Merge pull request #2530 from oesteban/enh/add-masks-overlap

ENH: Revise the implementation of FuzzyOverlap

Author: effigies

nipype/algorithms/metrics.py

@@ -20,11 +20,11 @@
 
 from .. import config, logging
 
-from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File,
-                               InputMultiPath, BaseInterfaceInputSpec,
-                               isdefined)
+from ..interfaces.base import (
+    SimpleInterface, BaseInterface, traits, TraitedSpec, File,
+    InputMultiPath, BaseInterfaceInputSpec,
+    isdefined)
 from ..interfaces.nipy.base import NipyBaseInterface
-from ..utils import NUMPY_MMAP
 
 iflogger = logging.getLogger('interface')
 
@@ -383,6 +383,7 @@ class FuzzyOverlapInputSpec(BaseInterfaceInputSpec):
         File(exists=True),
         mandatory=True,
         desc='Test image. Requires the same dimensions as in_ref.')
+    in_mask = File(exists=True, desc='calculate overlap only within mask')
     weighting = traits.Enum(
         'none',
         'volume',
@@ -403,10 +404,6 @@ class FuzzyOverlapInputSpec(BaseInterfaceInputSpec):
 class FuzzyOverlapOutputSpec(TraitedSpec):
     jaccard = traits.Float(desc='Fuzzy Jaccard Index (fJI), all the classes')
     dice = traits.Float(desc='Fuzzy Dice Index (fDI), all the classes')
-    diff_file = File(
-        exists=True,
-        desc=
-        'resulting difference-map of all classes, using the chosen weighting')
     class_fji = traits.List(
         traits.Float(),
         desc='Array containing the fJIs of each computed class')
@@ -415,7 +412,7 @@ class FuzzyOverlapOutputSpec(TraitedSpec):
         desc='Array containing the fDIs of each computed class')
 
 
-class FuzzyOverlap(BaseInterface):
+class FuzzyOverlap(SimpleInterface):
     """Calculates various overlap measures between two maps, using the fuzzy
     definition proposed in: Crum et al., Generalized Overlap Measures for
     Evaluation and Validation in Medical Image Analysis, IEEE Trans. Med.
@@ -439,77 +436,75 @@ class FuzzyOverlap(BaseInterface):
     output_spec = FuzzyOverlapOutputSpec
 
     def _run_interface(self, runtime):
-        ncomp = len(self.inputs.in_ref)
-        assert (ncomp == len(self.inputs.in_tst))
-        weights = np.ones(shape=ncomp)
-
-        img_ref = np.array([
-            nb.load(fname, mmap=NUMPY_MMAP).get_data()
-            for fname in self.inputs.in_ref
-        ])
-        img_tst = np.array([
-            nb.load(fname, mmap=NUMPY_MMAP).get_data()
-            for fname in self.inputs.in_tst
-        ])
-
-        msk = np.sum(img_ref, axis=0)
-        msk[msk > 0] = 1.0
-        tst_msk = np.sum(img_tst, axis=0)
-        tst_msk[tst_msk > 0] = 1.0
-
-        # check that volumes are normalized
-        # img_ref[:][msk>0] = img_ref[:][msk>0] / (np.sum( img_ref, axis=0 ))[msk>0]
-        # img_tst[tst_msk>0] = img_tst[tst_msk>0] / np.sum( img_tst, axis=0 )[tst_msk>0]
-
-        self._jaccards = []
-        volumes = []
-
-        diff_im = np.zeros(img_ref.shape)
-
-        for ref_comp, tst_comp, diff_comp in zip(img_ref, img_tst, diff_im):
-            num = np.minimum(ref_comp, tst_comp)
-            ddr = np.maximum(ref_comp, tst_comp)
-            diff_comp[ddr > 0] += 1.0 - (num[ddr > 0] / ddr[ddr > 0])
-            self._jaccards.append(np.sum(num) / np.sum(ddr))
-            volumes.append(np.sum(ref_comp))
-
-        self._dices = 2.0 * (np.array(self._jaccards) /
-                             (np.array(self._jaccards) + 1.0))
+        # Load data
+        refdata = nb.concat_images(self.inputs.in_ref).get_data()
+        tstdata = nb.concat_images(self.inputs.in_tst).get_data()
+
+        # Data must have same shape
+        if not refdata.shape == tstdata.shape:
+            raise RuntimeError(
+                'Size of "in_tst" %s must match that of "in_ref" %s.' %
+                (tstdata.shape, refdata.shape))
+
+        ncomp = refdata.shape[-1]
 
+        # Load mask
+        mask = np.ones_like(refdata, dtype=bool)
+        if isdefined(self.inputs.in_mask):
+            mask = nb.load(self.inputs.in_mask).get_data()
+            mask = mask > 0
+            mask = np.repeat(mask[..., np.newaxis], ncomp, -1)
+            assert mask.shape == refdata.shape
+
+        # Drop data outside mask
+        refdata = refdata[mask]
+        tstdata = tstdata[mask]
+
+        if np.any(refdata < 0.0):
+            iflogger.warning('Negative values encountered in "in_ref" input, '
+                             'taking absolute values.')
+            refdata = np.abs(refdata)
+
+        if np.any(tstdata < 0.0):
+            iflogger.warning('Negative values encountered in "in_tst" input, '
+                             'taking absolute values.')
+            tstdata = np.abs(tstdata)
+
+        if np.any(refdata > 1.0):
+            iflogger.warning('Values greater than 1.0 found in "in_ref" input, '
+                             'scaling values.')
+            refdata /= refdata.max()
+
+        if np.any(tstdata > 1.0):
+            iflogger.warning('Values greater than 1.0 found in "in_tst" input, '
+                             'scaling values.')
+            tstdata /= tstdata.max()
+
+        numerators = np.atleast_2d(
+            np.minimum(refdata, tstdata).reshape((-1, ncomp)))
+        denominators = np.atleast_2d(
+            np.maximum(refdata, tstdata).reshape((-1, ncomp)))
+
+        jaccards = numerators.sum(axis=0) / denominators.sum(axis=0)
+
+        # Calculate weights
+        weights = np.ones_like(jaccards, dtype=float)
         if self.inputs.weighting != "none":
-            weights = 1.0 / np.array(volumes)
+            volumes = np.sum((refdata + tstdata) > 0, axis=1).reshape((-1, ncomp))
+            weights = 1.0 / volumes
             if self.inputs.weighting == "squared_vol":
                 weights = weights**2
 
