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InCellReader.java
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InCellReader.java
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/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2017 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 2 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
* #L%
*/
package loci.formats.in;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import loci.common.DataTools;
import loci.common.Location;
import loci.common.RandomAccessInputStream;
import loci.common.xml.BaseHandler;
import loci.common.xml.XMLTools;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.IMinMaxStore;
import loci.formats.meta.MetadataStore;
import ome.xml.model.enums.Binning;
import ome.xml.model.primitives.NonNegativeInteger;
import ome.xml.model.primitives.PositiveInteger;
import ome.xml.model.primitives.Timestamp;
import ome.units.quantity.Length;
import ome.units.quantity.Temperature;
import ome.units.quantity.Time;
import ome.units.UNITS;
import org.xml.sax.Attributes;
import org.xml.sax.helpers.DefaultHandler;
/**
* InCellReader is the file format reader for InCell 1000/2000 datasets.
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class InCellReader extends FormatReader {
// -- Constants --
public static final String INCELL_MAGIC_STRING = "IN Cell Analyzer";
public static final String CYTELL_MAGIC_STRING = "Cytell";
private static final String[] PIXELS_SUFFIXES =
new String[] {"tif", "tiff", "im"};
private static final String[] METADATA_SUFFIXES =
new String[] {"xml", "xlog"};
// -- Fields --
private boolean[][] plateMap;
private Image[][][][] imageFiles;
private MinimalTiffReader tiffReader;
private List<Double> emWaves, exWaves;
private List<String> channelNames;
private int totalImages;
private transient int imagesNumber;
private int imageWidth, imageHeight;
private String creationDate;
private String rowName = "A", colName = "1";
private int fieldCount;
private int wellRows, wellCols;
private Map<Integer, int[]> wellCoordinates;
private Map<Integer, Length> posX, posY;
private int offsetPointCounter;
private boolean[][] exclude;
private List<Integer> channelsPerTimepoint;
private boolean oneTimepointPerSeries;
private int totalChannels;
private List<String> metadataFiles;
private Binning bin;
private Length x, y;
private Double gain;
private Double temperature;
private Double refractive;
private List<String> exFilters = new ArrayList<String>();
private List<String> emFilters = new ArrayList<String>();
// -- Constructor --
/** Constructs a new InCell 1000/2000 reader. */
public InCellReader() {
super("InCell 1000/2000",
new String[] {"xdce", "xml", "tiff", "tif", "xlog"});
suffixSufficient = false;
domains = new String[] {FormatTools.HCS_DOMAIN};
hasCompanionFiles = true;
datasetDescription = "One .xdce file with at least one .tif/.tiff or " +
".im file";
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
if (checkSuffix(name, "xdce") || checkSuffix(name, "xml")) {
return super.isThisType(name, open);
}
return false;
}
/* @see loci.formats.IFormatReader#isSingleFile(String) */
@Override
public boolean isSingleFile(String id) throws FormatException, IOException {
return false;
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 2048;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
String check = stream.readString(blockLen);
return check.indexOf(INCELL_MAGIC_STRING) >= 0 ||
check.indexOf(CYTELL_MAGIC_STRING) >= 0;
}
/* @see loci.formats.IFormatReader#fileGroupOption(String) */
@Override
public int fileGroupOption(String id) throws FormatException, IOException {
return FormatTools.MUST_GROUP;
}
/* @see loci.formats.IFormatReader#get8BitLookupTable() */
@Override
public byte[][] get8BitLookupTable() throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);
return tiffReader == null ? null : tiffReader.get8BitLookupTable();
}
/* @see loci.formats.IFormatReader#get16BitLookupTable() */
@Override
public short[][] get16BitLookupTable() throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);
return tiffReader == null ? null : tiffReader.get16BitLookupTable();
}
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
int[] coordinates = getZCTCoords(no);
int well = getWellFromSeries(getSeries());
int field = getFieldFromSeries(getSeries());
int timepoint = oneTimepointPerSeries ?
getSeries() % channelsPerTimepoint.size() : coordinates[2];
int image = getIndex(coordinates[0], coordinates[1], 0);
if (imageFiles[well][field][timepoint][image] == null) return buf;
String filename = imageFiles[well][field][timepoint][image].filename;
if (filename == null || !(new Location(filename).exists())) return buf;
if (imageFiles[well][field][timepoint][image].isTiff) {
try {
tiffReader.setId(filename);
return tiffReader.openBytes(0, buf, x, y, w, h);
}
catch (FormatException e) {
LOGGER.debug("", e);
}
catch (IOException e) {
LOGGER.debug("", e);
}
return buf;
}
// pixels are stored in .im files
RandomAccessInputStream s = new RandomAccessInputStream(filename);
if (s.length() > FormatTools.getPlaneSize(this)) {
s.seek(128);
readPlane(s, x, y, w, h, buf);
}
s.close();
return buf;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
final List<String> files = new ArrayList<String>();
files.add(currentId);
files.addAll(metadataFiles);
if (!noPixels && imageFiles != null) {
int well = getWellFromSeries(getSeries());
int field = getFieldFromSeries(getSeries());
for (Image[] timepoints : imageFiles[well][field]) {
for (Image plane : timepoints) {
if (plane != null && plane.filename != null) {
if (new Location(plane.filename).exists()) {
files.add(plane.filename);
}
if (plane.thumbnailFile != null && new Location(plane.thumbnailFile).exists()) {
files.add(plane.thumbnailFile);
}
}
}
}
}
return files.toArray(new String[files.size()]);
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (tiffReader != null) tiffReader.close(fileOnly);
if (!fileOnly) {
imageFiles = null;
tiffReader = null;
totalImages = 0;
imagesNumber = 0;
emWaves = exWaves = null;
channelNames = null;
wellCoordinates = null;
posX = null;
posY = null;
offsetPointCounter = 0;
creationDate = null;
wellRows = wellCols = 0;
fieldCount = 0;
exclude = null;
metadataFiles = null;
imageWidth = imageHeight = 0;
rowName = "A";
colName = "1";
channelsPerTimepoint = null;
oneTimepointPerSeries = false;
totalChannels = 0;
plateMap = null;
bin = null;
x = null;
y = null;
gain = null;
temperature = null;
refractive = null;
emFilters.clear();
exFilters.clear();
}
}
/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@Override
public int getOptimalTileWidth() {
FormatTools.assertId(currentId, true, 1);
for (Image[][][] well : imageFiles) {
for (Image[][] field : well) {
for (Image[] timepoint : field) {
for (Image img : timepoint) {
if (img != null) {
if (img.isTiff && tiffReader != null) {
return tiffReader.getOptimalTileWidth();
}
break;
}
}
}
}
}
return super.getOptimalTileWidth();
}
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
@Override
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
for (Image[][][] well : imageFiles) {
for (Image[][] field : well) {
for (Image[] timepoint : field) {
for (Image img : timepoint) {
if (img != null) {
if (img.isTiff && tiffReader != null) {
return tiffReader.getOptimalTileHeight();
}
break;
}
}
}
}
}
return super.getOptimalTileHeight();
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
// make sure that we have the .xdce (or .xml) file
if (checkSuffix(id, PIXELS_SUFFIXES) || checkSuffix(id, "xlog")) {
Location currentFile = new Location(id).getAbsoluteFile();
Location parent = currentFile.getParentFile();
String[] list = parent.list(true);
for (String f : list) {
if (checkSuffix(f, new String[] {"xdce", "xml"})) {
String path = new Location(parent, f).getAbsolutePath();
if (isThisType(path)) {
// make sure that the .xdce file references the current file
// this ensures that the correct file is chosen if multiple
// .xdce files are the same directory
String data = DataTools.readFile(path);
if (data.indexOf(currentFile.getName()) >= 0) {
id = path;
break;
}
}
}
}
}
super.initFile(id);
