Merge pull request #1647 from shoshber/partialvoluming

ENH signal extraction interface

Author: chrisgorgo

nipype/interfaces/nilearn.py

@@ -0,0 +1,141 @@
+# -*- 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:
+'''
+Algorithms to compute statistics on :abbr:`fMRI (functional MRI)`
+
+    Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname(os.path.realpath(__file__))
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
+    >>> os.chdir(datadir)
+
+'''
+from __future__ import (print_function, division, unicode_literals,
+                        absolute_import)
+
+import numpy as np
+import nibabel as nb
+
+from .. import logging
+from ..interfaces.base import (traits, TraitedSpec, BaseInterface,
+                               BaseInterfaceInputSpec, File, InputMultiPath)
+IFLOG = logging.getLogger('interface')
+
+class SignalExtractionInputSpec(BaseInterfaceInputSpec):
+    in_file = File(exists=True, mandatory=True, desc='4-D fMRI nii file')
+    label_files = InputMultiPath(File(exists=True), mandatory=True,
+                                 desc='a 3-D label image, with 0 denoting '
+                                 'background, or a list of 3-D probability '
+                                 'maps (one per label) or the equivalent 4D '
+                                 'file.')
+    class_labels = traits.List(mandatory=True,
+                               desc='Human-readable labels for each segment '
+                               'in the label file, in order. The length of '
+                               'class_labels must be equal to the number of '
+                               'segments (background excluded). This list '
+                               'corresponds to the class labels in label_file '
+                               'in ascending order')
+    out_file = File('signals.tsv', usedefault=True, exists=False,
+                    mandatory=False, desc='The name of the file to output to. '
+                    'signals.tsv by default')
+    incl_shared_variance = traits.Bool(True, usedefault=True, mandatory=False, desc='By default '
+                                       '(True), returns simple time series calculated from each '
+                                       'region independently (e.g., for noise regression). If '
+                                       'False, returns unique signals for each region, discarding '
+                                       'shared variance (e.g., for connectivity. Only has effect '
+                                       'with 4D probability maps.')
+    include_global = traits.Bool(False, usedefault=True, mandatory=False,
+                                 desc='If True, include an extra column '
+                                 'labeled "global", with values calculated from the entire brain '
+                                 '(instead of just regions).')
+    detrend = traits.Bool(False, usedefault=True, mandatory=False,
+                          desc='If True, perform detrending using nilearn.')
+
+class SignalExtractionOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='tsv file containing the computed '
+                    'signals, with as many columns as there are labels and as '
+                    'many rows as there are timepoints in in_file, plus a '
+                    'header row with values from class_labels')
+
+class SignalExtraction(BaseInterface):
+    '''
+    Extracts signals over tissue classes or brain regions
+
+    >>> seinterface = SignalExtraction()
+    >>> seinterface.inputs.in_file = 'functional.nii'
+    >>> seinterface.inputs.label_files = 'segmentation0.nii.gz'
+    >>> seinterface.inputs.out_file = 'means.tsv'
+    >>> segments = ['CSF', 'gray', 'white']
+    >>> seinterface.inputs.class_labels = segments
+    >>> seinterface.inputs.detrend = True
+    >>> seinterface.inputs.include_global = True
+    '''
+    input_spec = SignalExtractionInputSpec
+    output_spec = SignalExtractionOutputSpec
+
+    def _run_interface(self, runtime):
+        maskers = self._process_inputs()
+
+        signals = []
+        for masker in maskers:
+            signals.append(masker.fit_transform(self.inputs.in_file))
+        region_signals = np.hstack(signals)
+
+        output = np.vstack((self.inputs.class_labels, region_signals.astype(str)))
+
+        # save output
+        np.savetxt(self.inputs.out_file, output, fmt=b'%s', delimiter='\t')
+        return runtime
+
+    def _process_inputs(self):
+        ''' validate and  process inputs into useful form.
+        Returns a list of nilearn maskers and the list of corresponding label names.'''
+        import nilearn.input_data as nl
+        import nilearn.image as nli
+
+        label_data = nli.concat_imgs(self.inputs.label_files)
+        maskers = []
+
+        # determine form of label files, choose appropriate nilearn masker
+        if np.amax(label_data.get_data()) > 1: # 3d label file
+            n_labels = np.amax(label_data.get_data())
+            maskers.append(nl.NiftiLabelsMasker(label_data))
+        else: # 4d labels
+            n_labels = label_data.get_data().shape[3]
+            if self.inputs.incl_shared_variance: # 4d labels, independent computation
+                for img in nli.iter_img(label_data):
+                    maskers.append(nl.NiftiMapsMasker(self._4d(img.get_data(), img.affine)))
+            else: # 4d labels, one computation fitting all
+                maskers.append(nl.NiftiMapsMasker(label_data))
+
+        # check label list size
+        if len(self.inputs.class_labels) != n_labels:
+            raise ValueError('The length of class_labels {} does not '
+                             'match the number of regions {} found in '
+                             'label_files {}'.format(self.inputs.class_labels,
+                                                     n_labels,
+                                                     self.inputs.label_files))
+
+        if self.inputs.include_global:
+            global_label_data = label_data.get_data().sum(axis=3) # sum across all regions
+            global_label_data = np.rint(global_label_data).astype(int).clip(0, 1) # binarize
+            global_label_data = self._4d(global_label_data, label_data.affine)
+            global_masker = nl.NiftiLabelsMasker(global_label_data, detrend=self.inputs.detrend)
+            maskers.insert(0, global_masker)
+            self.inputs.class_labels.insert(0, 'global')
+
+        for masker in maskers:
+            masker.set_params(detrend=self.inputs.detrend)
+
+        return maskers
+
+    def _4d(self, array, affine):
+        ''' takes a 3-dimensional numpy array and an affine,
+        returns the equivalent 4th dimensional nifti file '''
+        return nb.Nifti1Image(array[:, :, :, np.newaxis], affine)
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['out_file'] = self.inputs.out_file
+        return outputs

nipype/interfaces/tests/test_nilearn.py

@@ -0,0 +1,199 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+import unittest
+import os
+import tempfile
+import shutil
+
+import numpy as np
+
+from ...testing import (assert_equal, utils, assert_almost_equal, raises,
+                        skipif)
+from .. import nilearn as iface
+
+no_nilearn = True
+try:
+    __import__('nilearn')
+    no_nilearn = False
+except ImportError:
+    pass
+
+class TestSignalExtraction(unittest.TestCase):
+
+    filenames = {
+        'in_file': 'fmri.nii',
+        'label_files': 'labels.nii',
+        '4d_label_file': '4dlabels.nii',
+        'out_file': 'signals.tsv'
+    }
+    labels = ['csf', 'gray', 'white']
+    global_labels = ['global'] + labels
+
+    def setUp(self):
+        self.orig_dir = os.getcwd()
+        self.temp_dir = tempfile.mkdtemp()
+        os.chdir(self.temp_dir)
+
+        utils.save_toy_nii(self.fake_fmri_data, self.filenames['in_file'])
+        utils.save_toy_nii(self.fake_label_data, self.filenames['label_files'])
+
+    @skipif(no_nilearn)
+    def test_signal_extract_no_shared(self):
+        # run
+        iface.SignalExtraction(in_file=self.filenames['in_file'],
+                               label_files=self.filenames['label_files'],
+                               class_labels=self.labels,
+                               incl_shared_variance=False).run()
+        # assert
+        self.assert_expected_output(self.labels, self.base_wanted)
+
+
+    @skipif(no_nilearn)
+    @raises(ValueError)
+    def test_signal_extr_bad_label_list(self):
+        # run
+        iface.SignalExtraction(in_file=self.filenames['in_file'],
+                               label_files=self.filenames['label_files'],
+                               class_labels=['bad'],
+                               incl_shared_variance=False).run()
+
+    @skipif(no_nilearn)
+    def test_signal_extr_equiv_4d_no_shared(self):
+        self._test_4d_label(self.base_wanted, self.fake_equiv_4d_label_data,
+                            incl_shared_variance=False)
+
+    @skipif(no_nilearn)
+    def test_signal_extr_4d_no_shared(self):
+        # set up & run & assert
+        self._test_4d_label(self.fourd_wanted, self.fake_4d_label_data, incl_shared_variance=False)
+
+    @skipif(no_nilearn)
+    def test_signal_extr_global_no_shared(self):
+        # set up
+        wanted_global = [[-4./6], [-1./6], [3./6], [-1./6], [-7./6]]
+        for i, vals in enumerate(self.base_wanted):
+            wanted_global[i].extend(vals)
+
+        # run
+        iface.SignalExtraction(in_file=self.filenames['in_file'],
+                               label_files=self.filenames['label_files'],
+                               class_labels=self.labels,
+                               include_global=True,
+                               incl_shared_variance=False).run()
+
+        # assert
+        self.assert_expected_output(self.global_labels, wanted_global)
+
+    @skipif(no_nilearn)
+    def test_signal_extr_4d_global_no_shared(self):
+        # set up
+        wanted_global = [[3./8], [-3./8], [1./8], [-7./8], [-9./8]]
+        for i, vals in enumerate(self.fourd_wanted):
+            wanted_global[i].extend(vals)
+
+        # run & assert
+        self._test_4d_label(wanted_global, self.fake_4d_label_data,
+                            include_global=True, incl_shared_variance=False)
+
+    @skipif(no_nilearn)
+    def test_signal_extr_shared(self):
+        # set up
+        wanted = []
+        for vol in range(self.fake_fmri_data.shape[3]):
+            volume = self.fake_fmri_data[:, :, :, vol].flatten()
+            wanted_row = []
+            for reg in range(self.fake_4d_label_data.shape[3]):
+                region = self.fake_4d_label_data[:, :, :, reg].flatten()
