help with Confidence Interval Autoscale method?

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

help with Confidence Interval Autoscale method?

Francis OBrien
Hello,

I am a total newbie so I am willing to learn if people can point me in the right direction. I am trying to get the following code for confidence interval autoscaling to work but I keep getting the errors in Fiji when I try to run the code.

https://github.com/imagej/imagej-common/blob/master/src/main/java/net/imagej/autoscale/ConfidenceIntervalAutoscaleMethod.java

 How do I use this code in ImageJ? Is it run as a macro?

 Best,

Francis

--
Regards,

Francis

Research graduate,
New York School of Medicine
New York

_______________________________________________
ImageJ-devel mailing list
[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel
Reply | Threaded
Open this post in threaded view
|

Re: help with Confidence Interval Autoscale method?

Mark Hiner
Hi Francis,

An AutoscaleMethod is a plugin to an AutoscaleService[1], and is either accessed directly (via getAutoscaleMethod) or indirectly (via getDefaultMethod or the getDefault...Range metods). To use this code in ImageJ you would either have to use a command that calls into the AutoscaleService, or write your own plugin/macro.

Here's an example of a simple python macro that prints the min/max calculated using the confidence interval method:

------
# @AutoscaleService asService
# @net.imagej.Dataset data

m = asService.getAutoscaleMethod('Confidence Interval')

r = m.getRange(data)

print 'Range min: ', r.getMin(), ', max: ', r.getMax()
----

The first two lines are script parameters[2]. The AutoscaleService is available by default, but for a Dataset you will have to open an image either with ImageJ2/SCIFIO enabled (Edit > Options > ImageJ2) or using the "File > Import > Image..." command directly.

Hope that helps. Let me know if you have any more questions.

Best,
Mark


On Mon, Jan 26, 2015 at 11:38 PM, Francis OBrien <[hidden email]> wrote:
Hello,

I am a total newbie so I am willing to learn if people can point me in the right direction. I am trying to get the following code for confidence interval autoscaling to work but I keep getting the errors in Fiji when I try to run the code.

https://github.com/imagej/imagej-common/blob/master/src/main/java/net/imagej/autoscale/ConfidenceIntervalAutoscaleMethod.java

 How do I use this code in ImageJ? Is it run as a macro?

 Best,

Francis

--
Regards,

Francis

Research graduate,
New York School of Medicine
New York

_______________________________________________
ImageJ-devel mailing list
[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel



_______________________________________________
ImageJ-devel mailing list
[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel