Optimizing Display

[Robert Lockwood]

I work for the USDA Forest Service and we have been using ImageJ to view
our own images and others for which we have no viewers.  I am working on a
view those of us who need to view our images and am able to do so.  I work
 in Java for this.  The problem I have is that the test images I have don't
have much contrast and they are displayed "as is".  I have written code in
the past in C/C++ in which the images are automatically enhanced for
contrast and a simple rubber band mapping.  Our images were created from C
with pixels as USHORT.  I calculate the minimum, maximum, and mean and they
are exactly what ImageJ calculates.  My attempts to map the data to improve
contrast are all failures but ImageJ displays a good image.

Is it possible to get the methods used by ImageJ?  I'm using Eclipse on
Ubuntu for development.

--
When I was 12 I thought I would live forever.
So far, so good.

[Senseney, Justin (NIH/CIT) [E]]

Robert,

Since the ImageJ source-code is freely available here: http://imagej.nih.gov/ij/download.html, I would recommend building ImageJ yourself within Eclipse as a new Java Project.  Then you can use Eclipse's debug mode to see exactly how ImageJ is adjusting contrast and how ImageJ works when you run any of the Image->Adjust->X tools from the menubar.  The only tricky part is you'll see the build has errors with the default JRE, but since those are contained in Compiler.java you can still run ImageJ from Eclipse even with those build errors (these would need the JDK to fix).  Just make a new Java Application in Run Configuration... in Eclipse with ij.ImageJ as your main class.

Justin Senseney
BIRSS/ISL/DCB/CIT/NIH
301-594-5887
301-480-0028 (fax)
Building 12A/2015



-----Original Message-----
From: Robert Lockwood [mailto:[hidden email]]
Sent: Thursday, May 17, 2012 4:12 PM
To: List IMAGEJ
Subject: Optimizing Display

I work for the USDA Forest Service and we have been using ImageJ to view our own images and others for which we have no viewers.  I am working on a view those of us who need to view our images and am able to do so.  I work  in Java for this.  The problem I have is that the test images I have don't have much contrast and they are displayed "as is".  I have written code in the past in C/C++ in which the images are automatically enhanced for contrast and a simple rubber band mapping.  Our images were created from C with pixels as USHORT.  I calculate the minimum, maximum, and mean and they are exactly what ImageJ calculates.  My attempts to map the data to improve contrast are all failures but ImageJ displays a good image.

Is it possible to get the methods used by ImageJ?  I'm using Eclipse on Ubuntu for development.

--
When I was 12 I thought I would live forever.
So far, so good.

[Robert Lockwood]

That was quick, thanks!
Does imagej use the tools on initial display?

On Thu, May 17, 2012 at 1:52 PM, Senseney, Justin (NIH/CIT) [E] <
[hidden email]> wrote:

> Robert,
>
> Since the ImageJ source-code is freely available here:
> http://imagej.nih.gov/ij/download.html, I would recommend building ImageJ
> yourself within Eclipse as a new Java Project.  Then you can use Eclipse's
> debug mode to see exactly how ImageJ is adjusting contrast and how ImageJ
> works when you run any of the Image->Adjust->X tools from the menubar.  The
> only tricky part is you'll see the build has errors with the default JRE,
> but since those are contained in Compiler.java you can still run ImageJ
> from Eclipse even with those build errors (these would need the JDK to
> fix).  Just make a new Java Application in Run Configuration... in Eclipse
> with ij.ImageJ as your main class.
>
> Justin Senseney
> BIRSS/ISL/DCB/CIT/NIH
> 301-594-5887
> 301-480-0028 (fax)
> Building 12A/2015
>
>
>
> -----Original Message-----
> From: Robert Lockwood [mailto:[hidden email]]
> Sent: Thursday, May 17, 2012 4:12 PM
> To: List IMAGEJ
> Subject: Optimizing Display
>
> I work for the USDA Forest Service and we have been using ImageJ to view
> our own images and others for which we have no viewers.  I am working on a
> view those of us who need to view our images and am able to do so.  I work
>  in Java for this.  The problem I have is that the test images I have don't
> have much contrast and they are displayed "as is".  I have written code in
> the past in C/C++ in which the images are automatically enhanced for
> contrast and a simple rubber band mapping.  Our images were created from C
> with pixels as USHORT.  I calculate the minimum, maximum, and mean and they
> are exactly what ImageJ calculates.  My attempts to map the data to improve
> contrast are all failures but ImageJ displays a good image.
>
> Is it possible to get the methods used by ImageJ?  I'm using Eclipse on
> Ubuntu for development.
>
> --
> When I was 12 I thought I would live forever.
> So far, so good.
>

