Differences

This shows you the differences between two versions of the page.

--- documents:201021ijmacrofragments [2020/10/21 14:06] – created kota
+++ documents:201021ijmacrofragments [2021/12/07 09:09] (current) – kota
@@ Line 1: / Line 1: @@
 ====== ImageJ Macro Fragments ======
 Some notes on ImageJ macro
-===== Getting the number of Threads =====
+===== Getting the number of Cores =====
-<code>
+<sxh js>
 th = eval("script","Runtime.getRuntime().availableProcessors();");
 print(th);
-</code>
+</sxh>
+===== Loading ROIs from a file in Internet =====
+shell command "curl" should be available in your local machine. [[https://help.ubidots.com/en/articles/2165289-learn-how-to-install-run-curl-on-windows-macosx-linux|See here for installation]].
+<sxh js>
+run("Blobs (25K)");
+path = getDirectory('imagej')+"RoiSet.zip";
+print(path)
+exec("curl", "-LJO", "https://github.com/mutterer/weird/raw/master/RoiSet.zip", "--output", path);
+roiManager("Open",path);
+roiManager("Show All");
+File.delete(path);
+</sxh>
+===== Getting Pixel Coordinates within a Polygon ROI =====
+<sxh js>
+Roi.getContainedPoints(xps, yps);
+for(i=0; i<xps.length; i++) {
+	xpos = xps[i];
+	ypos = yps[i];
+	pixval = getPixel(xpos, ypos);
+	print("("+ xpos + ", " + ypos + ") ", pixval);
+}
+</sxh>
+===== Ways of getting the file basename =====
+<sxh js>
+filepath = "/my/path/to/great_image.tif";
+//Method 1, string indexing
+basename = substring(filepath, lastIndexOf(filepath, "/")+1, lastIndexOf(filepath, "."));
+print("Method 1: ", basename);
+//Method 2, regular expression
+basename = replace(filepath, "(.*\\/)(.*)\\..{3,5}$", "$2");
+print("Method 2: ", basename);
+//... in this case, it's also possible to get the parent directry just with a small modification
+parent = replace(filepath, "(.*\\/)(.*)\\..{3,5}$", "$1");
+print(".... parent: ", parent);
+//Method 3, use a specific command
+//from ver. 1.52r
+basename = File.getNameWithoutExtension(filepath);
+print("Method 3: ", basename);
+//... it's also possible to get the parent directory with a command.
+parent = File.getDirectory(filepath);
+print(".... parent: ", parent);
+</sxh>
+===== Convert black pixels to white in RGB image =====
+<sxh js>
+for (j =0; j<getHeight();j++){
+	for (i=0; i<getWidth();i++){
+		pix =  getPixel(i, j);
+		sum = sumRGB(pix);
+		if (sum == 0){
+			setPixel(i, j, 0xffffff);
+		}
+	}
+}
+function sumRGB(RGBpixval){
+	sum = getR(pix) + getG(pix) + getB(pix);
+	return sum;
+}
+function getR(RGBpixval){
+	rf = (RGBpixval & 0xff0000)>>16;
+	return rf;
+}
+function getG(RGBpixval){
+	gf = (RGBpixval & 0x00ff00)>>8;
+	return gf;
+}
+function getB(RGBpixval){
+    bf = (RGBpixval & 0x0000ff);
+    return bf;
+}
+</sxh>