(ImagePlus imp, boolean replot)
| 262 | } |
| 263 | |
| 264 | void plotLanes(ImagePlus imp, boolean replot) { |
| 265 | int topMargin = 16; |
| 266 | int bottomMargin = 2; |
| 267 | double min = Double.MAX_VALUE; |
| 268 | double max = -Double.MAX_VALUE; |
| 269 | int plotWidth; |
| 270 | double[][] profiles; |
| 271 | profiles = new double[MAX_LANES+1][]; |
| 272 | IJ.showStatus("Plotting " + nLanes + " lanes"); |
| 273 | ImageProcessor ipRotated = imp.getProcessor(); |
| 274 | if (isVertical) |
| 275 | ipRotated = ipRotated.rotateLeft(); |
| 276 | ImagePlus imp2 = new ImagePlus("", ipRotated); |
| 277 | imp2.setCalibration(imp.getCalibration()); |
| 278 | if (uncalibratedOD && (imp2.getType()==ImagePlus.GRAY16 || imp2.getType()==ImagePlus.GRAY32)) |
| 279 | new ImageConverter(imp2).convertToGray8(); |
| 280 | if (invertPeaks) { |
| 281 | ImageProcessor ip2 = imp2.getProcessor().duplicate(); |
| 282 | ip2.invert(); |
| 283 | imp2.setProcessor(null, ip2); |
| 284 | } |
| 285 | //imp2.show(); |
| 286 | |
| 287 | for (int i=1; i<=nLanes; i++) { |
| 288 | if (isVertical) |
| 289 | imp2.setRoi(firstRect.y, |
| 290 | ipRotated.getHeight() - x[i] - firstRect.width, |
| 291 | firstRect.height, firstRect.width); |
| 292 | else |
| 293 | imp2.setRoi(firstRect.x, x[i], firstRect.width, firstRect.height); |
| 294 | ProfilePlot pp = new ProfilePlot(imp2); |
| 295 | profiles[i] = pp.getProfile(); |
| 296 | if (pp.getMin()<min) |
| 297 | min = pp.getMin(); |
| 298 | if (pp.getMax()>max) |
| 299 | max = pp.getMax(); |
| 300 | if (uncalibratedOD) |
| 301 | profiles[i] = od(profiles[i]); |
| 302 | } |
| 303 | if (uncalibratedOD) { |
| 304 | min = odMin; |
| 305 | max = odMax; |
| 306 | } |
| 307 | |
| 308 | if (isVertical) |
| 309 | plotWidth = firstRect.height; |
| 310 | else |
| 311 | plotWidth = firstRect.width; |
| 312 | if (plotWidth<650) |
| 313 | plotWidth = 650; |
| 314 | if (isVertical) { |
| 315 | if (plotWidth>4*firstRect.height) |
| 316 | plotWidth = 4*firstRect.height; |
| 317 | } else { |
| 318 | if (plotWidth>4*firstRect.width) |
| 319 | plotWidth = 4*firstRect.width; |
| 320 | } |
| 321 |
no test coverage detected