in = new RandomAccessInputStream(id);
channelNames = new ArrayList<String>();
emWaves = new ArrayList<Double>();
exWaves = new ArrayList<Double>();
channelsPerTimepoint = new ArrayList<Integer>();
metadataFiles = new ArrayList<String>();
// parse metadata from the .xdce or .xml file
wellCoordinates = new HashMap<Integer, int[]>();
posX = new HashMap<Integer, Length>();
posY = new HashMap<Integer, Length>();
offsetPointCounter = 0;
byte[] b = new byte[(int) in.length()];
in.read(b);
CoreMetadata ms0 = core.get(0);
ms0.dimensionOrder = "XYZCT";
MetadataStore store = makeFilterMetadata();
DefaultHandler handler = new MinimalInCellHandler();
XMLTools.parseXML(b, handler);
if (getSizeZ() == 0) ms0.sizeZ = 1;
if (getSizeC() == 0) ms0.sizeC = 1;
if (getSizeT() == 0) ms0.sizeT = 1;
if (totalImages == 0) {
ms0.imageCount = getSizeC() * getSizeZ() * getSizeT();
totalImages = getImageCount() * wellRows * wellCols * fieldCount;
Location parent = new Location(currentId).getAbsoluteFile().getParentFile();
for (int row=0; row<wellRows; row++) {
for (int col=0; col<wellCols; col++) {
plateMap[row][col] = true;
for (int field=0; field<fieldCount; field++) {
for (int t=0; t<getSizeT(); t++) {
for (int image=0; image<getSizeC() * getSizeZ(); image++) {
// this could be expanded to allow for timepoint indexes
// in the file name, as well as allowing the filter names to
// be omitted
int channel = getZCTCoords(image)[1];
Image plane = new Image();
String filename = FormatTools.getWellRowName(row) + " - " +
(col + 1) + "(fld " + (field + 1) +
" wv " + exFilters.get(channel) + " - " + emFilters.get(channel) + ").tif";
Location path = new Location(parent, filename);
if (path.exists()) {
plane.filename = path.getAbsolutePath();
}
else {
LOGGER.debug("Missing file {}", filename);
}
imageFiles[row * wellCols + col][field][t][image] = plane;
}
}
}
}
}
} else if (totalImages != imagesNumber) {
LOGGER.warn("Inconsistent number of Images {}: expected {} but found {}",
id, imagesNumber, totalImages);
}
for (int t=imageFiles[0][0].length-1; t>=0; t--) {
boolean allNull = true;
for (int well=0; well<imageFiles.length; well++) {
for (int field=0; field<imageFiles[well].length; field++) {
for (int p=0; p<imageFiles[well][field][t].length; p++) {
if (imageFiles[well][field][t][p] != null) {
allNull = false;
break;
}
}
}
}
if (allNull) {
ms0.sizeT--;
}
}
int seriesCount = 0;
if (exclude != null) {
for (int row=0; row<wellRows; row++) {
for (int col=0; col<wellCols; col++) {
if (!exclude[row][col]) {
int well = row * wellCols + col;
boolean hasNonNullImage = false;
for (int field=0; field<imageFiles[well].length; field++) {
for (int t=0; t<imageFiles[well][field].length; t++) {
for (int p=0; p<imageFiles[well][field][t].length; p++) {
if (imageFiles[well][field][t][p] != null) {
hasNonNullImage = true;
break;
}
}
}
}
if (hasNonNullImage) {
seriesCount += imageFiles[well].length;
}
}
}
}
int expectedSeries = totalImages / (getSizeZ() * getSizeC() * getSizeT());
if (expectedSeries > 0) {
seriesCount = (int) Math.min(seriesCount, expectedSeries);
}
}
else seriesCount = totalImages / (getSizeZ() * getSizeC() * getSizeT());
totalChannels = getSizeC();
oneTimepointPerSeries = false;
for (int i=1; i<channelsPerTimepoint.size(); i++) {
if (!channelsPerTimepoint.get(i).equals(channelsPerTimepoint.get(i - 1)))
{
oneTimepointPerSeries = true;
break;
}
}
if (oneTimepointPerSeries) {
int imageCount = 0;
for (Integer timepoint : channelsPerTimepoint) {
imageCount += timepoint.intValue() * getSizeZ();
}
seriesCount = (totalImages / imageCount) * getSizeT();
}
int sizeT = getSizeT();
int sizeC = getSizeC();
int z = getSizeZ();
int t = oneTimepointPerSeries ? 1 : getSizeT();
core.clear();
for (int i=0; i<seriesCount; i++) {
int c = oneTimepointPerSeries ?
channelsPerTimepoint.get(i % sizeT).intValue() : sizeC;
CoreMetadata ms = new CoreMetadata();
core.add(ms);
ms.sizeZ = z;
ms.sizeC = c;
ms.sizeT = t;
ms.imageCount = z * c * t;
ms.dimensionOrder = "XYZCT";
}
int wellIndex = getWellFromSeries(0);
int fieldIndex = getFieldFromSeries(0);
String filename = imageFiles[wellIndex][fieldIndex][0][0].filename;
boolean isTiff = imageFiles[wellIndex][fieldIndex][0][0].isTiff;
if (isTiff && filename != null) {
tiffReader = new MinimalTiffReader();
tiffReader.setId(filename);
for (int i=0; i<seriesCount; i++) {
CoreMetadata ms = core.get(i);
ms.sizeX = tiffReader.getSizeX();
ms.sizeY = tiffReader.getSizeY();
ms.interleaved = tiffReader.isInterleaved();
ms.indexed = tiffReader.isIndexed();
ms.rgb = tiffReader.isRGB();
ms.pixelType = tiffReader.getPixelType();
ms.littleEndian = tiffReader.isLittleEndian();
}
}
else {
for (int i=0; i<seriesCount; i++) {
CoreMetadata ms = core.get(i);
ms.sizeX = imageWidth;
ms.sizeY = imageHeight;
ms.interleaved = false;
ms.indexed = false;
ms.rgb = false;
ms.pixelType = FormatTools.UINT16;
ms.littleEndian = true;
}
}
MetadataTools.populatePixels(store, this, true);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
handler = new InCellHandler(store);
XMLTools.parseXML(b, handler);
}
String rowNaming =
Character.isDigit(rowName.charAt(0)) ? "Number" : "Letter";
String colNaming =
Character.isDigit(colName.charAt(0)) ? "Number" : "Letter";
String plateName = currentId;
int begin = plateName.lastIndexOf(File.separator) + 1;
int end = plateName.lastIndexOf(".");
plateName = plateName.substring(begin, end);
store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
store.setPlateName(plateName, 0);
store.setPlateRowNamingConvention(MetadataTools.getNamingConvention(rowNaming), 0);
store.setPlateColumnNamingConvention(MetadataTools.getNamingConvention(colNaming), 0);
store.setPlateRows(new PositiveInteger(wellRows), 0);
store.setPlateColumns(new PositiveInteger(wellCols), 0);
String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
store.setPlateAcquisitionID(plateAcqID, 0, 0);
PositiveInteger maxFieldCount = FormatTools.getMaxFieldCount(fieldCount);
if (maxFieldCount != null) {
store.setPlateAcquisitionMaximumFieldCount(maxFieldCount, 0, 0);
}
// populate Image data
String instrumentID = MetadataTools.createLSID("Instrument", 0);
String experimentID = MetadataTools.createLSID("Experiment", 0);
store.setInstrumentID(instrumentID, 0);
store.setExperimentID(experimentID, 0);
String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
store.setObjectiveID(objectiveID, 0, 0);
String detectorID = MetadataTools.createLSID("Detector", 0, 0);
store.setDetectorID(detectorID, 0, 0);
int prevWell = -1;
for (int i=0; i<seriesCount; i++) {
store.setObjectiveSettingsID(objectiveID, i);
if (refractive != null) {
store.setObjectiveSettingsRefractiveIndex(refractive, i);
}
if (x != null) {
store.setPixelsPhysicalSizeX(x, i);
}
if (y != null) {
store.setPixelsPhysicalSizeY(y, i);
}
int well = getWellFromSeries(i);
int field = getFieldFromSeries(i);
int totalTimepoints =
oneTimepointPerSeries ? channelsPerTimepoint.size() : 1;
int timepoint = oneTimepointPerSeries ? (i % totalTimepoints) + 1 : -1;
String imageID = MetadataTools.createLSID("Image", i);
store.setImageID(imageID, i);
store.setImageInstrumentRef(instrumentID, i);
store.setImageExperimentRef(experimentID, i);
int wellRow = well / wellCols;
int wellCol = well % wellCols;
wellIndex = i / (fieldCount * totalTimepoints);
if (well != prevWell) {
String wellID = MetadataTools.createLSID("Well", 0, wellIndex);
store.setWellID(wellID, 0, wellIndex);
store.setWellRow(new NonNegativeInteger(wellRow), 0, wellIndex);
