/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2015 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.BufferedReader;
import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;
import loci.common.DataTools;
import loci.common.DateTools;
import loci.common.IniList;
import loci.common.IniParser;
import loci.common.IniTable;
import loci.common.Location;
import loci.common.RandomAccessInputStream;
import loci.formats.ClassList;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.IFormatReader;
import loci.formats.ImageReader;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
import ome.units.quantity.Length;
import ome.units.UNITS;
import ome.xml.model.primitives.PositiveFloat;
import ome.xml.model.primitives.Timestamp;
import ome.units.quantity.Length;
/**
* HitachiReader is the file format reader for S-4800 files.
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class HitachiReader extends FormatReader {
// -- Constants --
private static final String MAGIC = "[SemImageFile]";
private static final String DATE_FORMAT = "MM/dd/yyyy HH:mm:ss";
// -- Fields --
private ImageReader helperReader;
// -- Constructor --
/** Constructs a new Hitachi reader. */
public HitachiReader() {
super("Hitachi", "txt");
suffixSufficient = false;
domains = new String[] {FormatTools.SEM_DOMAIN};
hasCompanionFiles = true;
datasetDescription =
"One .txt file plus one similarly-named .tif, .bmp, or .jpg file";
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isSingleFile(String) */
@Override
public boolean isSingleFile(String id) throws FormatException, IOException {
return false;
}
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
if (!open) {
return false;
}
String base = name;
if (base.indexOf(".") >= 0) {
base = base.substring(0, base.lastIndexOf("."));
}
if (checkSuffix(name, "txt")) {
Location bmp = new Location(base + ".bmp");
Location jpg = new Location(base + ".jpg");
Location tif = new Location(base + ".tif");
if (!bmp.exists() && !jpg.exists() && !tif.exists()) {
return false;
}
return super.isThisType(name, open);
}
String textFile = base + ".txt";
return new Location(textFile).exists() && isThisType(textFile, open);
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = MAGIC.length();
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return (stream.readString(blockLen)).indexOf(MAGIC) >= 0;
}
/**
* @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);
helperReader.openBytes(no, buf, x, y, w, h);
return buf;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
if (noPixels) {
return new String[] {currentId};
}
return new String[] {currentId, helperReader.getCurrentFile()};
}
/* @see loci.formats.IFormatReader#fileGroupOption(String) */
@Override
public int fileGroupOption(String id) throws FormatException, IOException {
return FormatTools.MUST_GROUP;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
if (helperReader != null) {
helperReader.close();
}
helperReader = null;
}
}
/* @see loci.formats.IFormatReader#reopenFile() */
@Override
public void reopenFile() throws IOException {
super.reopenFile();
helperReader.reopenFile();
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
if (!checkSuffix(id, "txt")) {
String base = id;
if (base.indexOf(".") >= 0) {
base = base.substring(0, base.lastIndexOf("."));
}
id = base + ".txt";
initFile(id);
return;
}
super.initFile(id);
String data = DataTools.readFile(id);
IniParser parser = new IniParser();
parser.setBackslashContinuesLine(false);
IniList ini = parser.parseINI(new BufferedReader(new StringReader(data)));
IniTable image = ini.getTable("SemImageFile");
if (image == null) {
throw new FormatException("Could not find 'SemImageFile' table.");
}
for (String key : image.keySet()) {
addGlobalMeta(key, image.get(key));
}
String imageName = image.get("SampleName");
String pixelsFile = image.get("ImageName");
String date = image.get("Date");
String time = image.get("Time");
Location parent = new Location(id).getAbsoluteFile().getParentFile();
pixelsFile = new Location(parent, pixelsFile).getAbsolutePath();
ClassList<IFormatReader> classes = ImageReader.getDefaultReaderClasses();
Class<? extends IFormatReader>[] classArray = classes.getClasses();
ClassList<IFormatReader> newClasses =
new ClassList<IFormatReader>(IFormatReader.class);
for (Class<? extends IFormatReader> c : classArray) {
if (!c.equals(HitachiReader.class)) {
newClasses.addClass(c);
}
}
helperReader = new ImageReader(newClasses);
helperReader.setId(pixelsFile);
core = new ArrayList<CoreMetadata>(helperReader.getCoreMetadataList());
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this,
getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM);
store.setImageName(imageName, 0);
date = DateTools.formatDate(date + " " + time, DATE_FORMAT);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
populateOMEMetadata(image, store);
}
// -- Helper methods --
private void populateOMEMetadata(IniTable image, MetadataStore store) {
if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) {
return;
}
String modelNumber = image.get("InstructName");
String serialNumber = image.get("SerialNumber");
Double pixelSize = new Double(image.get("PixelSize"));
String workingDistance = image.get("WorkingDistance");
final Double stagePosXn = Double.valueOf(image.get("StagePositionX"));
final Double stagePosYn = Double.valueOf(image.get("StagePositionY"));
final Double stagePosZn = Double.valueOf(image.get("StagePositionZ"));
final Length stagePosXl = new Length(stagePosXn, UNITS.REFERENCEFRAME);
final Length stagePosYl = new Length(stagePosYn, UNITS.REFERENCEFRAME);
final Length stagePosZl = new Length(stagePosZn, UNITS.REFERENCEFRAME);
Length sizeX = FormatTools.getPhysicalSizeX(pixelSize);
Length sizeY = FormatTools.getPhysicalSizeY(pixelSize);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
store.setPlanePositionX(stagePosXl, 0, 0);
store.setPlanePositionY(stagePosYl, 0, 0);
store.setPlanePositionZ(stagePosZl, 0, 0);
String instrument = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrument, 0);
store.setImageInstrumentRef(instrument, 0);
if (modelNumber != null) {
store.setMicroscopeModel(modelNumber, 0);
}
if (serialNumber != null) {
store.setMicroscopeSerialNumber(serialNumber, 0);
}
if (workingDistance != null) {
int end = workingDistance.indexOf(" ");
if (end < 0) end = workingDistance.length();
workingDistance = workingDistance.substring(0, end);
String objective = MetadataTools.createLSID("Objective", 0, 0);
store.setObjectiveID(objective, 0, 0);
store.setObjectiveSettingsID(objective, 0);
store.setObjectiveWorkingDistance(new Length(new Double(workingDistance), UNITS.MICROM), 0, 0);
}
}
}