Merge pull request #198 from oesteban/fix/ReadSidecarJSON

[RTM] Some love to sdc_unwarp

circle.yml

@@ -29,9 +29,9 @@ dependencies:
 test:
   override:
     - docker run -ti --rm --entrypoint="/usr/bin/run_unittests" poldracklab/fmriprep:latest
-    - docker run -ti --rm -v /etc/localtime:/etc/localtime:ro -v $HOME/nipype.cfg:/root/.nipype/nipype.cfg:ro -v $HOME/data:/data:ro -v $HOME/ds054/scratch:/scratch -v $HOME/ds054/out:/out poldracklab/fmriprep:latest /data/ds054 /out/ participant -t ds054 --debug --write-graph -w /scratch:
+    - docker run -ti --rm -v /etc/localtime:/etc/localtime:ro -v $HOME/nipype.cfg:/root/.nipype/nipype.cfg:ro -v $HOME/data:/data:ro -v $HOME/ds054/scratch:/scratch -v $HOME/ds054/out:/out poldracklab/fmriprep:latest /data/ds054 /out/ participant -t ds054 --debug -w /scratch:
         timeout: 4800
-    - docker run -ti --rm -v /etc/localtime:/etc/localtime:ro -v $HOME/nipype.cfg:/root/.nipype/nipype.cfg:ro -v $HOME/data:/data:ro -v $HOME/ds005/scratch:/scratch -v $HOME/ds005/out:/out poldracklab/fmriprep:latest /data/ds005 /out/ participant -t ds005 --debug --write-graph --no-skull-strip-ants -w /scratch:
+    - docker run -ti --rm -v /etc/localtime:/etc/localtime:ro -v $HOME/nipype.cfg:/root/.nipype/nipype.cfg:ro -v $HOME/data:/data:ro -v $HOME/ds005/scratch:/scratch -v $HOME/ds005/out:/out poldracklab/fmriprep:latest /data/ds005 /out/ participant -t ds005 --debug --no-skull-strip-ants -w /scratch:
         timeout: 4800
     - find ~/ds054/scratch -not -name "*.svg" -not -name "*.html" -not -name "*.svg" -not -name "*.rst" -type f -delete
     - find ~/ds005/scratch -not -name "*.svg" -not -name "*.html" -not -name "*.svg" -not -name "*.rst" -type f -delete

fmriprep/interfaces/bids.py

@@ -6,7 +6,7 @@
 # @Author: oesteban
 # @Date:   2016-06-03 09:35:13
 # @Last Modified by:   oesteban
-# @Last Modified time: 2016-10-05 15:03:25
+# @Last Modified time: 2016-12-02 17:31:40
 import os
 import os.path as op
 import pkg_resources as pkgr
@@ -16,7 +16,7 @@
 
 from nipype import logging
 from nipype.interfaces.base import (
-    traits, isdefined, TraitedSpec, BaseInterface, BaseInterfaceInputSpec, 
+    traits, isdefined, TraitedSpec, BaseInterface, BaseInterfaceInputSpec,
     File, InputMultiPath, OutputMultiPath
 )
 
@@ -158,38 +158,50 @@ class ReadSidecarJSONInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='the input nifti file')
     fields = traits.List(traits.Str, desc='get only certain fields')
 
-
 class ReadSidecarJSONOutputSpec(TraitedSpec):
+    subject_id = traits.Str()
+    session_id = traits.Str()
+    task_id = traits.Str()
+    acq_id = traits.Str()
+    rec_id = traits.Str()
+    run_id = traits.Str()
     out_dict = traits.Dict()
 
-
 class ReadSidecarJSON(BaseInterface):
     """
     An utility to find and read JSON sidecar files of a BIDS tree
     """
-
+    expr = re.compile('^sub-(?P<subject_id>[a-zA-Z0-9]+)(_ses-(?P<session_id>[a-zA-Z0-9]+))?'
+                      '(_task-(?P<task_id>[a-zA-Z0-9]+))?(_acq-(?P<acq_id>[a-zA-Z0-9]+))?'
+                      '(_rec-(?P<rec_id>[a-zA-Z0-9]+))?(_run-(?P<run_id>[a-zA-Z0-9]+))?')
     input_spec = ReadSidecarJSONInputSpec
     output_spec = ReadSidecarJSONOutputSpec
 
     def __init__(self, **inputs):
         self._results = {}
         super(ReadSidecarJSON, self).__init__(**inputs)
 