store.setWellColumn(new NonNegativeInteger(wellCol), 0, wellIndex);
prevWell = well;
}
char rowChar = rowName.charAt(rowName.length() - 1);
char colChar = colName.charAt(colName.length() - 1);
String row = rowName.substring(0, rowName.length() - 1);
String col = colName.substring(0, colName.length() - 1);
if (Character.isDigit(rowChar)) {
row += wellRow + Integer.parseInt(String.valueOf(rowChar));
}
else row += (char) (rowChar + wellRow);
if (Character.isDigit(colChar)) {
col += wellCol + Integer.parseInt(String.valueOf(colChar));
}
else col += (char) (colChar + wellCol);
String imageName = "Well " + row + "-" + col + ", Field #" + (field + 1);
if (timepoint >= 0) {
imageName += ", Timepoint #" + timepoint;
}
store.setImageName(imageName, i);
if (creationDate != null) {
store.setImageAcquisitionDate(new Timestamp(creationDate), i);
}
timepoint--;
if (timepoint < 0) timepoint = 0;
int sampleIndex = field * totalTimepoints + timepoint;
String wellSampleID =
MetadataTools.createLSID("WellSample", 0, wellIndex, sampleIndex);
store.setWellSampleID(wellSampleID, 0, wellIndex, sampleIndex);
store.setWellSampleIndex(new NonNegativeInteger(i), 0, wellIndex, sampleIndex);
store.setWellSampleImageRef(imageID, 0, wellIndex, sampleIndex);
if (posX.containsKey(field)) {
store.setWellSamplePositionX(posX.get(field), 0, wellIndex, sampleIndex);
}
if (posY.containsKey(field)) {
store.setWellSamplePositionY(posY.get(field), 0, wellIndex, sampleIndex);
}
store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, i);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
// populate PlaneTiming data
for (int i=0; i<seriesCount; i++) {
setSeries(i);
int well = getWellFromSeries(i);
int field = getFieldFromSeries(i);
int timepoint = oneTimepointPerSeries ?
i % channelsPerTimepoint.size() : 0;
Double[][] minMax = new Double[getEffectiveSizeC()][2];
for (int time=0; time<getSizeT(); time++) {
if (!oneTimepointPerSeries) timepoint = time;
int c = channelsPerTimepoint.get(timepoint).intValue();
for (int q=0; q<getSizeZ()*c; q++) {
Image img = imageFiles[well][field][timepoint][q];
if (img == null) continue;
int plane = time * getSizeZ() * c + q;
if (img.deltaT != null) {
store.setPlaneDeltaT(new Time(img.deltaT, UNITS.SECOND), i, plane);
}
if (img.exposure != null) {
store.setPlaneExposureTime(new Time(img.exposure, UNITS.SECOND), i, plane);
}
store.setPlanePositionX(posX.get(field), i, plane);
store.setPlanePositionY(posY.get(field), i, plane);
store.setPlanePositionZ(img.zPosition, i, plane);
int channel = getZCTCoords(plane)[1];
if (img.min != null && (minMax[channel][0] == null ||
img.min < minMax[channel][0]))
{
minMax[channel][0] = img.min;
}
if (img.max != null && (minMax[channel][1] == null ||
img.max > minMax[channel][1]))
{
minMax[channel][1] = img.max;
}
}
}
// populate LogicalChannel data
for (int q=0; q<getEffectiveSizeC(); q++) {
if (q < channelNames.size()) {
store.setChannelName(channelNames.get(q), i, q);
}
if (q < emWaves.size()) {
Double wave = emWaves.get(q);
Length emission = FormatTools.getEmissionWavelength(wave);
if (emission != null) {
store.setChannelEmissionWavelength(emission, i, q);
}
}
if (q < exWaves.size()) {
Double wave = exWaves.get(q);
Length excitation = FormatTools.getExcitationWavelength(wave);
if (excitation != null) {
store.setChannelExcitationWavelength(excitation, i, q);
}
}
if (detectorID != null) {
store.setDetectorSettingsID(detectorID, i, q);
if (bin != null) {
store.setDetectorSettingsBinning(bin, i, q);
}
if (gain != null) {
store.setDetectorSettingsGain(gain, i, q);
}
}
LOGGER.trace("series {} channel {}: min = {}, max = {}", i, q, minMax[q][0], minMax[q][1]);
if (store instanceof IMinMaxStore) {
IMinMaxStore minMaxStore = (IMinMaxStore) store;
