overlays
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I’ve written a macro that identifies hairs in a photomicrograph, outlines them and draws colored arrows across their Feret’s width with the arrowhead pointing to the thin end of the hair and with a color assigned correlating with the Feret’s angle (calculated over 360 degrees).
I’d like to overlay these arrow on the original image. It works well with a simpler macro making all the arrows are black or all are white, but when I used the colored arrows macro, the overlay is converted to green. Any idea why? Here’s the very end of the macro (whole macro below) for (i=0; i<nResults; i++) { r = getResult("R",i); g = getResult("G",i); b = getResult("B",i); xh = getResult("xh",i); xt = getResult("xt",i); yh = getResult("yh",i); yt = getResult("yt",i); run("Draw", "slice"); setTool("arrow"); run("Color Picker..."); setForegroundColor(r, g, b); makeArrow(xt, yt, xh, yh, "notched"); Roi.setStrokeWidth(width); Overlay.addSelection(); Overlay.copy; } run("Close"); open(path_name); run("Color Picker..."); setForegroundColor(r, g, b); Overlay.paste; ///////////////////////////////////////// Here’s the whole macro var path_name = getDirectory("image")+ getInfo("image.filename"); run("Revert"); setAutoThreshold("Default"); run("Set Measurements...", "centroid center feret's redirect=None decimal=3"); run("Analyze Particles...", " show=[Overlay Outlines] display exclude clear"); run("To ROI Manager"); roiManager("Show All without labels"); title = "Untitled"; width=512; height=512; Dialog.create("Set Arrow"); Dialog.addNumber("Width:", 51); Dialog.show(); width = Dialog.getNumber(); resetThreshold(); 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"); for (i=0; i<nResults; i++) { a = getResult("angle360",i); if (0 < a && a < 60){ r = 255; g = 4.25*a; b = 0; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (61 < a && a < 120){ r = -4.25*a + 510; g = 255; b = 0; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (121 < a && a< 180){ r = 0; g = 255; b = 4.25*a - 510; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (181 < a && a < 240){ r = 0; g = -4.25*a + 1020; b = 255; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (241 < a && a < 300){ r = 4.25*a - 1020; g = 0; b = 255; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (301 < a && a < 360){ r = 255; g = 0; b = -4.25*a + 1530; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } } for (i=0; i<nResults; i++) { r = getResult("R",i); g = getResult("G",i); b = getResult("B",i); xh = getResult("xh",i); xt = getResult("xt",i); yh = getResult("yh",i); yt = getResult("yt",i); run("Draw", "slice"); setTool("arrow"); run("Color Picker..."); setForegroundColor(r, g, b); makeArrow(xt, yt, xh, yh, "notched"); Roi.setStrokeWidth(width); Overlay.addSelection(); Overlay.copy; } run("Close"); open(path_name); run("Color Picker..."); setForegroundColor(r, g, b); Overlay.paste; Len Dobens 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]> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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> On Jan 3, 2017, at 5:36 PM, Dobens, Leonard <[hidden email]> wrote: > > I’ve written a macro that identifies hairs in a photomicrograph, outlines them and draws colored arrows across their Feret’s width with the arrowhead pointing to the thin end of the hair and with a color assigned correlating with the Feret’s angle (calculated over 360 degrees). > > I’d like to overlay these arrow on the original image. It works well with a simpler macro making all the arrows are black or all are white, but when I used the colored arrows macro, the overlay is converted to green. Any idea why? It would be very helpful if you could provide a small, self-contained macro that reproduces the problem. The following macro works as expected. It requires the latest ImageJ daily build (1.51j9), which