pytest and coverage improvements

- notebooks are considered in coverage analysis now
   -> custom notebook runner plugin adapted
- added images for documentation

datahandling/serial_datahandling.py

@@ -326,7 +326,7 @@ class SerialDataHandling(DataHandling):
                         cellData[name] = tuple(field)
                     else:
                         for i in range(fSize):
-                            cellData["%s[%d]" % (name, i)] = np.ascontiguousarray(field[...,i])
+                            cellData["%s[%d]" % (name, i)] = np.ascontiguousarray(field[..., i])
                 else:
                     assert False
             imageToVTK(fullFileName, cellData=cellData)

display_utils.py

@@ -121,6 +121,11 @@ display_animation_func = None
 
 
 def disp(*args, **kwargs):
+    from IPython import get_ipython
+    ipython = get_ipython()
+    if not ipython:
+        return
+
     if not display_animation_func:
         raise Exception("Call set_display_mode first")
     return display_animation_func(*args, **kwargs)

jupytersetup.py

@@ -3,7 +3,6 @@ import matplotlib.animation as animation
 from IPython.display import HTML
 from tempfile import NamedTemporaryFile
 import base64
-from IPython import get_ipython
 import sympy as sp
 
 
@@ -150,6 +149,11 @@ display_animation_func = None
 
 
 def disp(*args, **kwargs):
+    from IPython import get_ipython
+    ipython = get_ipython()
+    if not ipython:
+        return
+
     if not display_animation_func:
         raise Exception("Call set_display_mode first")
     return display_animation_func(*args, **kwargs)
@@ -174,10 +178,14 @@ def setDisplayMode(mode):
         raise Exception("Unknown mode. Available modes 'imageupdate', 'video' and 'window' ")
 
 
-ipython = get_ipython()
-if ipython:
-    setDisplayMode('imageupdate')
-    ipython.magic("config InlineBackend.rc = { }")
-    ipython.magic("matplotlib inline")
-    plt.rc('figure', figsize=(16, 6))
-    sp.init_printing()
+def activateIPython():
+    from IPython import get_ipython
+    ipython = get_ipython()
+    if ipython:
+        setDisplayMode('imageupdate')
+        ipython.magic("config InlineBackend.rc = { }")
+        ipython.magic("matplotlib inline")
+        plt.rc('figure', figsize=(16, 6))
+        sp.init_printing()
+
+activateIPython()

vtk.py

@@ -2,42 +2,56 @@ from pyevtk.vtk import VtkFile, VtkImageData
 from pyevtk.hl import _addDataToFile, _appendDataToFile
 
 
-def imageToVTK(path, origin=(0.0, 0.0, 0.0), spacing=(1.0, 1.0, 1.0), cellData=None, pointData=None):
-    """Patched version of same pyevtk function that also support vector data"""
-    assert cellData != None or pointData != None
+def imageToVTK(path, cellData, origin=(0.0, 0.0, 0.0), spacing=(1.0, 1.0, 1.0)):
+    """
+    Writes numpy data to VTK
+
+    Numpy arrays have to be contiguous in memory - if this is a problem call :func:`numpy.ascontiguousarray` first
+
+    Patched version of same pyevtk function that also supports vector-valued data
+
+    :param path: path with file name, without file ending (.vtk) where data should be stored
+    :param cellData: dictionary, mapping name of the data to a 3D numpy array, or to a 3-tuple of 3D numpy arrays
+                     in case of vector-valued data
+    :param origin: 3-tuple describing the origin of the field in 3D
+    :param spacing: 3-tuple describing the grid spacing in x,y, z direction
+    :returns path to file that was written
+
+
+    Example:
+
+    >>> from tempfile import TemporaryDirectory
+    >>> import os
+    >>> import numpy as np
+    >>> with TemporaryDirectory() as tmp_dir:
+    ...     path = os.path.join(tmp_dir, 'out')
+    ...     size = (20, 20, 20)
+    ...     resFile = imageToVTK(path, cellData = {'someScalarField': np.zeros(size),
+    ...                                            'someVectorField': (np.zeros(size), np.ones(size), np.zeros(size))
+    ...                                           })
+    """
 
     # Extract dimensions
     start = (0, 0, 0)
     end = None
-    if cellData:
-        keys = list(cellData.keys())
-        data = cellData[keys[0]]
-        if hasattr(data, 'shape'):
-            end = data.shape
-        elif isinstance(data, tuple):
-            shapes = set(d.shape for d in data)
-            if len(shapes) > 1:
-                raise ValueError("All components have to have the same shape")
-            end = shapes.pop()
-    elif pointData:
-        keys = list(pointData.keys())
-        data = pointData[keys[0]]
-        if hasattr(data, 'shape'):
-            end = data.shape
-            end = (end[0] - 1, end[1] - 1, end[2] - 1)
-        # Added for vector support...
-        elif data[0].ndim == 3 and data[1].ndim == 3 and data[0].ndim == 3:
-            keys = list(pointData.keys())
-            data = pointData[keys[0]]
-            end = data[0].shape
-            end = (end[0] - 1, end[1] - 1, end[2] - 1)
+
+    keys = list(cellData.keys())
+    data = cellData[keys[0]]
+    if hasattr(data, 'shape'):
+        end = data.shape
+    elif isinstance(data, tuple):
+        shapes = set(d.shape for d in data)
+        if len(shapes) > 1:
+            raise ValueError("All components have to have the same shape")
+        end = shapes.pop()
+
     # Write data to file
     w = VtkFile(path, VtkImageData)
     w.openGrid(start=start, end=end, origin=origin, spacing=spacing)
     w.openPiece(start=start, end=end)
-    _addDataToFile(w, cellData, pointData)
+    _addDataToFile(w, cellData, pointData=None)
     w.closePiece()
     w.closeGrid()
-    _appendDataToFile(w, cellData, pointData)
+    _appendDataToFile(w, cellData, pointData=None)
     w.save()
     return w.getFileName()