stitching_OPAL.groovy

/**
 * Convert TIFF fields of view to a pyramidal OME-TIFF.
 *
 */

import qupath.lib.common.GeneralTools
import qupath.lib.images.servers.ImageServerProvider
import qupath.lib.images.servers.ImageServers
import qupath.lib.images.servers.SparseImageServer
import qupath.lib.images.writers.ome.OMEPyramidWriter
import qupath.lib.regions.ImageRegion

import javax.imageio.ImageIO
import javax.imageio.plugins.tiff.BaselineTIFFTagSet
import javax.imageio.plugins.tiff.TIFFDirectory
import java.awt.image.BufferedImage

import static qupath.lib.gui.scripting.QPEx.*

boolean promptForFiles = true

File dir
List<File> files
String baseName = 'Merged image'
List<ImageRegion> image_regions = new ArrayList<>();

if (promptForFiles) {
    def qupath = getQuPath()
    files = Dialogs.promptForMultipleFiles("Choose input files", null, "TIFF files", ".tif", ".tiff")
} else {
    // Try to get the URI of the current image that is open
    def currentFile = new File(getCurrentServer().getURIs()[0])
    dir = currentFile.getParentFile()
    // This naming scheme works for me...
    String name = currentFile.getName()
    int ind = name.indexOf("_[")
    if (ind < 0)
        ind = name.toLowerCase().lastIndexOf('.tif')
    if (ind >= 0)
        baseName = currentFile.getName().substring(0, ind)
    // Get all the non-OME TIFF files in the same directory
    files = dir.listFiles().findAll {
        return it.isFile() &&
                !it.getName().endsWith('.ome.tif') &&
                (baseName == null || it.getName().startsWith(baseName))
        (it.getName().endsWith('.tiff') || it.getName().endsWith('.tif') || checkTIFF(file))
    }
}
if (!files) {
    print 'No TIFF files selected'
    return
}

File fileOutput
if (promptForFiles) {
    def qupath = getQuPath()
    fileOutput = Dialogs.promptToSaveFile("Output file", null, null, "OME-TIFF", ".ome.tif")
} else {
    // Ensure we have a unique output name
    fileOutput = new File(dir, baseName+'.ome.tif')
    int count = 1
    while (fileOutput.exists()) {
        fileOutput = new File(dir, baseName+'-'+count+'.ome.tif')
    }
}
if (fileOutput == null)
    return

// Parse image regions & create a sparse server
print 'Parsing regions from ' + files.size() + ' files...'
int[] temp = new int[500];
int cpt;
int i = 0;
def builder = new SparseImageServer.Builder()
files.forEach { f ->

    def filename = f.getName()
    int xVal = extractInt(filename).split(' ')[-2] as int 
    temp[i] = xVal;
    
    if (i>=1 && temp[i] != temp[i-1]){
        print('changing x value')
        cpt = cpt + 1
    }
       
    def region = parseRegion(f, cpt)
    i = i + 1
    
    image_regions.add(region)

    if (region == null) {
        print 'WARN: Could not parse region for ' + f
        return
    }
    def serverBuilder = ImageServerProvider.getPreferredUriImageSupport(BufferedImage.class, f.toURI().toString()).getBuilders().get(0)
    builder.jsonRegion(region, 1.0, serverBuilder)
}

print 'Building server...'
def server = builder.build()
server = ImageServers.pyramidalize(server)
print(server)

long startTime = System.currentTimeMillis()
String pathOutput = fileOutput.getAbsolutePath()
new OMEPyramidWriter.Builder(server)
    .downsamples(server.getPreferredDownsamples()) // Use pyramid levels calculated in the ImageServers.pyramidalize(server) method
    .tileSize(512)      // Requested tile size
    .channelsInterleaved()      // Because SparseImageServer returns all channels in a BufferedImage, it's more efficient to write them interleaved
    .parallelize()              // Attempt to parallelize requesting tiles (need to write sequentially)
    .losslessCompression()      // Use lossless compression (often best for fluorescence, by lossy compression may be ok for brightfield)
    .build()
    .writePyramid(pathOutput)
long endTime = System.currentTimeMillis()
print('Image written to ' + pathOutput + ' in ' + GeneralTools.formatNumber((endTime - startTime)/1000.0, 1) + ' s')
server.close()


static ImageRegion parseRegion(File file, int i, int z = 0, int t = 0) {
    if (checkTIFF(file)) {
        try {
            return parseRegionFromTIFF(file,i, z, t)
        } catch (Exception e) {
            print e.getLocalizedMessage()
        }
    }
}

