/* @see BaseTiffReader#initStandardMetadata() */ protected void initStandardMetadata() throws FormatException, IOException { super.initStandardMetadata(); delegate = new MinimalTiffReader(); delegate.setId(currentId); exposureTimes = new ArrayList<Double>(); String data = ifds.get(0).getComment(); // remove magic string data = data.substring(data.indexOf("\n") + 1); date = data.substring(0, data.indexOf("\n")); data = data.substring(data.indexOf("\n") + 1); data = data.replaceAll("ReadFromDoc", ""); IniParser parser = new IniParser(); parser.setCommentDelimiter(";"); IniList ini = parser.parseINI(new BufferedReader(new StringReader(data))); String objective = ini.getTable(" MICROSCOPE ").get("Objective"); int space = objective.indexOf(" "); if (space != -1) { magnification = new Integer(objective.substring(0, space - 1)); immersion = objective.substring(space + 1); } IniTable cameraTable = ini.getTable(" CAPTURE DEVICE "); binning = cameraTable.get("Binning") + "x" + cameraTable.get("Binning"); cameraType = cameraTable.get("Camera Type"); cameraName = cameraTable.get("Camera Name"); core[0].bitsPerPixel = Integer.parseInt(cameraTable.get("Display Depth")); IniTable captureTable = ini.getTable(" CAPTURE "); int index = 1; for (int i = 0; i < getSizeC(); i++) { if (captureTable.get("c_Filter" + index) != null) { exposureTimes.add(new Double(captureTable.get("c_Expos" + index))); } else i--; index++; } IniTable calibrationTable = ini.getTable(" CALIBRATION "); String units = calibrationTable.get("units"); scaling = Double.parseDouble(calibrationTable.get("factor")); core[0].imageCount *= getSizeC(); core[0].rgb = false; if (ifds.get(0).containsKey(CUSTOM_BITS)) { core[0].bitsPerPixel = ifds.get(0).getIFDIntValue(CUSTOM_BITS); } if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { HashMap<String, String> iniMap = ini.flattenIntoHashMap(); metadata.putAll(iniMap); } }
/* @see loci.formats.FormatReader#initFile(String) */ protected void initFile(String id) throws FormatException, IOException { // make sure we have the experiment file id = locateExperimentFile(id); super.initFile(id); Location dir = new Location(id).getAbsoluteFile().getParentFile(); for (String file : dir.list(true)) { Location f = new Location(dir, file); if (!f.isDirectory()) { if (checkSuffix(file, META_EXT)) { metadataFiles.add(f.getAbsolutePath()); } } } // parse Experiment metadata IniList experiment = readMetaData(id); if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { objective = experiment.getTable("Geometry").get("Name"); IniTable camera = experiment.getTable("Camera"); binning = camera.get("BinX") + "x" + camera.get("BinY"); parseChannelData(dir); addGlobalMeta("Objective", objective); addGlobalMeta("Camera binning", binning); } Vector<String> uniqueRows = new Vector<String>(); Vector<String> uniqueColumns = new Vector<String>(); for (String well : wellLabels) { String row = well.substring(0, 1).trim(); String column = well.substring(1).trim(); if (!uniqueRows.contains(row) && row.length() > 0) uniqueRows.add(row); if (!uniqueColumns.contains(column) && column.length() > 0) { uniqueColumns.add(column); } } int nSlices = getSizeZ() == 0 ? 1 : getSizeZ(); int nTimepoints = getSizeT(); int nWells = wellLabels.size(); int nChannels = getSizeC() == 0 ? channelNames.size() : getSizeC(); if (nChannels == 0) nChannels = 1; tiffs = getTiffs(dir.getAbsolutePath()); reader = new MinimalTiffReader(); reader.setId(tiffs[0][0]); int sizeX = reader.getSizeX(); int sizeY = reader.getSizeY(); int pixelType = reader.getPixelType(); boolean rgb = reader.isRGB(); boolean interleaved = reader.isInterleaved(); boolean indexed = reader.isIndexed(); boolean littleEndian = reader.isLittleEndian(); if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { IniParser parser = new IniParser(); for (String metadataFile : metadataFiles) { String filename = new Location(metadataFile).getName(); if (!checkSuffix(metadataFile, "txt")) { String data = DataTools.readFile(metadataFile); IniList ini = parser.parseINI(new