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CompareReader.java
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CompareReader.java
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package ch.epfl.biop.formats.in;
import ij.ImageJ;
import ij.ImagePlus;
import ij.io.FileSaver;
import ij.plugin.ContrastEnhancer;
import ij.plugin.Scaler;
import ij.process.ImageProcessor;
import loci.common.DebugTools;
import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.FormatException;
import loci.formats.IFormatReader;
import loci.formats.in.DynamicMetadataOptions;
import loci.formats.in.ZeissCZIReader;
import loci.formats.ome.OMEXMLMetadata;
import loci.formats.services.OMEXMLService;
import loci.plugins.BF;
import loci.plugins.in.ImporterOptions;
import ome.units.UNITS;
import ome.units.quantity.Length;
import ome.units.quantity.Time;
import ome.xml.meta.MetadataRetrieve;
import org.apache.commons.io.FilenameUtils;
import org.openjdk.jol.info.GraphLayout;
import org.scijava.util.VersionUtils;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.lang.reflect.Method;
import java.net.URLDecoder;
import java.text.DecimalFormat;
import java.time.Duration;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
import java.util.concurrent.Callable;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.function.Consumer;
import java.util.function.Function;
/*
TODO: mention improvement on split_hcr_probes_plasmid_pos_fov_tile3_Airyscan_Processing_Stitch.czi:
the image is cropped in the original reader and has black edges
*/
public class CompareReader {
public static final Set<String> criticalMethods = new HashSet<>(Arrays.asList(
"getPixelsSizeX",
"getPixelsSizeY",
"getPixelsSizeZ",
"getPixelsSizeC",
"getPixelsSizeT",
"getImageCount",
"getChannelSamplesPerPixel"));
public static final double timeStampDifferenceAllowedInS = 0.01; // 10 ms
public static final double positionDifferenceAllowedInUM = 0.001; // 1nm
static long nanoStart;
public static void tic() {
nanoStart = System.nanoTime();
}
public static Duration toc() {
long nanoEnd = System.nanoTime();
long delta = nanoEnd-nanoStart;
return Duration.ofNanos(delta);
}
public static String formatDuration(Duration period) {
if (period.minusMillis(1).isNegative()) {
return "<1 ms";
} else {
return period.toMillis()+" ms";
}
}
static List<Boolean> skipSeriesReader1 = new ArrayList<>(),
skipSeriesReader2 = new ArrayList<>();
public static void compareFileMeta(String imagePath, boolean flattenResolutions, boolean autoStitch, Consumer<String> logger, SummaryPerFile summary) throws DependencyException, ServiceException, IOException, FormatException {
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IFormatReader reader_1 = CompareReader.builder().quickStart(true).autoStitch(autoStitch).flattenResolutions(flattenResolutions).get();
OMEXMLMetadata omeXML_1 = service.createOMEXMLMetadata();
reader_1.setMetadataStore(omeXML_1);
tic();
reader_1.setId(imagePath);
if (flattenResolutions) {
int nSeries = reader_1.getSeriesCount();
for (int s=0; s<nSeries; s++) {
reader_1.setSeries(s);
skipSeriesReader1.add(
(reader_1.getSizeX()>MAX_PIXEL_READ)||(reader_1.getSizeY()>MAX_PIXEL_READ)
);
System.out.println("R1 Series "+s+": "+skipSeriesReader1.get(s));
}
}
Duration readerIniTime1 = toc();
String quickStartInit = formatDuration(readerIniTime1);
IFormatReader reader_2 = CompareReader.builder().quickStart(false).autoStitch(autoStitch).flattenResolutions(flattenResolutions).get();
OMEXMLMetadata omeXML_2 = service.createOMEXMLMetadata();
reader_2.setMetadataStore(omeXML_2);
tic();
reader_2.setId(imagePath);
Duration readerIniTime2 = toc();
String init = formatDuration(readerIniTime2);
if (flattenResolutions) {
int nSeries = reader_2.getSeriesCount();
for (int s=0; s<nSeries; s++) {
reader_2.setSeries(s);
skipSeriesReader2.add(
(reader_2.getSizeX()>MAX_PIXEL_READ)||(reader_2.getSizeY()>MAX_PIXEL_READ)
);
System.out.println("R2 Series "+s+": "+skipSeriesReader2.get(s)+" "+reader_1.getSizeX());
}
}
logger.accept(" Method | Parameters | Quick Start Reader | Original Reader | Delta ");
logger.accept("-------------------|------------------|--------------------|-----------------|-------");
logger.accept("Initialization | |"+quickStartInit+ "|"+init+ "| ");
summary.ratioReaderInitialisationDuration = (double) (readerIniTime2.toMillis()) / (double) (readerIniTime1.toMillis());
double reader1SizeInMb = (float) GraphLayout.parseInstance(reader_1).totalSize() / (1024.0*1024.0);
double reader2SizeInMb = (float) GraphLayout.parseInstance(reader_2).totalSize() / (1024.0*1024.0);
DecimalFormat df = new DecimalFormat("0.00");
logger.accept("Reader Size (Mb) | |"+df.format(reader1SizeInMb)+ "|"+df.format(reader2SizeInMb)+ "| ");
summary.ratioMem = reader2SizeInMb / reader1SizeInMb;
compareMeta(omeXML_1, omeXML_2, logger, summary);
reader_1.close();
reader_2.close();
}
public static void compareMeta(OMEXMLMetadata meta_1, OMEXMLMetadata meta_2, Consumer<String> logger, SummaryPerFile summary) {
// Methods without arguments
boolean allEqual = true;
Map<String, Method> methods = new TreeMap<>();
