Posted by
fabien on
URL: http://imagej.273.s1.nabble.com/Issues-with-analyze-particules-in-batch-mode-roi-became-black-tp5021305.html
hello, it makes somes days that i try to run an particules analysis with
thoses steps:
//00 - define image directory
//01 - rotates pictures with name finishing with"-07", “-08”, …, “-12”.
//02 - show active picture
//03 - create 3 “roy” .
//04 - Combine Roys
//05 - delete outside of the combined roy
//06 - select “paintbrush” tool
//07 - define the treshold level
//08 - Finalisation and validation by user of treshold settings
//09 - make binary
//10 - Convert picture in 8-bits.
//11 - fill holes
//12 - do an analyze of particules
//13 - saves results
//14 - close everything exept “Results” and “Log”
//15 - delete roys for the next picture
I got several issues:
FOR “//12 - do an analyze of particules” : if i choose Outlines or Masks
results are the same.
my program has worked for 26 pictures and now the second square become all
black whatever the treshold level defined (attached picture).
-the results excel built is in xls and a message appears when i open it, the
message says that the format and the extension of the document is dose’nt
match.
This is the program i built:
//00 - define image directory
dir = getDirectory(“image”); //define dir for saving names
name = getTitle; //define the name of the picture for savings
index = lastIndexOf(name, “.”); //define index for savings
//01 - rotates pictures with name finishing with"-07", "-08", ..., "-12".
list2=substring(name, 0, (lengthOf(name)-4)); //cut the end of the picture
name
if (endsWith(list2, “-07”)) //if the end of the picture name is “-07”
run("Rotate… “, “angle=180 interpolation=None”); // do a rotation of 180°
if (endsWith(list2, “-08”)) //if the end of the picture name is -08”
run("Rotate… ", “angle=180 interpolation=None”); // do a rotation of 180°
if (endsWith(list2, “-09”)) //if the end of the picture name is “-09”
run("Rotate… ", “angle=180 interpolation=None”); // do a rotation of 180°
if (endsWith(list2, “-10”)) //if the end of the picture name is “-10”
run("Rotate… ", “angle=180 interpolation=None”); // do a rotation of 180°
if (endsWith(list2, “-11”)) //if the end of the picture name is “-11”
run("Rotate… ", “angle=180 interpolation=None”); // do a rotation of 180°
if (endsWith(list2, “-12”)) //if the end of the picture name is “-12”
run("Rotate… ", “angle=180 interpolation=None”); // do a rotation of 180°
//02 - show active picture
setBatchMode(false); //show active picture
//03 - create 3 "roy" .
run(“ROI Manager…”); //lauch of roy manager
makeRectangle(504, 204, 215, 381); // define the first square
roiManager(“add”); // add first square to roi
makeRectangle(262, 204, 224, 362); // define the second square
roiManager(“add”); // add second square to roi
makeRectangle(537, 630, 149, 116); // define the third square
roiManager(“add”); // add third square to roi
roiManager(“select”, newArray(0,1,2)); // select all roys
//04 - Combine Roys
roiManager(“Combine”); // combine all roys
roiManager(“add”); // add to roy manager the combined roy
roiManager(“select”, 3); // select the combined roy
//05 - delete outside of the combined roy
run(“Clear Outside”); // clear outside the combined roy
//06 - select "paintbrush" tool
setTool( “Paintbrush Tool” ); // select “paintbrush” tool
//07 - define the treshold level
setThreshold(185, 255); // define the treshold level
run(“Threshold…”); // run threshold
//08 - Finalisation and validation by user of treshold settings
waitForUser(“définir le threshold et appuyer sur OK”); //wait user for
clicing to “ok”
//09 - make binary
run(“Make Binary”); //make binary
//10 - Convert picture in 8-bits.
run(“8-bit”); //Convert picture in 8-bits.
//11 - fill holes
run(“Fill Holes”); // fill holes
//12 - do an analyze particules
run(“Analyze Particles…”, “size=50-Infinity show=Outlines display exclude
include summarize”);
//13 - saves results
selectWindow(“Results”); // select “results windows”
getResult (“Area”, 0); // selectionne “Area column”
if (index!=-1) name = substring(name, 0, index); // too smart for me
name = name + “.xls”; // transform name for creating excel file
saveAs(“Results…”, dir+name); //saves results (step 1)
print(dir+name); //saves result (step 2)
//14 - close everything exept "Results" and "Log"
close();
//15 - delete roys for the next picture
roiManager(“Deselect”); //select all roys
roiManager(“Delete”); //delete all roys
I’m not a programmer, i founded parts of code on internet and on this forum
in order to create this program
If someone can help me, thank you A LOT. :slight_smile:
<
http://imagej.1557.x6.nabble.com/file/t382132/SO%2BGL-00007-01-05.jpg>
--
Sent from:
http://imagej.1557.x6.nabble.com/--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html