Changes between Version 3 and Version 4 of Examples/Brain

Timestamp:

04/11/17 12:37:34 (7 years ago)

Author:

Herwig Zilken

Comment:

--

Examples/Brain

@@ -56 +56 @@
    dset[i, : , :]=v
 
-
 print "success"
 fout.close()
-
 }}}
 
 == Creating XDMF Files
-!ParaView needs proper XDMF files to be able to read the data from a hdf5 file. We generated two xdfm files by hand. One for the fullsize dataset, and one for loading a spatial subsampled version via a hyperslab.
-
-The xdmf file for the fullsize dataset is quite simple an defines just the uniform rectilinear grid with one attribute. It is a very good practize to normalize the spatial extend of the grid by setting the grid spacing accordingly. We decided that the grid should have the extend "1.0" in the direction on its largest axis.
-So the grid spacing is 1.0/31076=3.21792e-5 for the Y- and Z-axis. The X-axis is the direction of the slice cutting, therefore it's grid spacing is larger by a factor of 40, resulting in 40*3.21792e-5=1.2872e-3.
+!ParaView needs proper XDMF files to be able to read the data from a hdf5 file. We generated two xdfm files by hand. One for the fullsize dataset, and one to be able to load a spatial subsampled version via a hyperslab.
+
+The xdmf file for the fullsize dataset is quite simple an defines just the uniform rectilinear grid with one attribute. It is a very good practise to normalize the spatial extend of the grid by setting the grid spacing accordingly. We decided that the grid should have the extend "1.0" in the direction on its largest axis.
+So the grid spacing is 1.0/31076=3.21792e-5 for the Y- and Z-axis. The X-axis is the direction where the slices are cut. Therefore it's grid spacing is larger by a factor of 40, resulting in 40*3.21792e-5=1.2872e-3.
+The origin of the grid was set to its center.
 
 '''Fullsize Version:'''
@@ -95 +94 @@
 }}}
 
-As the dataset is relatively large (200 GB), we decided to generate a second xdmf file which only reads a subsampled version of the data (every 4th pixel in Y- and Z-direction, 12.5 GB). This can be done via the "hyperslab" construct and adds a little bit more complexity to the description. Please note that the grid spacing has to be adapted to the subsampled grid size accordingly.
+As the dataset is relatively large (200 GB), we decided to generate a second xdmf file which only reads a subsampled version of the data (every 4th pixel in Y- and Z-direction, 12.5 GB). This is conventiant because the loading time is much shorter and the handling of the data is more fluent. The subsampling can be done via the "hyperslab" construct in the xdmf file and adds a little bit more complexity to the description. Please note that the grid spacing has to be adapted to the subsampled grid size accordingly.
 
