Merge branch 'nipy-dipy-master' into textactor2d

.travis.yml

@@ -17,7 +17,7 @@ addons:
 
 env:
     global:
-        - DEPENDS="cython numpy scipy matplotlib h5py nibabel cvxopt"
+        - DEPENDS="cython numpy scipy matplotlib h5py nibabel cvxpy"
         - VENV_ARGS="--python=python"
         - INSTALL_TYPE="setup"
         - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
@@ -88,6 +88,7 @@ before_install:
     # Needed for Python 3.5 wheel fetching
     - $PIPI --upgrade pip setuptools
     - $PIPI nose;
+    - $PIPI numpy;
     - if [ -n "$DEPENDS" ]; then $PIPI $DEPENDS; fi
     - if [ "${COVERAGE}" == "1" ]; then pip install coverage coveralls codecov; fi
     - if [ "${VTK}" == "1" ]; then

cythexts.py

@@ -38,7 +38,7 @@ def stamped_pyx_ok(exts, hash_stamp_fname):
     for mod in exts:
         for source in mod.sources:
             base, ext = splitext(source)
-            if not ext in ('.pyx', '.py'):
+            if ext not in ('.pyx', '.py'):
                 continue
             source_hash = sha1(open(source, 'rb').read()).hexdigest()
             c_fname = base + '.c'
@@ -58,7 +58,7 @@ def stamped_pyx_ok(exts, hash_stamp_fname):
         if line.startswith('#'):
             continue
         fname, hash = [e.strip() for e in line.split(',')]
-        if not hash in stamps:
+        if hash not in stamps:
             return False
         # Compare path made canonical for \/
         fname = fname.replace(filesep, '/')

dipy/io/dpy.py

@@ -1,12 +1,12 @@
-''' A class for handling large tractography datasets.
+""" A class for handling large tractography datasets.
 
     It is built using the pytables tools which in turn implement
     key features of the HDF5 (hierachical data format) API [1]_.
 
     References
     ----------
     .. [1] http://www.hdfgroup.org/HDF5/doc/H5.intro.html
-'''
+"""
 
 import numpy as np
 
@@ -22,8 +22,7 @@
 tables, have_tables, _ = optional_package('tables')
 
 # Useful variable for backward compatibility.
-if have_tables:
-    TABLES_LESS_3_0 = LooseVersion(tables.__version__) < "3.0"
+TABLES_LESS_3_0 = LooseVersion(tables.__version__) < "3.0" if have_tables else False
 
 # Make sure not to carry across setup module from * import
 __all__ = ['Dpy']
@@ -32,7 +31,7 @@
 class Dpy(object):
     @doctest_skip_parser
     def __init__(self, fname, mode='r', compression=0):
-        ''' Advanced storage system for tractography based on HDF5
+        """ Advanced storage system for tractography based on HDF5
 
         Parameters
         ------------
@@ -50,7 +49,7 @@ def __init__(self, fname, mode='r', compression=0):
         >>> from dipy.io.dpy import Dpy
         >>> def dpy_example():
         ...     fd,fname = mkstemp()
-        ...     fname = fname + '.dpy' #add correct extension
+        ...     fname += '.dpy'#add correct extension
         ...     dpw = Dpy(fname,'w')
         ...     A=np.ones((5,3))
         ...     B=2*A.copy()
@@ -67,7 +66,7 @@ def __init__(self, fname, mode='r', compression=0):
         ...     os.remove(fname) #delete file from disk
         >>> dpy_example()  # skip if not have_tables
 
