Python Dataset.get_mapped方法代码示例

# 需要导入模块: from mvpa.datasets.base import Dataset [as 别名]
# 或者: from mvpa.datasets.base.Dataset import get_mapped [as 别名]
def test_featuregroup_mapper():
    ds = Dataset(np.arange(24).reshape(3,8))
    ds.fa['roi'] = [0, 1] * 4
    # just to check
    ds.sa['chunks'] = np.arange(3)

    # correct results
    csamples = [[3, 4], [11, 12], [19, 20]]
    croi = [0, 1]
    cchunks = np.arange(3)

    m = mean_group_feature(['roi'])
    mds = m.forward(ds)
    assert_equal(mds.shape, (3, 2))
    assert_array_equal(mds.samples, csamples)
    assert_array_equal(mds.fa.roi, np.unique([0, 1] * 4))
    # FAs should simply remain the same
    assert_array_equal(mds.sa.chunks, np.arange(3))

    # now without grouping
    m = mean_feature()
    # forwarding just the samples should yield the same result
    assert_array_equal(m.forward(ds.samples),
                       m.forward(ds).samples)

    # And when operating on a dataset with >1D samples, then operate
    # only across "features", i.e. 1st dimension
    ds = Dataset(np.arange(24).reshape(3,2,2,2))
    mapped = ds.get_mapped(m)
    assert_array_equal(m.forward(ds.samples),
                       mapped.samples)
    assert_array_equal(mapped.samples.shape, (3, 2, 2))
    assert_array_equal(mapped.samples, np.mean(ds.samples, axis=1))
    # and still could map back? ;) not ATM, so just to ensure consistency
    assert_raises(NotImplementedError,
                  mapped.a.mapper.reverse, mapped.samples)
    # but it should also work with standard 2d sample arrays
    ds = Dataset(np.arange(24).reshape(3,8))
    mapped = ds.get_mapped(m)
    assert_array_equal(mapped.samples.shape, (3, 1))

# 需要导入模块: from mvpa.datasets.base import Dataset [as 别名]
# 或者: from mvpa.datasets.base.Dataset import get_mapped [as 别名]
def fmri_dataset(samples, targets=None, chunks=None, mask=None, sprefix="voxel", tprefix="time", add_fa=None):
    """Create a dataset from an fMRI timeseries image.

    The timeseries image serves as the samples data, with each volume becoming
    a sample. All 3D volume samples are flattened into one-dimensional feature
    vectors, optionally being masked (i.e. subset of voxels corresponding to
    non-zero elements in a mask image).

    In addition to (optional) samples attributes for targets and chunks the
    returned dataset contains a number of additional attributes:

    Samples attributes (per each volume):

      * volume index (time_indices)
      * volume acquisition time (time_coord)

    Feature attributes (per each voxel):

      * voxel indices (voxel_indices), sometimes referred to as ijk

    Dataset attributes:

      * dump of the NIfTI image header data (imghdr)
      * volume extent (voxel_dim)
      * voxel extent (voxel_eldim)

    The default attribute name is listed in parenthesis, but may be altered by
    the corresponding prefix arguments. The validity of the attribute values
    relies on correct settings in the NIfTI image header.

    Parameters
    ----------
    samples : str or NiftiImage or list
      fMRI timeseries, specified either as a filename (single file 4D image),
      an image instance (4D image), or a list of filenames or image instances
      (each list item corresponding to a 3D volume).
    targets : scalar or sequence
      Label attribute for each volume in the timeseries, or a scalar value that
      is assigned to all samples.
    chunks : scalar or sequence
      Chunk attribute for each volume in the timeseries, or a scalar value that
      is assigned to all samples.
    mask : str or NiftiImage
      Filename or image instance of a 3D volume mask. Voxels corresponding to
      non-zero elements in the mask will be selected. The mask has to be in the
      same space (orientation and dimensions) as the timeseries image
    sprefix : str or None
      Prefix for attribute names describing spatial properties of the
      timeseries. If None, no such attributes are stored in the dataset.
    tprefix : str or None
      Prefix for attribute names describing temporal properties of the
      timeseries. If None, no such attributes are stored in the dataset.
    add_fa : dict or None
      Optional dictionary with additional volumetric data that shall be stored
      as feature attributes in the dataset. The dictionary key serves as the
      feature attribute name. Each value might be of any type supported by the
      'mask' argument of this function.

