Merge pull request #60 from matthew-brett/dft-optional-packages

Make dicom / PIL.Image optional for tests

Author: mih

nibabel/dft.py

@@ -9,13 +9,18 @@
 # Copyright (C) 2011 Christian Haselgrove
 
 import os
-import struct
 import tempfile
 import StringIO
-import numpy
-import nibabel
 import sqlite3
-import dicom
+
+import numpy
+
+from .nifti1 import Nifti1Header
+
+# Shield optional dicom import
+from .optpkg import optional_package
+dicom, have_dicom, _ = optional_package('dicom')
+
 
 class DFTError(Exception):
     "base class for DFT exceptions"
@@ -176,7 +181,7 @@ def as_nifti(self):
 
         m = numpy.array(m)
 
-        hdr = nibabel.nifti1.Nifti1Header(endianness='<')
+        hdr = Nifti1Header(endianness='<')
         hdr.set_intent(0)
         hdr.set_qform(m, 1)
         hdr.set_xyzt_units(2, 8)

nibabel/optpkg.py

@@ -0,0 +1,86 @@
+""" Routines to support optional packages """
+
+try:
+    import nose
+except ImportError:
+    have_nose = False
+else:
+    have_nose = True
+
+from .tripwire import TripWire, is_tripwire
+
+def optional_package(name, trip_msg=None):
+    """ Return package-like thing and module setup for package `name`
+
+    Parameters
+    ----------
+    name : str
+        package name
+    trip_msg : None or str
+        message to give when someone tries to use the return package, but we
+        could not import it, and have returned a TripWire object instead.
+        Default message if None.
+
+    Returns
+    -------
+    pkg_like : module or ``TripWire`` instance
+        If we can import the package, return it.  Otherwise return an object
+        raising an error when accessed
+    have_pkg : bool
+        True if import for package was successful, false otherwise
+    module_setup : function
+        callable usually set as ``setup_module`` in calling namespace, to allow
+        skipping tests.
+
+    Example
+    -------
+    Typical use would be something like this at the top of a module using an
+    optional package:
+
+    >>> from nipy.utils.optpkg import optional_package
+    >>> pkg, have_pkg, setup_module = optional_package('not_a_package')
+
+    Of course in this case the package doesn't exist, and so, in the module:
+
+    >>> have_pkg
+    False
+
+    and
+
+    >>> pkg.some_function()
+    Traceback (most recent call last):
+        ...
+    TripWireError: We need package not_a_package for these functions, but ``import not_a_package`` raised an ImportError
+
+    If the module does exist - we get the module
+
+    >>> pkg, _, _ = optional_package('os')
+    >>> hasattr(pkg, 'path')
+    True
+
+    Or a submodule if that's what we asked for
+
+    >>> subpkg, _, _ = optional_package('os.path')
+    >>> hasattr(subpkg, 'dirname')
+    True
+    """
+    # fromlist=[''] results in submodule being returned, rather than the top
+    # level module.  See help(__import__)
+    try:
+        pkg = __import__(name, fromlist=[''])
+    except ImportError:
+        pass
+    else: # import worked
+        # top level module
+        return pkg, True, lambda : None
+    if trip_msg is None:
+        trip_msg = ('We need package %s for these functions, but '
+                    '``import %s`` raised an ImportError'
+                    % (name, name))
+    pkg = TripWire(trip_msg)
+    def setup_module():
+        if have_nose:
+            raise nose.plugins.skip.SkipTest('No %s for these tests'
+                                             % name)
+    return pkg, False, setup_module
+

nibabel/tests/test_dft.py

@@ -3,17 +3,28 @@
 
 from os.path import join as pjoin, dirname
 import StringIO
-import PIL.Image
-from nose.tools import assert_true, assert_false, assert_equal, assert_raises
+
+import numpy as np
+
 from .. import dft
 from .. import nifti1
 
+from nose.tools import (assert_true, assert_false, assert_equal, assert_raises)
+
+# Shield optional package imports
+from ..optpkg import optional_package
+# setup_module will raise SkipTest if no dicom to import
+dicom, have_dicom, setup_module = optional_package('dicom')
+PImage, have_pil, _ = optional_package('PIL.Image')
+pil_test = np.testing.dec.skipif(not have_pil, 'could not import PIL.Image')
+
 data_dir = pjoin(dirname(__file__), 'data')
 
+
 def test_init():
     dft.clear_cache()
     dft.update_cache(data_dir)
-    return
+
 
 def test_study():
     studies = dft.get_studies(data_dir)
@@ -42,32 +53,35 @@ def test_series():
     assert_equal(ser.bits_allocated, 16)
     assert_equal(ser.bits_stored, 12)
 
+
 def test_storage_instances():
     studies = dft.get_studies(data_dir)
     sis = studies[0].series[0].storage_instances
     assert_equal(len(sis), 2)
     assert_equal(sis[0].instance_number, 1)
     assert_equal(sis[1].instance_number, 2)
-    assert_equal(sis[0].uid, 
+    assert_equal(sis[0].uid,
                  '1.3.12.2.1107.5.2.32.35119.2010011420300180088599504.0')
-    assert_equal(sis[1].uid, 
+    assert_equal(sis[1].uid,
                  '1.3.12.2.1107.5.2.32.35119.2010011420300180088599504.1')
 
+
 def test_storage_instance():
-    return
+    pass
 
+
+@pil_test
 def test_png():
     studies = dft.get_studies(data_dir)
     data = studies[0].series[0].as_png()
-    im = PIL.Image.open(StringIO.StringIO(data))
+    im = PImage.open(StringIO.StringIO(data))
     assert_equal(im.size, (256, 256))
-    return
+
 
 def test_nifti():
     studies = dft.get_studies(data_dir)
     data = studies[0].series[0].as_nifti()
     assert_equal(len(data), 352 + 2*256*256*2)
     h = nifti1.Nifti1Header(data[:348])
     assert_equal(h.get_data_shape(), (256, 256, 2))
-    return
 

nibabel/tripwire.py

@@ -0,0 +1,48 @@
+""" Class to raise error for missing modules or other misfortunes
+"""
+
+class TripWireError(Exception):
+    """ Exception if trying to use TripWire object """
+
+
+def is_tripwire(obj):
+    """ Returns True if `obj` appears to be a TripWire object
+
+    Examples
+    --------
+    >>> is_tripwire(object())
+    False
+    >>> is_tripwire(TripWire('some message'))
+    True
+    """
+    try:
+        obj.any_attribute
+    except TripWireError:
+        return True
+    except:
+        pass
+    return False
+
+
+class TripWire(object):
+    """ Class raising error if used
+
+    Standard use is to proxy modules that we could not import
+
+    Examples
+    --------
+    >>> try:
+    ...     import silly_module_name
+    ... except ImportError:
+    ...    silly_module_name = TripWire('We do not have silly_module_name')
+    >>> silly_module_name.do_silly_thing('with silly string')
+    Traceback (most recent call last):
+        ...
+    TripWireError: We do not have silly_module_name
+    """
+    def __init__(self, msg):
+        self._msg = msg
+
+    def __getattr__(self, attr_name):
+        ''' Raise informative error accessing attributes '''
+        raise TripWireError(self._msg)