Add HMC dev from sprint 2020

Rename to EMC (Eddy Motion Correction) and fix several workflow bugs

MANIFEST.in

@@ -8,3 +8,4 @@ include dmriprep/_version.py
 
 # data
 include dmriprep/config/reports-spec.yml
+recursive-include * *.json

dmriprep/config/emc_coarse_Affine.json

@@ -0,0 +1,25 @@
+{
+    "dimension": 3,
+    "float": true,
+    "winsorize_lower_quantile": 0.002,
+    "winsorize_upper_quantile": 0.998,
+    "collapse_output_transforms": true,
+    "write_composite_transform": false,
+    "use_histogram_matching": [ false, false ],
+    "use_estimate_learning_rate_once": [ true, true ],
+    "transforms": [ "Rigid", "Affine" ],
+    "number_of_iterations": [ [ 100, 100 ], [ 100 ] ],
+    "output_warped_image": true,
+    "transform_parameters": [ [ 0.2 ], [ 0.15 ] ],
+    "convergence_threshold": [ 1e-06, 1e-06 ],
+    "convergence_window_size": [ 20, 20 ],
+    "metric": [ "Mattes", "Mattes" ],
+    "sampling_percentage": [ 0.15, 0.2 ],
+    "sampling_strategy": [ "Random", "Random" ],
+    "smoothing_sigmas": [ [ 8.0, 2.0 ], [ 2.0 ] ],
+    "sigma_units": [ "mm", "mm" ],
+    "metric_weight": [ 1.0, 1.0 ],
+    "shrink_factors": [ [ 2, 1 ], [ 1 ] ],
+    "radius_or_number_of_bins": [ 48, 48 ],
+    "interpolation": "BSpline"
+}

dmriprep/config/emc_coarse_Rigid.json

@@ -0,0 +1,25 @@
+{
+    "dimension": 3,
+    "float": true,
+    "winsorize_lower_quantile": 0.002,
+    "winsorize_upper_quantile": 0.998,
+    "collapse_output_transforms": true,
+    "write_composite_transform": false,
+    "use_histogram_matching": [ false ],
+    "use_estimate_learning_rate_once": [ true ],
+    "transforms": [ "Rigid" ],
+    "number_of_iterations": [ [ 100, 100 ] ],
+    "output_warped_image": true,
+    "transform_parameters": [ [ 0.2 ] ],
+    "convergence_threshold": [ 1e-06 ],
+    "convergence_window_size": [ 20 ],
+    "metric": [ "Mattes" ],
+    "sampling_percentage": [ 0.15 ],
+    "sampling_strategy": [ "Random" ],
+    "smoothing_sigmas": [ [ 8.0, 2.0 ] ],
+    "sigma_units": [ "mm"],
+    "metric_weight": [ 1.0 ],
+    "shrink_factors": [ [ 2, 1 ] ],
+    "radius_or_number_of_bins": [ 48 ],
+    "interpolation": "BSpline"
+}

dmriprep/config/emc_precise_Affine.json

@@ -0,0 +1,25 @@
+{
+    "dimension": 3,
+    "float": true,
+    "winsorize_lower_quantile": 0.002,
+    "winsorize_upper_quantile": 0.998,
+    "collapse_output_transforms": true,
+    "write_composite_transform": false,
+    "use_histogram_matching": [ false, false ],
+    "use_estimate_learning_rate_once": [ true, true ],
+    "transforms": [ "Rigid", "Affine" ],
+    "number_of_iterations": [ [ 1000, 1000 ], [ 1000 ] ],
+    "output_warped_image": true,
+    "transform_parameters": [ [ 0.2 ], [ 0.15 ] ],
+    "convergence_threshold": [ 1e-08, 1e-08 ],
+    "convergence_window_size": [ 20, 20 ],
+    "metric": [ "Mattes", "Mattes" ],
+    "sampling_percentage": [ 0.15, 0.2 ],
+    "sampling_strategy": [ "Random", "Random" ],
+    "smoothing_sigmas": [ [ 8.0, 2.0 ], [ 2.0 ] ],
+    "sigma_units": [ "mm", "mm" ],
+    "metric_weight": [ 1.0, 1.0 ],
+    "shrink_factors": [ [ 2, 1 ], [ 1 ] ],
+    "radius_or_number_of_bins": [ 48, 48 ],
+    "interpolation": "BSpline"
+}