+                wanted_row.append((volume*region).sum()/(region*region).sum())
+
+            wanted.append(wanted_row)
+        # run & assert
+        self._test_4d_label(wanted, self.fake_4d_label_data)
+
+    def _test_4d_label(self, wanted, fake_labels, include_global=False, incl_shared_variance=True):
+        # set up
+        utils.save_toy_nii(fake_labels, self.filenames['4d_label_file'])
+
+        # run
+        iface.SignalExtraction(in_file=self.filenames['in_file'],
+                               label_files=self.filenames['4d_label_file'],
+                               class_labels=self.labels,
+                               incl_shared_variance=incl_shared_variance,
+                               include_global=include_global).run()
+
+        wanted_labels = self.global_labels if include_global else self.labels
+
+        # assert
+        self.assert_expected_output(wanted_labels, wanted)
+
+    def assert_expected_output(self, labels, wanted):
+        with open(self.filenames['out_file'], 'r') as output:
+            got = [line.split() for line in output]
+            labels_got = got.pop(0) # remove header
+            assert_equal(labels_got, labels)
+            assert_equal(len(got), self.fake_fmri_data.shape[3],
+                         'num rows and num volumes')
+            # convert from string to float
+            got = [[float(num) for num in row] for row in got]
+            for i, time in enumerate(got):
+                assert_equal(len(labels), len(time))
+                for j, segment in enumerate(time):
+                    assert_almost_equal(segment, wanted[i][j], decimal=1)
+
+
+    def tearDown(self):
+        os.chdir(self.orig_dir)
+        shutil.rmtree(self.temp_dir)
+
+    fake_fmri_data = np.array([[[[2, -1, 4, -2, 3],
+                                 [4, -2, -5, -1, 0]],
+
+                                [[-2, 0, 1, 4, 4],
+                                 [-5, 3, -3, 1, -5]]],
+
+
+                               [[[2, -2, -1, -2, -5],
+                                 [3, 0, 3, -5, -2]],
+
+                                [[-4, -2, -2, 1, -2],
+                                 [3, 1, 4, -3, -2]]]])
+
+    fake_label_data = np.array([[[1, 0],
+                                 [3, 1]],
+
+                                [[2, 0],
+                                 [1, 3]]])
+
+    fake_equiv_4d_label_data = np.array([[[[1., 0., 0.],
+                                           [0., 0., 0.]],
+                                          [[0., 0., 1.],
+                                           [1., 0., 0.]]],
+                                         [[[0., 1., 0.],
+                                           [0., 0., 0.]],
+                                          [[1., 0., 0.],
+                                           [0., 0., 1.]]]])
+
+    base_wanted = [[-2.33333, 2, .5],
+                   [0, -2, .5],
+                   [-.3333333, -1, 2.5],
+                   [0, -2, .5],
+                   [-1.3333333, -5, 1]]
+
+    fake_4d_label_data = np.array([[[[0.2, 0.3, 0.5],
+                                     [0.1, 0.1, 0.8]],
+
+                                    [[0.1, 0.3, 0.6],
+                                     [0.3, 0.4, 0.3]]],
+
+                                   [[[0.2, 0.2, 0.6],
+                                     [0., 0.3, 0.7]],
+
+                                    [[0.3, 0.3, 0.4],
+                                     [0.3, 0.4, 0.3]]]])
+
+
+    fourd_wanted = [[-5.0652173913, -5.44565217391, 5.50543478261],
+                    [-7.02173913043, 11.1847826087, -4.33152173913],
+                    [-19.0869565217, 21.2391304348, -4.57608695652],
+                    [5.19565217391, -3.66304347826, -1.51630434783],
+                    [-12.0, 3., 0.5]]