    Returns
    -------
    Dataset
    """
    # load the samples
    niftisamples = _load_anynifti(samples, ensure=True, enforce_dim=4)
    samples = niftisamples.data

    # figure out what the mask is, but onyl handle known cases, the rest
    # goes directly into the mapper which maybe knows more
    niftimask = _load_anynifti(mask)
    if niftimask is None:
        pass
    elif isinstance(niftimask, np.ndarray):
        mask = niftimask
    else:
        mask = _get_nifti_data(niftimask)

    # compile the samples attributes
    sa = {}
    if not targets is None:
        sa["targets"] = _expand_attribute(targets, samples.shape[0], "targets")
    if not chunks is None:
        sa["chunks"] = _expand_attribute(chunks, samples.shape[0], "chunks")

    # create a dataset
    ds = Dataset(samples, sa=sa)
    if sprefix is None:
        inspace = None
    else:
        inspace = sprefix + "_indices"
    ds = ds.get_mapped(FlattenMapper(shape=samples.shape[1:], inspace=inspace))

    # now apply the mask if any
    if not mask is None:
        flatmask = ds.a.mapper.forward1(mask)
        # direct slicing is possible, and it is potentially more efficient,
        # so let's use it
        # mapper = FeatureSliceMapper(flatmask)
        # ds = ds.get_mapped(FeatureSliceMapper(flatmask))
        ds = ds[:, flatmask != 0]

#.........这里部分代码省略.........

# 需要导入模块: from mvpa.datasets.base import Dataset [as 别名]
# 或者: from mvpa.datasets.base.Dataset import get_mapped [as 别名]
def fmri_dataset(samples, targets=None, chunks=None, mask=None,
                 sprefix='voxel', tprefix='time', add_fa=None,):
    """Create a dataset from an fMRI timeseries image.

    The timeseries image serves as the samples data, with each volume becoming
    a sample. All 3D volume samples are flattened into one-dimensional feature
    vectors, optionally being masked (i.e. subset of voxels corresponding to
    non-zero elements in a mask image).

    In addition to (optional) samples attributes for targets and chunks the
    returned dataset contains a number of additional attributes:

    Samples attributes (per each volume):

      * volume index (time_indices)
      * volume acquisition time (time_coord)

    Feature attributes (per each voxel):

      * voxel indices (voxel_indices), sometimes referred to as ijk

    Dataset attributes:

      * dump of the image (e.g. NIfTI) header data (imghdr)
      * class of the image (e.g. Nifti1Image) (imgtype)
      * volume extent (voxel_dim)
      * voxel extent (voxel_eldim)

    The default attribute name is listed in parenthesis, but may be altered by
    the corresponding prefix arguments. The validity of the attribute values
    relies on correct settings in the NIfTI image header.

    Parameters
    ----------
    samples : str or NiftiImage or list
      fMRI timeseries, specified either as a filename (single file 4D image),
      an image instance (4D image), or a list of filenames or image instances
      (each list item corresponding to a 3D volume).
    targets : scalar or sequence
      Label attribute for each volume in the timeseries, or a scalar value that
      is assigned to all samples.
    chunks : scalar or sequence
      Chunk attribute for each volume in the timeseries, or a scalar value that
      is assigned to all samples.
    mask : str or NiftiImage
      Filename or image instance of a 3D volume mask. Voxels corresponding to
      non-zero elements in the mask will be selected. The mask has to be in the
      same space (orientation and dimensions) as the timeseries image
    sprefix : str or None
      Prefix for attribute names describing spatial properties of the
      timeseries. If None, no such attributes are stored in the dataset.
    tprefix : str or None
      Prefix for attribute names describing temporal properties of the
      timeseries. If None, no such attributes are stored in the dataset.
    add_fa : dict or None
      Optional dictionary with additional volumetric data that shall be stored
      as feature attributes in the dataset. The dictionary key serves as the
      feature attribute name. Each value might be of any type supported by the
      'mask' argument of this function.

    Returns
    -------
    Dataset
    """
    # load the samples
    imgdata, imghdr, imgtype = _load_anyimg(samples, ensure=True, enforce_dim=4)

    # figure out what the mask is, but only handle known cases, the rest
    # goes directly into the mapper which maybe knows more
    maskimg = _load_anyimg(mask)
    if maskimg is None:
        pass
    else:
        # take just data and ignore the header
        mask = maskimg[0]

    # compile the samples attributes
    sa = {}
    if not targets is None:
        sa['targets'] = _expand_attribute(targets, imgdata.shape[0], 'targets')
    if not chunks is None:
        sa['chunks'] = _expand_attribute(chunks, imgdata.shape[0], 'chunks')

    # create a dataset
    ds = Dataset(imgdata, sa=sa)
    if sprefix is None:
        space = None
    else:
        space = sprefix + '_indices'
    ds = ds.get_mapped(FlattenMapper(shape=imgdata.shape[1:], space=space))

    # now apply the mask if any
    if not mask is None:
        flatmask = ds.a.mapper.forward1(mask)
        # direct slicing is possible, and it is potentially more efficient,
        # so let's use it
        #mapper = StaticFeatureSelection(flatmask)
        #ds = ds.get_mapped(StaticFeatureSelection(flatmask))
        ds = ds[:, flatmask != 0]

#.........这里部分代码省略.........