/**
 * Check for TIFF 'magic number'.
 * @param file
 * @return
 */
static boolean checkTIFF(File file) {
    file.withInputStream {
        def bytes = it.readNBytes(4)
        short byteOrder = toShort(bytes[0], bytes[1])
        int val
        if (byteOrder == 0x4949) {
            // Little-endian
            val = toShort(bytes[3], bytes[2])
        } else if (byteOrder == 0x4d4d) {
            val = toShort(bytes[2], bytes[3])
        } else
            return false
        return val == 42 || val == 43
    }
}

/**
 * Combine two bytes to create a short, in the given order
 * @param b1
 * @param b2
 * @return
 */
static short toShort(byte b1, byte b2) {
    return (b1 << 8) + (b2 << 0)
}

/**
 * Parse an ImageRegion from a TIFF image, using the metadata.
 * @param file image file
 * @param z index of z plane
 * @param t index of timepoint
 * @return
 */
static ImageRegion parseRegionFromTIFF(File file, int i ,int z = 0, int t = 0) {
    int x, y, width, height, val
    String name 
    file.withInputStream {
        def reader = ImageIO.getImageReadersByFormatName("TIFF").next()
        reader.setInput(ImageIO.createImageInputStream(it))
        
        
        def metadata = reader.getImageMetadata(0)
        def tiffDir = TIFFDirectory.createFromMetadata(metadata)

        double xRes = getRational(tiffDir, BaselineTIFFTagSet.TAG_X_RESOLUTION)
        double yRes = getRational(tiffDir, BaselineTIFFTagSet.TAG_Y_RESOLUTION)
        
        //Get xPos and yPos for MIBI data
        //def stringDescription = tiffDir.getTIFFField(BaselineTIFFTagSet.TAG_IMAGE_DESCRIPTION).getAsString(0)
        //def s = stringDescription.findAll(/\[[0-9]+, [0-9]+\]/)
        //def f_0 = s[0].split(',')[0]
        //def f_1 = s[0].split(',')[1]
        //double xPos = f_0.substring(1,f_0.length()).toInteger() *0.0001
        //double yPos = f_1.substring(0,f_1.length()-1).toInteger()*0.0001
        
        //for processed data as coord saved as float
        //double xPos = Math.round(f_0.substring(1,f_0.length()).toFloat())*0.0001
        //double yPos = Math.round(f_1.substring(0,f_1.length()-1).toFloat())*0.0001
        
        double xPos = getRational(tiffDir, BaselineTIFFTagSet.TAG_X_POSITION)
        double yPos = getRational(tiffDir, BaselineTIFFTagSet.TAG_Y_POSITION)
       
        width = tiffDir.getTIFFField(BaselineTIFFTagSet.TAG_IMAGE_WIDTH).getAsLong(0) as int
        height = tiffDir.getTIFFField(BaselineTIFFTagSet.TAG_IMAGE_LENGTH).getAsLong(0) as int
        
        name = file.getName()
        //int yPos = extractInt(name).split(' ')[-1] as int 
        //int xPos = extractInt(name).split(' ')[-2] as int 
        x = Math.round(xRes * xPos) as int
        y = Math.round(yRes * yPos) as int
        
        //x_ = (x - 0.05 * x)  as int 
        //y_ = (y - 0.05 * y) as int 
      
        x = x - 2 * i
        
       // x = xRes * xPos
        //y = yRes * yPos
        
        //y = 8733
        //x = 69901
        //if (x != 12943){ //first tile on the x-axis 
        //    x = x-2
        //}
            
    }
    return ImageRegion.createInstance(x, y, width, height, z, t)
}

/**
 * Helper for parsing rational from TIFF metadata.
 * @param tiffDir
 * @param tag
 * @return
 */
static double getRational(TIFFDirectory tiffDir, int tag) {
    long[] rational = tiffDir.getTIFFField(tag).getAsRational(0);
    return rational[0] / (double)rational[1];
}

static String extractInt(String str) { 
    // Replacing every non-digit number 
    // with a space(" ") 
    str = str.replaceAll("[^\\d]", " "); 
  
    // Remove extra spaces from the beginning 
    // and the ending of the string 
    str = str.trim(); 
  
    // Replace all the consecutive white 
    // spaces with a single space 
    str = str.replaceAll(" +", " "); 
  
    if (str.equals("")) 
        return "-1"; 
  
    return str; 
}