 '''Subsampled Version:'''
@@ -129 +128 @@
 </Domain>
 </Xdmf>
-
 }}}
 
@@ -139 +137 @@
 
 == Generating the movie with a Python script
+In the next sections the resulting Python script is shown step by step.
+=== Preliminary Steps
+First of all one has to import paraview.simple and open a view of the correct size (e.g. 1920x1080=fullHD or 3840x2160=4K).
+{{{
+#!python
+#### import the simple module from the paraview
+from paraview.simple import *
+
+Connect() #connect to build in paraview
+#also possible to connect to pvserver, e.g. pv.Connect('localhost')
+
+paraview.simple._DisableFirstRenderCameraReset()
+
+# get active view
+renderView = CreateRenderView('RenderView')
+renderView.UseOffscreenRendering = 1
+renderView.ViewSize = [1920*2, 1080*2]
+}}}
+
+=== Loading the Data
+The data is loaded and then visualized with the [http://www.ospray.org/ OSPRay] volume renderer:
+{{{
+#!python
+vervet = XDMFReader(FileNames=['/homeb/zam/zilken/JURECA/projekte/hdf5_inm_converter/Vervet_Sehrinde_rightHem_direction/data/vervet_hyperslab.xdmf'])
+vervet.PointArrayStatus = ['PLI']
+vervet.GridStatus = ['Brain']
+print "loading vervet data"
+vervetDisplay = Show(vervet, renderView)
+vervetDisplay.VolumeRenderingMode = 'OSPRay Based'
+vervetDisplay.SetRepresentationType('Volume')
+vervetDisplay.ColorArrayName = ['POINTS', '']
+vervetDisplay.OSPRayScaleArray = 'PLI'
+vervetDisplay.OSPRayScaleFunction = 'PiecewiseFunction'
+vervetDisplay.SelectOrientationVectors = 'None'
+vervetDisplay.ScaleFactor = 0.09998712839442306
+vervetDisplay.SelectScaleArray = 'PLI'
+}}}
+
+=== Camera Animation: Path-based
+To orbit around the data (rotate the data), the camera can be animated in orbit mode. The CameraTrack and the AnimationScene are used in conjunction with two keyframes to render 100 images:
+{{{
+#!python
+cameraAnimationCue1 = GetCameraTrack(view=renderView)
+animationScene = GetAnimationScene()
+
+# create first keyframe
+# Note: this one keyframe stores all orbit camera position in PositionPathPoints
+keyFrame5157 = CameraKeyFrame()
+keyFrame5157.Position = [0.0, 0.0, 1.488]
+keyFrame5157.ViewUp = [-1.0, 0.0, 0.0]
+keyFrame5157.ParallelScale = 0.6825949417738006
+keyFrame5157.PositionPathPoints = [0.0, 0.0, 1.488, 0.0, 1.1563931906479727, 0.9364287418821582, 0.0, 1.455483629891903, -0.30937259593682587, 0.0, 0.6755378636124458, -1.3258177079922915, 0.0, -0.6052241248967907, -1.3593556409721905, 0.0, -1.437297629518134, -0.3851227391125512, 0.0, -1.2038172876299222, 0.8746244554111999]
+keyFrame5157.FocalPathPoints = [0.0, 0.0, 0.0]
+keyFrame5157.ClosedPositionPath = 1
+
+# create last keyframe
+keyFrame5158 = CameraKeyFrame()
+keyFrame5158.KeyTime = 1.0
+keyFrame5158.Position = [0.0, 0.0, 1.488]
+keyFrame5158.ViewUp = [-1.0, 0.0, 0.0]
+keyFrame5158.ParallelScale = 0.6825949417738006
+
+# initialize the animation track
+cameraAnimationCue1.Mode = 'Path-based'
+cameraAnimationCue1.KeyFrames = [keyFrame5157, keyFrame5158]
+
+numFrames = 100
+imageNum = 0
+animationScene.NumberOfFrames = numFrames
+animationScene.GoToFirst()
+for i in range(numFrames):
+  print ("orbit state: rendering image %04d" % (imageNum))
+  WriteImage("image_%04d.png" % (imageNum))
+  imageNum = imageNum + 1
+  animationScene.GoToNext()
+}}}
+
+=== Camera Animation: Interpolate Camera
+For whatever reason !ParaView offers a second option for camera animation, called "interpolate camera".
+In this mode, the Position-, !FocalPoint- and !ViewUp-vectors of a given number of keyframes are interpolated.
+This way a camera flight consisting of 2, 3 or more keyframes can be animated. Here is an example for 3 keyframes.
+{{{
+#!python
+# create key frame 1
+keyFrame1 = CameraKeyFrame()
+keyFrame1.KeyTime = 0.0
+keyFrame1.Position = [0.0, 0.0,  1.488]
+keyFrame1.FocalPoint = [0.0, 0.0, 0.0]
+keyFrame1.ViewUp = [-1.0, 0.0, 0.0]
+keyFrame1.ParallelScale = 0.8516115354228021
+# create key frame 2
+keyFrame2 = CameraKeyFrame()
+keyFrame2.KeyTime = 0.14
+keyFrame2.Position = [-0.28, -0.495, 1.375]
+keyFrame2.FocalPoint = [-0.00016, -0.0003, -4.22e-5]
+keyFrame2.ViewUp = [-0.981, 0.0255, -0.193]
+keyFrame2.ParallelScale = 0.8516115354228021
+# create key frame 2
+keyFrame3.KeyTime = 1.0
+keyFrame3.Position = [-0.0237, -0.092, 0.1564]
+keyFrame3.FocalPoint = [-0.000116651539708215, -0.000439441275715884, -9.75944360306001e-05]
+keyFrame3.ViewUp = [-0.98677511491576, -0.0207684556984332, -0.160759272923493]
+keyFrame3.ParallelScale = 0.8516115354228021
+
+cameraAnimationCue1.KeyFrames = [keyFrame1, keyFrame2, keyFrame3]
+cameraAnimationCue1.Mode = 'Interpolate Camera'
+numFrames = 200
+animationScene.NumberOfFrames = numFrames
+
+animationScene.GoToFirst()
+imageNum = 0
+
+for i in range(numFrames):
+  print ("rendering image %04d" % (imageNum))
+  WriteImage("picture_%04d.png" % (imageNum))
+  imageNum = imageNum + 1
+  animationScene.GoToNext()
+}}}