for (Method method: MetadataRetrieve.class.getMethods()) {
methods.put(method.getName(), method);
}
for (Method method: methods.values()) {
Class<?>[] paramTypes = method.getParameterTypes();
if (paramTypes.length == 0) {
allEqual = allEqual && isEqualExceptionAndNullSafe(() -> method.invoke(meta_1),
() -> method.invoke(meta_2), method.getName(),"|(No args)|", logger, summary);
}
}
compareExperimenter(meta_1, meta_2, methods, logger, summary);
compareInstrument(meta_1, meta_2, methods, logger, summary);
compareImageMethods(meta_1, meta_2, methods, logger, summary);
comparePlanes(meta_1, meta_2, methods, logger, summary);
compareChannels(meta_1, meta_2, methods, logger, summary);
comparePlate(meta_1, meta_2, methods, logger, summary);
//compareModulo(meta_1, meta_2, methods, logger); Not implemented yet
}
public static void compareModulo(OMEXMLMetadata meta_1, OMEXMLMetadata meta_2, Map<String, Method> methods, Consumer<String> logger) {
// TODO
}
public static void comparePlate(OMEXMLMetadata meta_1, OMEXMLMetadata meta_2, Map<String, Method> methods, Consumer<String> logger, SummaryPerFile summary) {
String[] methods_plateIdx = new String[] {
"getPlateID",
"getPlateAnnotationRefCount",
"getPlateColumnNamingConvention",
"getPlateColumns",
"getPlateDescription",
"getPlateAcquisitionCount",
"getPlateExternalIdentifier",
"getPlateName",
"getPlateRows",
"getPlateFieldIndex",
"getPlateRowNamingConvention",
"getPlateWellOriginX",
"getPlateWellOriginY",
"getPlateStatus"
};
int nPlates = Math.max(meta_1.getPlateCount(), meta_2.getPlateCount());
// Plate
for (int iPlate = 0; iPlate<nPlates; iPlate++) {
int i = iPlate;
for (String method:methods_plateIdx) {
isEqualExceptionAndNullSafe(
() -> methods.get(method).invoke(meta_1,i),
() -> methods.get(method).invoke(meta_2,i), method,"| Plate "+i+" | ", logger, summary);
}
}
}
public static void compareInstrument(OMEXMLMetadata meta_1, OMEXMLMetadata meta_2, Map<String, Method> methods, Consumer<String> logger, SummaryPerFile summary) {
String[] methods_instrIdx = new String[] {
"getInstrumentID",
"getInstrumentAnnotationRefCount"
};
int nInstruments = Math.max(meta_1.getInstrumentCount(), meta_2.getInstrumentCount());
// Experimenter
for (int iInstrument = 0; iInstrument<nInstruments; iInstrument++) {
int i = iInstrument;
for (String method:methods_instrIdx) {
isEqualExceptionAndNullSafe(
() -> methods.get(method).invoke(meta_1,i),
() -> methods.get(method).invoke(meta_2,i), method,"| Instrument "+i+" | ", logger, summary);
}
}
}
private static void comparePlanes(OMEXMLMetadata meta_1, OMEXMLMetadata meta_2, Map<String, Method> methods, Consumer<String> logger, SummaryPerFile summary) {
// Per image
String[] methods_ImageIdx_PlaneIdx = new String[] {
"getPlaneAnnotationRefCount",
"getPlaneDeltaT",
"getPlaneExposureTime",
"getPlaneHashSHA1",
"getPlanePositionX","getPlanePositionY",
"getPlanePositionZ",
"getPlaneTheC",
"getPlaneTheT",
"getPlaneTheZ"
};
int nImages = Math.max(meta_1.getImageCount(), meta_2.getImageCount());
for (int iImage = 0; iImage<nImages; iImage++) {
int iImageFinal = iImage;
if (isEqualExceptionAndNullSafe(
() -> meta_1.getPlaneCount(iImageFinal),
() -> meta_2.getPlaneCount(iImageFinal), "Different plane count found for image "+iImageFinal, "", logger, summary)) {
for (int iPlane = 0; iPlane < meta_1.getPlaneCount(iImage); iPlane++) {
int iPlaneFinal = iPlane;
for (String method : methods_ImageIdx_PlaneIdx) {
isEqualExceptionAndNullSafe(
() -> methods.get(method).invoke(meta_1, iImageFinal, iPlaneFinal),
() -> methods.get(method).invoke(meta_2, iImageFinal, iPlaneFinal), method , "| Image " + iImageFinal + " Plane " + iPlaneFinal + " | ", logger, summary);
}
}
}
}
}
private static void compareChannels(OMEXMLMetadata meta_1, OMEXMLMetadata meta_2, Map<String, Method> methods, Consumer<String> logger, SummaryPerFile summary) {
String[] methods_ImageIdx_ChannelIdx = new String[] {
"getChannelAcquisitionMode",
"getChannelAnnotationRefCount",
"getChannelColor",
"getChannelFluor",
"getChannelExcitationWavelength",
"getChannelEmissionWavelength",
"getChannelContrastMethod",
"getChannelIlluminationType",
"getChannelFilterSetRef",
"getChannelID",
"getChannelLightSourceSettingsAttenuation",
"getChannelLightSourceSettingsID",
"getChannelLightSourceSettingsWavelength",
"getChannelName",
"getChannelNDFilter",
"getChannelPockelCellSetting",
"getChannelSamplesPerPixel"
};
int nImages = Math.max(meta_1.getImageCount(), meta_2.getImageCount());
for (int iImage = 0; iImage<nImages; iImage++) {
int iImageFinal = iImage;
if (isEqualExceptionAndNullSafe(
() -> meta_1.getChannelCount(iImageFinal),
() -> meta_2.getChannelCount(iImageFinal), "Different channel count found for image "+iImageFinal, "", logger, summary)) {
for (int iChannel = 0; iChannel < meta_1.getChannelCount(iImage); iChannel++) {
int iChannelFinal = iChannel;
for (String method : methods_ImageIdx_ChannelIdx) {
isEqualExceptionAndNullSafe(
() -> methods.get(method).invoke(meta_1, iImageFinal, iChannelFinal),
