Creating 3D Image from two 2D arrays

[Victoria Price]

Hello,

So I've plotted the 2D numpy arrays as images beautifully.  I have a master image and a slave image that I'm hoping to combine together into an x,y,z system but I'm not entirely clear on how to do this.  The x and y axis are from the master image and the z coordinate comes from the slave image x coordinate, if that helps.  Any guidance would be appreciated, I'm a bit lost.

Thanks!

Victoria

[Luke Campagnola]

On Thu, Oct 18, 2012 at 3:16 PM, Victoria Price <victoria...@gmail.com> wrote:

So I've plotted the 2D numpy arrays as images beautifully.  I have a master image and a slave image that I'm hoping to combine together into an x,y,z system but I'm not entirely clear on how to do this.  The x and y axis are from the master image and the z coordinate comes from the slave image x coordinate, if that helps.  Any guidance would be appreciated, I'm a bit lost.

So you have 2 images; one in the x,y plane and one in the z,y plane. 

How exactly do you want to visualize this? 

Perhaps two image planes in a 3D view, like panel B in this image: http://c431376.r76.cf2.rackcdn.com/344/fninf-03-009/image_m/fninf-03-009-g005.jpg   ?

Luke

[Victoria Price]

Yes, that's exactly what I'm thinking!  Thank you for articulating that for me.  What is the best way to go about doing this? 

[Luke Campagnola]

We'll need a GLImageItem class for that. 

Should be very easy to put together.. I'll include one in the next release (probably tonight).

[Luke Campagnola]

Have a look at the latest revision, particularly examples/GLImageItem.py

[Victoria Price]

Those are excellent, thank you.  One question I have is, since I'm deriving the Z coordinate from a different data array, how to I merge the two to create the xz/yz planes? 

The arrays are 96x512... so would the shape be (96,512,96)?  

[Luke Campagnola]

On Fri, Oct 19, 2012 at 12:12 PM, Victoria Price <victoria...@gmail.com> wrote:

Those are excellent, thank you.  One question I have is, since I'm deriving the Z coordinate from a different data array, how to I merge the two to create the xz/yz planes? 

The arrays are 96x512... so would the shape be (96,512,96)?  

In the example, I use 2D slices taken from a 3D data set so that the images on the slice planes will match where they intersect.

It sounds like you already have two 2D planes selected from what (I presume) was originally a 3D volume, so it's not necessary to try to reconstruct a 3D array--just create one GLImageItem from each array and rotate/position them accordingly.

[Victoria Price]

I've attached the basic code, though it does call modules that I've written to read in the data from the file (and locate the appropriate image data array)...I receive this error:

Traceback (most recent call last):

  File "C:/Users/Tory/Desktop/3DTesting", line 17, in <module>

    image=pg.makeRGBA(frame.data[shape[0]])[0]

IndexError: index out of bounds

Am I on the right track?

Thank you again for all of your help!

Edit:  it seems to not want to let me attach a file...

from PyQt4.QtGui import *

from PyQt4.QtCore import *

from fileheader import FileHeader, Frame

import pyqtgraph as pg

import pyqtgraph.opengl as gl

from scipy import ndimage

import sys,os

filename="C:/Users/Tory/Desktop/PYTHON NOAA/test.ddf"

slaveFilename="C:/Users/Tory/Desktop/PYTHON NOAA/test.ddf"

fileheader=FileHeader(filename)

frame=fileheader.frameAtIndex(1)

slaveFileHeader=FileHeader(slaveFilename)

slaveFrame=slaveFileHeader.frameAtIndex(1)

shape=(96,512)

image=pg.makeRGBA(frame.data[shape[0]])[0]

slaveImage=pg.makeRGBA(slaveFrame.data[shape[1]])[0]

app=QApplication([])

w = gl.GLViewWidget()

w.show()

v1=gl.GLImageItem(image)

v1.translate(-shape[1],-shape[2])

w.addItem(v1)

v2=gl.GLImageItem(slaveImage)

v2.translate(-shape[0],-shape[2])

w.addItem(v2)

if sys.flags.interactive !=1:

    app.exec_()

[Luke Campagnola]

If 'frame.data' is a 2D array and 'shape' is the shape of that array, then one would expect the expression 'frame.data[shape[0]]' to generate this error.

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