Python ProbabilisticDirectionGetter.from_shcoeff方法代碼示例

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_shcoeff [as 別名]
def test_ProbabilisticDirectionGetter():
    # Test the constructors and errors of the ProbabilisticDirectionGetter

    class SillyModel(SphHarmModel):

        sh_order = 4

        def fit(self, data, mask=None):
            coeff = np.zeros(data.shape[:-1] + (15,))
            return SphHarmFit(self, coeff, mask=None)

    model = SillyModel(gtab=None)
    data = np.zeros((3, 3, 3, 7))

    # Test if the tracking works on different dtype of the same data.
    for dtype in [np.float32, np.float64]:
        fit = model.fit(data.astype(dtype))

        # Sample point and direction
        point = np.zeros(3)
        dir = unit_octahedron.vertices[0].copy()

        # make a dg from a fit
        dg = ProbabilisticDirectionGetter.from_shcoeff(fit.shm_coeff, 90,
                                                       unit_octahedron)
        state = dg.get_direction(point, dir)
        npt.assert_equal(state, 1)

        # Make a dg from a pmf
        N = unit_octahedron.theta.shape[0]
        pmf = np.zeros((3, 3, 3, N))
        dg = ProbabilisticDirectionGetter.from_pmf(pmf, 90, unit_octahedron)
        state = dg.get_direction(point, dir)
        npt.assert_equal(state, 1)

        # pmf shape must match sphere
        bad_pmf = pmf[..., 1:]
        npt.assert_raises(ValueError, ProbabilisticDirectionGetter.from_pmf,
                          bad_pmf, 90, unit_octahedron)

        # pmf must have 4 dimensions
        bad_pmf = pmf[0, ...]
        npt.assert_raises(ValueError, ProbabilisticDirectionGetter.from_pmf,
                          bad_pmf, 90, unit_octahedron)
        # pmf cannot have negative values
        pmf[0, 0, 0, 0] = -1
        npt.assert_raises(ValueError, ProbabilisticDirectionGetter.from_pmf,
                          pmf, 90, unit_octahedron)

        # Check basis_type keyword
        dg = ProbabilisticDirectionGetter.from_shcoeff(fit.shm_coeff, 90,
                                                       unit_octahedron,
                                                       basis_type="mrtrix")

        npt.assert_raises(ValueError,
                          ProbabilisticDirectionGetter.from_shcoeff,
                          fit.shm_coeff, 90, unit_octahedron,
                          basis_type="not a basis")

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_shcoeff [as 別名]
def tracking_prob(dir_src, dir_out, verbose=False):

    wm_name = 'wm_mask_' + par_b_tag + '_' + par_dim_tag + '.nii.gz'
    wm_mask, affine = load_nifti(pjoin(dir_src, wm_name), verbose)

    sh_name = 'sh_' + par_b_tag + '_' + par_dim_tag + '.nii.gz'
    sh, _ = load_nifti(pjoin(dir_src, sh_name), verbose)

    sphere = get_sphere('symmetric724') 

    classifier = ThresholdTissueClassifier(wm_mask.astype('f8'), .5)
    classifier = BinaryTissueClassifier(wm_mask)
    max_dg = ProbabilisticDirectionGetter.from_shcoeff(sh, max_angle=par_trk_max_angle, sphere=sphere)
    seeds = utils.seeds_from_mask(wm_mask, density=2, affine=affine)
    streamlines = LocalTracking(max_dg, classifier, seeds, affine, step_size=par_trk_step_size)
    streamlines = list(streamlines)

    trk_name = 'tractogram_' + par_b_tag + '_' + par_dim_tag + '_' + par_trk_prob_tag + '.trk'
    trk_out = os.path.join(dir_out, trk_name)
 
    save_trk(trk_out, streamlines, affine, wm_mask.shape)

    dpy_out = trk_out.replace('.trk', '.dpy')
    dpy = Dpy(dpy_out, 'w')
    dpy.write_tracks(streamlines)
    dpy.close()

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_shcoeff [as 別名]
    def _get_direction_getter(self, strategy_name, pam, pmf_threshold,
                              max_angle):
        """Get Tracking Direction Getter object.

        Parameters
        ----------
        strategy_name: str
            String representing direction getter name.
        pam: instance of PeaksAndMetrics
            An object with ``gfa``, ``peak_directions``, ``peak_values``,
            ``peak_indices``, ``odf``, ``shm_coeffs`` as attributes.
        pmf_threshold : float
            Threshold for ODF functions.
        max_angle : float
            Maximum angle between streamline segments.

