From 6436bc804cd57fcc847ba174d967df577067398a Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 27 Feb 2018 14:59:25 +0000
Subject: [PATCH] New module fsl.utils.assertions, migrated over from Sean's
DHCP project.
---
fsl/utils/assertions.py | 84 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 84 insertions(+)
create mode 100644 fsl/utils/assertions.py
diff --git a/fsl/utils/assertions.py b/fsl/utils/assertions.py
new file mode 100644
index 000000000..9d6d748c8
--- /dev/null
+++ b/fsl/utils/assertions.py
@@ -0,0 +1,84 @@
+#!/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"
--
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