From 99fdbb87402445f0925f9f823a63a43720ed2cab Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@desy.de>
Date: Fri, 20 Jan 2017 11:33:13 +0100
Subject: [PATCH] Updates from OnDA, testing branch, 20/01/17
---
cfel_fabio.py | 22 +-
cfel_optarg.py | 21 +-
cfelvtk.py | 543 +++++++++++++++++++++++++++++++++++++++++++++++++
3 files changed, 566 insertions(+), 20 deletions(-)
create mode 100644 cfelvtk.py
diff --git a/cfel_fabio.py b/cfel_fabio.py
index 7edc689..98c3373 100644
--- a/cfel_fabio.py
+++ b/cfel_fabio.py
@@ -51,24 +51,24 @@ def read_cbf_from_stream(stream):
infile = stream
cbf_obj._readheader(infile)
- if fabio.cbfimage.CIF_BINARY_BLOCK_KEY not in cbf_obj.cif:
- err = "Not key %s in CIF, no CBF image in stream" % fabio.cbfimage.CIF_BINARY_BLOCK_KEY
+ if cbf_obj.CIF_BINARY_BLOCK_KEY not in cbf_obj.cif:
+ err = "Not key %s in CIF, no CBF image in stream" % fabio.cbfobj.CIF_BINARY_BLOCK_KEY
logger.error(err)
for kv in cbf_obj.cif.items():
print("%s: %s" % kv)
raise RuntimeError(err)
- if cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY] == "CIF Binary Section":
- cbf_obj.cbs += infile.read(len(fabio.cbfimage.STARTER) + int(cbf_obj.header["X-Binary-Size"])
+ if cbf_obj.cif[cbf_obj.CIF_BINARY_BLOCK_KEY] == "CIF Binary Section":
+ cbf_obj.cbs += infile.read(len(cbf_obj.STARTER) + int(cbf_obj.header["X-Binary-Size"])
- len(cbf_obj.cbs) + cbf_obj.start_binary)
else:
- if len(cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY]) > int(
- cbf_obj.header["X-Binary-Size"]) + cbf_obj.start_binary + len(fabio.cbfimage.STARTER):
- cbf_obj.cbs = cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY][:int(cbf_obj.header["X-Binary-Size"]) +
- cbf_obj.start_binary +
- len(fabio.cbfimage.STARTER)]
+ if len(cbf_obj.cif[cbf_obj.CIF_BINARY_BLOCK_KEY]) > int(
+ cbf_obj.header["X-Binary-Size"]) + cbf_obj.start_binary + len(cbf_obj.STARTER):
+ cbf_obj.cbs = cbf_obj.cif[cbf_obj.CIF_BINARY_BLOCK_KEY][:int(cbf_obj.header["X-Binary-Size"]) +
+ cbf_obj.start_binary +
+ len(cbf_obj.STARTER)]
else:
- cbf_obj.cbs = cbf_obj.cif[fabio.cbfimage.CIF_BINARY_BLOCK_KEY]
- binary_data = cbf_obj.cbs[cbf_obj.start_binary + len(fabio.cbfimage.STARTER):]
+ cbf_obj.cbs = cbf_obj.cif[cbf_obj.CIF_BINARY_BLOCK_KEY]
+ binary_data = cbf_obj.cbs[cbf_obj.start_binary + len(cbf_obj.STARTER):]
if "Content-MD5" in cbf_obj.header:
ref = numpy.string_(cbf_obj.header["Content-MD5"])
diff --git a/cfel_optarg.py b/cfel_optarg.py
index a06978f..218980f 100644
--- a/cfel_optarg.py
+++ b/cfel_optarg.py
@@ -12,14 +12,6 @@
#
# You should have received a copy of the GNU General Public License
# along with cfelpyutils. If not, see <http://www.gnu.org/licenses/>.
-
-
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
-from __future__ import unicode_literals
-
-
"""
Utilities for parsing command line options and configuration files.
