/*
* #%L
* Bio-Formats Plugins for ImageJ: a collection of ImageJ plugins including the
* Bio-Formats Importer, Bio-Formats Exporter, Bio-Formats Macro Extensions,
* Data Browser and Stack Slicer.
* %%
* Copyright (C) 2006 - 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.plugins.in;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Hashtable;
import loci.formats.FormatTools;
import loci.formats.IFormatReader;
import loci.formats.MetadataTools;
/**
* Helper class for storing original metadata key/value pairs.
*/
public class ImporterMetadata extends HashMap<String, Object> {
// -- Constructor --
public ImporterMetadata(IFormatReader r, ImportProcess process,
boolean usePrefix)
{
// merge global metadata
putAll(r.getGlobalMetadata());
// merge location path
put("Location", process.getCurrentFile());
final ImporterOptions options = process.getOptions();
final int oldSeries = r.getSeries();
final int seriesCount = r.getSeriesCount();
final int digits = digits(seriesCount);
for (int i=0; i<seriesCount; i++) {
if (!options.isSeriesOn(i)) continue;
r.setSeries(i);
// build prefix from image name and/or series number
String s = "";
if (usePrefix) {
s = process.getOMEMetadata().getImageName(i);
if ((s == null || s.trim().length() == 0) && seriesCount > 1) {
StringBuffer sb = new StringBuffer();
sb.append("Series ");
int zeroes = digits - digits(i + 1);
for (int j=0; j<zeroes; j++) sb.append(0);
sb.append(i + 1);
sb.append(" ");
s = sb.toString();
}
else s += " ";
}
// merge series metadata
Hashtable<String, Object> seriesMeta = r.getSeriesMetadata();
MetadataTools.merge(seriesMeta, this, s);
// merge core values
final String pad = " "; // puts core values first when alphabetizing
put(pad + s + "SizeX", new Integer(r.getSizeX()));
put(pad + s + "SizeY", new Integer(r.getSizeY()));
put(pad + s + "SizeZ", new Integer(r.getSizeZ()));
put(pad + s + "SizeT", new Integer(r.getSizeT()));
put(pad + s + "SizeC", new Integer(r.getSizeC()));
put(pad + s + "IsRGB", new Boolean(r.isRGB()));
put(pad + s + "PixelType",
FormatTools.getPixelTypeString(r.getPixelType()));
put(pad + s + "LittleEndian", new Boolean(r.isLittleEndian()));
put(pad + s + "DimensionOrder", r.getDimensionOrder());
put(pad + s + "IsInterleaved", new Boolean(r.isInterleaved()));
put(pad + s + "BitsPerPixel", new Integer(r.getBitsPerPixel()));
String seriesName = process.getOMEMetadata().getImageName(i);
put(pad + "Series " + i + " Name", seriesName);
}
r.setSeries(oldSeries);
}
/** Returns a string with each key/value pair on its own line. */
public String getMetadataString(String separator) {
ArrayList<String> keys = new ArrayList<String>(keySet());
Collections.sort(keys);
StringBuffer sb = new StringBuffer();
for (String key : keys) {
sb.append(key);
sb.append(separator);
sb.append(get(key));
sb.append("\n");
}
return sb.toString();
}
// -- Object API methods --
@Override
public String toString() {
return getMetadataString(" = ");
}
// -- Helper methods --
/** Computes the given value's number of digits. */
private static int digits(int value) {
int digits = 0;
while (value > 0) {
value /= 10;
digits++;
}
return digits;
}
}