adds the Roi.setStrokeColor(r,g,b) macro function. -wayne requires("1.51j"); newImage("Untitled", "8-bit black", 720, 576, 1); makeArrow(337, 85, 205, 212, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(255, 200, 100); run("Add Selection..."); makeArrow(50, 130, 185, 213, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(255, 0, 0); run("Add Selection..."); makeArrow(201, 435, 195, 240, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(50, 100, 255); run("Add Selection..."); Overlay.copy; wait(2000); close; run("Boats (356K)"); Overlay.paste; > Here’s the very end of the macro (whole macro below) > > for (i=0; i<nResults; i++) { > r = getResult("R",i); > g = getResult("G",i); > b = getResult("B",i); > xh = getResult("xh",i); > xt = getResult("xt",i); > yh = getResult("yh",i); > yt = getResult("yt",i); > > run("Draw", "slice"); > setTool("arrow"); > run("Color Picker..."); > setForegroundColor(r, g, b); > makeArrow(xt, yt, xh, yh, "notched"); > Roi.setStrokeWidth(width); > Overlay.addSelection(); > Overlay.copy; > } > run("Close"); > open(path_name); > run("Color Picker..."); > setForegroundColor(r, g, b); > Overlay.paste; > > ///////////////////////////////////////// > > Here’s the whole macro > > var path_name = getDirectory("image")+ getInfo("image.filename"); > > run("Revert"); > > > setAutoThreshold("Default"); > run("Set Measurements...", "centroid center feret's redirect=None decimal=3"); > run("Analyze Particles...", " show=[Overlay Outlines] display exclude clear"); > run("To ROI Manager"); > roiManager("Show All without labels"); > > title = "Untitled"; > width=512; height=512; > Dialog.create("Set Arrow"); > Dialog.addNumber("Width:", 51); > Dialog.show(); > width = Dialog.getNumber(); > > resetThreshold(); > 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"); > > for (i=0; i<nResults; i++) { > a = getResult("angle360",i); > > if (0 < a && a < 60){ > r = 255; > g = 4.25*a; > b = 0; > setResult("R", i, r); > setResult("G", i, g); > setResult("B", i, b); > updateResults; > } > > if (61 < a && a < 120){ > r = -4.25*a + 510; > g = 255; > b = 0; > setResult("R", i, r); > setResult("G", i, g); > setResult("B", i, b); > updateResults; > } > if (121 < a && a< 180){ > r = 0; > g = 255; > b = 4.25*a - 510; > setResult("R", i, r); > setResult("G", i, g); > setResult("B", i, b); > updateResults; > } > if (181 < a && a < 240){ > r = 0; > g = -4.25*a + 1020; > b = 255; > setResult("R", i, r); > setResult("G", i, g); > setResult("B", i, b); > updateResults; > } > if (241 < a && a < 300){ > r = 4.25*a - 1020; > g = 0; > b = 255; > setResult("R", i, r); > setResult("G", i, g); > setResult("B", i, b); > updateResults; > } > if (301 < a && a < 360){ > r = 255; > g = 0; > b = -4.25*a + 1530; > setResult("R", i, r); > setResult("G", i, g); > setResult("B", i, b); > updateResults; > } > } > > for (i=0; i<nResults; i++) { > r = getResult("R",i); > g = getResult("G",i); > b = getResult("B",i); > xh = getResult("xh",i); > xt = getResult("xt",i); > yh = getResult("yh",i); > yt = getResult("yt",i); > > run("Draw", "slice"); > setTool("arrow"); > run("Color Picker..."); > setForegroundColor(r, g, b); > makeArrow(xt, yt, xh, yh, "notched"); > Roi.setStrokeWidth(width); > Overlay.addSelection(); > Overlay.copy; > } > run("Close"); > open(path_name); > run("Color Picker..."); > setForegroundColor(r, g, b); > Overlay.paste; > > > > Len Dobens > > > 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]> > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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A couple of problems in running your macro. The 1.51j version is not available, only 1.51i. Also when I do run your macro in “i” version, the command "Roi.setStrokeColor(255, 0, 0);” is not happy with RGB values - appears that only hex numbers are allowed (Does the “j” version permit RGB? that could address my problems).