() -> methods.get(method).invoke(meta_2, iImageFinal, iChannelFinal), method, "| Image " + iImageFinal + " Channel " + iChannelFinal + " | ", logger, summary);
}
}
}
}
}
private static void compareImageMethods(OMEXMLMetadata meta_1, OMEXMLMetadata meta_2, Map<String, Method> methods, Consumer<String> logger, SummaryPerFile summary) {
String[] methods_ImageIdx = new String[] {
"getImageName",
"getImageAcquisitionDate",
"getImageAnnotationRefCount",
"getImageDescription",
"getImageExperimenterGroupRef",
"getImageExperimenterRef",
"getImageInstrumentRef",
"getImageID",
"getImageROIRefCount",
"getPlaneCount",
"getChannelCount",
"getImageROIRefCount",
"getPixelsBinDataCount",
"getMicrobeamManipulationRefCount",
"getTiffDataCount",
"getStageLabelName",
"getStageLabelX",
"getStageLabelY",
"getStageLabelZ",
"getPixelsSizeX",
"getPixelsSizeY",
"getPixelsSizeZ",
"getPixelsSizeC",
"getPixelsSizeT",
"getPixelsPhysicalSizeX",
"getPixelsPhysicalSizeY",
"getPixelsPhysicalSizeZ",
"getPixelsInterleaved",
"getPixelsDimensionOrder",
"getPixelsBigEndian",
"getPixelsID"
};
int nImages = Math.max(meta_1.getImageCount(), meta_2.getImageCount());
for (int iImage = 0; iImage < nImages; iImage++) {
int i = iImage;
for (String method : methods_ImageIdx) {
isEqualExceptionAndNullSafe(
() -> methods.get(method).invoke(meta_1, i),
() -> methods.get(method).invoke(meta_2, i), method , "| Image " + i + " | ", logger, summary);
}
}
}
public static void compareExperimenter(OMEXMLMetadata meta_1, OMEXMLMetadata meta_2, Map<String, Method> methods, Consumer<String> logger, SummaryPerFile summary) {
String[] methods_expIdx = new String[] {
"getExperimenterEmail",
"getExperimenterID",
"getExperimenterAnnotationRefCount",
"getExperimenterInstitution",
"getExperimenterFirstName",
"getExperimenterLastName",
"getExperimenterUserName",
"getExperimenterMiddleName"
};
int nExperimenters = Math.max(meta_1.getExperimenterCount(), meta_2.getExperimenterCount());
// Experimenter
for (int iExperimenter = 0; iExperimenter<nExperimenters; iExperimenter++) {
int i = iExperimenter;
for (String method:methods_expIdx) {
isEqualExceptionAndNullSafe(
() -> methods.get(method).invoke(meta_1,i),
() -> methods.get(method).invoke(meta_2,i), method,"| Experimenter "+i+" | ", logger, summary);
}
}
}
private static void registerDiff(String methodName, SummaryPerFile summary) {
if (criticalMethods.contains(methodName)) {
summary.numberOfCriticalDifferences++;
} else if (explanations.get(summary.urlImage).keySet().contains(methodName)) {
summary.numberOfDifferencesIgnored++;
explanations.get(summary.urlImage).get(methodName).forEach(ignoreRule -> {
String key = summary.imageName+".autoStitch."+summary.autoStitch;
if (!ignoreRule.occurencesPerReader.containsKey(key)) {
ignoreRule.occurencesPerReader.put(key,0);
}
ignoreRule.occurencesPerReader.put(key,ignoreRule.occurencesPerReader.get(key)+1);
});
} else {
summary.numberOfDifferences++;
}
}
private static boolean isEqualExceptionAndNullSafe(Callable<Object> o1Getter,
Callable<Object> o2Getter,
String methodName,
String arguments,
Consumer<String> logger,
SummaryPerFile summary) {
String message = methodName+arguments;
DecimalFormat df = new DecimalFormat("0.000");
Object o1 = null, o2 = null;
boolean exception_1 = false, exception_2 = false;
try {
o1 = o1Getter.call();
} catch (Exception e) {
exception_1 = true;
}
try {
o2 = o2Getter.call();
} catch (Exception e) {
exception_2 = true;
}
if (Boolean.logicalXor(exception_1, exception_2)) {
logger.accept( message + " error: "+exception_1+" | error: "+exception_2+ "|");
registerDiff(methodName, summary);
return false;
} else {
if ((o1!=null)&&(o2!=null)) {
if (!o1.equals(o2)) {
if ((o1 instanceof Length) && (o2 instanceof Length)) {
Length l1 = (Length) o1;
Length l2 = (Length) o2;
if ((l1.unit().equals(UNITS.REFERENCEFRAME)) && (l2.unit().equals(UNITS.REFERENCEFRAME))) {
boolean res = (l1.value(UNITS.REFERENCEFRAME).doubleValue()-l2.value(UNITS.REFERENCEFRAME).doubleValue())==0;
if (!res) {
logger.accept(message + o1 + "| " + o2 + "|");
registerDiff(methodName, summary);
}
return res;
} else {
if ((((Length) o1).value(UNITS.MICROMETER)!=null) && (((Length) o2).value(UNITS.MICROMETER)!=null)) {
l1.value(UNITS.MICROMETER);
l1.value(UNITS.MICROMETER).doubleValue();
l2.value(UNITS.MICROMETER);
l2.value(UNITS.MICROMETER).doubleValue();
double diff = Math.abs(l1.value(UNITS.MICROMETER).doubleValue() - l2.value(UNITS.MICROMETER).doubleValue());
if (diff < positionDifferenceAllowedInUM) {
return true;
} else {
logger.accept(message + df.format(l1.value(UNITS.MICROMETER)) + " um | " + df.format(l2.value(UNITS.MICROMETER)) + " um | " + df.format(diff) + " um");
}
} else {
logger.accept(message + o1 + "| " + o2 + "|");
registerDiff(methodName, summary);
return false;
}
}
} else if ((o1 instanceof Time) && (o2 instanceof Time)) {
Time t1 = (Time) o1;
Time t2 = (Time) o2;
double diff = Math.abs(t1.value(UNITS.SECOND).doubleValue() - t2.value(UNITS.SECOND).doubleValue());
//System.out.println( message +"t diff = "+diff+ "\t 1: \t "+o1+"\t 2: \t "+o2);
if (diff<timeStampDifferenceAllowedInS) {
return true; // below 1 ms = equality, yep that's right.
