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Content-Type: text/plain; charset="iso-8859-1"
Message-ID:  <8C3ACF2AFE15D411AFFD00805FA6303B252980@PFINT1>
Date:         Wed, 22 May 2002 09:56:29 +0200
Reply-To:     ImageJ Interest Group <[log in to unmask]>
Sender:       ImageJ Interest Group <[log in to unmask]>
From:         Gary Chinga <[log in to unmask]>
Subject:      Re: Surface plots in VolumeJ/Matlab .m data files.

Michael,

I was also trying to make a plugin based on the macro I described. However,
my java knowledge is very limited. It seems that the only steps necessary
are
1.-     Make two stacks, one with the original image, the other the depth
coded stack
2.-     Stack substraction
3.-     Stack reverser

The rest can be done with your Volumej. Even the rotation of the surface
plot is better performed using your Volumej plugin.

It will be wonderful if the surface plot capability is integrated into your
plugin. Thanks.

Gary.


> -----Original Message-----
> From: Abramoff [SMTP:[log in to unmask]]
> Sent: 21. mai 2002 20:47
> To:   [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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