Merge pull request #160 from nipy/enh/autoload-linear

ENH: Guess open linear transform formats

Author: oesteban

nitransforms/io/__init__.py

@@ -1,11 +1,34 @@
 # emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Read and write transforms."""
-from . import afni, fsl, itk, lta
+from nitransforms.io import afni, fsl, itk, lta
+from nitransforms.io.base import TransformIOError, TransformFileError
 
 __all__ = [
     "afni",
     "fsl",
     "itk",
     "lta",
+    "get_linear_factory",
+    "TransformFileError",
+    "TransformIOError",
 ]
+
+_IO_TYPES = {
+    "itk": (itk, "ITKLinearTransform"),
+    "ants": (itk, "ITKLinearTransform"),
+    "elastix": (itk, "ITKLinearTransform"),
+    "lta": (lta, "FSLinearTransform"),
+    "fs": (lta, "FSLinearTransform"),
+    "fsl": (fsl, "FSLLinearTransform"),
+    "afni": (afni, "AFNILinearTransform"),
+}
+
+
+def get_linear_factory(fmt, is_array=True):
+    """Return the type required by a given format."""
+    if fmt.lower() not in _IO_TYPES:
+        raise TypeError(f"Unsupported transform format <{fmt}>.")
+
+    module, classname = _IO_TYPES[fmt.lower()]
+    return getattr(module, f"{classname}{'Array' * is_array}")

nitransforms/io/afni.py

@@ -95,12 +95,16 @@ def from_string(cls, string):
         if not lines:
             raise TransformFileError
 
-        parameters = np.vstack(
-            (
-                np.genfromtxt([lines[0].encode()], dtype="f8").reshape((3, 4)),
-                (0.0, 0.0, 0.0, 1.0),
+        try:
+            parameters = np.vstack(
+                (
+                    np.genfromtxt([lines[0].encode()], dtype="f8").reshape((3, 4)),
+                    (0.0, 0.0, 0.0, 1.0),
+                )
             )
-        )
+        except ValueError as e:
+            raise TransformFileError from e
+
         sa["parameters"] = parameters
         return tf
 

nitransforms/io/base.py

@@ -6,8 +6,12 @@
 from ..patched import LabeledWrapStruct
 
 
-class TransformFileError(Exception):
-    """A custom exception for transform files."""
+class TransformIOError(IOError):
+    """General I/O exception while reading/writing transforms."""
+
+
+class TransformFileError(TransformIOError):
+    """Specific I/O exception when a file does not meet the expected format."""
 
 
 class StringBasedStruct(LabeledWrapStruct):

nitransforms/io/fsl.py

@@ -10,6 +10,7 @@
     BaseLinearTransformList,
     LinearParameters,
     DisplacementsField,
+    TransformIOError,
     TransformFileError,
     _ensure_image,
 )
@@ -40,7 +41,7 @@ def from_ras(cls, ras, moving=None, reference=None):
             moving = reference
 
         if reference is None:
-            raise ValueError("Cannot build FSL linear transform without a reference")
+            raise TransformIOError("Cannot build FSL linear transform without a reference")
 
         reference = _ensure_image(reference)
         moving = _ensure_image(moving)
@@ -77,7 +78,7 @@ def from_string(cls, string):
     def to_ras(self, moving=None, reference=None):
         """Return a nitransforms internal RAS+ matrix."""
         if reference is None:
-            raise ValueError("Cannot build FSL linear transform without a reference")
+            raise TransformIOError("Cannot build FSL linear transform without a reference")
 
         if moving is None:
             warnings.warn(

nitransforms/io/itk.py

@@ -8,6 +8,7 @@
     BaseLinearTransformList,
     DisplacementsField,
     LinearParameters,
+    TransformIOError,
     TransformFileError,
 )
 
@@ -306,7 +307,7 @@ def from_filename(cls, filename):
         from h5py import File as H5File
 
         if not str(filename).endswith(".h5"):
-            raise RuntimeError("Extension is not .h5")
+            raise TransformFileError("Extension is not .h5")
 
         with H5File(str(filename)) as f:
             return cls.from_h5obj(f)
@@ -354,7 +355,7 @@ def from_h5obj(cls, fileobj, check=True):
                 )
                 continue
 
