wip: bidsy cli

Author: akeshavan

dmriprep/cli.py

@@ -3,14 +3,51 @@
 """Console script for dmriprep."""
 import sys
 import click
+from . import run
+from . import io
+import os
 
 
 @click.command()
-def main(args=None):
-    """Console script for dmriprep."""
-    click.echo("Replace this message by putting your code into "
-               "dmriprep.cli.main")
-    click.echo("See click documentation at http://click.pocoo.org/")
+@click.option('--participant-label', help="The label(s) of the participant(s) that should be"
+                                           "analyzed. The label corresponds to"
+                                           "sub-<participant_label> from the BIDS spec (so it does"
+                                           "not include 'sub-'). If this parameter is not provided"
+                                           "all subjects will be analyzed. Multiple participants"
+                                           "can be specified with a space separated list.",
+              default=None
+              )
+@click.argument('bids_dir',
+                )
+@click.argument('output_dir',
+                )
+@click.argument('analysis_level',
+                type=click.Choice(['participant', 'group']),
+                default='participant')
+def main(participant_label, bids_dir, output_dir, analysis_level="participant"):
+    """
+    BIDS_DIR: The directory with the input dataset formatted according to the BIDS standard.
+
+    OUTPUT_DIR: The directory where the output files should be stored.
+    If you are running a group level analysis, this folder
+    should be prepopulated with the results of
+    the participant level analysis.
+
+    ANALYSIS_LEVEL: Level of the analysis that will be performed. Multiple
+    participant level analyses can be run independently
+    (in parallel).
+    """
+
+    if analysis_level is not 'participant':
+        raise NotImplementedError('The only valid analysis level for dmriprep is participant at the moment.')
+
+    inputs = io.get_BIDS_files(participant_label, bids_dir)
+
+    # for subject_id, subject_inputs in inputs:
+    #     run.run_dmriprep_pe(**subject_inputs,
+    #                         working_dir=os.path.join(output_dir, 'scratch'),
+    #                         out_dir=output_dir)
+    click.echo('doing stuff {} {} {} {}'.format(participant_label, bids_dir, output_dir, analysis_level))
     return 0
 
 

dmriprep/dmriprep.py

@@ -11,46 +11,3 @@
 
 
 mod_logger = logging.getLogger(__name__)
-
-
-
-def pre_afq_individual(input_s3_keys, s3_prefix, out_bucket,
-                       in_bucket='fcp-indi', workdir=op.abspath('.')):
-    input_files = fetch.download_register(
-        subject_keys=input_s3_keys,
-        bucket=in_bucket,
-        directory=op.abspath(op.join(workdir, 'input')),
-    )
-
-    move_t1_to_freesurfer(input_files.files['t1w'][0])
-
-    scratch_dir = op.join(workdir, 'scratch')
-    out_dir = op.join(workdir, 'output')
-
-    run_dmriprep(
-        dwi_file=input_files.files['dwi'][0],
-        dwi_file_AP=input_files.files['epi_ap'][0],
-        dwi_file_PA=input_files.files['epi_pa'][0],
-        bvec_file=input_files.files['bvec'][0],
-        bval_file=input_files.files['bval'][0],
-        subjects_dir=op.dirname(input_files.files['t1w'][0]),
-        working_dir=scratch_dir,
-        out_dir=out_dir,
-    )
-
-    out_files = []
-    for root, dirs, filenames in os.walk(out_dir):
-        for filename in filenames:
-            rel_path = op.join(root, filename)
-            if op.isfile(rel_path):
-                out_files.append(rel_path.replace(out_dir + '/', '', 1))
-
-    s3_output = upload_to_s3(output_files=out_files,
-                             outdir=out_dir,
-                             bucket=out_bucket,
-                             prefix=s3_prefix,
-                             site=input_s3_keys.site,
-                             session=input_s3_keys.session,
-                             subject=input_s3_keys.subject)
-
-    return s3_output

dmriprep/io.py

@@ -0,0 +1,10 @@
+"""
+BIDS-functions to return inputs for the run.py functions.
+
+"""
+from glob import glob
+import os
+
+def get_BIDS_files(subject_id, bids_input_directory):
+    if not subject_id:
+        subjects = glob(os.path.join(bids_input_directory, "*"))

dmriprep/run.py

@@ -264,7 +264,7 @@ def run_dmriprep_pe(dwi_file, dwi_file_AP, dwi_file_PA, bvec_file, bval_file,
     prep.inputs.inputnode.in_bval = bval_file
     eddy = prep.get_node('fsl_eddy')
     eddy.inputs.repol = True
-    eddy.inputs.niter = 1  # TODO: change back to 5 when running for real
+    eddy.inputs.niter = 1  # TODO: make this a parameter to the function with default 5
 
     merge = pe.Node(fsl.Merge(dimension='t'), name="mergeAPPA")
     merge.inputs.in_files = [dwi_file_AP, dwi_file_PA]
@@ -429,7 +429,9 @@ def reportNodeFunc(dwi_corrected_file, eddy_rms, eddy_report,
     wf.connect(get_tensor, "color_fa_file", reportNode, 'color_fa_file')
 
     wf.connect(reportNode, 'report', datasink, 'dmriprep.report.@report')
+    wf.write_graph()
 
+    # TODO: take this out and just return workflow
     wf.run()
 
     copyfile(bval_file, op.join(