petebankhead/QuPath-Merge unmixed files to pyramid.groovy

## QuPath-Merge unmixed files to pyramid.groovy

/**
 * Convert TIFF fields of view to a pyramidal OME-TIFF.
 *
 * Locations are parsed from the baseline TIFF tags, therefore these need to be set.
 *
 * One application of this script is to combine spectrally-unmixed images.
 * Be sure to read the script and see where default settings could be changed, e.g.
 *   - Prompting the user to select files (or using the one currently open the viewer)
 *   - Using lossy or lossless compression
 *
 * Note: This version has been updated for QuPath v0.5.x.
 * Check the 'Revisions' tab on GitHub to see previous versions.
 *
 * @author Pete Bankhead
 */


import qupath.fx.dialogs.FileChoosers
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'
if (promptForFiles) {
    files = FileChoosers.promptForMultipleFiles("Choose input files",
            FileChoosers.createExtensionFilter("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))
    }
}
if (!files) {
    print 'No TIFF files selected'
    return
}

File fileOutput
if (promptForFiles) {
    fileOutput = FileChoosers.promptToSaveFile("Output file", null,
            FileChoosers.createExtensionFilter("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...'
def builder = new SparseImageServer.Builder()
files.parallelStream().forEach { f ->
    def region = parseRegion(f)
    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)

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 z = 0, int t = 0) {
    if (checkTIFF(file)) {
        try {
            return parseRegionFromTIFF(file, 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 z = 0, int t = 0) {
    int x, y, width, height
    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)

        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

        x = Math.round(xRes * xPos) as int
        y = Math.round(yRes * yPos) as int
    }
    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];
}

	/**
	* Convert TIFF fields of view to a pyramidal OME-TIFF.
	*
	* Locations are parsed from the baseline TIFF tags, therefore these need to be set.
	*
	* One application of this script is to combine spectrally-unmixed images.
	* Be sure to read the script and see where default settings could be changed, e.g.
	* - Prompting the user to select files (or using the one currently open the viewer)
	* - Using lossy or lossless compression
	*
	* Note: This version has been updated for QuPath v0.5.x.
	* Check the 'Revisions' tab on GitHub to see previous versions.
	*
	* @author Pete Bankhead
	*/


	import qupath.fx.dialogs.FileChoosers
	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'
	if (promptForFiles) {
	files = FileChoosers.promptForMultipleFiles("Choose input files",
	FileChoosers.createExtensionFilter("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))
	}
	}
	if (!files) {
	print 'No TIFF files selected'
	return
	}

	File fileOutput
	if (promptForFiles) {
	fileOutput = FileChoosers.promptToSaveFile("Output file", null,
	FileChoosers.createExtensionFilter("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...'
	def builder = new SparseImageServer.Builder()
	files.parallelStream().forEach { f ->
	def region = parseRegion(f)
	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)

	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 z = 0, int t = 0) {
	if (checkTIFF(file)) {
	try {
	return parseRegionFromTIFF(file, 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 z = 0, int t = 0) {
	int x, y, width, height
	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)

	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

	x = Math.round(xRes * xPos) as int
	y = Math.round(yRes * yPos) as int
	}
	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];
	}
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