minMaxStore.setChannelGlobalMinMax(q, minMax[q][0], minMax[q][1], i);
}
}
if (temperature != null) {
store.setImagingEnvironmentTemperature(
new Temperature(temperature, UNITS.CELSIUS), i);
}
}
setSeries(0);
// populate Plate data
store.setPlateWellOriginX(new Length(0.5, UNITS.MICROMETER), 0);
store.setPlateWellOriginY(new Length(0.5, UNITS.MICROMETER), 0);
}
}
// -- Helper methods --
private int getFieldFromSeries(int series) {
if (oneTimepointPerSeries) series /= channelsPerTimepoint.size();
return series % fieldCount;
}
private int getWellFromSeries(int series) {
if (oneTimepointPerSeries) series /= channelsPerTimepoint.size();
int well = series / fieldCount;
int counter = -1;
for (int row=0; row<plateMap.length; row++) {
for (int col=0; col<plateMap[row].length; col++) {
if (plateMap[row][col]) {
counter++;
}
if (counter == well) {
return row * wellCols + col;
}
}
}
return -1;
}
// -- Helper classes --
class MinimalInCellHandler extends BaseHandler {
private String currentImageFile;
private String currentThumbnail;
private int wellRow, wellCol;
private int nChannels = 0;
private boolean doT = true;
private boolean doZ = true;
private Image lastImage = null;
@Override
public void endElement(String uri, String localName, String qName) {
if (qName.equals("PlateMap")) {
int sizeT = getSizeT();
if (sizeT == 0) {
// There has been no <TimeSchedule> in the <PlateMap> defined to
// populate channelsPerTimepoint so we have to assume that there is
// only one timepoint otherwise the imageFiles array below will not
// be correctly initialized.
sizeT = 1;
}
if (channelsPerTimepoint.size() == 0) {
// There has been no <TimeSchedule> in the <PlateMap> defined to
// populate channelsPerTimepoint so we have to assume that all
// channels are being acquired.
CoreMetadata ms0 = core.get(0);
channelsPerTimepoint.add(ms0.sizeC);
}
imageFiles = new Image[wellRows * wellCols][fieldCount][sizeT][];
for (int well=0; well<wellRows*wellCols; well++) {
for (int field=0; field<fieldCount; field++) {
for (int t=0; t<sizeT; t++) {
int channels = channelsPerTimepoint.get(t).intValue();
imageFiles[well][field][t] = new Image[channels * getSizeZ()];
}
}
}
}
else if (qName.equals("TimePoint")) {
channelsPerTimepoint.add(nChannels);
nChannels = 0;
}
else if (qName.equals("Times")) {
if (channelsPerTimepoint.size() == 0) {
channelsPerTimepoint.add(getSizeC());
}
for (int i=0; i<channelsPerTimepoint.size(); i++) {
int c = channelsPerTimepoint.get(i).intValue();
if (c == 0) {
channelsPerTimepoint.set(i, getSizeC());
}
}
}
}
@Override
public void startElement(String uri, String localName, String qName,
Attributes attributes)
{
CoreMetadata ms0 = core.get(0);
if (qName.equals("Plate")) {
wellRows = Integer.parseInt(attributes.getValue("rows"));
wellCols = Integer.parseInt(attributes.getValue("columns"));
plateMap = new boolean[wellRows][wellCols];
}
else if (qName.equals("Exclude")) {
if (exclude == null) exclude = new boolean[wellRows][wellCols];
int row = Integer.parseInt(attributes.getValue("row")) - 1;
int col = Integer.parseInt(attributes.getValue("col")) - 1;
exclude[row][col] = true;
}
else if (qName.equals("Images")) {
imagesNumber = Integer.parseInt(attributes.getValue("number"));
}
else if (qName.equals("Image")) {
totalImages++;
String file = attributes.getValue("filename");
String thumb = attributes.getValue("thumbnail");
Location current = new Location(currentId).getAbsoluteFile();
Location imageFile = new Location(current.getParentFile(), file);
currentImageFile = imageFile.getAbsolutePath();
currentThumbnail =
new Location(current.getParentFile(), thumb).getAbsolutePath();
}
else if (qName.equals("Identifier")) {
int field = Integer.parseInt(attributes.getValue("field_index"));
