WIP: fix failure to write OpenDX file (Issue #21)

- change delta to DxD array if it is 1D
- added additional test (currently failing)
- use tempdir (added to travis and tests_require)

.travis.yml

@@ -20,10 +20,10 @@ install:
   - conda create --yes -q -n pyenv python=$TRAVIS_PYTHON_VERSION numpy=1.9.2 scipy=0.16.0 nose=1.3.7 six sphinx=1.3
   - source activate pyenv
   - case "$TRAVIS_PYTHON_VERSION" in 2.*) SPECIAL_PACKAGES="mock";; 3.*) SPECIAL_PACKAGES="";; esac
-  - pip install  coveralls $SPECIAL_PACKAGES
+  - pip install  coveralls tempdir $SPECIAL_PACKAGES
 
 script:
-  - nosetests -v --with-coverage --cover-package gridData --process-timeout=120 gridData
+  - nosetests -v --with-coverage --cover-package gridData --process-timeout=120 --processes=2 gridData
   - |
      test ${TRAVIS_PULL_REQUEST} == "false" && \
      test ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} && \

CHANGELOG

@@ -12,7 +12,7 @@ The rules for this file:
   * accompany each entry with github issue/PR number (Issue #xyz)
 
 ------------------------------------------------------------------------------
-??/??/?? 
+??/??/?? orbeckst
 
   * 0.3.1
 
@@ -22,6 +22,10 @@ The rules for this file:
 
   Fixes
 
+  * fixed writing of DX files failed with "NotImplementedError: Only
+    regularly spaced grids allowed." (issue #21 and
+    MDAnalysis/mdanalysis#544)
+
 09/10/22 kain88-de, holocronweavers, orbeckst
 
   * 0.3.0

gridData/OpenDX.py

@@ -139,11 +139,19 @@ def __init__(self,classid,shape=None,origin=None,delta=None,**kwargs):
         self.component = 'positions'
         self.shape = numpy.asarray(shape)      # D dimensional shape
         self.origin = numpy.asarray(origin)    # D vector
-        self.delta = numpy.asarray(delta)      # DxD array of grid spacings
         self.rank = len(self.shape)            # D === rank
-        if self.delta.shape != (self.rank,self.rank):
-            # check OpenDX specs for irreg spacing
-            raise NotImplementedError('Only regularly spaced grids allowed.')
+
+        self.delta = numpy.asarray(delta)      # DxD array of grid spacings
+        # gridDataFormats  actually provides a simple 1D array with the deltas because only
+        # regular grids are used but the following is a reminder that OpenDX should be able
+        # to handle more complicated volume elements
+        if len(self.delta.shape) == 1:
+            self.delta = numpy.diag(delta)
+        if self.delta.shape != (self.rank, self.rank):
+            # check OpenDX specs for irreg spacing if we want to implement
+            # anything more complicated
+            raise NotImplementedError('Only regularly spaced grids allowed, '
+                                      'not delta={}'.format(self.delta))
     def write(self,file):
         DXclass.write(self,file,
                       ('counts '+self.ndformat(' %d')) % tuple(self.shape))

gridData/tests/test_dx.py

@@ -1,14 +1,32 @@
+import tempdir
+import os
+
 import numpy as np
-from numpy.testing import assert_array_equal
+from numpy.testing import assert_array_equal, assert_array_almost_equal
 from nose.tools import assert_equal
 
 from gridData import Grid
 
 
-def test_dx():
+def test_read_dx():
     g = Grid('gridData/tests/test.dx')
     POINTS = 8
     assert_array_equal(g.grid.flat, np.ones(POINTS))
     assert_equal(g.grid.size, POINTS)
     assert_array_equal(g.delta, np.ones(3))
     assert_array_equal(g.origin, np.zeros(3))
+
+def test_write_dx(counts=100, ndim=3):
+    h, edges = np.histogramdd(np.random.random((counts, ndim)), bins=10)
+    g = Grid(h, edges)
+    assert_equal(g.grid.sum(), counts)
+
+    with tempdir.in_tempdir():
+        outfile = "grid.dx"
+        g.export(outfile)
+        g2 = Grid(outfile)
+
+    assert_array_almost_equal(g.grid, g2.grid,
+                              err_msg="written grid does not match original")
+    assert_array_almost_equal(g.delta, g2.delta,
+                              err_msg="deltas of written grid do not match original")

setup.py

@@ -28,6 +28,7 @@
       packages=find_packages(exclude=[]),
       package_data={},
       install_requires=['numpy>=1.0.3', 'six'],
+      tests_require=['nose', 'tempdir', 'numpy'],
       # extras can be difficult to install through setuptools and/or
       # you might prefer to use the version available through your
       # packaging system