@@ -27,6 +19,10 @@ This module contains utilities for parsing of command line options and
configuration files.
"""
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
import ast
@@ -76,6 +72,11 @@ def parse_parameters(config):
monitor_params[sect][op] = config.get(sect, op)
if monitor_params[sect][op].startswith("'") and monitor_params[sect][op].endswith("'"):
monitor_params[sect][op] = monitor_params[sect][op][1:-1]
+ try:
+ monitor_params[sect][op].encode('ascii')
+ except UnicodeEncodeError:
+ raise RuntimeError('Error parsing parameters. Only ASCII characters are allowed in parameter '
+ 'names and values.')
continue
if monitor_params[sect][op].startswith('"') and monitor_params[sect][op].endswith('"'):
monitor_params[sect][op] = monitor_params[sect][op][1:-1]
@@ -115,6 +116,8 @@ def parse_parameters(config):
monitor_params[sect][op] = float(monitor_params[sect][op])
continue
except ValueError:
- pass
+ raise RuntimeError('Error parsing parameters. The parameter {0}/{1} parameter has an invalid type. '
+ 'Allowed types are None, int, float, bool and str. Strings must be '
+ 'single-quoted.'.format(sect, op))
return monitor_params
diff --git a/cfelvtk.py b/cfelvtk.py
new file mode 100644
index 0000000..47bb0c7
--- /dev/null
+++ b/cfelvtk.py
@@ -0,0 +1,543 @@
+# This file is part of cfelpyutils.
+#
+# cfelpyutils is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# cfelpyutils is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with cfelpyutils. If not, see <http://www.gnu.org/licenses/>.
+"""
+Utilities for 3d data visualization using the Visualization Toolkit (VTK).
+"""
+import numpy
+import vtk
+
+VTK_VERSION = vtk.vtkVersion().GetVTKMajorVersion()
+
+
+def get_lookup_table(minimum_value, maximum_value, log=False, colorscale="jet", number_of_colors=1000):
+ """Create a vtkLookupTable with a specified range, and colorscale.
+
+ Args:
+ minimum_value (float): Lowest value the lookup table can display, lower values will be displayed as this value
+ maximum_value (float): Highest value the lookup table can display, higher values will be displayed as this value
+ log (Optional[bool]): True if the scale is logarithmic
+ colorscale (Optional[string]): Accepts the name of any matplotlib colorscale. The lookuptable will
+ replicate this scale.
+ number_of_colors (Optional[int]): The length of the table. Higher values corresponds to a smoother color scale.
+
+ Returns:
+ lookup_table (vtk.vtkLookupTable): A vtk lookup table
+ """
+
+ import matplotlib
+ import matplotlib.cm
+ if log:
+ lut = vtk.vtkLogLookupTable()
+ else:
+ lut = vtk.vtkLookupTable()
+ lut.SetTableRange(minimum_value, maximum_value)
+ lut.SetNumberOfColors(number_of_colors)
+ lut.Build()
+ for i in range(number_of_colors):
+ color = matplotlib.cm.cmap_d[colorscale](float(i) / float(number_of_colors))
+ lut.SetTableValue(i, color[0], color[1], color[2], 1.)
+ lut.SetUseBelowRangeColor(True)
+ lut.SetUseAboveRangeColor(True)
+ return lut
+
+
+def array_to_float_array(array_in, dtype=None):
+ """Convert a numpy array into a vtkFloatArray of vtkDoubleArray, depending on the type of the input.
+ This flattens the array and thus the shape is lost.
+
+ Args:
+ array_in (numpy.ndarray): The array to convert.
+ dtype (Optional[type]): Optionaly convert the array to the specified data. Otherwise the original
+ type will be preserved.
+
+ Returns:
+ float_array (vtk.vtkFloatArray): A float array of the specified type.