int z = Integer.parseInt(attributes.getValue("z_index"));
int c = Integer.parseInt(attributes.getValue("wave_index"));
int t = Integer.parseInt(attributes.getValue("time_index"));
int channels = channelsPerTimepoint.get(t).intValue();
int index = FormatTools.getIndex("XYZCT", getSizeZ(),
channels, 1, getSizeZ() * channels, z, c, 0);
Image img = new Image();
img.thumbnailFile = currentThumbnail;
Location file = new Location(currentImageFile);
img.filename = file.exists() ? currentImageFile : null;
if (img.filename == null) {
LOGGER.debug("{} does not exist.", currentImageFile);
}
currentImageFile = currentImageFile.toLowerCase();
img.isTiff = currentImageFile.endsWith(".tif") ||
currentImageFile.endsWith(".tiff");
imageFiles[wellRow * wellCols + wellCol][field][t][index] = img;
lastImage = img;
}
else if (qName.equals("MinMaxMean")) {
if (lastImage != null) {
lastImage.min = DataTools.parseDouble(attributes.getValue("min"));
lastImage.max = DataTools.parseDouble(attributes.getValue("max"));
}
}
else if (qName.equals("offset_point")) {
fieldCount++;
}
else if (qName.equals("TimePoint") && doT) {
ms0.sizeT++;
}
else if (qName.equals("Wavelength")) {
String fusion = attributes.getValue("fusion_wave");
if (fusion.equals("false")) ms0.sizeC++;
String mode = attributes.getValue("imaging_mode");
if (mode != null) {
doZ = mode.equals("3-D");
}
}
else if (qName.equals("AcqWave")) {
nChannels++;
}
else if (qName.equals("ZDimensionParameters")) {
String nz = attributes.getValue("number_of_slices");
if (nz != null && doZ) {
ms0.sizeZ = Integer.parseInt(nz);
}
else ms0.sizeZ = 1;
}
else if (qName.equals("Row")) {
wellRow = Integer.parseInt(attributes.getValue("number")) - 1;
}
else if (qName.equals("Column")) {
wellCol = Integer.parseInt(attributes.getValue("number")) - 1;
plateMap[wellRow][wellCol] = true;
}
else if (qName.equals("Size")) {
imageWidth = Integer.parseInt(attributes.getValue("width"));
imageHeight = Integer.parseInt(attributes.getValue("height"));
}
else if (qName.equals("NamingRows")) {
rowName = attributes.getValue("begin");
}
else if (qName.equals("NamingColumns")) {
colName = attributes.getValue("begin");
}
else if (qName.equals("TimeSchedule")) {
doT = Boolean.parseBoolean(attributes.getValue("enabled"));
}
else if (qName.equals("ExcitationFilter")) {
exFilters.add(attributes.getValue("name"));
}
else if (qName.equals("EmissionFilter")) {
emFilters.add(attributes.getValue("name"));
}
}
}
/** SAX handler for parsing XML. */
class InCellHandler extends BaseHandler {
private String currentQName;
private boolean openImage;
private MetadataStore store;
private int nextPlate = 0;
private int currentRow = -1, currentCol = -1;
private int currentField = 0;
private int currentImage, currentPlane;
private Double timestamp, exposure;
private Length zPosition;
public InCellHandler(MetadataStore store) {
this.store = store;
}
@Override
public void characters(char[] ch, int start, int length) {
if (currentQName.equals("UserComment")) {
String value = new String(ch, start, length);
store.setImageDescription(value, 0);
}
}
@Override
public void endElement(String uri, String localName, String qName) {
if (qName.equals("Image")) {
wellCoordinates.put(currentField,
new int[] {currentRow, currentCol});
openImage = false;
int well = currentRow * wellCols + currentCol;
Image img = imageFiles[well][currentField][currentImage][currentPlane];
if (img != null) {
img.deltaT = timestamp;
img.exposure = exposure;
}
}
}
@Override
public void startElement(String uri, String localName, String qName,
Attributes attributes)
{
currentQName = qName;
for (int i=0; i<attributes.getLength(); i++) {
String key = qName + " - " + attributes.getQName(i);