I need to visualize 2000 images each 2560x1440 and 8 bit color using Python3. The images are stored in a properietary 3d-printing format (RLE encoded). I have code to extract each image as an numpy array. Using vtk.vtkImageImport().CopyImportVoidPointer I could read this into vtk. Problem is that reading all images in one numpy-array causes memory problems (6GB of data).
I see a few possible solutions:
- use numpy.memmap but this is slow on linux, I could investigate this further;
- save all images to disk and use a vtk file reader, but saving to disk is slow, so also not optimal;
- write my own vtk file reader which directly reads the 3d-printing file, however I have found a way to do this in python.
- read each slice into a vtk.vtkVolume() and add it to the renderer using vtk.vtkRenderer(). I encountered the problem that the Z-order is not adjusted when rotating the scene.
Am I missing another way to handle this much data? If not which solution is the best to investigate further?
Below the code which shows my Z-order problem in solution 4:
import numpy as np
import vtk
from tempfile import mkdtemp
import os.path as path
import psutil
installpath=''
def init():
import sys,os
global installpath
if getattr(sys, 'frozen', False):# frozen
installpath = os.path.dirname(sys.executable)
else: # unfrozen
installpath = os.path.dirname(os.path.realpath(__file__))
print ("Installed at: ",installpath)
def addCube(offset,colorIndex):
dw,dh,dd=offset
w,h,d=75,75,75
data_matrix=np.zeros((d,h,w),dtype='uint8')
data_matrix[0+dd:35+dd,0+dh:35+dh,0+dw:35+dw] = colorIndex
# For VTK to be able to use the data, it must be stored as a VTK- image.
# This can be done by the vtkImageImport-class which
# imports raw data and stores it.
dataImporter = vtk.vtkImageImport()
# The previously created array is converted to a string of chars and imported.
data_string = data_matrix.tostring()
del (data_matrix)
dataImporter.CopyImportVoidPointer(data_string, len(data_string))
del (data_string)
# The type of the newly imported data is set to unsigned char (uint8)
dataImporter.SetDataScalarTypeToUnsignedChar()
# Because the data that is imported only contains an intensity value
# (it isnt RGB-coded or someting similar), the importer must be told this is the case.
dataImporter.SetNumberOfScalarComponents(1)
# The following two functions describe how the data is stored and the dimensions of the array it is stored in.
# For this simple case, all axes are of length 75 and begins with the first element.
# For other data, this is probably not the case.
# I have to admit however, that I honestly dont know the difference between SetDataExtent()
# and SetWholeExtent() although VTK complains if not both are used.
dataImporter.SetDataExtent(0, w-1, 0, h-1, 0, d-1)
dataImporter.SetWholeExtent(0, w-1, 0, h-1, 0, d-1)
# The following class is used to store transparency-values for later retrival.
# In our case, we want the value 0 to be
# completely opaque whereas the three different cubes are given different transparency-values to show how it works.
alphaChannelFunc = vtk.vtkPiecewiseFunction()
alphaChannelFunc.AddPoint(0, 0.0)
alphaChannelFunc.AddPoint(colorIndex, 1.0)#0.05)
# This class stores color data and can create color tables from a few color points.
# For this demo, we want the three cubes to be of the colors red green and blue.
colorFunc = vtk.vtkColorTransferFunction()
#colorFunc.AddRGBPoint(0, 0.0, 0.0, 0.0)
colorFunc.AddRGBPoint(1, 1.0, 0.0, 0.0)
colorFunc.AddRGBPoint(2, 0.0, 1.0, 0.0)
colorFunc.AddRGBPoint(3, 0.0, 0.0, 1.0)
colorFunc.AddRGBPoint(4, 1.0, 1.0, 0.0)
colorFunc.AddRGBPoint(5, 1.0, 0.0, 1.0)
colorFunc.AddRGBPoint(6, 0.0, 1.0, 1.0)
colorFunc.AddRGBPoint(7, 1.0, 1.0, 1.0)
# The previous two classes stored properties.
# Because we want to apply these properties to the volume we want to render,
# we have to store them in a class that stores volume properties.
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorFunc)
volumeProperty.SetScalarOpacity(alphaChannelFunc)
volumeProperty.ShadeOn()
volumeMapper = vtk.vtkFixedPointVolumeRayCastMapper()
volumeMapper.SetInputConnection(dataImporter.GetOutputPort())
# The class vtkVolume is used to pair the previously declared volume as well as the properties
# to be used when rendering that volume.
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
return volume
def main():
global installpath
colors = vtk.vtkNamedColors()
# We begin by creating the data we want to render.
volume1=addCube((0,0,0),4)
volume2=addCube((25,25,25),2)
# With almost everything else ready, its time to initialize the renderer and window, as well as
# creating a method for exiting the application
renderer = vtk.vtkRenderer()
renderWin = vtk.vtkRenderWindow()
renderWin.AddRenderer(renderer)
renderInteractor = vtk.vtkRenderWindowInteractor()
renderInteractor.SetRenderWindow(renderWin)
# We add the volume to the renderer ...
renderer.AddVolume(volume1)
renderer.AddVolume(volume2)
renderer.SetBackground(colors.GetColor3d("MistyRose"))
# ... and set window size.
renderWin.SetSize(400, 400)
# A simple function to be called when the user decides to quit the application.
def exitCheck(obj, event):
if obj.GetEventPending() != 0:
obj.SetAbortRender(1)
# Tell the application to use the function as an exit check.
renderWin.AddObserver("AbortCheckEvent", exitCheck)
renderInteractor.Initialize()
# Because nothing will be rendered without any input, we order the first render manually
# before control is handed over to the main-loop.
renderWin.Render()
renderInteractor.Start()
if __name__ == '__main__':
init()
main()