Merge pull request #69 from matthew-brett/load-save-benchmarks

NF - add image load save benchmarks

Author: matthew-brett

nibabel/__init__.py

@@ -63,6 +63,7 @@
 try:
     from numpy.testing import Tester
     test = Tester().test
+    bench = Tester().bench
     del Tester
 except ImportError:
     def test(*args, **kwargs): raise RuntimeError('Need numpy >= 1.2 for tests')

nibabel/benchmarks/__init__.py

@@ -0,0 +1 @@
+# Benchmarks for nibabel

nibabel/benchmarks/bench_load_save.py

@@ -0,0 +1,52 @@
+""" Benchmarks for load and save of image arrays
+
+Run benchmarks with::
+
+    >>> import nibabel as nib
+    >>> nib.bench()
+
+If you have doctests enabled by default in nose (with a noserc file or
+environment variable), or you have a numpy version > 1.6.1, this will also run
+the doctests, let's hope they pass.
+"""
+import sys
+
+import numpy as np
+
+from ..py3k import BytesIO
+from .. import Nifti1Image
+
+from numpy.testing import measure
+
+def bench_load_save():
+    rng = np.random.RandomState(20111001)
+    repeat = 4
+    img_shape = (128, 128, 64)
+    arr = rng.normal(size=img_shape)
+    img = Nifti1Image(arr, np.eye(4))
+    sio = BytesIO()
+    img.file_map['image'].fileobj = sio
+    hdr = img.get_header()
+    sys.stdout.flush()
+    print "\nImage load save"
+    print "----------------"
+    hdr.set_data_dtype(np.float32)
+    mtime = measure('img.to_file_map()', repeat)
+    print '%30s %6.2f' % ('Save float64 to float32', mtime)
+    mtime = measure('img.from_file_map(img.file_map)', repeat)
+    print '%30s %6.2f' % ('Load from float32', mtime)
+    hdr.set_data_dtype(np.int16)
+    mtime = measure('img.to_file_map()', repeat)
+    print '%30s %6.2f' % ('Save float64 to int16', mtime)
+    mtime = measure('img.from_file_map(img.file_map)', repeat)
+    print '%30s %6.2f' % ('Load from int16', mtime)
+    arr = np.random.random_integers(low=-1000,high=-1000, size=img_shape)
+    arr = arr.astype(np.int16)
+    img = Nifti1Image(arr, np.eye(4))
+    sio = BytesIO()
+    img.file_map['image'].fileobj = sio
+    hdr = img.get_header()
+    hdr.set_data_dtype(np.float32)
+    mtime = measure('img.to_file_map()', repeat)
+    print '%30s %6.2f' % ('Save Int16 to float32', mtime)
+    sys.stdout.flush()

setup.py

@@ -84,6 +84,7 @@ def main(**extra_args):
                           'nibabel.nicom.tests',
                           'nibabel.testing',
                           'nibabel.tests',
+                          'nibabel.benchmarks',
                           # install nisext as its own package
                           'nisext',
                           'nisext.tests'],