+ """
+ if dtype is None:
+ dtype = array_in.dtype
+ if dtype == "float32":
+ float_array = vtk.vtkFloatArray()
+ elif dtype == "float64":
+ float_array = vtk.vtkDoubleArray()
+ else:
+ raise ValueError("Wrong format of input array, must be float32 or float64")
+ if len(array_in.shape) == 2:
+ float_array.SetNumberOfComponents(array_in.shape[1])
+ elif len(array_in.shape) == 1:
+ float_array.SetNumberOfComponents(1)
+ else:
+ raise ValueError("Wrong shape of array must be 1D or 2D.")
+ float_array.SetVoidArray(numpy.ascontiguousarray(array_in, dtype), numpy.product(array_in.shape), 1)
+ return float_array
+
+
+def array_to_vtk(array_in, dtype=None):
+ """Convert a numpy array into a vtk array of the specified type. This flattens the array and thus the shape is lost.
+
+ Args:
+ array_in (numpy.ndarray): The array to convert.
+ dtype (Optional[type]): Optionaly convert the array to the specified data. Otherwise the original type
+ will be preserved.
+
+ Returns:
+ vtk_array (vtk.vtkFloatArray): A float array of the specified type.
+ """
+ if dtype is None:
+ dtype = numpy.dtype(array_in.dtype)
+ else:
+ dtype = numpy.dtype(dtype)
+ if dtype == numpy.float32:
+ vtk_array = vtk.vtkFloatArray()
+ elif dtype == numpy.float64:
+ vtk_array = vtk.vtkDoubleArray()
+ elif dtype == numpy.uint8:
+ vtk_array = vtk.vtkUnsignedCharArray()
+ elif dtype == numpy.int8:
+ vtk_array = vtk.vtkCharArray()
+ else:
+ raise ValueError("Wrong format of input array, must be float32 or float64")
+ if len(array_in.shape) != 1 and len(array_in.shape) != 2:
+ raise ValueError("Wrong shape: array must be 1D")
+ vtk_array.SetNumberOfComponents(1)
+ vtk_array.SetVoidArray(numpy.ascontiguousarray(array_in.flatten(), dtype), numpy.product(array_in.shape), 1)
+ return vtk_array
+
+
+def array_to_image_data(array_in, dtype=None):
+ """Convert a numpy array to vtkImageData. Image data is a 3D object, thus the input must be 3D.
+
+ Args:
+ array_in (numpy.ndarray): Array to convert to vtkImageData. Must be 3D.
+ dtype (Optional[type]): Optionaly convert the array to the specified data. Otherwise the original
+ type will be preserved.
+
+ Returns:
+ image_data (vtk.vtkImageData): Image data containing the data from the array.
+ """
+ if len(array_in.shape) != 3:
+ raise ValueError("Array must be 3D for conversion to vtkImageData")
+ array_flat = array_in.flatten()
+ float_array = array_to_float_array(array_flat, dtype)
+ image_data = vtk.vtkImageData()
+ image_data.SetDimensions(*array_in.shape)
+ image_data.GetPointData().SetScalars(float_array)
+ return image_data
+
+
+def window_to_png(render_window, file_name, magnification=1):
+ """Take a screen shot of a specific vt render window and save it to file.
+
+ Args:
+ render_window (vtk.vtkRenderWindow): The render window window to capture.
+ file_name (string): A png file with this name will be created from the provided window.
+ magnification (Optional[int]): Increase the resolution of the output file by this factor
+ """
+ magnification = int(magnification)
+ window_to_image_filter = vtk.vtkWindowToImageFilter()
+ window_to_image_filter.SetInput(render_window)
+ window_to_image_filter.SetMagnification(magnification)
+ window_to_image_filter.SetInputBufferTypeToRGBA()
+ window_to_image_filter.Update()
+
+ writer = vtk.vtkPNGWriter()
+ writer.SetFileName(file_name)
+ writer.SetInputConnection(window_to_image_filter.GetOutputPort())
+ writer.Write()
+
+
+def poly_data_to_actor(poly_data, lut):
+ """Create a vtkActor from a vtkPolyData. This circumvents the need to create a vtkMapper by internally
+ using a very basic vtkMapper
+
+ Args:
+ poly_data (vtk.vtkPolyData): vtkPolyData object.
