Merge pull request #410 from brian-team/spatialneuron

Spatialneuron

.travis.yml

@@ -2,17 +2,21 @@ language: python
 matrix:
   include:
     - python: "2.6"
-      env: STANDALONE=no CYTHON=yes
+      env: STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=no
     - python: "2.7"
-      env: STANDALONE=no CYTHON=yes
+      env: STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=no
+    - python: "2.7"
+      env: STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=yes
+    - python: "3.3"
+      env: STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=no
     - python: "3.3"
-      env: STANDALONE=no CYTHON=yes
+      env: STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=yes
     - python: "3.4"
-      env: STANDALONE=no CYTHON=yes
+      env: STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=no
     - python: "2.7"
-      env: STANDALONE=yes CYTHON=no
+      env: STANDALONE=yes CYTHON=no MINIMAL_VERSIONS=no
     - python: "2.7"  # test without installed cython
-      env: STANDALONE=no CYTHON=no
+      env: STANDALONE=no CYTHON=no MINIMAL_VERSIONS=no
 
 # Use miniconda to install binary versions of numpy etc. from continuum
 # analytic's repository. Follows an approach described by Dan Blanchard:
@@ -28,7 +32,11 @@ before_install:
 # command to install dependencies
 install:
   - conda update --yes conda
-  - conda create -n travis_conda --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy nose sphinx ipython sympy pyparsing
+  - if [[ $MINIMAL_VERSIONS == 'yes' ]]; then
+    conda create -n travis_conda --yes pip python=$TRAVIS_PYTHON_VERSION numpy==1.8.0 scipy==0.13.3 nose sphinx ipython sympy==0.7.6 jinja2==2.7 pyparsing;
+    else
+    conda create -n travis_conda --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy nose sphinx ipython sympy pyparsing jinja2;
+    fi
   - source activate travis_conda
   - if [[ $CYTHON == 'yes' ]]; then conda install --yes cython; SETUP_ARGS=--with-cython; else SETUP_ARGS=""; fi
   - pip install -q coveralls --use-mirrors

brian2/spatialneuron/morphology.py

@@ -16,12 +16,6 @@
 
 logger = get_logger(__name__)
 
-try:
-    from pylab import figure
-    from mpl_toolkits.mplot3d import Axes3D
-except ImportError:
-    logger.warn('matplotlib 0.99.1 is required for 3D plots', once=True)
-
 __all__ = ['Morphology', 'MorphologyData', 'Cylinder', 'Soma']
 
 
@@ -207,10 +201,6 @@ def create_from_segments(self, segments, origin=0):
         self.diameter, self.length, self.area, self.x, self.y, self.z = \
             zip(*[(seg['diameter'], seg['length'], seg['area'], seg['x'],
                    seg['y'], seg['z']) for seg in branch])
-        (self.diameter, self.length, self.area,
-         self.x, self.y, self.z) = (array(self.diameter), array(self.length),
-                                    array(self.area), array(self.x),
-                                    array(self.y), array(self.z))
         self.type = segments[n]['T']  # normally same type for all compartments
                                      # in the branch
         self.set_distance()
@@ -463,6 +453,11 @@ def plot(self, axes=None, simple=True, origin=None):
             if ``True``, the diameter of branches is ignored
             (defaults to ``True``)
         """
+        try:
+            from pylab import figure
+            from mpl_toolkits.mplot3d import Axes3D
+        except ImportError:
+            raise ImportError('matplotlib 0.99.1 is required for 3d plots')
         if axes is None:  # new figure
             fig = figure()
             axes = Axes3D(fig)

brian2/spatialneuron/spatialneuron.py

@@ -417,9 +417,10 @@ def _pre_calc_iteration(self, morphology, counter=0):
         self._temp_morph_parent_i[counter] = morphology.parent + 1
         self._temp_starts[counter] = morphology._origin
         self._temp_ends[counter] = morphology._origin + len(morphology.x) - 1
+        total_count = 1
         for child in morphology.children:
-            counter += 1
-            self._pre_calc_iteration(child, counter)
+            total_count += self._pre_calc_iteration(child, counter+total_count)
+        return total_count
 
     def number_branches(self, morphology, n=0, parent=-1):
         '''

brian2/tests/test_spatialneuron.py

@@ -3,12 +3,14 @@
 from nose.plugins.attrib import attr
 from brian2 import *
 
+@attr('codegen-independent')
 @with_setup(teardown=restore_initial_state)
 def test_construction():
     BrianLogger.suppress_name('resolution_conflict')
     morpho = Soma(diameter=30*um)
     morpho.L = Cylinder(length=10*um, diameter=1*um, n=10)
     morpho.LL = Cylinder(length=5*um, diameter=2*um, n=5)
+    morpho.LR = Cylinder(length=5*um, diameter=2*um, n=10)
     morpho.right = Cylinder(length=3*um, diameter=1*um, n=7)
     morpho.right.nextone = Cylinder(length=2*um, diameter=1*um, n=3)
     gL=1e-4*siemens/cm**2
@@ -42,6 +44,11 @@ def test_construction():
     assert_allclose(neuron.L.main.area,morpho.L.area)
     assert_allclose(neuron.L.main.length,morpho.L.length)
 
+    # Check basic consistency of the flattened representation
+    assert len(np.unique(neuron.diffusion_state_updater._morph_i[:])) == len(neuron.diffusion_state_updater._morph_i)
+    assert all(neuron.diffusion_state_updater._ends[:].flat >=
+               neuron.diffusion_state_updater._starts[:].flat)
+
 
 @attr('long')
 @with_setup(teardown=restore_initial_state)
@@ -207,4 +214,4 @@ def test_rall():
     test_construction()
     test_infinitecable()
     test_finitecable()
-    test_rall()
+    test_rall()

setup.py

@@ -139,13 +139,13 @@ def build_extension(self, ext):
                     # include default_preferences file
                     'brian2': ['default_preferences']
                     },
-      install_requires=['numpy>=1.4.1',
-                        'scipy>=0.7.0',
+      install_requires=['numpy>=1.8.0',
+                        'scipy>=0.13.3',
                         'sympy>=0.7.6',
                         'pyparsing',
                         'jinja2>=2.7',
                        ],
-      setup_requires=['numpy>=1.4.1'],
+      setup_requires=['numpy>=1.8.0'],
       cmdclass={'build_ext': optional_build_ext},
       provides=['brian2'],
       extras_require={'test': ['nosetests>=1.0'],