NeuroPy: MATLAB-ParaView

on Quarry:  provide a MATLAB function that dumps VTK Image formatted file (.vti):


  • test_vti.m

  • TE2vti.m

.../TEpackage0.6>  more test_vti.m 
load ../data_oct2010/2010_09_14_0_000_ASDF.mat
TEmatrix = ASDFTEdelay(asdf_raw,1);
fname = 'm150.vti'
TE2vti(fname,TEmatrix);
  • paraview.org (download)

    Need to open Preferences and toggle on "Auto Accept" for real-time actions. 

    File -> Open (the m150.vti file)
  display window: left (or middle) mouse button drags object; right mouse button scales

Object Inspector/Display panel > Edit Color Map > 
   (top) Color Scale 
      > Choose Preset (select whatever colormap)
      > "Rescale Range" or "Rescale to Data Range"
   (top) Color Legend
      > toggle "Show Color Legend"  (mousing over colorbar allows drag/scale)


    Filters -> Common -> Extract Subset 
  - lets you select subset of entire data
Filters -> Data Analysis -> Plot Over Line 
  - lets you create and (hold down Shift) drag up/down a "line source", generating a 2D plot
You can then File->Save State then later File->Load State
(~/dev/paraview-play/neurons_m150.pvsm)

    PV 3.8 vs. PV 3.10

    Loading the same PV state file into each version, I see that 3.10 offers additional (unwanted) plots for the PlotOverLine filter:

    I manually entered the Point1 & Point2 coords. Ideally, I'd like to be able to translate in Y by a integral (+/- 1) unit, not a continuous (float) amount. Shift-select the line will at least constrain it in X and Z.

    Here's the underlying image data - showing the single scalar array (TE): 

    % more m150.vti 
⟨?xml version="1.0"?>
⟨VTKFile type="ImageData" version="0.1" byte_order="LittleEndian">
⟨ImageData WholeExtent="0 149 0 149 0 0" Origin="0 0 0" Spacing="1 1 1">
⟨Piece Extent="0 149 0 149 0 0">
⟨PointData Scalars="TE">
⟨DataArray type="Float64" Name="TE" NumberOfComponents="1" format="ascii">
0.000000000000 0.000000504614 0.000000001189 0.000000233241 0.000000339648 ...

    Another difference in 3.8 vs. 3.10 is the "Information" on the PlotOverLine1 object - in 3.8, the range of the vtkValidPointMask is [0,1]; in 3.10, it's [1,1].

    Also, fwiw, I get an error msg:

    The fix seems to be: select the plot window, select the Display tab on the Obj Inspector, check another var and then un-check it. This will display only the TE, as desired. (Note that on this last screen capture, we also made the line resolution=150 instead of 100).

  • firing page
  • up