-        '''
+        """
 
         self.mode = mode
         self.f = tables.openFile(fname, mode=self.mode) if TABLES_LESS_3_0 else tables.open_file(fname, mode=self.mode)
@@ -116,30 +115,30 @@ def version(self):
         return ver[0].decode()
 
     def write_track(self, track):
-        ''' write on track each time
-        '''
+        """ write on track each time
+        """
         self.tracks.append(track.astype(np.float32))
         self.curr_pos += track.shape[0]
         self.offsets.append(np.array([self.curr_pos]).astype(np.int64))
 
     def write_tracks(self, T):
-        ''' write many tracks together
-        '''
+        """ write many tracks together
+        """
         for track in T:
             self.tracks.append(track.astype(np.float32))
             self.curr_pos += track.shape[0]
             self.offsets.append(np.array([self.curr_pos]).astype(np.int64))
 
     def read_track(self):
-        ''' read one track each time
-        '''
+        """ read one track each time
+        """
         off0, off1 = self.offsets[self.offs_pos:self.offs_pos + 2]
         self.offs_pos += 1
         return self.tracks[off0:off1]
 
     def read_tracksi(self, indices):
-        ''' read tracks with specific indices
-        '''
+        """ read tracks with specific indices
+        """
         T = []
         for i in indices:
             # print(self.offsets[i:i+2])
@@ -148,8 +147,8 @@ def read_tracksi(self, indices):
         return T
 
     def read_tracks(self):
-        ''' read the entire tractography
-        '''
+        """ read the entire tractography
+        """
         I = self.offsets[:]
         TR = self.tracks[:]
         T = []

dipy/io/peaks.py

@@ -3,24 +3,21 @@
 import os
 import numpy as np
 
-from dipy.core.sphere import Sphere
 from dipy.direction.peaks import (PeaksAndMetrics,
                                   reshape_peaks_for_visualization)
+from dipy.core.sphere import Sphere
+from dipy.io.image import save_nifti
+
 from distutils.version import LooseVersion
 
 # Conditional import machinery for pytables
 from dipy.utils.optpkg import optional_package
 
 # Allow import, but disable doctests, if we don't have pytables
-tables, have_tables, _ = optional_package('tables')
+tables, have_tables, _ = optional_package('tables', 'PyTables is not installed')
 
 # Useful variable for backward compatibility.
-if have_tables:
-    TABLES_LESS_3_0 = LooseVersion(tables.__version__) < "3.0"
-
-from dipy.data import get_sphere
-from dipy.core.sphere import Sphere
-from dipy.io.image import save_nifti
+TABLES_LESS_3_0 = LooseVersion(tables.__version__) < "3.0" if have_tables else False
 
 
 def _safe_save(f, group, array, name):
@@ -34,10 +31,11 @@ def _safe_save(f, group, array, name):
     name : string
     """
 
-    if TABLES_LESS_3_0:
-        func_create_carray = f.createCArray
-    else:
-        func_create_carray = f.create_carray
+    if not have_tables:
+        # We generate a TripWireError via this call
+        _ = tables.any_attributes
+
+    func_create_carray = f.createCArray if TABLES_LESS_3_0 else f.create_carray
 
     if array is not None:
         atom = tables.Atom.from_dtype(array.dtype)
@@ -189,20 +187,9 @@ def save_peaks(fname, pam, affine=None, verbose=False):
                                 [b"0.0.1"], 'PAM5 version number')
     version_string = f.root.version[0].decode()
 
-    try:
-        affine = pam.affine
-    except AttributeError:
-        pass
-
-    try:
-        shm_coeff = pam.shm_coeff
-    except AttributeError:
-        shm_coeff = None
-
-    try:
-        odf = pam.odf
-    except AttributeError:
-        odf = None
+    affine = pam.affine if hasattr(pam, 'affine') else affine
+    shm_coeff = pam.shm_coeff if hasattr(pam, 'shm_coeff') else None
+    odf = pam.odf if hasattr(pam, 'odf') else None
 
     _safe_save(f, group, affine, 'affine')
     _safe_save(f, group, pam.peak_dirs, 'peak_dirs')
@@ -271,4 +258,3 @@ def peaks_to_niftis(pam,
         save_nifti(fname_indices, pam.peak_indices, pam.affine)
 
         save_nifti(fname_gfa, pam.gfa, pam.affine)
-

dipy/io/tests/test_io_peaks.py

@@ -4,31 +4,26 @@
 import numpy as np
 import numpy.testing as npt
 
-from distutils.version import LooseVersion
-from dipy.reconst.peaks import PeaksAndMetrics
 from nibabel.tmpdirs import InTemporaryDirectory
 