} else {
logger.accept( message +" "+df.format(t1.value(UNITS.SECOND))+" s | "+df.format(t2.value(UNITS.SECOND))+" s | "+df.format(diff)+" s");
}
} else {
logger.accept(message + o1 + "| " + o2 + "|");
}
registerDiff(methodName, summary);
return false;
} else {
return true;
}
} else {
if ((o1==null)&&(o2==null)) {
return true;
} else {
logger.accept( message + " 1: "+(o1==null?"null":o1)+"| 2: "+(o2==null?"null":o2));
registerDiff(methodName, summary);
return false;
}
}
}
}
static final int MAX_LINES = 500;
static final int MAX_SERIES = 5000;
static final int MAX_PIXEL_READ = 10_000;
static final double THUMB_SIZE = 150;
static int ruleNumber = 0;
public static int getNumberOfDifferentPixels(ImagePlus imp1, ImagePlus imp2) {
ImageProcessor ip1 = imp1.getProcessor();
ImageProcessor ip2 = imp2.getProcessor();
int width = Math.min(ip1.getWidth(), ip2.getWidth());
int height = Math.min(ip1.getHeight(), ip2.getHeight());
int differences = 0;
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
int pixelValue1 = ip1.getPixel(x, y);
int pixelValue2 = ip2.getPixel(x, y);
if (pixelValue1 != pixelValue2) {
differences++;
}
}
}
//System.out.println("Number of different pixels: " + differences);
return differences;
}
public static void makeReport(String imageFolderPath, String imageName, boolean autoStitch, boolean flattenRes,
String originalURL, SummaryPerFile summary) {
summary.imageName = imageName;
summary.urlImage = originalURL;
summary.flattenRes = flattenRes;
summary.autoStitch = autoStitch;
String imagePath = imageFolderPath + imageName;
String imageNameNoExt = FilenameUtils.removeExtension(imageName);
//ZeissQuickStartCZIReader.allowAutoStitch = autoStitch;
ij.Prefs.set("bioformats.zeissczi.allow.autostitch", autoStitch);
String reportFolderPath = "compare"+File.separator;
String reportImagePath = "compare"+File.separator+imageNameNoExt+File.separator;
String reportFilePath = reportFolderPath+imageNameNoExt+".flat_"+flattenRes+".stitch_"+autoStitch+".md";
summary.urlFullReport = "compare/"+imageNameNoExt+".flat_"+flattenRes+".stitch_"+autoStitch+".md";
if (!new File(reportFolderPath).exists()) {
if (!new File(reportFolderPath).mkdirs()) {
System.err.println("Couldn't create folder "+reportFolderPath+", exiting");
return;
}
}
if (!new File(reportImagePath).exists()) {
if (!new File(reportImagePath).mkdirs()) {
System.err.println("Couldn't create folder "+reportImagePath+", exiting");
return;
}
}
try (BufferedWriter bw = new BufferedWriter(new FileWriter(reportFilePath))) {
Consumer<String> logTo = (str) ->
{
try {
bw.write(str+"\n");
} catch (IOException e) {
throw new RuntimeException(e);
}
};
// Build the rest of the comparison
AtomicInteger counter = new AtomicInteger();
counter.set(0);
compareFileMeta(imagePath, flattenRes, autoStitch, (str) -> {
int count = counter.incrementAndGet();
if (count<MAX_LINES) {
logTo.accept("| " + str + " |");
} else if (count==MAX_LINES) {
logTo.accept("");
logTo.accept(" More than "+MAX_LINES+" differences.");
}
}, summary);
logTo.accept("# ["+imageName+"]("+originalURL+") report" );
logTo.accept(" - **Autostitch** = "+autoStitch);
logTo.accept(" - ZeissCZIReader v"+ VersionUtils.getVersion(ZeissCZIReader.class));
logTo.accept(" - ZeissQuickStartCZIReader v"+ VersionUtils.getVersion(ZeissQuickStartCZIReader.class));
logTo.accept("");
logTo.accept("# Images ");
logTo.accept("");
// Collect images
if (flattenRes) { // Skips images if flatten = false
List<String> qImages = new ArrayList<>();
List<String> qImagesSize = new ArrayList<>();
List<String> images = new ArrayList<>();
List<String> imagesSize = new ArrayList<>();
List<Integer> pixelsDiffs = new ArrayList<>();
// Importer settings
ImporterOptions options = new ImporterOptions();
options.setAutoscale(true);
options.setId(imagePath);
options.setOpenAllSeries(true);
options.setShowOMEXML(false);
options.setVirtual(true);
ImagePlus[] imps;
// Quick Start
ij.Prefs.set("bioformats.enabled.ZeissCZI", false);
ij.Prefs.set("bioformats.enabled.ZeissQuickStartCZI", true);
tic();
imps = BF.openImagePlus(options);
Duration readTimeQuickStartReader = toc();
String readTimeQuick = formatDuration(readTimeQuickStartReader);//System.out.println("init quick = "+toc());
int nSeriesQStart = imps.length;
List<ImagePlus> qthumbs = new ArrayList<>();
for (int i = 0; i < nSeriesQStart; i++) {
if (!skipSeriesReader1.get(i)) {
ImagePlus temp = new ImagePlus("", imps[i].getProcessor());
temp.setLut(imps[i].getLuts()[0]);
//temp.show();
double scaleFactor = temp.getWidth() > temp.getWidth() ? THUMB_SIZE / (double) temp.getWidth() : THUMB_SIZE / (double) temp.getHeight();
