Macro with if statement and how to save as txt

[valeriaberno]

Dear all

I am quite new on writing Macro on ImageJ and I cannot figure out 2
options I would like to include.
this is my MAcro and it works perfectly but I would like to add 2 things
see at the end of the macro:
dir1 = getDirectory("Choose source directory");
dir2 = getDirectory("Choose destination directory");
list = getFileList(dir1);

//setBatchMode(true);
sigma = getNumber("sigma?", 20);
min = getNumber("min?", 200000);
for (i=0; i<list.length; i++) {
     print(i);
     showProgress(i+1, list.length);
     path = dir1 + list[i];
        open (path);

     run("Grays");
print("Grays have been run");

run("Find Edges");
print("Edges done");

run("Gaussian Blur...", "sigma");
print ("Gaussian Blur was done with parameter "+sigma);

run("Auto Threshold", "method=Triangle white");
print("Auto Threshold done with Triangle");

run("Properties...", "channels=1 slices=1 frames=1 unit=px pixel_width=1
pixel_height=1 voxel_depth=1.0000000 frame=[0 sec] origin=0,0");
print("Properties adjusted");


run("3D Objects Counter", "threshold=128 slice=0 min.=min max.=1440744
objects statistics");
//run("Brightness/Contrast...");
print("3D object Counter");
//close window automatically when no object found

run("Apply LUT");

         SavePath =  dir2 + "spot_"+i+".TIF";

saveAs("TIFF", SavePath);
//remove close all if it is in a batch mode
close();
close();

}

dir4 = getDirectory("Choose source nuclei directory");

dir3 = getDirectory("Choose Nuclei directory");
list = getFileList(dir4);
for (i=0; i<list.length; i++) {
     print(i);
     showProgress(i+1, list.length);
     path = dir4 + list[i];

     open (path);


           run("8-bit");

         run("Invert LUT");

         run("Subtract Background...", "rolling=30");

         SavePath = dir3 + "nuclei_"+i+".TIF";

         saveAs("TIFF", SavePath);
         //remove close all if it is in a batch mode
         close();

     }

My files are named array0001_B, array0001_D and array0001_R and so on.
On the first part of the macro I would like to add the "if" in order to
open only the images that ends with B...but it doesn't work as the macro
open all the files anyway. what is wrong?

path = dir1 + list[i];
     if (endsWith(path, "B.TIF")){
     open (path);
     }

At the end of the macro I also would like to save a string as a txt file
but it never work out. This is how I wrote it:

//To run Farsight
dir1 = getDirectory("Choose source directory");
list = getFileList(dir1);
for (i=0; i<list.length; i++) {
path = dir1 + list[i];
     if (endsWith(path, "D.TIF")){
         RunSegmentation = "cd dir1 segment_nuclei "+list[i]+"
nuclei_"+i+"TIF"

         run("Text...", "save=[dir1]");

         saveAs("text",RunSegmentation);


thanks in advance for all your help

Valeria

--
Valeria Berno,PhD
Microscopy Facility Manager
MRC Centre for Regenerative Medicine
SCRM building
The University of Edinburgh
Edinburgh bioQuarter
5 Little France Drive
Edinburgh
EH16 4UU
Tel Office 0131 6519521


The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Rocco D'Antuono]

Hi Valeria:
1. try to change "B.TIF" in "B.tif";
2. I would assign this value to variable: RunSegmentation=dir1+"segment nuclei "+list[i];
Hope this would work,
Best regards,
Rocco