I recognized that Roi.setStrokeColor() arrows drawn manually and colored by a hex value could be overplayed properly and I have tried to put together a hex converter for my RGB values, and while that change in the macro effectively removes the green arrows, the colors are now black with a couple of blue arrows, so my hex converter (as written) is not good. The “green arrows” that come from the macro code cited below: run("Color Picker..."); setForegroundColor(r, g, b); makeArrow(xt, yt, xh, yh, "notched"); Roi.setStrokeWidth(width); Overlay.addSelection(); Overlay.copy; may result from a "select arrow” appearance (green), that if I could “de-select” all, may reveal their underlying proper color Len On Jan 3, 2017, at 10:17 PM, Rasband, Wayne (NIH/NIMH) [E] <[hidden email]<mailto:[hidden email]>> wrote: On Jan 3, 2017, at 5:36 PM, Dobens, Leonard <[hidden email]<mailto:[hidden email]>> wrote: I’ve written a macro that identifies hairs in a photomicrograph, outlines them and draws colored arrows across their Feret’s width with the arrowhead pointing to the thin end of the hair and with a color assigned correlating with the Feret’s angle (calculated over 360 degrees). I’d like to overlay these arrow on the original image. It works well with a simpler macro making all the arrows are black or all are white, but when I used the colored arrows macro, the overlay is converted to green. Any idea why? It would be very helpful if you could provide a small, self-contained macro that reproduces the problem. The following macro works as expected. It requires the latest ImageJ daily build (1.51j9), which adds the Roi.setStrokeColor(r,g,b) macro function. -wayne requires("1.51j"); newImage("Untitled", "8-bit black", 720, 576, 1); makeArrow(337, 85, 205, 212, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(255, 200, 100); run("Add Selection..."); makeArrow(50, 130, 185, 213, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(255, 0, 0); run("Add Selection..."); makeArrow(201, 435, 195, 240, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(50, 100, 255); run("Add Selection..."); Overlay.copy; wait(2000); close; run("Boats (356K)"); Overlay.paste; Here’s the very end of the macro (whole macro below) for (i=0; i<nResults; i++) { r = getResult("R",i); g = getResult("G",i); b = getResult("B",i); xh = getResult("xh",i); xt = getResult("xt",i); yh = getResult("yh",i); yt = getResult("yt",i); run("Draw", "slice"); setTool("arrow"); run("Color Picker..."); setForegroundColor(r, g, b); makeArrow(xt, yt, xh, yh, "notched"); Roi.setStrokeWidth(width); Overlay.addSelection(); Overlay.copy; } run("Close"); open(path_name); run("Color Picker..."); setForegroundColor(r, g, b); Overlay.paste; ///////////////////////////////////////// Here’s the whole macro var path_name = getDirectory("image")+ getInfo("image.filename"); run("Revert"); setAutoThreshold("Default"); run("Set Measurements...", "centroid center feret's redirect=None decimal=3"); run("Analyze Particles...", " show=[Overlay Outlines] display exclude clear"); run("To ROI Manager"); roiManager("Show All without labels"); title = "Untitled"; width=512; height=512; Dialog.create("Set Arrow"); Dialog.addNumber("Width:", 51); Dialog.show(); width = Dialog.getNumber(); resetThreshold(); 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"); for (i=0; i<nResults; i++) { a = getResult("angle360",i); if (0 < a && a < 60){ r = 255; g = 4.25*a; b = 0; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (61 < a && a < 120){ r = -4.25*a + 510; g = 255; b = 0; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (121 < a && a< 180){ r = 0; g = 255; b = 4.25*a - 510; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (181 < a && a < 240){ r = 0; g = -4.25*a + 1020; b = 255; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (241 < a && a < 300){ r = 4.25*a - 1020; g = 0; b = 255; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (301 < a && a < 360){ r = 255; g = 0; b = -4.25*a + 1530; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } } for (i=0; i<nResults; i++) { r = getResult("R",i); g = getResult("G",i); b = getResult("B",i); xh = getResult("xh",i); xt = getResult("xt",i); yh = getResult("yh",i); yt = getResult("yt",i); run("Draw", "slice"); setTool("arrow"); run("Color Picker..."); setForegroundColor(r, g, b); makeArrow(xt, yt, xh, yh, "notched"); Roi.setStrokeWidth(width); Overlay.addSelection(); Overlay.copy; } run("Close"); open(path_name); run("Color Picker..."); setForegroundColor(r, g, b); Overlay.paste; Len Dobens 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]><mailto:[hidden email]> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html 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]> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Len,
If you do "Help->Update_ImageJ..." and from there you choose the "daily build" version you will end up with the version v1.51j9. And I tried the macro Wayne sent you on this daily build version and it is working as a charm. And the same macro is not working properly if you stay within the version 1.51i. My best regards, Philippe -----Message d'origine----- De : ImageJ Interest Group [mailto:[hidden email]] De la part de Dobens, Leonard Envoyé : jeudi 5 janvier 2017 01:33 À : [hidden email] Objet : Re: overlays A couple of problems in running your macro. The 1.51j version is not available, only 1.51i. Also when I do run your macro in “i” version, the command "Roi.setStrokeColor(255, 0, 0);” is not happy with RGB values - appears that only hex numbers are allowed (Does the “j” version permit RGB? that could address my problems). I recognized that Roi.setStrokeColor() arrows drawn manually and colored by a hex value could be overplayed properly and I have tried to put together a hex converter for my RGB values, and while that change in the macro effectively removes the green arrows, the colors are now black with a couple of blue arrows, so my hex converter (as written) is not good. The “green arrows” that come from the macro code cited below: run("Color Picker..."); setForegroundColor(r, g, b); makeArrow(xt, yt, xh, yh, "notched"); Roi.setStrokeWidth(width); Overlay.addSelection(); Overlay.copy; may result from a "select arrow” appearance (green), that if I could “de-select” all, may reveal their underlying proper color Len On Jan 3, 2017, at 10:17 PM, Rasband, Wayne (NIH/NIMH) [E] <[hidden email]<mailto:[hidden email]>> wrote: On Jan 3, 2017, at 5:36 PM, Dobens, Leonard <[hidden email]<mailto:[hidden email]>> wrote: I’ve written a macro that identifies hairs in a photomicrograph, outlines them and draws colored arrows across their Feret’s width with the arrowhead pointing to the thin end of the hair and with a color assigned correlating with the Feret’s angle (calculated over 360 degrees). I’d like to overlay these arrow on the original image. It works well with a simpler macro making all the arrows are black or all are white, but when I used the colored arrows macro, the overlay is converted to green. Any idea why? It would be very helpful if you could provide a small, self-contained macro that reproduces the problem. The following macro works as expected. It requires the latest ImageJ daily build (1.51j9), which adds the Roi.setStrokeColor(r,g,b) macro function. -wayne requires("1.51j"); newImage("Untitled", "8-bit black", 720, 576, 1); makeArrow(337, 85, 205, 212, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(255, 200, 100); run("Add Selection..."); makeArrow(50, 130, 185, 213, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(255, 0, 0); run("Add Selection..."); makeArrow(201, 435, 195, 240, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(50, 100, 255); run("Add Selection..."); Overlay.copy; wait(2000); close; run("Boats (356K)"); Overlay.paste; Here’s the very end of the macro (whole macro below) for (i=0; i<nResults; i++) { r = getResult("R",i); g = getResult("G",i); b = getResult("B",i); xh = getResult("xh",i); xt = getResult("xt",i); yh = getResult("yh",i); yt = getResult("yt",i); run("Draw", "slice"); setTool("arrow"); run("Color Picker..."); setForegroundColor(r, g, b); makeArrow(xt, yt, xh, yh, "notched"); Roi.setStrokeWidth(width); Overlay.addSelection(); Overlay.copy; } run("Close"); open(path_name); run("Color