ImagePlus thumb = Scaler.resize(temp, (int) (temp.getWidth() * scaleFactor), (int) (temp.getHeight() * scaleFactor), 1, "");
thumb.setTitle(imps[i].getTitle());
new ContrastEnhancer().equalize(thumb);
qImages.add(imageNameNoExt + ".quick_true.flat_" + flattenRes + ".stitch_" + autoStitch + ".series_" + i + ".jpg");
new FileSaver(thumb).saveAsJpeg(reportImagePath + qImages.get(qImages.size() - 1));
qthumbs.add(thumb);
qImagesSize.add("X:" + imps[i].getWidth() + "<br>" +
"Y:" + imps[i].getHeight() + "<br>" +
"C:" + imps[i].getNChannels() + "<br>" +
"Z:" + imps[i].getNSlices() + "<br>" +
"T:" + imps[i].getNFrames()
);
temp.close();
//thumb.close();
imps[i].close();
}
}
// Default reader
ij.Prefs.set("bioformats.enabled.ZeissCZI", true);
ij.Prefs.set("bioformats.enabled.ZeissQuickStartCZI", false);
tic();
imps = BF.openImagePlus(options);
Duration readTimeReader = toc();
String readTime = formatDuration(readTimeReader);//System.out.println("init quick = "+toc());
int nSeries = imps.length;
List<ImagePlus> thumbs = new ArrayList<>();
for (int i = 0; i < nSeries; i++) {
if (!skipSeriesReader2.get(i)) {
ImagePlus temp = new ImagePlus("", imps[i].getProcessor());
temp.setLut(imps[i].getLuts()[0]);
//temp.show();
double scaleFactor = temp.getWidth() > temp.getWidth() ? THUMB_SIZE / (double) temp.getWidth() : THUMB_SIZE / (double) temp.getHeight();
ImagePlus thumb = Scaler.resize(temp, (int) (temp.getWidth() * scaleFactor), (int) (temp.getHeight() * scaleFactor), 1, "");
thumb.setTitle(imps[i].getTitle());
new ContrastEnhancer().equalize(thumb);
images.add(imageNameNoExt + ".quick_false.flat_" + flattenRes + ".stitch_" + autoStitch + ".series_" + i + ".jpg");
new FileSaver(thumb).saveAsJpeg(reportImagePath + images.get(images.size() - 1));
thumbs.add(thumb);
imagesSize.add("X:" + imps[i].getWidth() + "<br>" +
"Y:" + imps[i].getHeight() + "<br>" +
"C:" + imps[i].getNChannels() + "<br>" +
"Z:" + imps[i].getNSlices() + "<br>" +
"T:" + imps[i].getNFrames()
);
temp.close();
//thumb.close();
imps[i].close();
if (i < qthumbs.size()) {
// let's compute the diff
ImagePlus qthumb = qthumbs.get(i);
int numberOfDiffs = getNumberOfDifferentPixels(qthumb, thumb);
pixelsDiffs.add(numberOfDiffs);
summary.numberOfDiffsPixels += numberOfDiffs;
}
}
}
for (ImagePlus image :thumbs) {
image.close();
}
for (ImagePlus image :qthumbs) {
image.close();
}
logTo.accept("| Series | Quick Start Reader | Size | Original Reader | Size | #Diffs |");
logTo.accept("|-------------------|--------------------|------|-----------------|------|--------|");
logTo.accept("| Read time (all) |"+readTimeQuick+ "|------|"+readTime +"|------|--------|");
summary.ratioFirstPlaneReadingTime = (double) (readTimeReader.toMillis()) / (double) (readTimeQuickStartReader.toMillis());
int nImages = Math.max(qImages.size(), images.size());
for (int i = 0; i<nImages; i++) {
String imgQ;
if (i<qImages.size()) {
imgQ = "!["+qImages.get(i)+"]("+imageNameNoExt+"/"+qImages.get(i)+")"+"|"+qImagesSize.get(i);
} else imgQ = " | ";
String img;
if (i<images.size()) {
img = "!["+images.get(i)+"]("+imageNameNoExt+"/"+images.get(i)+")"+"|"+imagesSize.get(i);
} else img = " | ";
int nDiffs = -1;
if (pixelsDiffs.size()>i) nDiffs = pixelsDiffs.get(i);
logTo.accept("|"+i+"|"+imgQ+"|"+img+"|"+nDiffs+"|");
}
}
logTo.accept("");
logTo.accept("# Metadata");
logTo.accept("");
} catch (Exception e) {
e.printStackTrace();
}
}
public static class IgnoreDiffExplanation {
public String explanation;
public Note note;
enum Note {BETTER, WORSE, SAME}
public Map<String, Integer> occurencesPerReader = new HashMap<>();
}
static List<IgnoreDiffExplanation> allExplanations = new ArrayList<>();
static Map<String, Map<String, List<IgnoreDiffExplanation>>> explanations = new HashMap<>();
public static void addIgnoreRule(
String reason, IgnoreDiffExplanation.Note note,
String[] cziURLs,
String[] methods
) {
IgnoreDiffExplanation explanation = new IgnoreDiffExplanation();
explanation.explanation = reason;
explanation.note = note;
for (String url: cziURLs) {
if (explanations.containsKey(url)) {
for (String method : methods) {
if (!explanations.get(url).containsKey(method)) {
explanations.get(url).put(method, new ArrayList<>());
}
explanations.get(url).get(method).add(explanation);
}
}
}
allExplanations.add(explanation);
}
public static void main(String... args) {
//ImageJ imageJ = new ImageJ();
//imageJ.setVisible(true);
DebugTools.setRootLevel("TRACE");
DebugTools.setRootLevel("WARN");
DebugTools.setRootLevel("OFF");
Function<String, String> decoder = (str) -> {
try {
return URLDecoder.decode(str, "UTF-8");
} catch(Exception e){
e.printStackTrace();