+from dipy.reconst.peaks import PeaksAndMetrics
+from dipy.data import get_sphere
+from dipy.io.peaks import load_peaks, save_peaks, peaks_to_niftis, _safe_save
+
 # Conditional import machinery for pytables
 from dipy.utils.optpkg import optional_package
+from dipy.utils.tripwire import TripWireError
 
 # Allow import, but disable doctests, if we don't have pytables
 tables, have_tables, _ = optional_package('tables')
 
-from dipy.data import get_sphere
-from dipy.core.sphere import Sphere
-
-from dipy.io.peaks import load_peaks, save_peaks, peaks_to_niftis
-
 # Decorator to protect tests from being run without pytables present
-iftables = npt.dec.skipif(not have_tables,
-                          'Pytables does not appear to be installed')
+iftables = npt.dec.skipif(not have_tables, 'Pytables does not appear to be installed')
 
 
 @iftables
 def test_io_peaks():
-
     with InTemporaryDirectory():
-
         fname = 'test.pam5'
 
         sphere = get_sphere('repulsion724')
@@ -54,7 +49,9 @@ def test_io_peaks():
         pam2.affine = None
 
         fname2 = 'test2.pam5'
-        save_peaks(fname2, pam2)
+        save_peaks(fname2, pam2, np.eye(4))
+        pam2_res = load_peaks(fname2, verbose=True)
+        npt.assert_array_equal(pam.peak_dirs, pam2_res.peak_dirs)
 
         pam3 = load_peaks(fname2, verbose=False)
 
@@ -97,7 +94,6 @@ def test_io_peaks():
 
         del pam.shm_coeff
         save_peaks(fname6, pam, verbose=True)
-        pam_tmp = load_peaks(fname6, True)
 
         fname_shm = 'shm.nii.gz'
         fname_dirs = 'dirs.nii.gz'
@@ -116,6 +112,47 @@ def test_io_peaks():
         os.path.isfile(fname_gfa)
 
 
-if __name__ == '__main__':
+def test_io_save_peaks_error():
+    with InTemporaryDirectory():
+        fname = 'test.pam5'
+
+        pam = PeaksAndMetrics()
 
+        npt.assert_raises(IOError, save_peaks, 'test.pam', pam)
+        npt.assert_raises(ValueError, save_peaks, fname, pam)
+
+        sphere = get_sphere('repulsion724')
+
+        pam.affine = np.eye(4)
+        pam.peak_dirs = np.random.rand(10, 10, 10, 5, 3)
+        pam.peak_values = np.zeros((10, 10, 10, 5))
+        pam.peak_indices = np.zeros((10, 10, 10, 5))
+        pam.shm_coeff = np.zeros((10, 10, 10, 45))
+        pam.sphere = sphere
+        pam.B = np.zeros((45, sphere.vertices.shape[0]))
+        pam.total_weight = 0.5
+        pam.ang_thr = 60
+        pam.gfa = np.zeros((10, 10, 10))
+        pam.qa = np.zeros((10, 10, 10, 5))
+        pam.odf = np.zeros((10, 10, 10, sphere.vertices.shape[0]))
+
+        if not have_tables:
+            npt.assert_raises(TripWireError, save_peaks, fname, pam)
+
+
+@npt.dec.skipif(have_tables)
+def test_io_safe_save_error():
+
+    class Mock(object):
+        pass
+
+    fake_hdf5 = Mock()
+    fake_group = Mock()
+    fake_array = np.eye(4)
+    fake_name = "function_tester"
+
+    npt.assert_raises(TripWireError, _safe_save, fake_hdf5, fake_group, fake_array, fake_name)
+
+
+if __name__ == '__main__':
     npt.run_module_suite()