Merge pull request #3 from nipy/master

Update to current master

Author: blakedewey

nipype/interfaces/base.py

@@ -1349,9 +1349,9 @@ def _terminal_output_update(self):
     def set_default_terminal_output(cls, output_type):
         """Set the default terminal output for CommandLine Interfaces.
 
-        This method is used to set default terminal output for 
-        CommandLine Interfaces.  However, setting this will not 
-        update the output type for any existing instances.  For these, 
+        This method is used to set default terminal output for
+        CommandLine Interfaces.  However, setting this will not
+        update the output type for any existing instances.  For these,
         assign the <instance>.inputs.terminal_output.
         """
 

nipype/interfaces/dipy/__init__.py

@@ -1,3 +1,4 @@
 from .tracks import TrackDensityMap
 from .tensors import TensorMode, DTI
 from .preprocess import Resample, Denoise
+from .simulate import SimulateMultiTensor

nipype/interfaces/dipy/simulate.py

@@ -0,0 +1,338 @@
+# -*- coding: utf-8 -*-
+"""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 nipype.interfaces.base import (
+    traits, TraitedSpec, BaseInterface, BaseInterfaceInputSpec, File,
+    InputMultiPath, isdefined)
+from nipype.utils.filemanip import split_filename
+import os.path as op
+import nibabel as nb
+import numpy as np
+from nipype.utils.misc import package_check
+import warnings
+
+from multiprocessing import (Process, Pool, cpu_count, pool,
+                             Manager, TimeoutError)
+
+from ... import logging
+iflogger = logging.getLogger('interface')
+
+have_dipy = True
+try:
+    package_check('dipy', version='0.8.0')
+except Exception, e:
+    have_dipy = False
+else:
+    import numpy as np
+    from dipy.sims.voxel import (multi_tensor, add_noise,
+                                 all_tensor_evecs)
+    from dipy.core.gradients import gradient_table
+
+
+class SimulateMultiTensorInputSpec(BaseInterfaceInputSpec):
+    in_dirs = InputMultiPath(File(exists=True), mandatory=True,
+                             desc='list of fibers (principal directions)')
+    in_frac = InputMultiPath(File(exists=True), mandatory=True,
+                             desc=('volume fraction of each fiber'))
+    in_vfms = InputMultiPath(File(exists=True), mandatory=True,
+                             desc=('volume fractions of isotropic '
+                                   'compartiments'))
+    in_mask = File(exists=True, desc='mask to simulate data')
+
+    diff_iso = traits.List(
+        [3000e-6, 960e-6, 680e-6], traits.Float, usedefault=True,
+        desc='Diffusivity of isotropic compartments')
+    diff_sf = traits.Tuple(
+        (1700e-6, 200e-6, 200e-6),
+        traits.Float, traits.Float, traits.Float, usedefault=True,
+        desc='Single fiber tensor')
+
+    n_proc = traits.Int(0, usedefault=True, desc='number of processes')
+    baseline = File(exists=True, mandatory=True, desc='baseline T2 signal')
+    gradients = File(exists=True, desc='gradients file')
+    in_bvec = File(exists=True, desc='input bvecs file')
+    in_bval = File(exists=True, desc='input bvals file')
+    num_dirs = traits.Int(32, usedefault=True,
+                          desc=('number of gradient directions (when table '
+                                'is automatically generated)'))
+    bvalues = traits.List(traits.Int, value=[1000, 3000], usedefault=True,
+                          desc=('list of b-values (when table '
+                                'is automatically generated)'))
+    out_file = File('sim_dwi.nii.gz', usedefault=True,
+                    desc='output file with fractions to be simluated')
+    out_mask = File('sim_msk.nii.gz', usedefault=True,
+                    desc='file with the mask simulated')
+    out_bvec = File('bvec.sim', usedefault=True, desc='simulated b vectors')
+    out_bval = File('bval.sim', usedefault=True, desc='simulated b values')
+    snr = traits.Int(0, usedefault=True, desc='signal-to-noise ratio (dB)')
+
+
+class SimulateMultiTensorOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='simulated DWIs')
+    out_mask = File(exists=True, desc='mask file')
+    out_bvec = File(exists=True, desc='simulated b vectors')
+    out_bval = File(exists=True, desc='simulated b values')
+
+
+class SimulateMultiTensor(BaseInterface):
+
+    """
+    Interface to MultiTensor model simulator in dipy
+    http://nipy.org/dipy/examples_built/simulate_multi_tensor.html