return str;
}
};
// These are parts from a multi-part file: they need to be downloaded, but they are not analyzed
DatasetHelper.getDataset("https://zenodo.org/record/8263451/files/Image_1_2023_08_18__14_32_31_964%281%29.czi", decoder);
DatasetHelper.getDataset("https://zenodo.org/record/8263451/files/Image_1_2023_08_18__14_32_31_964%282%29.czi", decoder);
DatasetHelper.getDataset("https://zenodo.org/record/8263451/files/Image_1_2023_08_18__14_32_31_964%283%29.czi", decoder);
DatasetHelper.getDataset("https://zenodo.org/record/8263451/files/test_gray.czi", decoder);
DatasetHelper.getDataset("https://zenodo.org/record/8263451/files/Image_1_2023_08_18__14_32_31_964.czi", decoder);
DatasetHelper.getDataset("https://zenodo.org/record/8305531/files/MouseBrain_41Slices_2x2Tiles_3Channels_2Illuminations_1Angle.czi", decoder);
String[] cziURLs ={
"https://zenodo.org/record/8263451/files/Demo%20LISH%204x8%2015pct%20647.czi",
"https://zenodo.org/record/8263451/files/test_gray.czi",
"https://zenodo.org/record/8263451/files/Image_1_2023_08_18__14_32_31_964.czi",
// "https://zenodo.org/record/7147844/files/test-fullplate.czi", // 13.7 GB test full plate -> out of memory
"https://zenodo.org/record/7129425/files/test-plate.czi", // test plate, 3.3 GB
"https://zenodo.org/record/7254229/files/P1.czi", // Cytoskeleton stack image, 125 MB
"https://zenodo.org/record/4662053/files/2021-02-25-tulip_Airyscan.czi", // Airyscan processed, 42.1 MB
"https://zenodo.org/record/4662053/files/2021-02-25-tulip_unprocessed-Airyscan.czi", // Unprocessed Airyscan 2.9Gb
"https://zenodo.org/record/6848342/files/Airyscan%20Lines%20Pattern.czi", //2 MB
"https://zenodo.org/record/6848342/files/Confocal%20Lines%20Pattern.czi", //2.2 MB
"https://zenodo.org/record/7015307/files/S%3D1_3x3_T%3D3_Z%3D4_CH%3D2.czi", // 107MB (demo camera images by Sebastien Rhode)
"https://zenodo.org/record/7015307/files/S%3D1_CH%3D2.czi", // 1.6MB
"https://zenodo.org/record/7015307/files/S%3D2_2x2_CH%3D1.czi", // 2.6MB
"https://zenodo.org/record/7015307/files/S%3D2_2x2_T%3D1_Z%3D4_CH%3D1.czi", //6.5MB
"https://zenodo.org/record/7015307/files/S%3D2_2x2_T%3D3_CH%3D1.czi", // 5.2MB
"https://zenodo.org/record/7015307/files/S%3D2_2x2_T%3D3_Z%3D4_CH%3D1.czi", // 16.8 MB
"https://zenodo.org/record/7015307/files/S%3D2_2x2_Z%3D4_CH%3D1.czi", // 6.5 MB
"https://zenodo.org/record/7015307/files/S%3D2_3x3_T%3D1_Z%3D4_CH%3D2.czi", // 72.6MB
"https://zenodo.org/record/7015307/files/S%3D2_3x3_T%3D3_CH%3D2.czi", // 55.3 MB
"https://zenodo.org/record/7015307/files/S%3D2_3x3_T%3D3_Z%3D1_CH%3D2.czi", // 54.6 MB
"https://zenodo.org/record/7015307/files/S%3D2_T%3D3_CH%3D1.czi", // 2.1 MB
"https://zenodo.org/record/7015307/files/S%3D2_T%3D3_Z%3D5_CH%3D1.czi", // 5.3 MB
"https://zenodo.org/record/7015307/files/S%3D3_1Pos_2Mosaic_T%3D2%3DZ%3D3_CH%3D2.czi", // 57.1 MB
"https://zenodo.org/record/7015307/files/S%3D3_CH%3D2.czi", // 2.1 MB
"https://zenodo.org/record/7015307/files/T%3D1_CH%3D2.czi", // 1.6 MB
"https://zenodo.org/record/7015307/files/T%3D1_Z%3D5_CH%3D1.czi", // 2.0 MB
"https://zenodo.org/record/7015307/files/T%3D2_CH%3D1.czi", // 1.6 MB
"https://zenodo.org/record/7015307/files/T%3D2_Z%3D5_CH%3D1.czi", // 2.6 MB
"https://zenodo.org/record/7015307/files/T%3D2_Z%3D5_CH%3D2.czi", // 4.0MB
"https://zenodo.org/record/7015307/files/T%3D3_CH%3D2.czi", // 2.1 MB
"https://zenodo.org/record/7015307/files/T%3D3_Z%3D5_CH%3D2.czi", // 5.3 MB
"https://zenodo.org/record/7015307/files/W96_B2%2BB4_S%3D2_T%3D1%3DZ%3D1_C%3D1_Tile%3D5x9.czi", // 31.3 MB
"https://zenodo.org/record/7015307/files/W96_B2%2BB4_S%3D2_T%3D2%3DZ%3D4_C%3D3_Tile%3D5x9.czi", // 737.7 MB
"https://zenodo.org/record/7015307/files/Z%3D5_CH%3D1.czi", // 2.0 MB
"https://zenodo.org/record/7015307/files/Z%3D5_CH%3D2.czi", // 2.6 MB
"https://zenodo.org/record/7117784/files/RBC_full_one_timepoint.czi", // 1.0 GB RBC full one timepoint
"https://zenodo.org/record/7117784/files/RBC_full_time_series.czi", // 3.1 GB RBC full time series
"https://zenodo.org/record/7117784/files/RBC_medium_LLSZ.czi", // 700 MB RBC series LLSZ
"https://zenodo.org/record/7117784/files/RBC_tiny.czi", // 48.9 MB RBC tiny
"https://zenodo.org/record/7260610/files/20221019_MixedGrain.czi", // 113 MB Mixed Grain confocal
"https://zenodo.org/record/7260610/files/20221019_MixedGrain2.czi", // 78.6 MB Mixed Grain2
"https://zenodo.org/record/5101351/files/Ph488.czi", // 43.1 MB*/
"https://zenodo.org/record/3991919/files/v.zanotelli_20190509_p165_031.czi", // 964 MB
"https://zenodo.org/record/3991919/files/v.zanotelli_20190509_p165_031_pt1.czi", // 3 MB
"https://zenodo.org/record/3991919/files/v.zanotelli_20190509_p165_031_pt2.czi", // 7.3 MB