--
When I was 12 I thought I would live forever.
So far, so good.

[dscho]

Hi,

On Thu, 17 May 2012, Senseney, Justin (NIH/CIT) [E] wrote:

> Since the ImageJ source-code is freely available here:
> http://imagej.nih.gov/ij/download.html, I would recommend building
> ImageJ yourself within Eclipse as a new Java Project.  Then you can use
> Eclipse's debug mode to see exactly how ImageJ is adjusting contrast and
> how ImageJ works when you run any of the Image->Adjust->X tools from the
> menubar.  The only tricky part is you'll see the build has errors with
> the default JRE, but since those are contained in Compiler.java you can
> still run ImageJ from Eclipse even with those build errors (these would
> need the JDK to fix).  Just make a new Java Application in Run
> Configuration... in Eclipse with ij.ImageJ as your main class.

To make things easier, we have a Mavenized ImageJ in
http://github.com/fiji/ImageJA which works great once you installed the
m2e plugin as described here:

        http://developer.imagej.net/eclipse

Ciao,
Johannes

[Robert Lockwood]

I'll give it a shot.

This project came about because we need to replace aging research
equipment, mostly the now 13 or 14 year old computer and 5 remote imaging
cameras (expensive cameras which we turned into imaging radiometers) and
are used for research into wildfire.  Since the band width would increase
by a factor of 4 for each of 3 cameras and by a factor of 10 for two others
I suggested that we should use distributed computing with small specialized
 LINUX computers running one or two sensors each and one as a master which
would host the GUI for the operator.  My super visor said "Make it so."
 and "by the way it must be done in Java."  I've never done any of this
before.  I quickly became immersed in names maven, git, eclipse, java
beans, and many more each of which had their own learning curve.  Now I
guess I'll need to learn maven, sigh.






On Thu, May 17, 2012 at 2:14 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Thu, 17 May 2012, Senseney, Justin (NIH/CIT) [E] wrote:
>
> > Since the ImageJ source-code is freely available here:
> > http://imagej.nih.gov/ij/download.html, I would recommend building
> > ImageJ yourself within Eclipse as a new Java Project.  Then you can use
> > Eclipse's debug mode to see exactly how ImageJ is adjusting contrast and
> > how ImageJ works when you run any of the Image->Adjust->X tools from the
> > menubar.  The only tricky part is you'll see the build has errors with
> > the default JRE, but since those are contained in Compiler.java you can
> > still run ImageJ from Eclipse even with those build errors (these would
> > need the JDK to fix).  Just make a new Java Application in Run
> > Configuration... in Eclipse with ij.ImageJ as your main class.
>
> To make things easier, we have a Mavenized ImageJ in
> http://github.com/fiji/ImageJA which works great once you installed the
> m2e plugin as described here:
>
>        http://developer.imagej.net/eclipse
>
> Ciao,
> Johannes
>

--
When I was 12 I thought I would live forever.
So far, so good.

[ctrueden]

Hi everyone,

On Thu, May 17, 2012 at 4:14 PM, Johannes Schindelin <
[hidden email]> wrote:

> To make things easier, we have a Mavenized ImageJ in
> http://github.com/fiji/ImageJA which works great once you installed the
> m2e plugin as described here:
>
>        http://developer.imagej.net/eclipse
>

Actually, if you install the "Eclipse for Java developers" bundle, it comes
with M2E preinstalled. Then all you have to do is File > Import > Existing
Maven Projects, if you have already cloned the source.