BufferedReader(new StringReader(data))); HashMap<String, String> h = ini.flattenIntoHashMap(); for (String key : h.keySet()) { addGlobalMeta(filename + " " + key, h.get(key)); } } } } for (int i = 0; i < getSeriesCount(); i++) { core[i] = new CoreMetadata(); core[i].sizeC = nChannels; core[i].sizeZ = nSlices; core[i].sizeT = nTimepoints; core[i].sizeX = sizeX / fieldCols; core[i].sizeY = sizeY / fieldRows; core[i].pixelType = pixelType; core[i].rgb = rgb; core[i].interleaved = interleaved; core[i].indexed = indexed; core[i].littleEndian = littleEndian; core[i].dimensionOrder = "XYZTC"; core[i].imageCount = nSlices * nTimepoints * nChannels; } MetadataStore store = makeFilterMetadata(); boolean populatePlanes = getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM; MetadataTools.populatePixels(store, this, populatePlanes); String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0); store.setPlateAcquisitionID(plateAcqID, 0, 0); if (fieldRows * fieldCols > 0) { store.setPlateAcquisitionMaximumFieldCount(new PositiveInteger(fieldRows * fieldCols), 0, 0); } else { LOGGER.warn("Expected positive value for MaximumFieldCount; got {}", fieldRows * fieldCols); } for (int row = 0; row < wellRows; row++) { for (int col = 0; col < wellCols; col++) { int index = row * wellCols + col; store.setWellID(MetadataTools.createLSID("Well", 0, index), 0, index); store.setWellRow(new NonNegativeInteger(row), 0, index); store.setWellColumn(new NonNegativeInteger(col), 0, index); } } for (int i = 0; i < getSeriesCount(); i++) { int well = i / (fieldRows * fieldCols); int field = i % (fieldRows * fieldCols); MetadataTools.setDefaultCreationDate(store, tiffs[well][0], i); String name = wellLabels.get(well); String row = name.substring(0, 1); Integer col = Integer.parseInt(name.substring(1)); int index = (row.charAt(0) - 'A') * wellCols + col - 1; String wellSampleID = MetadataTools.createLSID("WellSample", 0, index, field); store.setWellSampleID(wellSampleID, 0, index, field); store.setWellSampleIndex(new NonNegativeInteger(i), 0, index, field); String imageID = MetadataTools.createLSID("Image", i); store.setWellSampleImageRef(imageID, 0, index, field); store.setImageID(imageID, i); store.setImageName(name + " Field #" + (field + 1), i); store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, i); } MetadataLevel level = getMetadataOptions().getMetadataLevel(); if (level != MetadataLevel.MINIMUM) { String instrumentID = MetadataTools.createLSID("Instrument", 0); store.setInstrumentID(instrumentID, 0); String objectiveID = MetadataTools.createLSID("Objective", 0, 0); store.setObjectiveID(objectiveID, 0, 0); if (objective != null) { String[] tokens = objective.split(" "); String mag = tokens[0].replaceAll("[xX]", ""); String na = null; int naIndex = 0; for (int i = 0; i < tokens.length; i++) { if (tokens[i].equals("NA")) { naIndex = i + 1; na = tokens[naIndex]; break; } } Integer magnification = new Integer(mag); if (magnification > 0) { store.setObjectiveNominalMagnification(new PositiveInteger(magnification), 0, 0); } else { LOGGER.warn("Expected positive value for NominalMagnification; got {}", magnification); } if (na != null) { na = na.substring(0, 1) + "." + na.substring(1); store.setObjectiveLensNA(new Double(na), 0, 0); } if (naIndex + 1 < tokens.length) { store.setObjectiveManufacturer(tokens[naIndex + 1], 0, 0); } } // populate LogicalChannel data for (int i = 0; i < getSeriesCount(); i++) { store.setImageInstrumentRef(instrumentID, i); store.setObjectiveSettingsID(objectiveID, i); for (int c = 0; c < getSizeC(); c++) { store.setChannelName(channelNames.get(c), i, c); if (emWave[c] > 0) { store.setChannelEmissionWavelength(new PositiveInteger(emWave[c]), i, c); } else { LOGGER.warn("Expected positive value for EmissionWavelength; got {}", emWave[c]); } if (exWave[c] > 0) { store.setChannelExcitationWavelength(new PositiveInteger(exWave[c]), i, c); } else { LOGGER.warn("Expected positive value for ExcitationWavelength; got {}", exWave[c]); } String detectorID = MetadataTools.createLSID("Detector", 0, c); store.setDetectorID(detectorID, 0, c); store.setDetectorSettingsID(detectorID, i, c); store.setDetectorSettingsGain(gain[c], i, c); store.setDetectorSettingsOffset(offset[c], i, c); store.setDetectorSettingsBinning(getBinning(binning), i, c); } long firstPlane = 0; for (int p = 0; p < getImageCount(); p++) { int[] zct = getZCTCoords(p); store.setPlaneExposureTime(exposure[zct[1]], i, p); String file = getFilename(i, p); if (file != null) { long plane = getTimestamp(file); if (p == 0) { firstPlane = plane; } double timestamp = (plane - firstPlane) / 1000.0; store.setPlaneDeltaT(timestamp, i, p); } } } store.setPlateID(MetadataTools.createLSID("Plate", 0), 0); store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0); store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0); store.setPlateName(plateName, 0); store.setPlateDescription(plateDescription, 0); if (level != MetadataLevel.NO_OVERLAYS) { parseROIs(store); } } }
private IniList readMetaData(String id) throws IOException { IniParser parser = new IniParser(); IniList exp = parser.parseINI( new BufferedReader(new InputStreamReader(new FileInputStream(id), Constants.ENCODING))); IniList plate = null; // Read Plate File for (String filename : metadataFiles) { if (checkSuffix(filename, "plt")) { plate = parser.parseINI( new BufferedReader( new InputStreamReader(new FileInputStream(filename), Constants.ENCODING))); } else if (filename.endsWith("RoiSummary.txt")) { roiFile = filename; if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { RandomAccessInputStream s = new RandomAccessInputStream(filename); String line = s.readLine().trim(); while (!line.endsWith(".adf\"")) { line = s.readLine().trim(); } plateName = line.substring(line.indexOf(":")).trim(); plateName = plateName.replace('/', File.separatorChar); plateName = plateName.replace('\\', File.separatorChar); for (int i = 0; i < 3; i++) { plateName = plateName.substring(0, plateName.lastIndexOf(File.separator)); } plateName = plateName.substring(plateName.lastIndexOf(File.separator) + 1); s.close(); } } } if (plate == null) throw new IOException("No Plate File"); IniTable plateType = plate.getTable("PlateType"); if (plateName == null) { plateName = plateType.get("Brand"); } plateDescription = plateType.get("Brand") + " " + plateType.get("Description"); int nWells = Integer.parseInt(plateType.get("Wells")); if (nWells == 96) { wellRows = 8; wellCols = 12; } else if (nWells == 384) { wellRows = 16; wellCols = 24; } Location dir = new Location(id).getAbsoluteFile().getParentFile(); String[] wellList = dir.list(); Arrays.sort(wellList); for (String filename : wellList) { if (filename.startsWith("Well ")) { wellLabels.add(filename.split("\\s|\\.")[1]); } } IniTable imageTable = exp.getTable("Image"); boolean montage = imageTable.get("Montaged").equals("1"); if (montage) { fieldRows = Integer.parseInt(imageTable.get("TilesY")); fieldCols = Integer.parseInt(imageTable.get("TilesX")); } else { fieldRows = 1; fieldCols = 1; } core = new CoreMetadata[wellLabels.size() * fieldRows * fieldCols]; core[0] = new CoreMetadata(); // Hack for current testing/development purposes // Not all channels have the same Z!!! How to handle??? // FIXME FIXME FIXME core[0].sizeZ = 1; // FIXME FIXME FIXME // END OF HACK core[0].sizeC = Integer.parseInt(exp.getTable("General").get("Dyes")); core[0].bitsPerPixel = Integer.parseInt(exp.getTable("Camera").get("BitdepthUsed")); IniTable dyeTable = exp.getTable("Dyes"); for (int i = 1; i <= getSizeC(); i++) { channelNames.add(dyeTable.get(Integer.toString(i))); } // Count Images core[0].sizeT = 0; Location well = new Location(dir.getAbsolutePath(), "Well " + wellLabels.get(1)); for (String channelName : channelNames) { int timepoints = 0; for (String filename : well.list()) { if (filename.startsWith(channelName) && filename.endsWith(".tif")) { timepoints++; } } if (timepoints > getSizeT()) { core[0].sizeT = timepoints; } } return exp; }