         weights = weights / np.sum(weights)
+        dices = 2.0 * jaccards / (jaccards + 1.0)
 
-        setattr(self, '_jaccard', np.sum(weights * self._jaccards))
-        setattr(self, '_dice', np.sum(weights * self._dices))
-
-        diff = np.zeros(diff_im[0].shape)
-
-        for w, ch in zip(weights, diff_im):
-            ch[msk == 0] = 0
-            diff += w * ch
-
-        nb.save(
-            nb.Nifti1Image(diff,
-                           nb.load(self.inputs.in_ref[0]).affine,
-                           nb.load(self.inputs.in_ref[0]).header),
-            self.inputs.out_file)
-
+        # Fill-in the results object
+        self._results['jaccard'] = float(weights.dot(jaccards))
+        self._results['dice'] = float(weights.dot(dices))
+        self._results['class_fji'] = [float(v) for v in jaccards]
+        self._results['class_fdi'] = [float(v) for v in dices]
         return runtime
 
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        for method in ("dice", "jaccard"):
-            outputs[method] = getattr(self, '_' + method)
-        # outputs['volume_difference'] = self._volume
-        outputs['diff_file'] = os.path.abspath(self.inputs.out_file)
-        outputs['class_fji'] = np.array(self._jaccards).astype(float).tolist()
-        outputs['class_fdi'] = self._dices.astype(float).tolist()
-        return outputs
-
 
 class ErrorMapInputSpec(BaseInterfaceInputSpec):
     in_ref = File(

nipype/algorithms/tests/test_auto_FuzzyOverlap.py

@@ -10,6 +10,7 @@ def test_FuzzyOverlap_inputs():
             nohash=True,
             usedefault=True,
         ),
+        in_mask=dict(),
         in_ref=dict(mandatory=True, ),
         in_tst=dict(mandatory=True, ),
         out_file=dict(usedefault=True, ),
@@ -25,7 +26,6 @@ def test_FuzzyOverlap_outputs():
         class_fdi=dict(),
         class_fji=dict(),
         dice=dict(),
-        diff_file=dict(),
         jaccard=dict(),
     )
     outputs = FuzzyOverlap.output_spec()

nipype/algorithms/tests/test_metrics.py

@@ -0,0 +1,58 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+import numpy as np
+import nibabel as nb
+from nipype.testing import example_data
+from ..metrics import FuzzyOverlap
+
+
+def test_fuzzy_overlap(tmpdir):
+    tmpdir.chdir()
+
+    # Tests with tissue probability maps
+    in_mask = example_data('tpms_msk.nii.gz')
+    tpms = [example_data('tpm_%02d.nii.gz' % i) for i in range(3)]
+    out = FuzzyOverlap(in_ref=tpms[0], in_tst=tpms[0]).run().outputs
+    assert out.dice == 1
+
+    out = FuzzyOverlap(
+        in_mask=in_mask, in_ref=tpms[0], in_tst=tpms[0]).run().outputs
+    assert out.dice == 1
+
+    out = FuzzyOverlap(
+        in_mask=in_mask, in_ref=tpms[0], in_tst=tpms[1]).run().outputs
+    assert 0 < out.dice < 1
+
+    out = FuzzyOverlap(in_ref=tpms, in_tst=tpms).run().outputs
+    assert out.dice == 1.0
+
+    out = FuzzyOverlap(
+        in_mask=in_mask, in_ref=tpms, in_tst=tpms).run().outputs
+    assert out.dice == 1.0
+
+    # Tests with synthetic 3x3x3 images
+    data = np.zeros((3, 3, 3), dtype=float)
+    data[0, 0, 0] = 0.5
+    data[2, 2, 2] = 0.25
+    data[1, 1, 1] = 0.3
+    nb.Nifti1Image(data, np.eye(4)).to_filename('test1.nii.gz')
+
+    data = np.zeros((3, 3, 3), dtype=float)
+    data[0, 0, 0] = 0.6
+    data[1, 1, 1] = 0.3
+    nb.Nifti1Image(data, np.eye(4)).to_filename('test2.nii.gz')
+
+    out = FuzzyOverlap(in_ref='test1.nii.gz', in_tst='test2.nii.gz').run().outputs
+    assert np.allclose(out.dice, 0.82051)
+
+    # Just considering the mask, the central pixel
+    # that raised the index now is left aside.
+    data = np.zeros((3, 3, 3), dtype=int)
+    data[0, 0, 0] = 1
+    data[2, 2, 2] = 1
+    nb.Nifti1Image(data, np.eye(4)).to_filename('mask.nii.gz')
+
+    out = FuzzyOverlap(in_ref='test1.nii.gz', in_tst='test2.nii.gz',
+                       in_mask='mask.nii.gz').run().outputs
+    assert np.allclose(out.dice, 0.74074)