        Returns
        -------
        direction_getter : instance of DirectionGetter
            Used to get directions for fiber tracking.

        """
        dg, msg = None, ''
        if strategy_name.lower() in ["deterministic", "det"]:
            msg = "Deterministic"
            dg = DeterministicMaximumDirectionGetter.from_shcoeff(
                pam.shm_coeff,
                sphere=pam.sphere,
                max_angle=max_angle,
                pmf_threshold=pmf_threshold)
        elif strategy_name.lower() in ["probabilistic", "prob"]:
            msg = "Probabilistic"
            dg = ProbabilisticDirectionGetter.from_shcoeff(
                pam.shm_coeff,
                sphere=pam.sphere,
                max_angle=max_angle,
                pmf_threshold=pmf_threshold)
        elif strategy_name.lower() in ["closestpeaks", "cp"]:
            msg = "ClosestPeaks"
            dg = ClosestPeakDirectionGetter.from_shcoeff(
                pam.shm_coeff,
                sphere=pam.sphere,
                max_angle=max_angle,
                pmf_threshold=pmf_threshold)
        elif strategy_name.lower() in ["eudx", ]:
            msg = "Eudx"
            dg = pam
        else:
            msg = "No direction getter defined. Eudx"
            dg = pam

        logging.info('{0} direction getter strategy selected'.format(msg))
        return dg

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_shcoeff [as 別名]
    def _get_direction_getter(self, strategy_name, pam, pmf_threshold=0.1,
                              max_angle=30.):
        """Get Tracking Direction Getter object.

        Parameters
        ----------
        strategy_name: str
            string representing direction getter name

        Returns
        -------
        direction_getter : instance of DirectionGetter
            Used to get directions for fiber tracking.

        """
        dg, msg = None, ''
        if strategy_name.lower() in ["deterministic", "det"]:
            msg = "Deterministic"
            dg = DeterministicMaximumDirectionGetter.from_shcoeff(
                pam.shm_coeff,
                sphere=pam.sphere,
                max_angle=max_angle,
                pmf_threshold=pmf_threshold)
        elif strategy_name.lower() in ["probabilistic", "prob"]:
            msg = "Probabilistic"
            dg = ProbabilisticDirectionGetter.from_shcoeff(
                pam.shm_coeff,
                sphere=pam.sphere,
                max_angle=max_angle,
                pmf_threshold=pmf_threshold)
        elif strategy_name.lower() in ["closestpeaks", "cp"]:
            msg = "ClosestPeaks"
            dg = ClosestPeakDirectionGetter.from_shcoeff(
                pam.shm_coeff,
                sphere=pam.sphere,
                max_angle=max_angle,
                pmf_threshold=pmf_threshold)
        elif strategy_name.lower() in ["eudx", ]:
            msg = "Eudx"
            dg = pam
        else:
            msg = "No direction getter defined. Deterministic"
            dg = DeterministicMaximumDirectionGetter.from_shcoeff(
                pam.shm_coeff,
                sphere=pam.sphere,
                max_angle=max_angle,
                pmf_threshold=pmf_threshold)

        logging.info('{0} direction getter strategy selected'.format(msg))
        return dg

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_shcoeff [as 別名]
response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=0.7)
csd_model = ConstrainedSphericalDeconvModel(gtab, response, sh_order=6)
csd_fit = csd_model.fit(data, mask=white_matter)

"""
Next we'll need to make a ``ProbabilisticDirectionGetter``. Because the CSD
model represents the FOD using the spherical harmonic basis, we can use the
``from_shcoeff`` method to create the direction getter. This direction getter
will randomly sample directions from the FOD each time the tracking algorithm
needs to take another step.
"""

from dipy.direction import ProbabilisticDirectionGetter

prob_dg = ProbabilisticDirectionGetter.from_shcoeff(csd_fit.shm_coeff,
                                                    max_angle=30.,
                                                    sphere=default_sphere)

"""
As with deterministic tracking, we'll need to use a tissue classifier to
restrict the tracking to the white matter of the brain. One might be tempted
to use the GFA of the CSD FODs to build a tissue classifier, however the GFA
values of these FODs don't classify gray matter and white matter well. We will
therefore use the GFA from the CSA model which we fit for the first section of
this example. Alternatively, one could fit a ``TensorModel`` to the data and use
the fractional anisotropy (FA) to build a tissue classifier.
"""

classifier = ThresholdTissueClassifier(csa_peaks.gfa, .25)

