,
         custom_confounds=opts.custom_confounds,

xcp_d/workflow/base.py

@@ -44,6 +44,7 @@ def init_xcpd_wf(layout,
                  head_radius,
                  params,
                  subject_list,
+                 analysis_level,
                  smoothing,
                  custom_confounds,
                  output_dir,
@@ -79,6 +80,7 @@ def init_xcpd_wf(layout,
                 brain_template,
                 subject_list,
                 smoothing,
+                analysis_level,
                 custom_confounds,
                 output_dir,
                 work_dir,
@@ -96,6 +98,8 @@ def init_xcpd_wf(layout,
         BIDS dataset layout
     despike: bool
         afni depsike
+    analysis_level: str
+        only option is 'participant'
     motion_filter_type: str
         respiratory motion filter type: lp or notch
     motion_filter_order: str