+ lut (vtk.vtkLookupTable): The vtkLookupTable specifies the colorscale to use for the maper.
+
+ Returns:
+ actor (vtk.vtkActor): Actor to display the provided vtkPolyData
+ """
+ mapper = vtk.vtkPolyDataMapper()
+ mapper.SetInputData(poly_data)
+ mapper.SetLookupTable(lut)
+ mapper.SetUseLookupTableScalarRange(True)
+ actor = vtk.vtkActor()
+ actor.SetMapper(mapper)
+ return actor
+
+
+class IsoSurface(object):
+ """Create and plot isosurfaces.
+
+ Args:
+ volume (numpy.ndimage): 3D floating point array.
+ level (float or list of float): The threshold level for the isosurface, or a list of such levels.
+ """
+ def __init__(self, volume, level=None):
+ self._surface_algorithm = None
+ self._renderer = None
+ self._actor = None
+ self._mapper = None
+ self._volume_array = None
+
+ self._float_array = vtk.vtkFloatArray()
+ self._image_data = vtk.vtkImageData()
+ self._image_data.GetPointData().SetScalars(self._float_array)
+ self._setup_data(volume)
+
+ self._surface_algorithm = vtk.vtkMarchingCubes()
+ self._surface_algorithm.SetInputData(self._image_data)
+ self._surface_algorithm.ComputeNormalsOn()
+
+ if level is not None:
+ try:
+ self.set_multiple_levels(iter(level))
+ except TypeError:
+ self.set_level(0, level)
+
+ self._mapper = vtk.vtkPolyDataMapper()
+ self._mapper.SetInputConnection(self._surface_algorithm.GetOutputPort())
+ self._mapper.ScalarVisibilityOn()
+ self._actor = vtk.vtkActor()
+ self._actor.SetMapper(self._mapper)
+
+ def _setup_data(self, volume):
+ """Create the numpy array self._volume_array and vtk array self._float_array and make them share data.
+
+ Args:
+ volume (numpy.ndimage): This data will populate both the created numpy and vtk objects.
+ """
+ self._volume_array = numpy.zeros(volume.shape, dtype="float32", order="C")
+ self._volume_array[:] = volume
+ self._float_array.SetNumberOfValues(numpy.product(volume.shape))
+ self._float_array.SetNumberOfComponents(1)
+ self._float_array.SetVoidArray(self._volume_array, numpy.product(volume.shape), 1)
+ self._image_data.SetDimensions(*self._volume_array.shape)
+
+ def set_renderer(self, renderer):
+ """Set the renderer of the isosurface and remove any existing renderer.
+
+ Args:
+ renderer (vtk.vtkRenderer): Give this renderer controll over all the surface actors.
+ """
+ if self._actor is None:
+ raise RuntimeError("Actor does not exist.")
+ if self._renderer is not None:
+ self._renderer.RemoveActor(self._actor)
+ self._renderer = renderer
+ self._renderer.AddActor(self._actor)
+
+ def set_multiple_levels(self, levels):
+ """Remova any current surface levels and add the ones from the provided list.
+
+ Args:
+ levels (list of float): Levels for the isosurface, in absolute values (not e.g. ratios)
+ """
+ self._surface_algorithm.SetNumberOfContours(0)
+ for index, this_level in enumerate(levels):
+ self._surface_algorithm.SetValue(index, this_level)
+ self._render()
+
+ def get_levels(self):
+ """Return a list of the current surface levels.
+
+ Returns:
+ levels (list of floats): The current surface levels.
+ """
+ return [self._surface_algorithm.GetValue(index)
+ for index in range(self._surface_algorithm.GetNumberOfContours())]
+
+ def add_level(self, level):
+ """Add a single surface level.