// There are many more of the same kind that I do not use
"https://zenodo.org/record/7430767/files/10.5%20dpc%20vegfc%20gapdh%20Pecam%20wt%201.czi",
// There are many more of the same kind
"https://downloads.openmicroscopy.org/images/Zeiss-CZI/idr0011/Plate1-Blue-A_TS-Stinger/Plate1-Blue-A-12-Scene-3-P3-F2-03.czi",
// There are many more of the same kind //,
"https://zenodo.org/record/8303129/files/xt-scan-lsm980.czi",
"https://zenodo.org/record/8303129/files/xz-scan-lsm980.czi",
"https://zenodo.org/record/8303129/files/xzt-scan-lsm980.czi",
// Multi illumination, multi angle
"https://zenodo.org/record/8305531/files/MouseBrain_41Slices_1Tile_1Channel_2Illuminations_2Angles.czi",
"https://zenodo.org/record/8305531/files/MouseBrain_41Slices_1Tile_3Channel_2Illuminations_2Angles.czi",
"https://zenodo.org/record/8305531/files/MouseBrain_41Slices_2x2Tiles_3Channels_2Illuminations_1Angle.czi",
// LSM880
"https://zenodo.org/record/8321543/files/3Dexample.czi",
//
"https://zenodo.org/record/5911450/files/mf20_NF_sox9_Paroedura_PO18_2.czi",
"https://zenodo.org/record/5823010/files/2_mouse_02_01.czi",
"https://zenodo.org/record/3737795/files/qDII-CLV3-DR5-E27-LD-SAM11-T10.czi",
// "https://zenodo.org/record/7149674/files/raw_TMA_images.czi", too big
"https://zenodo.org/record/7884760/files/Skin-Positive.czi", // Takes too long
"https://zenodo.org/record/4017923/files/03_12_2020_DSGN0673_fov_11_561.czi",
"https://zenodo.org/record/8015721/files/split_hcr_probes_plasmid_pos_fov_tile3_Airyscan_Processing_Stitch.czi",
"https://zenodo.org/record/4994280/files/Nyre_5-1_Strep_100_DBE_500_mikro.czi",
"https://zenodo.org/record/3457096/files/09_10_2018_hiprfish_mix_1_fov_10_561.czi",
"https://zenodo.org/record/3457096/files/09_10_2018_hiprfish_mix_1_fov_15_405.czi",
"https://zenodo.org/record/6385351/files/Figure2_G.czi",
"https://zenodo.org/record/7240927/files/group1-08.czi",
"https://zenodo.org/record/8139356/files/CHMP2B_IF_A13410_CR-Gauss-15.czi",
"https://zenodo.org/record/7818783/files/Rat_100um_MOR1_x500_TSA.czi",
"https://zenodo.org/record/6865142/files/SIM%20Synapsed%20homologs%20of%20meiotic%20mouse%20chromosomes%20full%20FOV.czi",
//"https://zenodo.org/record/6637864/files/ferret-slices-mosaic-encoding.czi", // Too big
"https://zenodo.org/record/5172827/files/example_image_2c_1z_1t_.czi",
"https://zenodo.org/record/7994589/files/190731_EV38_1_Collagen_ITSwithAsc%2BDexa%2BIGF%2BTGF_63x_zstack_3.czi",
"https://zenodo.org/record/5068754/files/HepG2_ND100_ctrl_FASTZ.czi",
"https://zenodo.org/record/5016179/files/Fig1-source_data_1-B__Max.czi",
"https://zenodo.org/record/5016179/files/Fig1-source_data_1-B_.czi",
"https://zenodo.org/record/4627738/files/19juil05a1.czi",
"https://zenodo.org/record/6685822/files/Fig1B_left.czi",
"https://zenodo.org/record/6795923/files/0.7_L_side_LSO_b6_7_Nissl_first.czi",
"https://zenodo.org/record/4283106/files/190729S%20LP%20x63Z%20mCK13rCK17.czi",
"https://zenodo.org/record/4942564/files/NIP51_Int1570_mRNA670_%20%282%29.czi",
"https://zenodo.org/record/5908580/files/Figure2D-eGFPCdt1_2MKCl.czi",
// "https://zenodo.org/record/8015833/files/GFP_plasmid_Ecoli_plus_plaque_sample_ecoli_fov_01tile_Airyscan_Processing_stitch.czi", line too long
"https://zenodo.org/record/4243557/files/63x_tile_du145_tf_647_k27ac_488_dapi_r2.czi",
"https://zenodo.org/record/5602160/files/daf-12%20L1%201.czi",
"https://zenodo.org/record/5714530/files/dO%2030%20min%20nr%2013.czi"
};
// Local files - too big and/or private, not available on Zenodo
/* cziURLs = new String[] {
//"F:/czis/27052022_MouseE11_ToPRO_test_5x_z1.czi"
// "C:\\Users\\nicol\\Dropbox\\czis\\xt-scan-lsm980.czi",
// "C:\\Users\\nicol\\Dropbox\\czis\\xz-scan-lsm980.czi",
// "C:\\Users\\nicol\\Dropbox\\czis\\xzt-scan-lsm980.czi"
//"F:\\czis\\TL-03.czi",
// "\\\\sv-01-154\\d$\\SWAP\\Data\\2023-02-16_Marine\\2023-02-16\\New-02.czi" // never ends remotely
//"\\\\sv-01-154\\d$\\SWAP\\Data\\Marine\\2023-03-16\\Cfra_LS2-02.czi", // 27 Gb, remote
//"\\\\sv-01-154\\d$\\SWAP\\Data\\2022-11-07-Omaya\\2022-11-07\\New-04.czi" // 155 Gb, on server
//"\\\\sv-01-154\\d$\\SWAP\\Data\\NicoBIOP\\2022-06-30\\New-07.czi"
// "F:\\czis\\Tiles_small_1chanels_stitch_Zen3-8.czi"
};*/
for (String url: cziURLs) {
explanations.put(url, new HashMap<>());
}
// Set of rules explaining particular choices
addIgnoreRule("The quick reader reads the czi stage label name, instead of iterating scene indices."+
" This fits better with the original CZI file.",
IgnoreDiffExplanation.Note.BETTER,
cziURLs,
new String[]{"getStageLabelName"});
