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Fix reader
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@cjfuller
cjfuller committed Mar 3, 2024
1 parent 27cebbb commit afab732
Showing 1 changed file with 79 additions and 78 deletions.
157 changes: 79 additions & 78 deletions src/main/kotlin/edu/stanford/cfuller/imageanalysistools/image/io/ImageReader.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -3,91 +3,82 @@ package edu.stanford.cfuller.imageanalysistools.image.io
import edu.stanford.cfuller.imageanalysistools.frontend.LoggingUtilities
import edu.stanford.cfuller.imageanalysistools.image.Image
import edu.stanford.cfuller.imageanalysistools.image.ImageFactory
import edu.stanford.cfuller.imageanalysistools.image.ImageCoordinate

import edu.stanford.cfuller.imageanalysistools.image.PixelDataFactory
import edu.stanford.cfuller.imageanalysistools.image.PixelData


import java.util.Hashtable

/**
* This class reads an Image from a file on disk.
*
* Uses the LOCI bio-formats library to do the reading (http://www.loci.wisc.edu/software/bio-formats), so
* all formats supported by that library are supported in this reader.
* Uses the LOCI bio-formats library to do the reading
* (http://www.loci.wisc.edu/software/bio-formats), so all formats supported by that library are
* supported in this reader.
*
* For image formats that support multiple series per file (that is, multiple (X,Y,Z,C,T) 5D images per file), the reader
* will return only a single series at a time, keeps track of what series it has last read, and will return the subsequent series
* on subsequent calls to the read method.
* For image formats that support multiple series per file (that is, multiple (X,Y,Z,C,T) 5D images
* per file), the reader will return only a single series at a time, keeps track of what series it
* has last read, and will return the subsequent series on subsequent calls to the read method.
* @author Colin J. Fuller
*/


open class ImageReader {
protected var lociReader: loci.formats.ImageReader = loci.formats.ImageReader()
protected var lociReader: loci.formats.IFormatReader? = null
protected var seriesCounts: java.util.HashMap<String, Int> = java.util.HashMap<String, Int>()
protected var currentSeries: java.util.HashMap<String, Int> = java.util.HashMap<String, Int>()

/**
* Checks if the file specified in the supplied filename has more 5D image series that have not yet been read by this reader.
* @param filename The full absolute filename of the image file to check.
* @return true if there are more series that have not yet been read; false otherwise
* Checks if the file specified in the supplied filename has more 5D image series that have not
* yet been read by this reader.
* @param filename The full absolute filename of the image file to check.
* @return true if there are more series that have not yet been read; false otherwise
*/
fun hasMoreSeries(filename: String): Boolean {
if (!currentSeries.containsKey(filename)) return true
return currentSeries[filename]!! < seriesCounts[filename]!!
}

/**
* Gets the number of 5D image series in the file specified in the supplied filename.
* This can only be called after the read method has been called on this filename at least once; otherwise it
* will cause an exception.
* @param filename The full absolute filename of the image file to check.
* @return The number of 5D image series in the specified file.
* Gets the number of 5D image series in the file specified in the supplied filename. This can
* only be called after the read method has been called on this filename at least once;
* otherwise it will cause an exception.
* @param filename The full absolute filename of the image file to check.
* @return The number of 5D image series in the specified file.
*/
fun getSeriesCount(filename: String): Int {
return seriesCounts[filename] ?: throw IllegalArgumentException("Must call .read() on the same filename first.")
return seriesCounts[filename]
?: throw IllegalArgumentException("Must call .read() on the same filename first.")
}


/**
* Gets the index (starting at zero) of the next 5D image series that would be read by a call to the read method.
* This method can only be called after the read method has been called on this filename at least once; otherwise it
* will cause an exception.
* Gets the index (starting at zero) of the next 5D image series that would be read by a call to
* the read method. This method can only be called after the read method has been called on this
* filename at least once; otherwise it will cause an exception.
*
* Note that the value returned by this method will always be between 1 and the result of getSeriesCount(filename), inclusive.
* Since the read method must have been called once before calling this method, the 0th series will always have been read already,
* so at minimum the next series will be the first series. If there are no more series remaining in the file, the next that
* would be read would be one more than the maximal series index (which is getSeriesCount(filename) - 1).
* @param filename The full absolute filename of the image file to check.
* @return The series that will be the next to be read by this reader.
* Note that the value returned by this method will always be between 1 and the result of
* getSeriesCount(filename), inclusive. Since the read method must have been called once before
* calling this method, the 0th series will always have been read already, so at minimum the
* next series will be the first series. If there are no more series remaining in the file, the
* next that would be read would be one more than the maximal series index (which is
* getSeriesCount(filename) - 1).
* @param filename The full absolute filename of the image file to check.
* @return The series that will be the next to be read by this reader.
*/
fun getCurrentSeries(filename: String): Int {
return currentSeries[filename] ?: throw IllegalArgumentException("Must call .read() on the same filename first.")
return currentSeries[filename]
?: throw IllegalArgumentException("Must call .read() on the same filename first.")
}