Picker..."); setForegroundColor(r, g, b); Overlay.paste; ///////////////////////////////////////// Here’s the whole macro var path_name = getDirectory("image")+ getInfo("image.filename"); run("Revert"); setAutoThreshold("Default"); run("Set Measurements...", "centroid center feret's redirect=None decimal=3"); run("Analyze Particles...", " show=[Overlay Outlines] display exclude clear"); run("To ROI Manager"); roiManager("Show All without labels"); title = "Untitled"; width=512; height=512; Dialog.create("Set Arrow"); Dialog.addNumber("Width:", 51); Dialog.show(); width = Dialog.getNumber(); resetThreshold(); 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"); for (i=0; i<nResults; i++) { a = getResult("angle360",i); if (0 < a && a < 60){ r = 255; g = 4.25*a; b = 0; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (61 < a && a < 120){ r = -4.25*a + 510; g = 255; b = 0; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (121 < a && a< 180){ r = 0; g = 255; b = 4.25*a - 510; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (181 < a && a < 240){ r = 0; g = -4.25*a + 1020; b = 255; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (241 < a && a < 300){ r = 4.25*a - 1020; g = 0; b = 255; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (301 < a && a < 360){ r = 255; g = 0; b = -4.25*a + 1530; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } } for (i=0; i<nResults; i++) { r = getResult("R",i); g = getResult("G",i); b = getResult("B",i); xh = getResult("xh",i); xt = getResult("xt",i); yh = getResult("yh",i); yt = getResult("yt",i); run("Draw", "slice"); setTool("arrow"); run("Color Picker..."); setForegroundColor(r, g, b); makeArrow(xt, yt, xh, yh, "notched"); Roi.setStrokeWidth(width); Overlay.addSelection(); Overlay.copy; } run("Close"); open(path_name); run("Color Picker..."); setForegroundColor(r, g, b); Overlay.paste; Len Dobens 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]><mailto:[hidden email]> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html 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]> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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That did the trick and my own macro magically starts working perfectly as well. Thanks so much everybody!
Len Dobens On Jan 5, 2017, at 3:22 AM, Philippe CARL <[hidden email]<mailto:[hidden email]>> wrote: Dear Len, If you do "Help->Update_ImageJ..." and from there you choose the "daily build" version you will end up with the version v1.51j9. And I tried the macro Wayne sent you on this daily build version and it is working as a charm. And the same macro is not working properly if you stay within the version 1.51i. My best regards, Philippe -----Message d'origine----- De : ImageJ Interest Group [mailto:[hidden email]] De la part de Dobens, Leonard Envoyé : jeudi 5 janvier 2017 01:33 À : [hidden email]<mailto:[hidden email]> Objet : Re: overlays A couple of problems in running your macro. The 1.51j version is not available, only 1.51i. Also when I do run your macro in “i” version, the command "Roi.setStrokeColor(255, 0, 0);” is not happy with RGB values - appears that only hex numbers are allowed (Does the “j” version permit RGB? that could address my problems). I recognized that Roi.setStrokeColor() arrows drawn manually and colored by a hex value could be overplayed properly and I have tried to put together a hex converter for my RGB values, and while that change in the macro effectively removes the green arrows, the colors are now black with a couple of blue arrows, so my hex converter (as written) is not good. The “green arrows” that come from the macro code cited below: run("Color Picker..."); setForegroundColor(r, g, b); makeArrow(xt, yt, xh, yh, "notched"); Roi.setStrokeWidth(width); Overlay.addSelection(); Overlay.copy; may result from a "select arrow” appearance (green), that if I could “de-select” all, may reveal their underlying proper color Len On Jan 3, 2017, at 10:17 PM, Rasband, Wayne (NIH/NIMH) [E] <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote: On Jan 3, 2017, at 5:36 PM, Dobens, Leonard <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote: I’ve written a macro that identifies hairs in a photomicrograph, outlines them and draws colored arrows across their Feret’s width with the arrowhead pointing to the thin end of the hair and with a color assigned correlating with the Feret’s angle (calculated over 360 degrees). I’d like to overlay these arrow on the original image. It works well with a simpler macro making all the arrows are black or all are white, but when I used the colored arrows macro, the overlay is converted to green. Any idea why? It would be very helpful if you could provide a small, self-contained macro that reproduces the problem. The following macro works as expected. It requires the latest ImageJ daily build (1.51j9), which adds the Roi.setStrokeColor(r,g,b) macro function. -wayne requires("1.51j"); newImage("Untitled", "8-bit black", 720, 576, 1); makeArrow(337, 85, 205, 212, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(255, 200, 100); run("Add Selection..."); makeArrow(50, 130, 185, 213, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(255, 0, 0); run("Add Selection..."); makeArrow(201, 435, 195, 240, "notched large"); Roi.setStrokeWidth(3); Roi.setStrokeColor(50, 100, 255); run("Add Selection..."); Overlay.copy; wait(2000); close; run("Boats (356K)"); Overlay.paste; Here’s the very end of the macro (whole macro below) for (i=0; i<nResults; i++) { r = getResult("R",i); g = getResult("G",i); b = getResult("B",i); xh = getResult("xh",i); xt = getResult("xt",i); yh = getResult("yh",i); yt = getResult("yt",i); run("Draw", "slice"); setTool("arrow"); run("Color Picker..."); setForegroundColor(r, g, b); makeArrow(xt, yt, xh, yh, "notched"); Roi.setStrokeWidth(width); Overlay.addSelection(); Overlay.copy; } run("Close"); open(path_name); run("Color Picker..."); setForegroundColor(r, g, b); Overlay.paste; ///////////////////////////////////////// Here’s the whole macro var path_name = getDirectory("image")+ getInfo("image.filename"); run("Revert"); setAutoThreshold("Default"); run("Set Measurements...", "centroid center feret's redirect=None decimal=3"); run("Analyze Particles...", " show=[Overlay Outlines] display exclude clear"); run("To ROI Manager"); roiManager("Show All without labels"); title = "Untitled"; width=512; height=512; Dialog.create("Set Arrow"); Dialog.addNumber("Width:", 51); Dialog.show(); width = Dialog.getNumber(); resetThreshold(); 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"); for (i=0; i<nResults; i++) { a = getResult("angle360",i); if (0 < a && a < 60){ r = 255; g = 4.25*a; b = 0; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (61 < a && a < 120){ r = -4.25*a + 510; g = 255; b = 0; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (121 < a && a< 180){ r = 0; g = 255; b = 4.25*a - 510; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (181 < a && a < 240){ r = 0; g = -4.25*a + 1020; b = 255; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (241 < a && a < 300){ r = 4.25*a - 1020; g = 0; b = 255; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } if (301 < a && a < 360){ r = 255; g = 0; b = -4.25*a + 1530; setResult("R", i, r); setResult("G", i, g); setResult("B", i, b); updateResults; } } for (i=0; i<nResults; i++) { r = getResult("R",i); g = getResult("G",i); b = getResult("B",i); xh = getResult("xh",i); xt = getResult("xt",i); yh = getResult("yh",i); yt = getResult("yt",i); run("Draw", "slice"); setTool("arrow"); run("Color Picker..."); setForegroundColor(r, g, b); makeArrow(xt, yt, xh, yh, "notched"); Roi.setStrokeWidth(width); Overlay.addSelection(); Overlay.copy; } run("Close"); open(path_name); run("Color Picker..."); setForegroundColor(r, g, b); Overlay.paste; Len Dobens 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]><mailto:[hidden email]><mailto:[hidden email]> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html 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]><mailto:[hidden email]> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html 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]> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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