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.dipy as dipy
+    >>> sim = dipy.SimulateMultiTensor()
+    >>> sim.inputs.in_dirs = ['fdir00.nii', 'fdir01.nii']
+    >>> sim.inputs.in_frac = ['ffra00.nii', 'ffra01.nii']
+    >>> sim.inputs.in_vfms = ['tpm_00.nii.gz', 'tpm_01.nii.gz',
+    ...                       'tpm_02.nii.gz']
+    >>> sim.inputs.baseline = 'b0.nii'
+    >>> sim.inputs.in_bvec = 'bvecs'
+    >>> sim.inputs.in_bval = 'bvals'
+    >>> sim.run()                                   # doctest: +SKIP
+    """
+    input_spec = SimulateMultiTensorInputSpec
+    output_spec = SimulateMultiTensorOutputSpec
+
+    def _run_interface(self, runtime):
+        # Gradient table
+        if isdefined(self.inputs.in_bval) and isdefined(self.inputs.in_bvec):
+            # Load the gradient strengths and directions
+            bvals = np.loadtxt(self.inputs.in_bval)
+            bvecs = np.loadtxt(self.inputs.in_bvec).T
+            gtab = gradient_table(bvals, bvecs)
+        else:
+            gtab = _generate_gradients(self.inputs.num_dirs,
+                                       self.inputs.bvalues)
+        ndirs = len(gtab.bvals)
+        np.savetxt(op.abspath(self.inputs.out_bvec), gtab.bvecs.T)
+        np.savetxt(op.abspath(self.inputs.out_bval), gtab.bvals)
+
+        # Load the baseline b0 signal
+        b0_im = nb.load(self.inputs.baseline)
+        hdr = b0_im.get_header()
+        shape = b0_im.get_shape()
+        aff = b0_im.get_affine()
+
+        # Check and load sticks and their volume fractions
+        nsticks = len(self.inputs.in_dirs)
+        if len(self.inputs.in_frac) != nsticks:
+            raise RuntimeError(('Number of sticks and their volume fractions'
+                                ' must match.'))
+
+        # Volume fractions of isotropic compartments
+        nballs = len(self.inputs.in_vfms)
+        vfs = np.squeeze(nb.concat_images(
+            [nb.load(f) for f in self.inputs.in_vfms]).get_data())
+        if nballs == 1:
+            vfs = vfs[..., np.newaxis]
+        total_vf = np.sum(vfs, axis=3)
+
+        # Generate a mask
+        if isdefined(self.inputs.in_mask):
+            msk = nb.load(self.inputs.in_mask).get_data()
+            msk[msk > 0.0] = 1.0
+            msk[msk < 1.0] = 0.0
+        else:
+            msk = np.zeros(shape)
+            msk[total_vf > 0.0] = 1.0
+
+        msk = np.clip(msk, 0.0, 1.0)
+        nvox = len(msk[msk > 0])
+
+        # Fiber fractions
+        ffsim = nb.concat_images([nb.load(f) for f in self.inputs.in_frac])
+        ffs = np.nan_to_num(np.squeeze(ffsim.get_data()))  # fiber fractions
+        ffs = np.clip(ffs, 0., 1.)
+        if nsticks == 1:
+            ffs = ffs[..., np.newaxis]
+
+        for i in range(nsticks):
+            ffs[..., i] *= msk
+
+        total_ff = np.sum(ffs, axis=3)
+
+        # Fix incongruencies in fiber fractions
+        for i in range(1, nsticks):
+            if np.any(total_ff > 1.0):
+                errors = np.zeros_like(total_ff)
+                errors[total_ff > 1.0] = total_ff[total_ff > 1.0] - 1.0
+                ffs[..., i] -= errors
+                ffs[ffs < 0.0] = 0.0
+            total_ff = np.sum(ffs, axis=3)
+
+        for i in range(vfs.shape[-1]):
+            vfs[..., i] -= total_ff
+        vfs = np.clip(vfs, 0., 1.)
+
+        fractions = np.concatenate((ffs, vfs), axis=3)
+
+        nb.Nifti1Image(fractions, aff, None).to_filename('fractions.nii.gz')
+        nb.Nifti1Image(np.sum(fractions, axis=3), aff, None).to_filename(
+            'total_vf.nii.gz')
+
+        mhdr = hdr.copy()
+        mhdr.set_data_dtype(np.uint8)
+        mhdr.set_xyzt_units('mm', 'sec')
+        nb.Nifti1Image(msk, aff, mhdr).to_filename(
+            op.abspath(self.inputs.out_mask))
+
+        # Initialize stack of args
+        fracs = fractions[msk > 0]
+
+        # Stack directions
+        dirs = None
+        for i in range(nsticks):
+            f = self.inputs.in_dirs[i]
+            fd = np.nan_to_num(nb.load(f).get_data())
+            w = np.linalg.norm(fd, axis=3)[..., np.newaxis]
+            w[w < np.finfo(float).eps] = 1.0
+            fd /= w
+            if dirs is None:
+                dirs = fd[msk > 0].copy()
+            else:
+                dirs = np.hstack((dirs, fd[msk > 0]))
+
+        # Add random directions for isotropic components
+        for d in range(nballs):
+            fd = np.random.randn(nvox, 3)
+            w = np.linalg.norm(fd, axis=1)