/**
* Reads an image file from disk to an Image.
* @param filename The full absolute filename of the image file to read.
* @return An Image containing the pixel data and (if supported by the format) metadata from the image file.
* @throws java.io.IOException if there is an error reading the Image file from disk.
* @param filename The full absolute filename of the image file to read.
* @return An Image containing the pixel data and (if supported by the format) metadata from the
* image file.
* @throws java.io.IOException if there is an error reading the Image file from disk.
*/
@Synchronized @Throws(java.io.IOException::class)
@Synchronized
@Throws(java.io.IOException::class)
open fun read(filename: String): Image? {
try {
val meta = loci.common.services.ServiceFactory().getInstance(loci.formats.services.OMEXMLService::class.java).createOMEXMLMetadata()
try {
lociReader.metadataStore = meta
} catch (e: IllegalStateException) {
lociReader.close()
lociReader.metadataStore = meta
}
} catch (e: loci.common.services.ServiceException) {
e.printStackTrace()
} catch (e: loci.common.services.DependencyException) {
e.printStackTrace()
}
val reader: loci.formats.IFormatReader =
lociReader ?: loci.formats.ImageReader().getReader(filename)

lociReader = reader

try {
lock(filename)
Expand All @@ -98,35 +89,43 @@ open class ImageReader {

try {
try {
lociReader.setId(filename)
reader.setId(filename)
} catch (e: IllegalStateException) {
lociReader.close()
lociReader.setId(filename)
reader.close()
reader.setId(filename)
}

} catch (e: loci.formats.FormatException) {
throw java.io.IOException(e)
}

loci.formats.MetadataTools.populatePixels(lociReader.metadataStore, lociReader)
val p = PixelDataFactory.createPixelData(
lociReader.sizeX, lociReader.sizeY, lociReader.sizeZ, lociReader.sizeC, lociReader.sizeT,
lociReader.pixelType, lociReader.dimensionOrder)

if (!(lociReader.metadataStore as loci.formats.meta.IMetadata).getPixelsBinDataBigEndian(0, 0)) {
loci.formats.MetadataTools.populatePixels(reader.metadataStore, lociReader, true, true)
val p =
PixelDataFactory.createPixelData(
reader.sizeX,
reader.sizeY,
reader.sizeZ,
reader.sizeC,
reader.sizeT,
reader.pixelType,
reader.dimensionOrder
)

if (!((reader.metadataStore as loci.formats.meta.IMetadata).getPixelsBinDataBigEndian(0, 0)
?: false)
) {
p.setByteOrder(java.nio.ByteOrder.LITTLE_ENDIAN)
}

try {
if (!seriesCounts.containsKey(filename) || !hasMoreSeries(filename)) {
seriesCounts.put(filename, lociReader.seriesCount)
seriesCounts.put(filename, reader.seriesCount)
currentSeries.put(filename, 0)
}
lociReader.series = currentSeries[filename]!!
reader.series = currentSeries[filename]!!

for (i in 0..lociReader.imageCount - 1) {
val currPlane = lociReader.openBytes(i)
val zct = lociReader.getZCTCoords(i)
for (i in 0..reader.imageCount - 1) {
val currPlane = reader.openBytes(i)
val zct = reader.getZCTCoords(i)
p.setPlane(zct[0], zct[1], zct[2], currPlane)
}
} catch (e: loci.formats.FormatException) {
Expand All @@ -137,17 +136,17 @@ open class ImageReader {
return null
}

val toReturn = ImageFactory.create(lociReader.metadataStore as loci.formats.meta.IMetadata, p)
lociReader.close()
val toReturn = ImageFactory.create(reader.metadataStore as loci.formats.meta.IMetadata, p)
reader.close()
currentSeries.put(filename, currentSeries[filename]!! + 1)
release(filename, Thread.currentThread())
return toReturn
}

/**
* Releases the lock on the specified file, with the specified Thread that holds the lock.
* @param filename The file to unlock.
* @param lockObject The Thread that holds the lock.
* @param filename The file to unlock.
* @param lockObject The Thread that holds the lock.
*/
protected fun release(filename: String, lockObject: Thread) {
synchronized(ImageReader::class.java) {
Expand All @@ -163,10 +162,10 @@ open class ImageReader {

/**
* Locks the file at the specified filename for reading by an ImageReader.
* @param filename The file to lock.
* @return The Thread that holds the lock. This should always be the current thread on normal return.
* @throws InterruptedException
* TODO(colin): why do we need to lock for reading?
* @param filename The file to lock.
* @return The Thread that holds the lock. This should always be the current thread on
* normal return.
* @throws InterruptedException TODO(colin): why do we need to lock for reading?
*/
@Throws(InterruptedException::class)
fun lock(filename: String): Thread {
Expand All @@ -188,11 +187,13 @@ open class ImageReader {
}

/**
* Locks the file at the specified filename for reading by a specified Thread.
* The current Thread must still be the holder of the lock, or the file must be unlocked, or this method will block.
* @param filename The file to lock.
* @param toHoldLock The Thread that should hold the lock.
* @return The Thread that holds the lock. This should always be the specified thread on normal return.
* Locks the file at the specified filename for reading by a specified Thread. The current
* Thread must still be the holder of the lock, or the file must be unlocked, or this method
* will block.
* @param filename The file to lock.
* @param toHoldLock The Thread that should hold the lock.
* @return The Thread that holds the lock. This should always be the specified thread on
* normal return.
* @throws InterruptedException
*/
@Throws(InterruptedException::class)
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