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mia-algorithms/src/main/java/io/github/mianalysis/mia/process/imagej/ImageTiler.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,196 @@ | ||
| package io.github.mianalysis.mia.process.imagej; | ||
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| import ij.IJ; | ||
| import ij.ImagePlus; | ||
| import ij.ImageStack; | ||
| import ij.gui.Roi; | ||
| import ij.plugin.CanvasResizer; | ||
| import ij.process.ImageProcessor; | ||
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| public class ImageTiler { | ||
| public interface TileAxes { | ||
| String CHANNEL = "C"; | ||
| String T = "T"; | ||
| String Z = "Z"; | ||
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| String[] ALL = new String[] { CHANNEL, T, Z }; | ||
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| } | ||
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| public static ImagePlus tile(ImagePlus inputIpl, int xNumTiles, int yNumTiles, int xOverlapPx, int yOverlapPx, | ||
| String tileAxis) { | ||
| String title = "Tiled_" + inputIpl.getTitle(); | ||
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| int coreTileWidth = (int) Math.round(Math.ceil((double) (inputIpl.getWidth()-xOverlapPx) / (double) xNumTiles)); | ||
| int tileWidth = coreTileWidth + xOverlapPx; | ||
| int coreTileHeight = (int) Math.round(Math.ceil((double) (inputIpl.getHeight()-yOverlapPx) / (double) yNumTiles)); | ||
| int tileHeight = coreTileHeight + yOverlapPx; | ||
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| int nChannels = inputIpl.getNChannels(); | ||
| int nSlices = inputIpl.getNSlices(); | ||
| int nFrames = inputIpl.getNFrames(); | ||
| int bitDepth = inputIpl.getBitDepth(); | ||
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| int c0 = 0; | ||
| int z0 = 0; | ||
| int t0 = 0; | ||
| switch (tileAxis) { | ||
| case TileAxes.CHANNEL: | ||
| c0 = inputIpl.getNChannels(); | ||
| nChannels = nChannels * xNumTiles * yNumTiles; | ||
| break; | ||
| case TileAxes.Z: | ||
| z0 = inputIpl.getNSlices(); | ||
| nSlices = nSlices * xNumTiles * yNumTiles; | ||
| break; | ||
| case TileAxes.T: | ||
| t0 = inputIpl.getNFrames(); | ||
| nFrames = nFrames * xNumTiles * yNumTiles; | ||
| break; | ||
| } | ||
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| ImagePlus outputIpl = IJ.createHyperStack(title, tileWidth, tileHeight, nChannels, nSlices, nFrames, bitDepth); | ||
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| ImageStack outputIst = outputIpl.getStack(); | ||
| int count = 0; | ||
| for (int y = 0; y < yNumTiles; y++) { | ||
| for (int x = 0; x < xNumTiles; x++) { | ||
| int x0 = x * coreTileWidth; | ||
| int y0 = y * coreTileHeight; | ||
| inputIpl.setRoi(new Roi(x0, y0, tileWidth, tileHeight)); | ||
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| ImagePlus tileIpl = inputIpl.crop("stack"); | ||
| if (tileIpl.getWidth() < tileWidth || tileIpl.getHeight() < tileHeight) | ||
| tileIpl.setStack(new CanvasResizer().expandStack(tileIpl.getStack(), tileWidth, tileHeight, 0, 0)); | ||
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| ImageStack tileIst = tileIpl.getStack(); | ||
| for (int c = 0; c < inputIpl.getNChannels(); c++) { | ||
| for (int z = 0; z < inputIpl.getNSlices(); z++) { | ||
| for (int t = 0; t < inputIpl.getNFrames(); t++) { | ||
| int tileIdx = tileIpl.getStackIndex(c + 1, z + 1, t + 1); | ||
| int outputIdx = outputIpl.getStackIndex(c + c0 * count + 1, z + z0 * count + 1, | ||
| t + t0 * count + 1); | ||
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| ImageProcessor tileIpr = tileIst.getProcessor(tileIdx); | ||
| outputIst.setProcessor(tileIpr, outputIdx); | ||
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| } | ||
| } | ||
| } | ||
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| count++; | ||
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| } | ||
| } | ||
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| return outputIpl; | ||
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| } | ||
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| public static ImagePlus stitch(ImagePlus inputIpl, int xNumTiles, int yNumTiles, int xOverlapPx, int yOverlapPx, | ||
| int outputWidth, int outputHeight, | ||
| String tileAxis) { | ||
| String title = "Stitched_" + inputIpl.getTitle(); | ||
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| int tileWidth = inputIpl.getWidth(); | ||
| int coreTileWidth = tileWidth - xOverlapPx; | ||
| int tileHeight = inputIpl.getHeight(); | ||
| int coreTileHeight = tileHeight - yOverlapPx; | ||
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| int nChannels = inputIpl.getNChannels(); | ||
| int nSlices = inputIpl.getNSlices(); | ||
| int nFrames = inputIpl.getNFrames(); | ||
| int bitDepth = inputIpl.getBitDepth(); | ||
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| int c0 = 0; | ||
| int z0 = 0; | ||
| int t0 = 0; | ||
| switch (tileAxis) { | ||
| case TileAxes.CHANNEL: | ||
| nChannels = nChannels / (xNumTiles * yNumTiles); | ||
| c0 = nChannels; | ||
| break; | ||
| case TileAxes.Z: | ||
| nSlices = nSlices / (xNumTiles * yNumTiles); | ||
| z0 = nSlices; | ||
| break; | ||
| case TileAxes.T: | ||
| nFrames = nFrames / (xNumTiles * yNumTiles); | ||
| t0 = nFrames; | ||
| break; | ||
| } | ||
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| ImagePlus outputIpl = IJ.createHyperStack(title, outputWidth, outputHeight, nChannels, nSlices, nFrames, | ||
| 32); | ||
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| // Converting to 32 bit for this operation to get better results | ||
| IJ.run(inputIpl,"32-bit",null); | ||
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| ImageStack inputIst = inputIpl.getStack(); | ||
| ImageStack outputIst = outputIpl.getStack(); | ||
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| int count = 0; | ||
| for (int y = 0; y < yNumTiles; y++) { | ||
| for (int x = 0; x < xNumTiles; x++) { | ||
| int x0 = x * coreTileWidth; | ||
| int y0 = y * coreTileHeight; | ||
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| for (int c = 0; c < nChannels; c++) { | ||
| for (int z = 0; z < nSlices; z++) { | ||
| for (int t = 0; t < nFrames; t++) { | ||
| int inputIdx = inputIpl.getStackIndex(c + c0 * count + 1, z + z0 * count + 1, | ||
| t + t0 * count + 1); | ||
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| int outputIdx = outputIpl.getStackIndex(c + 1, z + 1, t + 1); | ||
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| ImageProcessor inputIpr = inputIst.getProcessor(inputIdx); | ||
| ImageProcessor outputIpr = outputIst.getProcessor(outputIdx); | ||
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| for (int xx = 0; xx < tileWidth; xx++) { | ||
| if (xx + x0 >= outputWidth) | ||
| break; | ||
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| for (int yy = 0; yy < tileHeight; yy++) { | ||
| if (yy + y0 >= outputHeight) | ||
| break; | ||
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| float multiplier = 1; | ||
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| if (xx < xOverlapPx && x != 0) | ||
| multiplier *= (1 - (xOverlapPx - xx) / (float) xOverlapPx); | ||
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| if (xx >= coreTileWidth && x != xNumTiles - 1) | ||
| multiplier *= (tileWidth - xx) / (float) xOverlapPx; | ||
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| if (yy < yOverlapPx && y != 0) | ||
| multiplier *= (1 - (yOverlapPx - yy) / (float) yOverlapPx); | ||
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| if (yy >= coreTileHeight && y != yNumTiles - 1) | ||
| multiplier *= (tileHeight - yy) / (float) yOverlapPx; | ||
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| outputIpr.setf(xx + x0, yy + y0, outputIpr.getf(xx+x0,yy+y0) + inputIpr.getf(xx, yy) * multiplier); | ||
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| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| count++; | ||
| } | ||
| } | ||
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| switch (bitDepth) { | ||
| case 8: | ||
| inputIpl.setDisplayRange(0,255); | ||
| break; | ||
| case 16: | ||
| inputIpl.setDisplayRange(0,65535); | ||
| break; | ||
| } | ||
| IJ.run(inputIpl,"8-bit",null); | ||
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| return outputIpl; | ||
|
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| } | ||
| } |
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