If you already have an Eclipse (3.7+) installation that does not have M2E
installed, you can install it by doing Help > Install New Software, Work
with "-- All Available Sites--", type "m2e" in the filter box, and then
install "m2e - Maven Integration for Eclipse" under Collaboration.

Using M2E makes managing dependencies in Eclipse much more flexible. E.g.:
if you have a Maven-based project open in Eclipse, it will be added as a
project dependency for in downstream project classpaths. If you close the
project, the downstream project classpaths will automatically switch to
using binary JAR dependencies.

Regards,
Curtis


On Thu, May 17, 2012 at 4:14 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Thu, 17 May 2012, Senseney, Justin (NIH/CIT) [E] wrote:
>
> > Since the ImageJ source-code is freely available here:
> > http://imagej.nih.gov/ij/download.html, I would recommend building
> > ImageJ yourself within Eclipse as a new Java Project.  Then you can use
> > Eclipse's debug mode to see exactly how ImageJ is adjusting contrast and
> > how ImageJ works when you run any of the Image->Adjust->X tools from the
> > menubar.  The only tricky part is you'll see the build has errors with
> > the default JRE, but since those are contained in Compiler.java you can
> > still run ImageJ from Eclipse even with those build errors (these would
> > need the JDK to fix).  Just make a new Java Application in Run
> > Configuration... in Eclipse with ij.ImageJ as your main class.
>
> To make things easier, we have a Mavenized ImageJ in
> http://github.com/fiji/ImageJA which works great once you installed the
> m2e plugin as described here:
>
>        http://developer.imagej.net/eclipse
>
> Ciao,
> Johannes
>

[Robert Lockwood]

I've decided to install the Mavenized ImageJ but when I get to the line in
the installation to look for Maven Projects in Eclipse: File->Import
 there's no Maven there.  Which Maven plugin do I install?



On Thu, May 17, 2012 at 2:51 PM, Curtis Rueden <[hidden email]> wrote:

> Hi everyone,
>
> On Thu, May 17, 2012 at 4:14 PM, Johannes Schindelin <
> [hidden email]> wrote:
>
> > To make things easier, we have a Mavenized ImageJ in
> > http://github.com/fiji/ImageJA which works great once you installed the
> > m2e plugin as described here:
> >
> >        http://developer.imagej.net/eclipse
> >
>
> Actually, if you install the "Eclipse for Java developers" bundle, it comes
> with M2E preinstalled. Then all you have to do is File > Import > Existing
> Maven Projects, if you have already cloned the source.
>
> If you already have an Eclipse (3.7+) installation that does not have M2E
> installed, you can install it by doing Help > Install New Software, Work
> with "-- All Available Sites--", type "m2e" in the filter box, and then
> install "m2e - Maven Integration for Eclipse" under Collaboration.
>
> Using M2E makes managing dependencies in Eclipse much more flexible. E.g.:
> if you have a Maven-based project open in Eclipse, it will be added as a
> project dependency for in downstream project classpaths. If you close the
> project, the downstream project classpaths will automatically switch to
> using binary JAR dependencies.
>
> Regards,
> Curtis
>
>
> On Thu, May 17, 2012 at 4:14 PM, Johannes Schindelin <
> [hidden email]> wrote:
>
> > Hi,
> >
> > On Thu, 17 May 2012, Senseney, Justin (NIH/CIT) [E] wrote:
> >
> > > Since the ImageJ source-code is freely available here:
> > > http://imagej.nih.gov/ij/download.html, I would recommend building
> > > ImageJ yourself within Eclipse as a new Java Project.  Then you can use
> > > Eclipse's debug mode to see exactly how ImageJ is adjusting contrast
> and
> > > how ImageJ works when you run any of the Image->Adjust->X tools from
> the
> > > menubar.  The only tricky part is you'll see the build has errors with
> > > the default JRE, but since those are contained in Compiler.java you can
> > > still run ImageJ from Eclipse even with those build errors (these would
> > > need the JDK to fix).  Just make a new Java Application in Run
> > > Configuration... in Eclipse with ij.ImageJ as your main class.
> >
> > To make things easier, we have a Mavenized ImageJ in
> > http://github.com/fiji/ImageJA which works great once you installed the
> > m2e plugin as described here:
> >
> >        http://developer.imagej.net/eclipse
> >
> > Ciao,
> > Johannes
> >
>

--
When I was 12 I thought I would live forever.
So far, so good.