"""

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_shcoeff [as 別名]
	def _run_interface(self, runtime):
		import numpy as np
		import nibabel as nib
		from dipy.io import read_bvals_bvecs
		from dipy.core.gradients import gradient_table
		from nipype.utils.filemanip import split_filename

		# Loading the data
		fname = self.inputs.in_file
		img = nib.load(fname)
		data = img.get_data()
		affine = img.get_affine()

		FA_fname = self.inputs.FA_file
		FA_img = nib.load(FA_fname)
		fa = FA_img.get_data()
		affine = FA_img.get_affine()
		affine = np.matrix.round(affine)

		mask_fname = self.inputs.brain_mask
		mask_img = nib.load(mask_fname)
		mask = mask_img.get_data()

		bval_fname = self.inputs.bval
		bvals = np.loadtxt(bval_fname)

		bvec_fname = self.inputs.bvec
		bvecs = np.loadtxt(bvec_fname)
		bvecs = np.vstack([bvecs[0,:],bvecs[1,:],bvecs[2,:]]).T
		gtab = gradient_table(bvals, bvecs)

		# Creating a white matter mask
		fa = fa*mask
		white_matter = fa >= 0.2

		# Creating a seed mask
		from dipy.tracking import utils
		seeds = utils.seeds_from_mask(white_matter, density=[2, 2, 2], affine=affine)

		# Fitting the CSA model
		from dipy.reconst.shm import CsaOdfModel
		from dipy.data import default_sphere
		from dipy.direction import peaks_from_model
		csa_model = CsaOdfModel(gtab, sh_order=8)
		csa_peaks = peaks_from_model(csa_model, data, default_sphere,
		                             relative_peak_threshold=.8,
		                             min_separation_angle=45,
		                             mask=white_matter)

		from dipy.tracking.local import ThresholdTissueClassifier
		classifier = ThresholdTissueClassifier(csa_peaks.gfa, .25)

		# CSD model
		from dipy.reconst.csdeconv import (ConstrainedSphericalDeconvModel, auto_response)
		response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=0.7)
		csd_model = ConstrainedSphericalDeconvModel(gtab, response, sh_order=8)
		csd_fit = csd_model.fit(data, mask=white_matter)

		from dipy.direction import ProbabilisticDirectionGetter
		prob_dg = ProbabilisticDirectionGetter.from_shcoeff(csd_fit.shm_coeff,
		                                                    max_angle=45.,
		                                                    sphere=default_sphere)

		# Tracking
		from dipy.tracking.local import LocalTracking
		streamlines = LocalTracking(prob_dg, classifier, seeds, affine,
		                            step_size=.5, maxlen=200, max_cross=1)

		# Compute streamlines and store as a list.
		streamlines = list(streamlines)

		# Saving the trackfile
		from dipy.io.trackvis import save_trk
		_, base, _ = split_filename(fname)
		save_trk(base + '_CSDprob.trk', streamlines, affine, fa.shape)

		return runtime

# 需要導入模塊: from dipy.direction import ProbabilisticDirectionGetter [as 別名]
# 或者: from dipy.direction.ProbabilisticDirectionGetter import from_shcoeff [as 別名]
det_streamline_generator = LocalTracking(pam,
                                         cmc_classifier,
                                         seeds,
                                         affine,
                                         step_size=step_size)

# The line below is failing not sure why
# detstreamlines = Streamlines(det_streamline_generator)

detstreamlines = list(det_streamline_generator)
detstreamlines = Streamlines(detstreamlines)
save_trk('det.trk', detstreamlines, affine=np.eye(4),
         vox_size=vox_size, shape=shape)

dg = ProbabilisticDirectionGetter.from_shcoeff(pam.shm_coeff,
                                               max_angle=20.,
                                               sphere=sphere)

# Particle Filtering Tractography
pft_streamline_generator = ParticleFilteringTracking(dg,
                                                     cmc_classifier,
                                                     seeds,
                                                     affine,
                                                     max_cross=1,
                                                     step_size=step_size,
                                                     maxlen=1000,
                                                     pft_back_tracking_dist=2,
                                                     pft_front_tracking_dist=1,
                                                     particle_count=15,
                                                     return_all=False)
# The line below is failing not sure why