Source code for

"""Read/write linear transforms."""
from pathlib import Path
import numpy as np
from nibabel import load as loadimg

from ..patched import LabeledWrapStruct

[docs]class TransformIOError(IOError): """General I/O exception while reading/writing transforms."""
[docs]class TransformFileError(TransformIOError): """Specific I/O exception when a file does not meet the expected format."""
[docs]class StringBasedStruct(LabeledWrapStruct): """File data structure from text files.""" def __init__(self, binaryblock=None, endianness=None, check=True): """Create a data structure based off of a string.""" _dtype = getattr(binaryblock, "dtype", None) if binaryblock is not None and _dtype == self.dtype: self._structarr = binaryblock.copy() return super().__init__(binaryblock, endianness, check) def __array__(self): """Return the internal structure array.""" return self._structarr
[docs] def to_string(self): """Convert to a string directly writeable to file.""" raise NotImplementedError
[docs] @classmethod def from_string(cls, string): """Read the struct from string.""" raise NotImplementedError
[docs]class LinearTransformStruct(StringBasedStruct): """File data structure from linear transforms."""
[docs] def to_filename(self, filename): """Store this transform to a file with the appropriate format.""" with open(str(filename), "w") as f: f.write(self.to_string())
[docs] def to_ras(self, moving=None, reference=None): """Return a nitransforms internal RAS+ matrix.""" raise NotImplementedError
[docs] @classmethod def from_filename(cls, filename): """Read the struct from a file given its path.""" with open(str(filename)) as f: string = return cls.from_string(string)
[docs] @classmethod def from_fileobj(cls, fileobj, check=True): """Read the struct from a file object.""" return cls.from_string(
[docs] @classmethod def from_ras(cls, ras, moving=None, reference=None): """Create an affine from a nitransform's RAS+ matrix.""" raise NotImplementedError
[docs]class LinearParameters(LinearTransformStruct): """ A string-based structure for linear transforms. Examples -------- >>> lp = LinearParameters() >>> np.all(lp.structarr['parameters'] == np.eye(4)) True >>> p = np.diag([2., 2., 2., 1.]) >>> lp = LinearParameters(p) >>> np.all(lp.structarr['parameters'] == p) True """ template_dtype = np.dtype([("parameters", "f8", (4, 4))]) dtype = template_dtype def __init__(self, parameters=None): """ Initialize with default parameters. """ super().__init__() self.structarr["parameters"] = np.eye(4) if parameters is not None: self.structarr["parameters"] = parameters
[docs]class BaseLinearTransformList(LinearTransformStruct): """A string-based structure for series of linear transforms.""" template_dtype = np.dtype([("nxforms", "i4")]) dtype = template_dtype _xforms = None _inner_type = LinearParameters def __init__(self, xforms=None, binaryblock=None, endianness=None, check=True): """Initialize with (optionally) a list of transforms.""" super().__init__(binaryblock, endianness, check) self.xforms = [self._inner_type(parameters=mat) for mat in xforms or []] @property def xforms(self): """Get the list of internal transforms.""" return self._xforms @xforms.setter def xforms(self, value): self._xforms = list(value) def __getitem__(self, idx): """Allow dictionary access to the transforms.""" if idx == "xforms": return self._xforms if idx == "nxforms": return len(self._xforms) raise KeyError(idx)
[docs]class DisplacementsField: """A data structure representing displacements fields."""
[docs] @classmethod def from_filename(cls, filename): """Import a displacements field from a NIfTI file.""" imgobj = loadimg(str(filename)) return cls.from_image(imgobj)
[docs] @classmethod def from_image(cls, imgobj): """Import a displacements field from a nibabel image object.""" raise NotImplementedError
[docs] @classmethod def to_filename(cls, img, filename): """Export a displacements field to a NIfTI file.""" imgobj = cls.to_image(img) imgobj.to_filename(filename)
[docs] @classmethod def to_image(cls, imgobj): """Export a displacements field image from a nitransforms image object.""" raise NotImplementedError
def _ensure_image(img): if isinstance(img, (str, Path)): return loadimg(img) return img