/* @see BaseTiffReader#initStandardMetadata() */ @Override protected void initStandardMetadata() throws FormatException, IOException { super.initStandardMetadata(); boolean helios = ifds.get(0).containsKey(HELIOS_TAG); boolean titan = ifds.get(0).containsKey(TITAN_TAG); // Helios etc data might have a stray Titan tag if (titan && ifds.get(0).getIFDTextValue(TITAN_TAG).trim().isEmpty()) { titan = false; } // Titan data (always?) has an empty Helios tag as well, so the Titan tag is checked first String software = "S-FEG"; if (titan) { software = "Titan"; } else if (helios) { software = "Helios NanoLab"; } addGlobalMeta("Software", software); int tagKey = SFEG_TAG; if (titan) { tagKey = TITAN_TAG; } else if (helios) { tagKey = HELIOS_TAG; } String tag = ifds.get(0).getIFDTextValue(tagKey); if (tag == null) { return; } tag = tag.trim(); if (tag.isEmpty()) { return; // fall back to regular reader } // store metadata for later conversion to OME-XML if (tag.startsWith("<")) { XMLTools.parseXML(tag, new FEIHandler()); } else { IniParser parser = new IniParser(); IniList ini = parser.parseINI(new BufferedReader(new StringReader(tag))); detectors = new ArrayList<String>(); if (helios) { IniTable userTable = ini.getTable("User"); date = userTable.get("Date") + " " + userTable.get("Time"); if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { userName = userTable.get("User"); IniTable systemTable = ini.getTable("System"); if (systemTable == null) { systemTable = ini.getTable("SYSTEM"); } if (systemTable != null) { microscopeModel = systemTable.get("SystemType"); } IniTable beamTable = ini.getTable("Beam"); if (beamTable != null) { String beamTableName = beamTable.get("Beam"); if (beamTableName != null) { beamTable = ini.getTable(beamTableName); } } if (beamTable != null) { String beamX = beamTable.get("StageX"); String beamY = beamTable.get("StageY"); String beamZ = beamTable.get("StageZ"); IniTable stageTable = ini.getTable("Stage"); if (beamX != null) { final Double number = Double.valueOf(beamX); stageX = new Length(number, UNITS.REFERENCEFRAME); } else if (stageTable != null) { final Double number = Double.valueOf(stageTable.get("StageX")); stageX = new Length(number, UNITS.REFERENCEFRAME); } if (beamY != null) { final Double number = Double.valueOf(beamY); stageY = new Length(number, UNITS.REFERENCEFRAME); } else if (stageTable != null) { final Double number = Double.valueOf(stageTable.get("StageY")); stageY = new Length(number, UNITS.REFERENCEFRAME); } if (beamZ != null) { final Double number = Double.valueOf(beamZ); stageZ = new Length(number, UNITS.REFERENCEFRAME); } else if (stageTable != null) { final Double number = Double.valueOf(stageTable.get("StageZ")); stageZ = new Length(number, UNITS.REFERENCEFRAME); } } IniTable scanTable = ini.getTable("Scan"); // physical sizes are stored in meters sizeX = new Double(scanTable.get("PixelWidth")) * 1000000; sizeY = new Double(scanTable.get("PixelHeight")) * 1000000; timeIncrement = new Double(scanTable.get("FrameTime")); } } else { IniTable dataTable = ini.getTable("DatabarData"); imageName = dataTable.get("ImageName"); imageDescription = dataTable.get("szUserText"); String magnification = ini.getTable("Vector").get("Magnification"); sizeX = new Double(magnification) * MAG_MULTIPLIER; sizeY = new Double(magnification) * MAG_MULTIPLIER; IniTable scanTable = ini.getTable("Vector.Sysscan"); final Double posX = Double.valueOf(scanTable.get("PositionX")); final Double posY = Double.valueOf(scanTable.get("PositionY")); stageX = new Length(posX, UNITS.REFERENCEFRAME); stageY = new Length(posY, UNITS.REFERENCEFRAME); IniTable detectorTable = ini.getTable("Vector.Video.Detectors"); int detectorCount = Integer.parseInt(detectorTable.get("NrDetectorsConnected")); for (int i = 0; i < detectorCount; i++) { detectors.add(detectorTable.get("Detector_" + i + "_Name")); } } // store everything else in the metadata hashtable if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { HashMap<String, String> iniMap = ini.flattenIntoHashMap(); metadata.putAll(iniMap); } } }