Jeremy's comment about terminology. Clearly "Heat Map" should refer only
"false color" or even better "pseudocolor". In any case, one would be
expected to provide a key to the color map in any image. The additional
Joel B. Sheffield, Ph.D
> I find the increasing use of "heat maps" unhelpful.
> Some false color LUTs do resemble the color sequence that a heated object
> could display, but most do not. It is therefore unclear if a "heat map"
> refers to a subset of LUTs or is intended as a generic reference to all
> LUTs.
>
> "LUTs", a longer but more precise "display LUTs" or "false color LUTs"
> seem to be provide greater clarity.
>
>
>
> ________________________________________
> From: ImageJ Interest Group [
[hidden email]] on behalf of Dobens,
> Leonard [
[hidden email]]
> Sent: 16 February 2017 22:37
> To:
[hidden email]
> Subject: problem overlaying from ROI manager in macro
>
> I am writing a macro to overlay a heat map of particle orientation
> measurements (over 360 degrees) as colors filling the particles overlayed
> back onto the original image. The macro works fine until the last step when
> I would like to recall the original image and from ROI overlay the colors.
> Interestingly, I can not close the ramp legend nor the thresholded
> particles image with this:
>
> run("Close All");
>
> open(path_name);
> run("RGB Color");
> run("From ROI Manager”);
>
> I can close the windows if I open a new macro with
>
> run("Close All");
>
>
> Here is the whole macro, using the “blobs” as an example; if you try it,
> just hit “return” to move past the dialog box; scroll to the last lines of
> the macro to see what I’ve written and if you could explain what the
> problem is down there, I’d be eternally grateful!
>
>
> best,
>
> Len Dobens
>
> ////////////////////
> var path_name = getDirectory("image")+ getInfo("image.filename");
>
>
> run("Blobs (25K)");
>
> run("Make Binary");
> run("Set Measurements...", "centroid center feret's redirect=None
> decimal=3");
>
> Dialog.create("Settings");
> Dialog.addNumber("Particle width:", 5);
> Dialog.addNumber("Opacity", 50);
> Dialog.addChoice("Lut:", newArray("32_Colors", "Ice", "Spectrum",
> "20_Colors"));
> Dialog.show();
> z = Dialog.getNumber();
> opac = Dialog.getNumber();
> heatmap = Dialog.getChoice();
>
>
> run("Analyze Particles...", "size=z-Infinity show=Overlay display exclude
> clear add");
>
>
> run("To ROI Manager");
> roiManager("Show All without labels");
>
> Overlay.drawLabels(false);
>
> for (i=0; i<nResults; i++) {
> x11 = getResult("FeretX",i);
> y11 = getResult("FeretY",i);
> length = getResult("Feret",i);
> degrees = getResult("FeretAngle",i);
> if (degrees>90)
> degrees -= 180;
> angle = degrees*PI/180;
> x21 = x11 + cos(angle)*length;
> setResult("x21", i, x21);
> y21 = y11 - sin(angle)*length;
> setResult("y21", i, y21);
>
> x31 = getResult("X",i);
> y31 = getResult("Y",i);
>
> makeLine(x31, y31, x11, y11);
> getPixelSize(unit, pw, ph);
> dz = (x31 - x11)*pw;
> da = (y31 - y11)*ph;
> distance1 = sqrt(dz*dz + da*da);
> setResult("D1", i, distance1);
> updateResults;
>
> makeLine(x31, y31, x21, y21);
> getPixelSize(unit, pw, ph);
> dx = (x31 - x21)*pw;
> dy = (y31 - y21)*ph;
> distance2 = sqrt(dx*dx + dy*dy);
> setResult("D2", i, distance2);
> updateResults;
>
> }
>
> for (i=0; i<nResults; i++) {
>
> D1 = getResult("D1",i);
> D2 = getResult("D2",i);
> x11 = getResult("FeretX",i);
> y11 = getResult("FeretY",i);
> x21 = getResult("x21",i);
> y21 = getResult("y21",i);
>
> if (D1 > D2) {
> setResult("xh", i, x11);
> setResult("xt", i, x21);
> setResult("yh", i, y11);
> setResult("yt", i, y21);
> updateResults;setTool("arrow");
>
> } else {
>
> setResult("xh", i, x21);
> setResult("xt", i, x11);
> setResult("yh", i, y21);
> setResult("yt", i, y11);
> }
> }
>
> for (i=0; i<nResults; i++) {
> xh = getResult("xh",i);
> xt = getResult("xt",i);
> yh = getResult("yh",i);
> yt = getResult("yt",i);
> degrees = getResult("FeretAngle",i);
>
>
> if (xh > xt && yh < yt){
> angle2 = degrees + 180;
> setResult("angle360", i, angle2);
> updateResults;
> }
>
> if (xh < xt && yh > yt){
> angle2 = degrees + 0;
> setResult("angle360", i, angle2);
> updateResults;
> }
>
> if (xh > xt && yh > yt){
> angle2 = degrees + 0;
> setResult("angle360", i, angle2);
> updateResults;
> }
>
> if (xh < xt && yh < yt){
> angle2 = degrees + 180;
> setResult("angle360", i, angle2);
> }
> }
>
> run("RGB Color");
> roiManager("Show All without labels");
>
> if (heatmap == "32_Colors") {
> run("ROI Color Coder", "measurement=angle360 lut=32_Colors width=0
> opacity="+ opac +" range=Min-Max n.=5 decimal=0 ramp=[256 pixels]
> font=SansSerif font_sie=14 draw");
>
> } else {
>
> if (heatmap == "Ice") {
> run("ROI Color Coder", "measurement=angle360 lut=Ice width=0 opacity="+
> opac +" range=Min-Max n.=5 decimal=0 ramp=[256 pixels] font=SansSerif
> font_size=14 draw");
>
> } else {
>
> if (heatmap == "Spectrum") {
> run("ROI Color Coder", "measurement=angle360 lut= Spectrum width=0
> opacity="+ opac +" range=Min-Max n.=5 decimal=0 ramp=[256 pixels]
> font=SansSerif font_size=14 draw");
>
> } else {
>
> if (heatmap == "20_Colors") {
> run("ROI Color Coder", "measurement=angle360 lut=20_Colors width=0
> opacity="+ opac +" range=Min-Max n.=5 decimal=0 ramp=[256 pixels]
> font=SansSerif font_size=14 draw");
>
> }
> }
>
> run("Close All");
>
> open(path_name);
> run("RGB Color");
> run("From ROI Manager");
>
>
>
>
>
> ///////////////////
>
>
> Leonard Dobens, PhD
> Professor of Molecular Biology and Biochemistry
> SCB312
> School of Biological Sciences
> University of Missouri-Kansas City
> 5007 Rockhill Road
> Kansas City, MO 64110
> 8162356272
>
[hidden email]<mailto:
[hidden email]>
>
>
>
>
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