-            raise NotImplementedError(
+            raise TransformIOError(
                 f"Unsupported transform type {xfm['TransformType'][0]}"
             )
 

nitransforms/linear.py

@@ -14,14 +14,14 @@
 
 from nibabel.loadsave import load as _nbload
 
-from .base import (
+from nitransforms.base import (
     ImageGrid,
     TransformBase,
     SpatialReference,
     _as_homogeneous,
     EQUALITY_TOL,
 )
-from . import io
+from nitransforms.io import get_linear_factory, TransformFileError
 
 
 class Affine(TransformBase):
@@ -183,51 +183,40 @@ def _to_hdf5(self, x5_root):
             self.reference._to_hdf5(x5_root.create_group("Reference"))
 
     def to_filename(self, filename, fmt="X5", moving=None):
-        """Store the transform in BIDS-Transforms HDF5 file format (.x5)."""
-        if fmt.lower() in ["itk", "ants", "elastix"]:
-            itkobj = io.itk.ITKLinearTransform.from_ras(self.matrix)
-            itkobj.to_filename(filename)
-            return filename
-
-        # Rest of the formats peek into moving and reference image grids
-        moving = ImageGrid(moving) if moving is not None else self.reference
-
-        _factory = {
-            "afni": io.afni.AFNILinearTransform,
-            "fsl": io.fsl.FSLLinearTransform,
-            "lta": io.lta.FSLinearTransform,
-            "fs": io.lta.FSLinearTransform,
-        }
-
-        if fmt not in _factory:
-            raise NotImplementedError(f"Unsupported format <{fmt}>")
-
-        _factory[fmt].from_ras(
-            self.matrix, moving=moving, reference=self.reference
-        ).to_filename(filename)
-        return filename
+        """Store the transform in the requested output format."""
+        writer = get_linear_factory(fmt, is_array=False)
 
-    @classmethod
-    def from_filename(cls, filename, fmt="X5", reference=None, moving=None):
-        """Create an affine from a transform file."""
         if fmt.lower() in ("itk", "ants", "elastix"):
-            _factory = io.itk.ITKLinearTransformArray
-        elif fmt.lower() in ("lta", "fs"):
-            _factory = io.lta.FSLinearTransformArray
-        elif fmt.lower() == "fsl":
-            _factory = io.fsl.FSLLinearTransformArray
-        elif fmt.lower() == "afni":
-            _factory = io.afni.AFNILinearTransformArray
+            writer.from_ras(self.matrix).to_filename(filename)
         else:
-            raise NotImplementedError
+            # Rest of the formats peek into moving and reference image grids
+            writer.from_ras(
+                self.matrix,
+                reference=self.reference,
+                moving=ImageGrid(moving) if moving is not None else self.reference,
+            ).to_filename(filename)
+        return filename
 
-        struct = _factory.from_filename(filename)
-        matrix = struct.to_ras(reference=reference, moving=moving)
-        if cls == Affine:
-            if np.shape(matrix)[0] != 1:
-                raise TypeError("Cannot load transform array '%s'" % filename)
-            matrix = matrix[0]
-        return cls(matrix, reference=reference)
+    @classmethod
+    def from_filename(cls, filename, fmt=None, reference=None, moving=None):
+        """Create an affine from a transform file."""
+        fmtlist = [fmt] if fmt is not None else ("itk", "lta", "afni", "fsl")
+
+        for potential_fmt in fmtlist:
+            try:
+                struct = get_linear_factory(potential_fmt).from_filename(filename)
+                matrix = struct.to_ras(reference=reference, moving=moving)
+                if cls == Affine:
+                    if np.shape(matrix)[0] != 1:
+                        raise TypeError("Cannot load transform array '%s'" % filename)
+                    matrix = matrix[0]
+                return cls(matrix, reference=reference)
+            except (TransformFileError, FileNotFoundError):
+                continue
+
+        raise TransformFileError(
+            f"Could not open <{filename}> (formats tried: {', '.join(fmtlist)})."
+        )
 
     def __repr__(self):
         """
@@ -353,31 +342,18 @@ def map(self, x, inverse=False):
         return np.swapaxes(affine.dot(coords), 1, 2)
 
     def to_filename(self, filename, fmt="X5", moving=None):
-        """Store the transform in BIDS-Transforms HDF5 file format (.x5)."""
-        if fmt.lower() in ("itk", "ants", "elastix"):
-            itkobj = io.itk.ITKLinearTransformArray.from_ras(self.matrix)
-            itkobj.to_filename(filename)
-            return filename
+        """Store the transform in the requested output format."""
+        writer = get_linear_factory(fmt, is_array=True)
 