+
+ Args:
+ level (float): The level of the new surface.
+ """
+ self._surface_algorithm.SetValue(self._surface_algorithm.GetNumberOfContours(), level)
+ self._render()
+
+ def remove_level(self, index):
+ """Remove a singel surface level at the provided index.
+
+ Args:
+ index (int): The index of the level. If levels were added one by one this corresponds
+ to the order in which they were added.
+ """
+ for index in range(index, self._surface_algorithm.GetNumberOfContours()-1):
+ self._surface_algorithm.SetValue(index, self._surface_algorithm.GetValue(index+1))
+ self._surface_algorithm.SetNumberOfContours(self._surface_algorithm.GetNumberOfContours()-1)
+ self._render()
+
+ def set_level(self, index, level):
+ """Change the value of an existing surface level.
+
+ Args:
+ index (int): The index of the level to change. If levels were added one by one this corresponds to
+ the order in which they were added.
+ level (float): The new level of the surface.
+ """
+ self._surface_algorithm.SetValue(index, level)
+ self._render()
+
+ def set_cmap(self, cmap):
+ """Set the colormap. The color is a function of surface level and mainly of relevance when plotting multiple surfaces.
+
+ Args:
+ cmap (string): Name of the colormap to use. Supports all colormaps provided by matplotlib.
+ """
+ self._mapper.ScalarVisibilityOn()
+ self._mapper.SetLookupTable(get_lookup_table(self._volume_array.min(), self._volume_array.max(),
+ colorscale=cmap))
+ self._render()
+
+ def set_color(self, color):
+ """Plot all surfaces in this provided color.
+
+ Args:
+ color (length 3 iterable): The RGB value of the color.
+ """
+ self._mapper.ScalarVisibilityOff()
+ self._actor.GetProperty().SetColor(color[0], color[1], color[2])
+ self._render()
+
+ def set_opacity(self, opacity):
+ """Set the opacity of all surfaces. (seting it individually for each surface is not supported)
+
+ Args:
+ opacity (float): Value between 0. and 1. where 0. is completely transparent and 1. is completely opaque.
+ """
+ self._actor.GetProperty().SetOpacity(opacity)
+ self._render()
+
+ def _render(self):
+ """Render if a renderer is set, otherwise do nothing."""
+ if self._renderer is not None:
+ self._renderer.GetRenderWindow().Render()
+
+ def set_data(self, volume):
+ """Change the data displayed.
+
+ Args:
+ volume (numpy.ndarray): The new array. Must have the same shape as the old array."""
+ if volume.shape != self._volume_array.shape:
+ raise ValueError("New volume must be the same shape as the old one")
+ self._volume_array[:] = volume
+ self._float_array.Modified()
+ self._render()
+
+
+def plot_isosurface(volume, level=None, opacity=1.):
+ """Plot isosurfaces of the provided module.
+
+ Args:
+ volume (numpy.ndarray): The 3D numpy array that will be plotted.
+ level (float or list of floats): Levels can be iterable or singel value.
+ opacity (float): Float between 0. and 1. where 0. is completely transparent and 1. is completely opaque.
+ """
+
+ surface_object = IsoSurface(volume, level)
+ surface_object.set_opacity(opacity)
+
+ renderer = vtk.vtkRenderer()
+ if opacity != 1.:
+ renderer.SetUseDepthPeeling(True)
+ render_window = vtk.vtkRenderWindow()
+ render_window.AddRenderer(renderer)
+ interactor = vtk.vtkRenderWindowInteractor()
+ interactor.SetRenderWindow(render_window)
+ interactor.SetInteractorStyle(vtk.vtkInteractorStyleRubberBandPick())
+
+ surface_object.set_renderer(renderer)
+
+ renderer.SetBackground(0., 0., 0.)
+ render_window.SetSize(800, 800)
+ interactor.Initialize()
+ render_window.Render()
+ interactor.Start()
+
+
+def plot_planes(array_in, log=False, cmap=None):
+ """Plot the volume at two interactive planes that cut the volume.
+
+ Args:
+ array_in (numpy.ndarray): Input array must be 3D.
+ log (bool): If true the data will be plotted in logarithmic scale.
+ cmap (string): Name of the colormap to use. Supports all colormaps provided by matplotlib.
+ """
+ array_in = numpy.float64(array_in)
+ renderer = vtk.vtkRenderer()
+ render_window = vtk.vtkRenderWindow()
+ render_window.AddRenderer(renderer)
+ interactor = vtk.vtkRenderWindowInteractor()
+ interactor.SetRenderWindow(render_window)
+ interactor.SetInteractorStyle(vtk.vtkInteractorStyleRubberBandPick())
+
+ if cmap is None:
+ import matplotlib as _matplotlib
+ cmap = _matplotlib.rcParams["image.cmap"]
+ lut = get_lookup_table(max(0., array_in.min()), array_in.max(), log=log, colorscale=cmap)
+ picker = vtk.vtkCellPicker()
+ picker.SetTolerance(0.005)
+
+ image_data = array_to_image_data(array_in)
+
+ def setup_plane():
+ """Create and setup a singel plane."""
+ plane = vtk.vtkImagePlaneWidget()
+ if VTK_VERSION >= 6:
+ plane.SetInputData(image_data)
+ else:
+ plane.SetInput(image_data)
+ plane.UserControlledLookupTableOn()
+ plane.SetLookupTable(lut)
+ plane.DisplayTextOn()
+ plane.SetPicker(picker)
+ plane.SetLeftButtonAction(1)
+ plane.SetMiddleButtonAction(2)
+ plane.SetRightButtonAction(0)
+ plane.SetInteractor(interactor)
+ return plane
+
+ plane_1 = setup_plane()
+ plane_1.SetPlaneOrientationToXAxes()
+ plane_1.SetSliceIndex(array_in.shape[0]//2)
+ plane_1.SetEnabled(1)
+ plane_2 = setup_plane()
+ plane_2.SetPlaneOrientationToYAxes()
+ plane_2.SetSliceIndex(array_in.shape[1]//2)
+ plane_2.SetEnabled(1)
+
+ renderer.SetBackground(0., 0., 0.)
+ render_window.SetSize(800, 800)
+ interactor.Initialize()
+ render_window.Render()
+ interactor.Start()
+
+
+def setup_window(size=(400, 400), background=(1., 1., 1.)):
+ """Create a renderer, render_window and interactor and setup connections between them.
+
+ Args:
+ size (Optional[length 2 iterable of int]): The size of the window in pixels.
+ background (Optional[length 3 iterable of float]): RGB value of the background color.
+
+ Returns:
+ renderer (vtk.vtkRenderer): A standard renderer connected to the window.
+ render_window (vtk.vtkRenderWindow): With dimensions given in the arguments, or oterwise 400x400 pixels.
+ interactor (vtk.vtkRenderWindowInteractor): The interactor will be given the rubber band pick interactor style.
+ """
+ renderer = vtk.vtkRenderer()
+ render_window = vtk.vtkRenderWindow()
+ render_window.AddRenderer(renderer)
+ interactor = vtk.vtkRenderWindowInteractor()
+ interactor.SetInteractorStyle(vtk.vtkInteractorStyleRubberBandPick())
+ interactor.SetRenderWindow(render_window)
+
+ renderer.SetBackground(background[0], background[1], background[2])
+ render_window.SetSize(size[0], size[1])
+
+ interactor.Initialize()
+ render_window.Render()
+ return renderer, render_window, interactor
+
+
+def scatterplot_3d(data, color=None, point_size=None, cmap="jet", point_shape=None):
+ """3D scatter plot.
+
+ Args:
+ data (numpy.ndimage): The array must have shape Nx3 where N is the number of points.
