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References: <[log in to unmask]>
Content-Type: text/plain; charset="iso-8859-1"
Message-ID:  <[log in to unmask]>
Date:         Tue, 21 May 2002 20:46:56 +0200
Reply-To:     ImageJ Interest Group <[log in to unmask]>
Sender:       ImageJ Interest Group <[log in to unmask]>
From:         Abramoff <[log in to unmask]>
Subject:      Re: Surface plots in VolumeJ/Matlab .m data files.

Hello,

I am having major problems with my ASDL, so havent been able to update the
VolumeJ/Flowj website for a week now (100MB of data). Thanks for all the bug
reports you sent me. At home, I am now using a 28k8 modem.

I was working on a suggestion by Paulo Magelhaes to do the surface rendering
automatically within VolumeJ, he is currently testing it. Very soon, there
will be a button on the VolumeJ user interface.
However, I have to admit I never even thought of writing a short plugin like
Gary did.
So in the future there may be three alternatives for making surface plots.
It may be even better to seperate the two plugins and create a 'SurfaceJ' or
similar.

Let me just wait for Magelhaes's verdict and I will send it to Wayne.
Updating the website will have to wait a while though.

Now that I have your attention, I also wrote a plugin to read the data
arrays in Matlab .m files. In my case, to read RTA (Retinal Thickness
Analyzer) files (I am an ophthalmologist). Please note: not the macros, just
the data structures.
In case anyone is interested I will upload it to Wayne also pending my
dysfunctional ASDL.

The real time volume renderer has run into problems with the rotated
rendering algorithm due to misalignments. Real Soon Now.

Thanks for your patience,

Michael Abramoff
____________________________________________________________________________
_________
Michael Abramoff, MD, PhD
Dept. of Ophthalmology, Room 4A65,
Vrije Universiteit University Hospital, 1117, de Boelelaan, 1080 MB
Amsterdam, The Netherlands

Image Sciences Institute, Room E01.334
University Medical Center Utrecht, 100, Heidelberglaan, 3584 CX Utrecht, The
Netherlands
[log in to unmask]
____________________________________________________________________________
_________


----- Original Message -----
From: "Wayne Rasband" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Tuesday, May 21, 2002 8:12 PM
Subject: Fwd: Surface plots...


> > From: GC <[log in to unmask]>
> > Date: Mon May 20, 2002  07:59:33 AM US/Eastern
> > To: [log in to unmask]
> > Subject: Surface plots...
> >
> > Hi!
> > The procedure described by Michael Abramoff and Tony Collins yields
> > excellent
> > surface plots!!. It may be however easier to generate such surface
> > plots by
> > recording the procedure into a macro. I have recorded a simple macro
> > (plugin) following the instructions and it works fine. Just remember to
> > unmark
> > the "create new window for result" to avoid creating several images.
> >
> > Gary.
> >
> >
/************************************************************************
> > **/
> > import ij.*;
> > import ij.process.*;
> > import ij.gui.*;
> > import java.awt.*;
> > import ij.plugin.*;
> >
> > /** Based on the procedure described by Michael Abramoff and Tony
> > Collins. The
> > Transformj, Volumej and Stack Reverser
> > plugins are required.
> >  */
> >
> > public class Surface_plot implements PlugIn {
> >
> >       public void run(String arg) {
> >               IJ.run("8-bit");
> >               IJ.run("Rotate ");              // rotation around the
z-axis only
> >                                       //Mark adjust size to fit result
> >                                       //Unmark create new window for
result
> >               IJ.run("Scale ");               //Generates a stack
containg the number of images
> >                                       //specified in the Scaling factor
in
> > Z-dimension field, try with >50
> > slices
> >                                       //Unmark create new window for
result
> >               IJ.run("Depth Coded Stack");    //OK
> >               IJ.run("Image Calculator...");  //Original stack -
depth_coded image
> >                                       //Unmark create new window for
result
> >               IJ.run("Stack Reverser");
> >               IJ.run("Volume Renderer");      //Follows the instructions
given
> > by Tony Collins
> >
//http://www.isi.uu.nl/people/michael/surfaceplots.htm
> >       }
> >
> > }
> >
> >
> >

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