-        # Rest of the formats peek into moving and reference image grids
-        if moving is not None:
-            moving = ImageGrid(moving)
+        if fmt.lower() in ("itk", "ants", "elastix"):
+            writer.from_ras(self.matrix).to_filename(filename)
         else:
-            moving = self.reference
-
-        _factory = {
-            "afni": io.afni.AFNILinearTransformArray,
-            "fsl": io.fsl.FSLLinearTransformArray,
-            "lta": io.lta.FSLinearTransformArray,
-            "fs": io.lta.FSLinearTransformArray,
-        }
-
-        if fmt not in _factory:
-            raise NotImplementedError(f"Unsupported format <{fmt}>")
-
-        _factory[fmt].from_ras(
-            self.matrix, moving=moving, reference=self.reference
-        ).to_filename(filename)
+            # Rest of the formats peek into moving and reference image grids
+            writer.from_ras(
+                self.matrix,
+                reference=self.reference,
+                moving=ImageGrid(moving) if moving is not None else self.reference,
+            ).to_filename(filename)
         return filename
 
     def apply(
@@ -486,17 +462,17 @@ def apply(
         return resampled
 
 
-def load(filename, fmt="X5", reference=None, moving=None):
+def load(filename, fmt=None, reference=None, moving=None):
     """
     Load a linear transform file.
 
     Examples
     --------
-    >>> xfm = load(regress_dir / "affine-LAS.itk.tfm", fmt="itk")
+    >>> xfm = load(regress_dir / "affine-LAS.itk.tfm")
     >>> isinstance(xfm, Affine)
     True
 
-    >>> xfm = load(regress_dir / "itktflist.tfm", fmt="itk")
+    >>> xfm = load(regress_dir / "itktflist.tfm")
     >>> isinstance(xfm, LinearTransformsMapping)
     True
 

nitransforms/tests/test_io.py

@@ -1,12 +1,14 @@
 # emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """I/O test cases."""
+import os
 from subprocess import check_call
 from io import StringIO
 import filecmp
 import shutil
 import numpy as np
 import pytest
+from h5py import File as H5File
 
 import nibabel as nb
 from nibabel.eulerangles import euler2mat
@@ -24,7 +26,7 @@
     FSLinearTransform as LT,
     FSLinearTransformArray as LTA,
 )
-from ..io.base import LinearParameters, TransformFileError
+from ..io.base import LinearParameters, TransformIOError, TransformFileError
 
 LPS = np.diag([-1, -1, 1, 1])
 ITK_MAT = LPS.dot(np.ones((4, 4)).dot(LPS))
@@ -224,7 +226,7 @@ def test_Linear_common(tmpdir, data_path, sw, image_orientation, get_testdata):
 
     # Test without images
     if sw == "fsl":
-        with pytest.raises(ValueError):
+        with pytest.raises(TransformIOError):
             factory.from_ras(RAS)
     else:
         xfm = factory.from_ras(RAS)
@@ -408,7 +410,7 @@ def test_afni_Displacements():
         afni.AFNIDisplacementsField.from_image(field)
 
 
-def test_itk_h5(testdata_path):
+def test_itk_h5(tmpdir, testdata_path):
     """Test displacements fields."""
     assert (
         len(
@@ -422,14 +424,29 @@ def test_itk_h5(testdata_path):
         == 2
     )
 
-    with pytest.raises(RuntimeError):
+    with pytest.raises(TransformFileError):
         list(
             itk.ITKCompositeH5.from_filename(
                 testdata_path
                 / "ds-005_sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.x5"
             )
         )
 
+    tmpdir.chdir()
+    shutil.copy(
+        testdata_path / "ds-005_sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5",
+        "test.h5",
+    )
+    os.chmod("test.h5", 0o666)
+
+    with H5File("test.h5", "r+") as h5file:
+        h5group = h5file["TransformGroup"]
+        xfm = h5group[list(h5group.keys())[1]]
+        xfm["TransformType"][0] = b"InventTransform"
+
+    with pytest.raises(TransformIOError):
+        itk.ITKCompositeH5.from_filename("test.h5")
+
 
 @pytest.mark.parametrize(
     "file_type, test_file", [(LTA, "from-fsnative_to-scanner_mode-image.lta")]