diff --git a/datahandling/serial_datahandling.py b/datahandling/serial_datahandling.py
index 888b82ffd0aa32e3c0f152297759fd137ea4e175..758b074f8d7f8aaf5df887e6f1c1b972cd9f8b66 100644
--- a/datahandling/serial_datahandling.py
+++ b/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)
diff --git a/display_utils.py b/display_utils.py
index ef49d810752a369e7131b7f72f350b41ca6e705e..1c4248c76dbc5c15a6a7d7d978c09acc5f786d0f 100644
--- a/display_utils.py
+++ b/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)
diff --git a/jupytersetup.py b/jupytersetup.py
index 1e46d707c03d505675fd11cee90a69136c5e82de..d11f81f631b251d0acb995bf006fed411af0e594 100644
--- a/jupytersetup.py
+++ b/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()
diff --git a/vtk.py b/vtk.py
index 2b5408180bb1ea9f6bfc62edea57d9b70610a348..caf9ca1aa411e065856315f196f51af8d7d2801c 100644
--- a/vtk.py
+++ b/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()