To plot mean values in results table

[cwc]

Hi everyone,

My apology if my question is too basic. I am trying to search the related topics but still confused. My need is to plot x-y graph (x = nResults and y = mean in results table) and thus I try to modify the example code but fail (please see below). Could everyone help me to figure it out?  Thank you very much.


n = nResults;  

    macro "Plot" {
         yValues = getResult('mean');
         Plot.create("Plot", "X", "Y");
         Plot.setLimits(0, n, 0, 10000);
         Plot.setLineWidth(2);
         Plot.setColor("lightGray");
         Plot.add("line",yValues);
         Plot.setColor("red");
         Plot.add("circles", yValues);
         Plot.show();
}

[Michael Entrup]

Hi cwc,

here is some Jython code (tested with Fiji) that plots the mean value of
a stack vs the slice number:


from ij import IJ
from ij import WindowManager as WM
from ij.gui import Plot

image = WM.getCurrentImage()
stack = image.getStack()
x = []
y = []
for i in range(1, stack.getSize() + 1):
        ip = stack.getProcessor(i)
        stat = ip.getStatistics()
        x.append(i)
        y.append(stat.mean)

plot = Plot("title", "slice", "mean", x, y)
plot.show()


The following code will create a results table first and reads the mean
values from there (2nd for loop):


from ij import IJ
from ij import WindowManager as WM
from ij.measure import ResultsTable as RT
from ij.gui import Plot

image = WM.getCurrentImage()
stack = image.getStack()
x = []
y = []

IJ.run("Set Measurements...", "mean display redirect=None decimal=3");
IJ.run("Clear Results", "")
for i in range(1, stack.getSize() + 1):
        image.setSlice(i)
        IJ.run(image, "Measure", "")

table = RT.getResultsTable()
counter = table.getCounter()
for i in range(0,counter):
        row =  table.getRowAsString(i)
        cells = row.split()
        x.append(i)
        # the table consists of 3 columns
        # cells[0]: index
        # cells[1]: slice name
        # cells[2]: mean value
        y.append(float(cells[2]))

plot = Plot("title", "slice", "mean", x, y)
plot.show()


For me it's much easier to write macros with Jython than with the basic
macro language, because you can use the full ImageJ API that is well
documented. I hope this examples will help you.

Best regards
Michael


Am 27.10.2014 um 16:53 schrieb cwc:

> Hi everyone,
>
> My apology if my question is too basic. I am trying to search the related
> topics but still confused. My need is to plot x-y graph (x = nResults and y
> = mean in results table) and thus I try to modify the example code but fail
> (please see below). Could everyone help me to figure it out?  Thank you very
> much.
>
>
> n = nResults;
>
>      macro "Plot" {
>           yValues = getResult('mean');
>           Plot.create("Plot", "X", "Y");
>           Plot.setLimits(0, n, 0, 10000);
>           Plot.setLineWidth(2);
>           Plot.setColor("lightGray");
>           Plot.add("line",yValues);
>           Plot.setColor("red");
>           Plot.add("circles", yValues);
>           Plot.show();
> }
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/To-plot-mean-values-in-results-table-tp5010204.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Emanuele Martini]

Hi,
I also suggest to use some other languages (I use Jython too) to have full access to ImageJ API, and overall you can use some IDE like Eclipse to debug your code in a more or less easy way.
Have a nice day,
Emanuele

[Rocco D'Antuono]

Hi user "cwc", to have your code working you could simply change the line

----------------------
yValues = getResult('mean');

----------------------

in

----------------------
yValues=newArray(n);
         for(i=0;i<n;i++)
          {
          yValues[i]=getResult('Mean',i);
          }

----------------------
Best regards,
Rocco

[cwc]

Hi Michael and Emanuele,

Thank you for your time and replies. It is my bad since I am not familiar with Fiji and thus it is my first time to hear the Jython code and others. I've read the related instructions in Fiji and felt interesting to learn them. My appreciation for your kind advices.  :)

Regards,
cwc

[cwc]

Hi Rocco,

Yes, I got the same answer as yours. I feel grateful because I figure out the problem and agree with someone even though the question is small. Very thanks for your time and reply. :)

Regards,
cwc    

[Kota Miura]

Hi cwc,

You do not need to write a macro. Use "Plot Results" function from BAR
package written by Tiago Ferreira.

https://github.com/tferr/Scripts/blob/master/README.md#data-analysis

BAR is listed in the update sites.
http://fiji.sc/List_of_update_sites

HTH
Kota

On Mon, Oct 27, 2014 at 4:53 PM, cwc <[hidden email]> wrote:

> Hi everyone,
>
> My apology if my question is too basic. I am trying to search the related
> topics but still confused. My need is to plot x-y graph (x = nResults and y
> = mean in results table) and thus I try to modify the example code but fail
> (please see below). Could everyone help me to figure it out?  Thank you
> very
> much.
>
>
> n = nResults;
>
>     macro "Plot" {
>          yValues = getResult('mean');
>          Plot.create("Plot", "X", "Y");
>          Plot.setLimits(0, n, 0, 10000);
>          Plot.setLineWidth(2);
>          Plot.setColor("lightGray");
>          Plot.add("line",yValues);
>          Plot.setColor("red");
>          Plot.add("circles", yValues);
>          Plot.show();
> }
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/To-plot-mean-values-in-results-table-tp5010204.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Centre for Molecular and Cellular Imaging,
European Molecular Biology Laboratory
Meyerhofstr. 1
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