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effigieseffigies
committedMay 25, 2019
ENH: LinearTransformArray
1 parent 97447e2 commit dacf547

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‎nibabel/freesurfer/lta.py

+233
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import numpy as np
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from ..wrapstruct import LabeledWrapStruct
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from ..volumeutils import Recoder
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transform_codes = Recoder((
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(0, 'LINEAR_VOX_TO_VOX'),
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(1, 'LINEAR_RAS_TO_RAS'),
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(2, 'LINEAR_PHYSVOX_TO_PHYSVOX'),
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(14, 'REGISTER_DAT'),
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(21, 'LINEAR_COR_TO_COR')),
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fields=('code', 'label'))
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class StringBasedStruct(LabeledWrapStruct):
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def __init__(self,
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binaryblock=None,
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endianness=None,
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check=True):
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if binaryblock is not None and getattr(binaryblock, 'dtype',
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None) == self.dtype:
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self._structarr = binaryblock.copy()
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return
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super(StringBasedStruct, self).__init__(binaryblock, endianness, check)
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def __array__(self):
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return self._structarr
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class VolumeGeometry(StringBasedStruct):
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template_dtype = np.dtype([
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('valid', 'i4'), # Valid values: 0, 1
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('volume', 'i4', (3, 1)), # width, height, depth
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('voxelsize', 'f4', (3, 1)), # xsize, ysize, zsize
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('xras', 'f4', (3, 1)), # x_r, x_a, x_s
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('yras', 'f4', (3, 1)), # y_r, y_a, y_s
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('zras', 'f4', (3, 1)), # z_r, z_a, z_s
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('cras', 'f4', (3, 1)), # c_r, c_a, c_s
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('filename', 'U1024')]) # Not conformant (may be >1024 bytes)
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dtype = template_dtype
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def as_affine(self):
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affine = np.eye(4)
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sa = self.structarr
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A = np.hstack((sa['xras'], sa['yras'], sa['zras'])) * sa['voxelsize']
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b = sa['cras'] - A.dot(sa['volume']) / 2
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affine[:3, :3] = A
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affine[:3, [3]] = b
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return affine
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def to_string(self):
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sa = self.structarr
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lines = [
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'valid = {} # volume info {:s}valid'.format(
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sa['valid'], '' if sa['valid'] else 'in'),
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'filename = {}'.format(sa['filename']),
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'volume = {:d} {:d} {:d}'.format(*sa['volume'].flatten()),
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'voxelsize = {:.15e} {:.15e} {:.15e}'.format(
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*sa['voxelsize'].flatten()),
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'xras = {:.15e} {:.15e} {:.15e}'.format(*sa['xras'].flatten()),
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'yras = {:.15e} {:.15e} {:.15e}'.format(*sa['yras'].flatten()),
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'zras = {:.15e} {:.15e} {:.15e}'.format(*sa['zras'].flatten()),
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'cras = {:.15e} {:.15e} {:.15e}'.format(*sa['cras'].flatten()),
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]
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return '\n'.join(lines)
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@classmethod
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def from_image(klass, img):
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volgeom = klass()
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sa = volgeom.structarr
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sa['valid'] = 1
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sa['volume'][:, 0] = img.shape[:3] # Assumes xyzt-ordered image
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sa['voxelsize'][:, 0] = img.header.get_zooms()[:3]
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A = img.affine[:3, :3]
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b = img.affine[:3, [3]]
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cols = A * (1 / sa['voxelsize'])
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sa['xras'] = cols[:, [0]]
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sa['yras'] = cols[:, [1]]
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sa['zras'] = cols[:, [2]]
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sa['cras'] = b + A.dot(sa['volume']) / 2
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try:
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sa['filename'] = img.file_map['image'].filename
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except:
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pass
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return volgeom
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@classmethod
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def from_string(klass, string):
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volgeom = klass()
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sa = volgeom.structarr
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lines = string.splitlines()
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for key in ('valid', 'filename', 'volume', 'voxelsize',
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'xras', 'yras', 'zras', 'cras'):
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label, valstring = lines.pop(0).split(' = ')
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assert label.strip() == key
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val = np.genfromtxt([valstring.encode()],
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dtype=klass.dtype[key])
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sa[key] = val.reshape(sa[key].shape) if val.size else ''
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return volgeom
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class LinearTransform(StringBasedStruct):
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template_dtype = np.dtype([
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('mean', 'f4', (3, 1)), # x0, y0, z0
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('sigma', 'f4'),
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('m_L', 'f4', (4, 4)),
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('m_dL', 'f4', (4, 4)),
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('m_last_dL', 'f4', (4, 4)),
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('src', VolumeGeometry),
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('dst', VolumeGeometry),
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('label', 'i4')])
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dtype = template_dtype
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def __getitem__(self, idx):
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val = super(LinearTransform, self).__getitem__(idx)
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if idx in ('src', 'dst'):
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val = VolumeGeometry(val)
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return val
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def to_string(self):
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sa = self.structarr
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lines = [
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'mean = {:6.4f} {:6.4f} {:6.4f}'.format(
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*sa['mean'].flatten()),
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'sigma = {:6.4f}'.format(float(sa['sigma'])),
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'1 4 4',
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('{:18.15e} ' * 4).format(*sa['m_L'][0]),
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('{:18.15e} ' * 4).format(*sa['m_L'][1]),
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('{:18.15e} ' * 4).format(*sa['m_L'][2]),
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('{:18.15e} ' * 4).format(*sa['m_L'][3]),
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'src volume info',
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self['src'].to_string(),
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'dst volume info',
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self['dst'].to_string(),
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]
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return '\n'.join(lines)
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@classmethod
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def from_string(klass, string):
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lt = klass()
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sa = lt.structarr
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lines = string.splitlines()
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for key in ('mean', 'sigma'):
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label, valstring = lines.pop(0).split(' = ')
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assert label.strip() == key
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val = np.genfromtxt([valstring.encode()],
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dtype=klass.dtype[key])
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sa[key] = val.reshape(sa[key].shape)
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assert lines.pop(0) == '1 4 4'
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val = np.genfromtxt([valstring.encode() for valstring in lines[:4]],
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dtype='f4')
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sa['m_L'] = val
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lines = lines[4:]
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assert lines.pop(0) == 'src volume info'
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sa['src'] = np.asanyarray(VolumeGeometry.from_string('\n'.join(lines[:8])))
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lines = lines[8:]
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assert lines.pop(0) == 'dst volume info'
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sa['dst'] = np.asanyarray(VolumeGeometry.from_string('\n'.join(lines)))
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return lt
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class LinearTransformArray(StringBasedStruct):
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template_dtype = np.dtype([
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('type', 'i4'),
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('nxforms', 'i4'),
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('subject', 'U1024'),
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('fscale', 'f4')])
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dtype = template_dtype
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_xforms = None
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def __init__(self,
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binaryblock=None,
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endianness=None,
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check=True):
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super(LinearTransformArray, self).__init__(binaryblock, endianness, check)
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self._xforms = [LinearTransform()
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for _ in range(self.structarr['nxforms'])]
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def __getitem__(self, idx):
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if idx == 'xforms':
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return self._xforms
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if idx == 'nxforms':
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return len(self._xforms)
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return super(LinearTransformArray, self).__getitem__(idx)
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def to_string(self):
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code = int(self['type'])
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header = [
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'type = {} # {}'.format(code, transform_codes.label[code]),
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'nxforms = {}'.format(self['nxforms'])]
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xforms = [xfm.to_string() for xfm in self._xforms]
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footer = [
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'subject {}'.format(self['subject']),
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'fscale {:.6f}'.format(float(self['fscale']))]
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return '\n'.join(header + xforms + footer)
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@classmethod
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def from_string(klass, string):
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lta = klass()
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sa = lta.structarr
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lines = string.splitlines()
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for key in ('type', 'nxforms'):
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label, valstring = lines.pop(0).split(' = ')
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assert label.strip() == key
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val = np.genfromtxt([valstring.encode()],
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dtype=klass.dtype[key])
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sa[key] = val.reshape(sa[key].shape) if val.size else ''
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for _ in range(sa['nxforms']):
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lta._xforms.append(
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LinearTransform.from_string('\n'.join(lines[:25])))
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lines = lines[25:]
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for key in ('subject', 'fscale'):
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# Optional keys
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if not lines[0].startswith(key):
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continue
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label, valstring = lines.pop(0).split(' ')
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assert label.strip() == key
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val = np.genfromtxt([valstring.encode()],
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dtype=klass.dtype[key])
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sa[key] = val.reshape(sa[key].shape) if val.size else ''
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assert len(lta._xforms) == sa['nxforms']
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return lta
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@classmethod
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def from_fileobj(klass, fileobj, check=True):
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return klass.from_string(fileobj.read())

‎nibabel/wrapstruct.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -323,7 +323,7 @@ def __setitem__(self, item, value):
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>>> wstr['integer']
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array(3, dtype=int16)
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'''
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self._structarr[item] = value
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self._structarr[item] = np.asanyarray(value)
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def __iter__(self):
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return iter(self.keys())

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