+
+ color (Optional[numpy.ndimage]): 1D Array of floating points with same length as the data array.
+ These numbers give the color of each point.
+ point_size (Optional[float]): The size of each points. Behaves differently depending on the point_shape.
+ If shape is spheres the size is relative to the scene and if squares the size is relative to the window.
+ point_shape (Optional["spheres" or "squares"]): "spheres" plots each point as a sphere, recommended for
+ small data sets. "squares" plot each point as a square without any 3D structure, recommended for
+ large data sets.
+ """
+ if len(data.shape) != 2 or data.shape[1] != 3:
+ raise ValueError("data must have shape (n, 3) where n is the number of points.")
+ if point_shape is None:
+ if len(data) <= 1000:
+ point_shape = "spheres"
+ else:
+ point_shape = "squares"
+ data = numpy.float32(data)
+ data_vtk = array_to_float_array(data)
+ point_data = vtk.vtkPoints()
+ point_data.SetData(data_vtk)
+ points_poly_data = vtk.vtkPolyData()
+ points_poly_data.SetPoints(point_data)
+
+ if color is not None:
+ lut = get_lookup_table(color.min(), color.max())
+ color_scalars = array_to_vtk(numpy.float32(color.copy()))
+ color_scalars.SetLookupTable(lut)
+ points_poly_data.GetPointData().SetScalars(color_scalars)
+
+ if point_shape == "spheres":
+ if point_size is None:
+ point_size = numpy.array(data).std() / len(data)**(1./3.) / 3.
+ glyph_filter = vtk.vtkGlyph3D()
+ glyph_filter.SetInputData(points_poly_data)
+ sphere_source = vtk.vtkSphereSource()
+ sphere_source.SetRadius(point_size)
+ glyph_filter.SetSourceConnection(sphere_source.GetOutputPort())
+ glyph_filter.SetScaleModeToDataScalingOff()
+ if color is not None:
+ glyph_filter.SetColorModeToColorByScalar()
+ else:
+ glyph_filter.SetColorMode(0)
+ glyph_filter.Update()
+ elif point_shape == "squares":
+ if point_size is None:
+ point_size = 3
+ glyph_filter = vtk.vtkVertexGlyphFilter()
+ glyph_filter.SetInputData(points_poly_data)
+ glyph_filter.Update()
+ else:
+ raise ValueError("{0} is not a valid entry for points".format(point_shape))
+
+ poly_data = vtk.vtkPolyData()
+ poly_data.ShallowCopy(glyph_filter.GetOutput())
+
+ renderer, render_window, interactor = setup_window()
+
+ mapper = vtk.vtkPolyDataMapper()
+ mapper.SetInputData(poly_data)
+ if color is not None:
+ mapper.SetLookupTable(lut)
+ mapper.SetUseLookupTableScalarRange(True)
+
+ points_actor = vtk.vtkActor()
+ points_actor.SetMapper(mapper)
+ points_actor.GetProperty().SetPointSize(point_size)
+ points_actor.GetProperty().SetColor(0., 0., 0.)
+
+ axes_actor = vtk.vtkCubeAxesActor()
+ axes_actor.SetBounds(points_actor.GetBounds())
+ axes_actor.SetCamera(renderer.GetActiveCamera())
+ axes_actor.SetFlyModeToStaticTriad()
+ axes_actor.GetXAxesLinesProperty().SetColor(0., 0., 0.)
+ axes_actor.GetYAxesLinesProperty().SetColor(0., 0., 0.)
+ axes_actor.GetZAxesLinesProperty().SetColor(0., 0., 0.)
+ for i in range(3):
+ axes_actor.GetLabelTextProperty(i).SetColor(0., 0., 0.)
+ axes_actor.GetTitleTextProperty(i).SetColor(0., 0., 0.)
+
+ renderer.AddActor(points_actor)
+ renderer.AddActor(axes_actor)
+
+ render_window.Render()
+ interactor.Start()
--
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