dmriprep/config/emc_precise_Rigid.json

@@ -0,0 +1,25 @@
+{
+    "dimension": 3,
+    "float": true,
+    "winsorize_lower_quantile": 0.002,
+    "winsorize_upper_quantile": 0.998,
+    "collapse_output_transforms": true,
+    "write_composite_transform": false,
+    "use_histogram_matching": [ false ],
+    "use_estimate_learning_rate_once": [ true ],
+    "transforms": [ "Rigid" ],
+    "number_of_iterations": [ [ 1000, 1000 ] ],
+    "output_warped_image": true,
+    "transform_parameters": [ [ 0.2 ], [ 0.15 ] ],
+    "convergence_threshold": [ 1e-08, 1e-08 ],
+    "convergence_window_size": [ 20, 20 ],
+    "metric": [ "Mattes" ],
+    "sampling_percentage": [ 0.15 ],
+    "sampling_strategy": [ "Random" ],
+    "smoothing_sigmas": [ [ 8.0, 2.0 ] ],
+    "sigma_units": [ "mm" ],
+    "metric_weight": [ 1.0 ],
+    "shrink_factors": [ [ 2, 1 ] ],
+    "radius_or_number_of_bins": [ 48 ],
+    "interpolation": "BSpline"
+}

dmriprep/interfaces/bids.py

@@ -0,0 +1,139 @@
+import os
+import re
+from pathlib import Path
+from nipype.interfaces.base import (
+    traits, TraitedSpec, BaseInterfaceInputSpec, SimpleInterface, File, isdefined,
+    InputMultiObject, OutputMultiPath, OutputMultiObject,
+)
+from ..utils.bids import splitext as _splitext, _copy_any
+
+__all__ = ['BIDS_NAME']
+
+BIDS_NAME = re.compile(
+    r'^(.*\/)?(?P<subject_id>sub-[a-zA-Z0-9]+)(_(?P<session_id>ses-[a-zA-Z0-9]+))?'
+    '(_(?P<task_id>task-[a-zA-Z0-9]+))?(_(?P<acq_id>acq-[a-zA-Z0-9]+))?'
+    '(_(?P<rec_id>rec-[a-zA-Z0-9]+))?(_(?P<run_id>run-[a-zA-Z0-9]+))?')
+
+
+class DerivativesDataSinkInputSpec(BaseInterfaceInputSpec):
+    base_directory = traits.Directory(
+        desc='Path to the base directory for storing data.')
+    in_file = InputMultiObject(File(exists=True), mandatory=True,
+                               desc='the object to be saved')
+    source_file = File(exists=False, mandatory=True, desc='the original file')
+    prefix = traits.Str(mandatory=False, desc='prefix for output files')
+    space = traits.Str('', usedefault=True, desc='Label for space field')
+    desc = traits.Str('', usedefault=True, desc='Label for description field')
+    suffix = traits.Str('', usedefault=True, desc='suffix appended to source_file')
+    keep_dtype = traits.Bool(False, usedefault=True, desc='keep datatype suffix')
+    extra_values = traits.List(traits.Str)
+    compress = traits.Bool(desc="force compression (True) or uncompression (False)"
+                                " of the output file (default: same as input)")
+    extension = traits.Str()
+
+
+class DerivativesDataSinkOutputSpec(TraitedSpec):
+    out_file = OutputMultiObject(File(exists=True, desc='written file path'))
+    compression = OutputMultiPath(
+        traits.Bool, desc='whether ``in_file`` was compressed/uncompressed '
+                          'or `it was copied directly.')
+
+
+class DerivativesDataSink(SimpleInterface):
+    """
+    Saves the `in_file` into a BIDS-Derivatives folder provided
+    by `base_directory`, given the input reference `source_file`.
+    >>> from pathlib import Path
+    >>> import tempfile
+    >>> from dmriprep.utils.bids import collect_data
+    >>> tmpdir = Path(tempfile.mkdtemp())
+    >>> tmpfile = tmpdir / 'a_temp_file.nii.gz'
+    >>> tmpfile.open('w').close()  # "touch" the file
+    >>> dsink = DerivativesDataSink(base_directory=str(tmpdir))
+    >>> dsink.inputs.in_file = str(tmpfile)
+    >>> dsink.inputs.source_file = collect_data('ds114', '01')[0]['t1w'][0]
+    >>> dsink.inputs.keep_dtype = True
+    >>> dsink.inputs.suffix = 'target-mni'
+    >>> res = dsink.run()
