New module fsl.utils.assertions, migrated over from Sean's DHCP project.

fsl/utils/assertions.py

+#!/usr/bin/env python
+#
+# Miscellaneous assertion functions.
+#
+# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk
+#         Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""This module contains a handful of miscellaneous assertion routines.
+"""
+
+
+import os.path as op
+import nibabel as nib
+
+
+def assertFileExists(*args):
+    """Raise an exception if the specified file/folder/s do not exist."""
+    for f in args:
+        assert op.exists(f), "file/folder does not exist: {0}".format(f)
+
+
+def assertIsNifti3D(*args):
+    """Raise an exception if the specified file/s are not 3D nifti."""
+    for f in args:
+        assertIsNifti(f)
+        d = nib.load(f)
+        assert len(d.shape) == 3, \
+            "incorrect shape for 3D nifti: {0}:{1}".format(d.shape, f)
+
+
+def assertIsNifti4D(*args):
+    """Raise an exception if the specified file/s are not 4D nifti."""
+    for f in args:
+        assertIsNifti(f)
+        d = nib.load(f)
+        assert len(d.shape) == 4, \
+            "incorrect shape for 4D nifti: {0}:{1}".format(d.shape, f)
+
+
+def assertIsNifti(*args):
+    """Raise an exception if the specified file/s are not nifti."""
+    for f in args:
+        assert isinstance(f, nib.nifti1.Nifti1Image) or \
+            f.endswith('.nii.gz') or f.endswith('.nii'), \
+            "file must be a nifti (.nii or .nii.gz): {0}".format(f)
+
+
+def assertNiftiShape(shape, *args):
+    """Raise an exception if the specified nifti/s are not specified shape."""
+    for fname in args:
+        d = nib.load(fname)
+        assert d.shape == shape, \
+            "incorrect shape ({2}) for nifti: {0}:{1}".format(d.shape, fname,
+                                                              shape)
+
+
+def assertIsSurfGifti(*args):
+    """Raise an exception if the specified file/s are not surface gifti."""
+    for fname in args:
+        assert fname.endswith('.surf.gii'), \
+            "file must be a surface gifti (surf.gii): {0}".format(fname)
+
+
+def assertIsFuncGifti(*args):
+    """Raise an exception if the specified file/s are not functional gifti."""
+    for fname in args:
+        assert fname.endswith('.func.gii'), \
+            "file must be a functional gifti (func.gii): {0}".format(fname)
+
+def assertIsMelodicDir(path):
+    """Raise an exception if the specified path is not a melodic directory.
+
+    :arg path:     Path to melodic directory
+    :type path:    string
+    """
+    assert op.exists(path), "melodic dir does not exist: {0}".format(path)
+    assert path.endswith('.ica'), \
+        "melodic directory must end in *.ica: {0}".format(path)
+    assert op.exists(op.join(path, 'melodic_IC.nii.gz')), \
+        "melodic directy must contain a file called melodic_IC.nii.gz"
+    assert op.exists(op.join(path, 'melodic_mix')), \
+        "melodic directy must contain a file called melodic_mix"
+    assert op.exists(op.join(path, 'melodic_FTmix')), \
+        "melodic directy must contain a file called melodic_FTmix"