+    def _list_outputs(self):
+        return self._results
+
     def _run_interface(self, runtime):
         metadata = get_metadata_for_nifti(self.inputs.in_file)
+        output_keys = [key for key in list(self.output_spec().get().keys()) if key.endswith('_id')]
+        outputs = self.expr.search(op.basename(self.inputs.in_file)).groupdict()
+
+        for key in output_keys:
+            id_value = outputs.get(key)
+            if id_value is not None:
+                self._results[key] = outputs.get(key)
 
         if isdefined(self.inputs.fields) and self.inputs.fields:
             for fname in self.inputs.fields:
                 self._results[fname] = metadata[fname]
         else:
-            self._results = metadata
+            self._results['out_dict'] = metadata
 
         return runtime
 
-    def _list_outputs(self):
-        out = self.output_spec().get()
-        out['out_dict'] = self._results
-        return out
 
 def get_metadata_for_nifti(in_file):
     """Fetchs metadata for a given nifi file"""
@@ -201,7 +213,7 @@ def get_metadata_for_nifti(in_file):
         ext = ext2 + ext
 
     side_json = fname + '.json'
-    fname_comps = side_json.split('/')[-1].split("_")
+    fname_comps = op.basename(side_json).split("_")
 
     session_comp_list = []
     subject_comp_list = []
@@ -221,15 +233,19 @@ def get_metadata_for_nifti(in_file):
                 else:
                     top_comp_list.append(comp)
 
+    if any([comp.startswith('ses') for comp in fname_comps]):
+        bids_dir = '/'.join(op.dirname(in_file).split('/')[:-3])
+    else:
+        bids_dir = '/'.join(op.dirname(in_file).split('/')[:-2])
 
-    top_json = "/" + "_".join(top_comp_list)
+    top_json = op.join(bids_dir, "_".join(top_comp_list))
     potential_json = [top_json]
 
-    subject_json = "/" + sub + "/" + "_".join(subject_comp_list)
+    subject_json = op.join(bids_dir, sub, "_".join(subject_comp_list))
     potential_json.append(subject_json)
 
     if ses:
-        session_json = "/" + sub + "/" + ses + "/" + "_".join(session_comp_list)
+        session_json = op.join(bids_dir, sub, ses, "_".join(session_comp_list))
         potential_json.append(session_json)
 
     potential_json.append(side_json)

fmriprep/workflows/fieldmap/__init__.py

@@ -6,6 +6,6 @@
 Fieldmap-processing workflows.
 
 """
-from fmriprep.workflows.fieldmap.base import create_encoding_file, mcflirt2topup
+from fmriprep.workflows.fieldmap.utils import create_encoding_file, mcflirt2topup
 from fmriprep.workflows.fieldmap.phase_diff_and_magnitudes import phase_diff_and_magnitudes
 from fmriprep.workflows.fieldmap.unwarp import sdc_unwarp

fmriprep/workflows/fieldmap/base.py

@@ -1,10 +1,26 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+Base fieldmap handling utilities.
+
+Possible fieldmap specifications according to BIDS 1.0.0
+--------------------------------------------------------
+
+8.9.1 one phase diff image, at least one magnitude image
+8.9.2 two phase images, two magnitude images
+8.9.3 fieldmap image (and one magnitude image)
+8.9.4 multiple phase encoded directions (topup)
+
+"""
+from __future__ import print_function, division, absolute_import, unicode_literals
 from future.utils import raise_from
 
 from nipype import logging
 
 LOGGER = logging.getLogger('workflow')
 
-
 def is_fmap_type(fmap_type, filename):
     from fmriprep.utils import misc
     import re
@@ -25,13 +41,6 @@ def sort_fmaps(fieldmaps):  # i.e. filenames
 def fieldmap_decider(fieldmap_data, settings):
     ''' Run fieldmap_decider to automatically find a
     Fieldmap preprocessing workflow '''
-
-    # POSSIBLE FILES ACCORDING TO BIDS 1.0.0
-    # 8.9.1 one phase diff image, at least one magnitude image
-    # 8.9.2 two phase images, two magnitude images
-    # 8.9.3 fieldmap image (and one magnitude image)
-    # 8.9.4 multiple phase encoded directions (topup)
-
     # inputs = { 'fieldmaps': None }
     # outputs = { 'fieldmaps': None,
     #             'outputnode.mag_brain': None,
@@ -58,60 +67,3 @@ def fieldmap_decider(fieldmap_data, settings):
             return se_fmap_workflow(settings=settings)
 