[ctrueden]

Hi Robert,

On Thu, May 17, 2012 at 6:09 PM, Robert Lockwood <[hidden email]>wrote:

> I've decided to install the Mavenized ImageJ but when I get to the line in
> the installation to look for Maven Projects in Eclipse: File->Import
>  there's no Maven there.  Which Maven plugin do I install?
>

The plugin is called M2E:

On Thu, May 17, 2012 at 4:51 PM, Curtis Rueden <[hidden email]> wrote:

> If you already have an Eclipse (3.7+) installation that does not have M2E
> installed, you can install it by doing Help > Install New Software, Work
> with "-- All Available Sites--", type "m2e" in the filter box, and then
> install "m2e - Maven Integration for Eclipse" under Collaboration.
>

HTH,
Curtis


On Thu, May 17, 2012 at 6:09 PM, Robert Lockwood <[hidden email]>wrote:

> I've decided to install the Mavenized ImageJ but when I get to the line in
> the installation to look for Maven Projects in Eclipse: File->Import
>  there's no Maven there.  Which Maven plugin do I install?
>
>
>
> On Thu, May 17, 2012 at 2:51 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi everyone,
> >
> > On Thu, May 17, 2012 at 4:14 PM, Johannes Schindelin <
> > [hidden email]> wrote:
> >
> > > To make things easier, we have a Mavenized ImageJ in
> > > http://github.com/fiji/ImageJA which works great once you installed
> the
> > > m2e plugin as described here:
> > >
> > >        http://developer.imagej.net/eclipse
> > >
> >
> > Actually, if you install the "Eclipse for Java developers" bundle, it
> comes
> > with M2E preinstalled. Then all you have to do is File > Import >
> Existing
> > Maven Projects, if you have already cloned the source.
> >
> > If you already have an Eclipse (3.7+) installation that does not have M2E
> > installed, you can install it by doing Help > Install New Software, Work
> > with "-- All Available Sites--", type "m2e" in the filter box, and then
> > install "m2e - Maven Integration for Eclipse" under Collaboration.
> >
> > Using M2E makes managing dependencies in Eclipse much more flexible.
> E.g.:
> > if you have a Maven-based project open in Eclipse, it will be added as a
> > project dependency for in downstream project classpaths. If you close the
> > project, the downstream project classpaths will automatically switch to
> > using binary JAR dependencies.
> >
> > Regards,
> > Curtis
> >
> >
> > On Thu, May 17, 2012 at 4:14 PM, Johannes Schindelin <
> > [hidden email]> wrote:
> >
> > > Hi,
> > >
> > > On Thu, 17 May 2012, Senseney, Justin (NIH/CIT) [E] wrote:
> > >
> > > > Since the ImageJ source-code is freely available here:
> > > > http://imagej.nih.gov/ij/download.html, I would recommend building
> > > > ImageJ yourself within Eclipse as a new Java Project.  Then you can
> use
> > > > Eclipse's debug mode to see exactly how ImageJ is adjusting contrast
> > and
> > > > how ImageJ works when you run any of the Image->Adjust->X tools from
> > the
> > > > menubar.  The only tricky part is you'll see the build has errors
> with
> > > > the default JRE, but since those are contained in Compiler.java you
> can
> > > > still run ImageJ from Eclipse even with those build errors (these
> would
> > > > need the JDK to fix).  Just make a new Java Application in Run
> > > > Configuration... in Eclipse with ij.ImageJ as your main class.
> > >
> > > To make things easier, we have a Mavenized ImageJ in
> > > http://github.com/fiji/ImageJA which works great once you installed
> the
> > > m2e plugin as described here:
> > >
> > >        http://developer.imagej.net/eclipse
> > >
> > > Ciao,
> > > Johannes
> > >
> >
>
>
>
> --
> When I was 12 I thought I would live forever.
> So far, so good.
>