+            fd[w < np.finfo(float).eps, ...] = np.array([1., 0., 0.])
+            w[w < np.finfo(float).eps] = 1.0
+            fd /= w[..., np.newaxis]
+            dirs = np.hstack((dirs, fd))
+
+        sf_evals = list(self.inputs.diff_sf)
+        ba_evals = list(self.inputs.diff_iso)
+
+        mevals = [sf_evals] * nsticks + \
+            [[ba_evals[d]] * 3 for d in range(nballs)]
+
+        b0 = b0_im.get_data()[msk > 0]
+        args = []
+        for i in range(nvox):
+            args.append(
+                {'fractions': fracs[i, ...].tolist(),
+                 'sticks': [tuple(dirs[i, j:j + 3])
+                            for j in range(nsticks + nballs)],
+                 'gradients': gtab,
+                 'mevals': mevals,
+                 'S0': b0[i],
+                 'snr': self.inputs.snr
+                 })
+
+        n_proc = self.inputs.n_proc
+        if n_proc == 0:
+            n_proc = cpu_count()
+
+        try:
+            pool = Pool(processes=n_proc, maxtasksperchild=50)
+        except TypeError:
+            pool = Pool(processes=n_proc)
+
+        # Simulate sticks using dipy
+        iflogger.info(('Starting simulation of %d voxels, %d diffusion'
+                       ' directions.') % (len(args), ndirs))
+        result = np.array(pool.map(_compute_voxel, args))
+        if np.shape(result)[1] != ndirs:
+            raise RuntimeError(('Computed directions do not match number'
+                                'of b-values.'))
+
+        signal = np.zeros((shape[0], shape[1], shape[2], ndirs))
+        signal[msk > 0] = result
+
+        simhdr = hdr.copy()
+        simhdr.set_data_dtype(np.float32)
+        simhdr.set_xyzt_units('mm', 'sec')
+        nb.Nifti1Image(signal.astype(np.float32), aff,
+                       simhdr).to_filename(op.abspath(self.inputs.out_file))
+
+        return runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['out_file'] = op.abspath(self.inputs.out_file)
+        outputs['out_mask'] = op.abspath(self.inputs.out_mask)
+        outputs['out_bvec'] = op.abspath(self.inputs.out_bvec)
+        outputs['out_bval'] = op.abspath(self.inputs.out_bval)
+
+        return outputs
+
+
+def _compute_voxel(args):
+    """
+    Simulate DW signal for one voxel. Uses the multi-tensor model and
+    three isotropic compartments.
+
+    Apparent diffusivity tensors are taken from [Alexander2002]_
+    and [Pierpaoli1996]_.
+
+    .. [Alexander2002] Alexander et al., Detection and modeling of non-Gaussian
+      apparent diffusion coefficient profiles in human brain data, MRM
+      48(2):331-340, 2002, doi: `10.1002/mrm.10209
+      <http://dx.doi.org/10.1002/mrm.10209>`_.
+    .. [Pierpaoli1996] Pierpaoli et al., Diffusion tensor MR imaging
+      of the human brain, Radiology 201:637-648. 1996.
+    """
+
+    ffs = args['fractions']
+    gtab = args['gradients']
+    signal = np.zeros_like(gtab.bvals, dtype=np.float32)
+
+    # Simulate dwi signal
+    sf_vf = np.sum(ffs)
+    if sf_vf > 0.0:
+        ffs = ((np.array(ffs) / sf_vf) * 100)
+        snr = args['snr'] if args['snr'] > 0 else None
+
+        try:
+            signal, _ = multi_tensor(
+                gtab, args['mevals'], S0=args['S0'],
+                angles=args['sticks'], fractions=ffs, snr=snr)
+        except Exception as e:
+            pass
+            # iflogger.warn('Exception simulating dwi signal: %s' % e)
+
+    return signal.tolist()
+
+
+def _generate_gradients(ndirs=64, values=[1000, 3000], nb0s=1):
+    """
+    Automatically generate a `gradient table
+    <http://nipy.org/dipy/examples_built/gradients_spheres.html#example-gradients-spheres>`_
+
+    """
+    import numpy as np
+    from dipy.core.sphere import (disperse_charges, Sphere, HemiSphere)
+    from dipy.core.gradients import gradient_table
+
+    theta = np.pi * np.random.rand(ndirs)
+    phi = 2 * np.pi * np.random.rand(ndirs)
+    hsph_initial = HemiSphere(theta=theta, phi=phi)
+    hsph_updated, potential = disperse_charges(hsph_initial, 5000)
+
+    values = np.atleast_1d(values).tolist()
+    vertices = hsph_updated.vertices
+    bvecs = vertices.copy()
+    bvals = np.ones(vertices.shape[0]) * values[0]
+
+    for v in values[1:]:
+        bvecs = np.vstack((bvecs, vertices))
+        bvals = np.hstack((bvals, v * np.ones(vertices.shape[0])))
+
+    for i in xrange(0, nb0s):
+        bvals = bvals.tolist()
+        bvals.insert(0, 0)
+
+        bvecs = bvecs.tolist()
+        bvecs.insert(0, np.zeros(3))
+
+    return gradient_table(bvals, bvecs)