     raise IOError("Unrecognized fieldmap structure")
-
-
-def create_encoding_file(input_images, in_dict):
-    """Creates a valid encoding file for topup"""
-    import json
-    import nibabel as nb
-    import numpy as np
-    import os
-
-    if not isinstance(input_images, list):
-        input_images = [input_images]
-    if not isinstance(in_dict, list):
-        in_dict = [in_dict]
-
-    pe_dirs = {'i': 0, 'j': 1, 'k': 2}
-    enc_table = []
-    for fmap, meta in zip(input_images, in_dict):
-        line_values = [0, 0, 0, meta['TotalReadoutTime']]
-        line_values[pe_dirs[meta['PhaseEncodingDirection'][0]]] = 1 + (
-            -2*(len(meta['PhaseEncodingDirection']) == 2))
-
-        nvols = 1
-        if len(nb.load(fmap).shape) > 3:
-            nvols = nb.load(fmap).shape[3]
-
-        enc_table += [line_values] * nvols
-
-    np.savetxt(os.path.abspath('parameters.txt'), enc_table, fmt=['%0.1f', '%0.1f', '%0.1f', '%0.20f'])
-    return os.path.abspath('parameters.txt')
-
-
-def mcflirt2topup(in_files, in_mats, out_movpar=None):
-    """
-    Converts a list of matrices from MCFLIRT to the movpar input
-    of TOPUP (a row per file with 6 parameters - 3 translations and 3 rotations
-    in this particular order).
-
-    """
-
-    import os.path as op
-    import numpy as np
-    params = np.zeros((len(in_files), 6))
-
-    if in_mats:
-        if len(in_mats) != len(in_files):
-            raise RuntimeError('Number of input matrices and files do not match')
-        else:
-            raise NotImplementedError
-
-    if out_movpar is None:
-        fname, fext = op.splitext(op.basename(in_files[0]))
-        if fext == '.gz':
-            fname, _ = op.splitext(fname)
-        out_movpar = op.abspath('./%s_movpar.txt' % fname)
-
-    np.savetxt(out_movpar, params)
-    return out_movpar

fmriprep/workflows/fieldmap/phase_diff_and_magnitudes.py

@@ -1,4 +1,13 @@
-from __future__ import division
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+Fieldmap preprocessing workflow for fieldmap data structure
+8.9.1 in BIDS 1.0.0: one phase diff and at least one magnitude image
+
+"""
+from __future__ import print_function, division, absolute_import, unicode_literals
 
 import logging
 import os.path as op
@@ -16,9 +25,6 @@
 from fmriprep.utils.misc import fieldmap_suffixes
 from fmriprep.viz import stripped_brain_overlay
 
-''' Fieldmap preprocessing workflow for fieldmap data structure
-8.9.1 in BIDS 1.0.0: one phase diff and at least one magnitude image'''
-
 
 def _sort_fmaps(input_images):
     ''' just a little data massaging'''
@@ -56,7 +62,7 @@ def _pick1st(inlist):
         return inlist[0]
 
     # Read phasediff echo times
-    meta = pe.Node(ReadSidecarJSON(fields=['EchoTime1', 'EchoTime2']), name='metadata')
+    meta = pe.Node(ReadSidecarJSON(), name='metadata')
     dte = pe.Node(niu.Function(input_names=['in_values'], output_names=['delta_te'],
                                function=_delta_te), name='ComputeDeltaTE')
 
@@ -199,14 +205,18 @@ def phdiff2fmap(in_file, delta_te, out_file=None):
     return out_file
 
 
-def _delta_te(in_values):
+def _delta_te(in_values, te1=None, te2=None):
     if isinstance(in_values, float):
         te2 = in_values
         te1 = 0.
 
     if isinstance(in_values, dict):
-        te1 = in_values['EchoTime1']
-        te2 = in_values['EchoTime2']
+        te1 = in_values.get('EchoTime1')
+        te2 = in_values.get('EchoTime2')
+
+        if not all((te1, te2)):
+            te2 = in_values.get('EchoTimeDifference')
+            te1 = 0
 
     if isinstance(in_values, list):
         te2, te1 = in_values
@@ -215,4 +225,8 @@ def _delta_te(in_values):
         if isinstance(te2, list):
             te2 = te2[1]
 
+    if te1 is None or te2 is None:
+        raise RuntimeError(
+            'No echo time information found')
+
     return abs(float(te2)-float(te1))

fmriprep/workflows/fieldmap/se_fmap_workflow.py

@@ -13,7 +13,7 @@
 from fmriprep.utils.misc import _first, gen_list
 from fmriprep.interfaces import ImageDataSink, ReadSidecarJSON
 from fmriprep.viz import stripped_brain_overlay
-from fmriprep.workflows.fieldmap.base import create_encoding_file
+from fmriprep.workflows.fieldmap.utils import create_encoding_file
 
 WORKFLOW_NAME = 'Fieldmap_SEs'