(String arg)
| 19 | private int frames = 1; |
| 20 | |
| 21 | public void run(String arg) { |
| 22 | ImagePlus imp = IJ.getImage(); |
| 23 | //Check if Roi is defined |
| 24 | if (imp.getRoi() == null) { |
| 25 | IJ.error("Stack Plotter", "Line or rectangular selection required"); |
| 26 | return; |
| 27 | } |
| 28 | //Check if Image is a Stack |
| 29 | int dim = imp.getNDimensions(); |
| 30 | if (dim < 3) { |
| 31 | IJ.error("Stack Plotter","This plugin requires a stack"); |
| 32 | return; |
| 33 | } |
| 34 | //Get Stack size |
| 35 | int length = 0; |
| 36 | if (dim==3) |
| 37 | length = imp.getImageStackSize(); |
| 38 | // Plot stack over frames information, improvement will be to select the dimension to plot over |
| 39 | boolean plotFrames = true; |
| 40 | if (dim>3) { |
| 41 | channel = imp.getChannel(); |
| 42 | slice = imp.getSlice(); |
| 43 | frame = imp.getFrame(); |
| 44 | length = frames = imp.getNFrames(); |
| 45 | if (dim==4 && length==1) { |
| 46 | plotFrames = false; |
| 47 | length = imp.getNSlices(); |
| 48 | } |
| 49 | } else |
| 50 | slice = imp.getCurrentSlice(); |
| 51 | |
| 52 | //Get a profile plot for each frame in the stack |
| 53 | //Store min and max value of all Profile across the stack |
| 54 | ProfilePlot[] pPlot = new ProfilePlot[length]; |
| 55 | double ymin = 0; |
| 56 | double ymax = 0; |
| 57 | for (int i=0; i<length; i++) { |
| 58 | if (dim == 3) imp.setPosition(i+1); |
| 59 | if (dim > 3) { |
| 60 | if (plotFrames) |
| 61 | imp.setPosition(channel,slice,i+1); |
| 62 | else |
| 63 | imp.setPosition(channel,i+1,frame); |
| 64 | } |
| 65 | pPlot[i] = new ProfilePlot(imp); |
| 66 | if (pPlot[i] == null) return; |
| 67 | if (pPlot[i].getMin() < ymin) ymin = pPlot[i].getMin(); |
| 68 | if (pPlot[i].getMax() > ymax) ymax = pPlot[i].getMax(); |
| 69 | } |
| 70 | //Save current Min and Max values of profile plot |
| 71 | double pp_min = ProfilePlot.getFixedMin(); |
| 72 | double pp_max = ProfilePlot.getFixedMax(); |
| 73 | //Set same Min Max values for all plots |
| 74 | ProfilePlot.setMinAndMax(ymin,ymax); |
| 75 | |
| 76 | //Make a profile stack |
| 77 | Plot plot = pPlot[0].getPlot(); |
| 78 | Dimension size = plot.getSize(); |
nothing calls this directly
no test coverage detected