addIgnoreRule("The quick reader reads the Z location correctly, and not the original reader.",
IgnoreDiffExplanation.Note.BETTER,
new String[]{
"https://zenodo.org/record/7117784/files/RBC_full_one_timepoint.czi",
"https://zenodo.org/record/7117784/files/RBC_full_time_series.czi",
"https://zenodo.org/record/7117784/files/RBC_medium_LLSZ.czi",
"https://zenodo.org/record/7117784/files/RBC_tiny.czi",
"https://downloads.openmicroscopy.org/images/Zeiss-CZI/idr0011/Plate1-Blue-A_TS-Stinger/Plate1-Blue-A-12-Scene-3-P3-F2-03.czi"
},
new String[]{
"getPlanePositionZ",
"https://downloads.openmicroscopy.org/images/Zeiss-CZI/idr0011/Plate1-Blue-A_TS-Stinger/Plate1-Blue-A-12-Scene-3-P3-F2-03.czi"
});
addIgnoreRule("The quick reader reads correctly the physical pixel for the lower resolution levels, in contrast to the original reader, " +
" which sets the same pixel size for all resolution levels (the one of the highest resolution).",
IgnoreDiffExplanation.Note.BETTER,
new String[]{
"https://zenodo.org/record/7015307/files/S%3D2_2x2_CH%3D1.czi",
"https://zenodo.org/record/7015307/files/S%3D2_2x2_T%3D1_Z%3D4_CH%3D1.czi",
"https://zenodo.org/record/7015307/files/S%3D2_2x2_T%3D3_CH%3D1.czi", // 5.2MB
"https://zenodo.org/record/7015307/files/S%3D2_2x2_T%3D3_Z%3D4_CH%3D1.czi", // 16.8 MB
"https://zenodo.org/record/7015307/files/S%3D2_2x2_Z%3D4_CH%3D1.czi", // 6.5 MB
"https://zenodo.org/record/7015307/files/S%3D2_3x3_T%3D1_Z%3D4_CH%3D2.czi", // 72.6MB
"https://zenodo.org/record/7015307/files/S%3D2_3x3_T%3D3_CH%3D2.czi", // 55.3 MB
"https://zenodo.org/record/7015307/files/S%3D2_3x3_T%3D3_Z%3D1_CH%3D2.czi",
"https://zenodo.org/record/7015307/files/S%3D3_1Pos_2Mosaic_T%3D2%3DZ%3D3_CH%3D2.czi",
"https://zenodo.org/record/7015307/files/W96_B2%2BB4_S%3D2_T%3D1%3DZ%3D1_C%3D1_Tile%3D5x9.czi", // 31.3 MB
"https://zenodo.org/record/7015307/files/W96_B2%2BB4_S%3D2_T%3D2%3DZ%3D4_C%3D3_Tile%3D5x9.czi"
},
new String[]{
"getPixelsPhysicalSizeX",
"getPixelsPhysicalSizeY"
});
addIgnoreRule("getPlaneDeltaT returns a wrong value (timestamp from first series) for the lower resolution levels in the original reader",
IgnoreDiffExplanation.Note.BETTER,
new String[]{
"https://zenodo.org/record/7015307/files/S%3D2_2x2_CH%3D1.czi",
"https://zenodo.org/record/7015307/files/S%3D1_3x3_T%3D3_Z%3D4_CH%3D2.czi",
"https://zenodo.org/record/7015307/files/S%3D2_2x2_T%3D1_Z%3D4_CH%3D1.czi",
"https://zenodo.org/record/7015307/files/S%3D2_2x2_T%3D3_CH%3D1.czi", // 5.2MB
"https://zenodo.org/record/7015307/files/S%3D2_2x2_T%3D3_Z%3D4_CH%3D1.czi", // 16.8 MB
"https://zenodo.org/record/7015307/files/S%3D2_2x2_Z%3D4_CH%3D1.czi", // 6.5 MB
"https://zenodo.org/record/7015307/files/S%3D2_3x3_T%3D1_Z%3D4_CH%3D2.czi", // 72.6MB
"https://zenodo.org/record/7015307/files/S%3D2_3x3_T%3D3_CH%3D2.czi", // 55.3 MB
"https://zenodo.org/record/7015307/files/S%3D2_3x3_T%3D3_Z%3D1_CH%3D2.czi",
"https://zenodo.org/record/7015307/files/S%3D3_1Pos_2Mosaic_T%3D2%3DZ%3D3_CH%3D2.czi",
"https://zenodo.org/record/7015307/files/W96_B2%2BB4_S%3D2_T%3D1%3DZ%3D1_C%3D1_Tile%3D5x9.czi", // 31.3 MB
"https://zenodo.org/record/7015307/files/W96_B2%2BB4_S%3D2_T%3D2%3DZ%3D4_C%3D3_Tile%3D5x9.czi"
},
new String[]{
"getPlaneDeltaT"
});
addIgnoreRule(
"Metadata not present for modulo planes in original reader",
IgnoreDiffExplanation.Note.SAME,
new String[]{
"https://zenodo.org/record/4662053/files/2021-02-25-tulip_unprocessed-Airyscan.czi"
},
new String[]{
"getPlaneDeltaT", "getPlanePositionZ", "getPlanePositionY", "getPlanePositionX"
});
addIgnoreRule("The stage label is null in the original reader.",
IgnoreDiffExplanation.Note.BETTER,
new String[]{
"https://zenodo.org/record/8263451/files/Image_1_2023_08_18__14_32_31_964.czi",
"https://zenodo.org/record/8263451/files/Demo%20LISH%204x8%2015pct%20647.czi"
},
new String[]{
"getStageLabelZ",
});
addIgnoreRule("When the pixel size is not defined (label / overview), the stage and plane location is in reference frame in"+
" the quick reader, and in micrometer in the original reader.",
IgnoreDiffExplanation.Note.SAME,
new String[]{
"https://zenodo.org/record/3991919/files/v.zanotelli_20190509_p165_031_pt1.czi",
},
new String[]{
"getStageLabelX", "getStageLabelY",
"getPlanePositionX", "getPlanePositionY"
});
addIgnoreRule("An edge case when the pixel size in Z is not defined, so one has to add a 0 in reference frame unit"+
" and a micrometer value in the metadata. The new reader chooses to set this operation as null,"+
" while the original reader keeps the micrometer value only",
IgnoreDiffExplanation.Note.WORSE,
new String[]{
"https://zenodo.org/record/3991919/files/v.zanotelli_20190509_p165_031_pt1.czi",
},
new String[]{