+    >>> res.outputs.out_file  # doctest: +ELLIPSIS
+    '.../dmriprep/sub-01/ses-retest/anat/sub-01_ses-retest_target-mni_T1w.nii.gz'
+    >>> bids_dir = tmpdir / 'bidsroot' / 'sub-02' / 'ses-noanat' / 'func'
+    >>> bids_dir.mkdir(parents=True, exist_ok=True)
+    >>> tricky_source = bids_dir / 'sub-02_ses-noanat_task-rest_run-01_bold.nii.gz'
+    >>> tricky_source.open('w').close()
+    >>> dsink = DerivativesDataSink(base_directory=str(tmpdir))
+    >>> dsink.inputs.in_file = str(tmpfile)
+    >>> dsink.inputs.source_file = str(tricky_source)
+    >>> dsink.inputs.keep_dtype = True
+    >>> dsink.inputs.desc = 'preproc'
+    >>> res = dsink.run()
+    >>> res.outputs.out_file  # doctest: +ELLIPSIS
+    '.../dmriprep/sub-02/ses-noanat/func/sub-02_ses-noanat_task-rest_run-01_\
+desc-preproc_bold.nii.gz'
+    """
+    input_spec = DerivativesDataSinkInputSpec
+    output_spec = DerivativesDataSinkOutputSpec
+    out_path_base = "dmriprep"
+    _always_run = True
+
+    def __init__(self, out_path_base=None, **inputs):
+        super(DerivativesDataSink, self).__init__(**inputs)
+        self._results['out_file'] = []
+        if out_path_base:
+            self.out_path_base = out_path_base
+
+    def _run_interface(self, runtime):
+        src_fname, _ = _splitext(self.inputs.source_file)
+        src_fname, dtype = src_fname.rsplit('_', 1)
+        _, ext = _splitext(self.inputs.in_file[0])
+        if self.inputs.compress is True and not ext.endswith('.gz'):
+            ext += '.gz'
+        elif self.inputs.compress is False and ext.endswith('.gz'):
+            ext = ext[:-3]
+
+        m = BIDS_NAME.search(src_fname)
+
+        mod = os.path.basename(os.path.dirname(self.inputs.source_file))
+
+        base_directory = runtime.cwd
+        if isdefined(self.inputs.base_directory):
+            base_directory = str(self.inputs.base_directory)
+
+        out_path = '{}/{subject_id}'.format(self.out_path_base, **m.groupdict())
+        if m.groupdict().get('session_id') is not None:
+            out_path += '/{session_id}'.format(**m.groupdict())
+        out_path += '/{}'.format(mod)
+
+        out_path = os.path.join(base_directory, out_path)
+
+        os.makedirs(out_path, exist_ok=True)
+
+        if isdefined(self.inputs.prefix):
+            base_fname = os.path.join(out_path, self.inputs.prefix)
+        else:
+            base_fname = os.path.join(out_path, src_fname)
+
+        formatstr = '{bname}{space}{desc}{suffix}{dtype}{ext}'
+        if len(self.inputs.in_file) > 1 and not isdefined(self.inputs.extra_values):
+            formatstr = '{bname}{space}{desc}{suffix}{i:04d}{dtype}{ext}'
+
+        space = '_space-{}'.format(self.inputs.space) if self.inputs.space else ''
+        desc = '_desc-{}'.format(self.inputs.desc) if self.inputs.desc else ''
+        suffix = '_{}'.format(self.inputs.suffix) if self.inputs.suffix else ''
+        dtype = '' if not self.inputs.keep_dtype else ('_%s' % dtype)
+
+        self._results['compression'] = []
+        for i, fname in enumerate(self.inputs.in_file):
+            out_file = formatstr.format(
+                bname=base_fname,
+                space=space,
+                desc=desc,
+                suffix=suffix,
+                i=i,
+                dtype=dtype,
+                ext=ext)
+            if isdefined(self.inputs.extra_values):
+                out_file = out_file.format(extra_value=self.inputs.extra_values[i])
+            self._results['out_file'].append(out_file)
+            self._results['compression'].append(_copy_any(fname, out_file))
+        return runtime