//
// IPLabReader.java
//
/*
LOCI Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ Melissa Linkert, Curtis Rueden, Chris Allan,
Eric Kjellman and Brian Loranger.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU Library 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 Library General Public License for more details.
You should have received a copy of the GNU Library General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package loci.formats.in;
import java.io.IOException;
import loci.formats.*;
/**
* IPLabReader is the file format reader for IPLab (.IPL) files.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/in/IPLabReader.java">Trac</a>,
* <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/in/IPLabReader.java">SVN</a></dd></dl>
*
* @author Melissa Linkert linkert at wisc.edu
* @author Curtis Rueden ctrueden at wisc.edu
*/
public class IPLabReader extends FormatReader {
// -- Fields --
/** Bytes per pixel. */
private int bps;
/** Total number of pixel bytes. */
private int dataSize;
// -- Constructor --
/** Constructs a new IPLab reader. */
public IPLabReader() { super("IPLab", "ipl"); }
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(byte[]) */
public boolean isThisType(byte[] block) {
if (block.length < 12) return false; // block length too short
String s = new String(block, 0, 4);
boolean big = s.equals("iiii");
boolean little = s.equals("mmmm");
if (!big && !little) return false;
int size = DataTools.bytesToInt(block, 4, 4, little);
if (size != 4) return false; // first block size should be 4
int version = DataTools.bytesToInt(block, 8, 4, little);
return version >= 0x100e;
}
/* @see loci.formats.IFormatReader#openBytes(int, byte[]) */
public byte[] openBytes(int no, byte[] buf)
throws FormatException, IOException
{
FormatTools.assertId(currentId, true, 1);
FormatTools.checkPlaneNumber(this, no);
FormatTools.checkBufferSize(this, buf.length);
int numPixels = core.sizeX[0] * core.sizeY[0] * core.sizeC[0] * bps;
in.seek(numPixels * (no / core.sizeC[0]) + 44);
in.read(buf);
return buf;
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
if (debug) debug("IPLabReader.initFile(" + id + ")");
super.initFile(id);
in = new RandomAccessStream(id);
status("Populating metadata");
core.littleEndian[0] = in.readString(4).equals("iiii");
in.order(core.littleEndian[0]);
// populate standard metadata hashtable and OME root node
in.skipBytes(12);
dataSize = in.readInt() - 28;
core.sizeX[0] = in.readInt();
core.sizeY[0] = in.readInt();
core.sizeC[0] = in.readInt();
core.sizeZ[0] = in.readInt();
core.sizeT[0] = in.readInt();
int filePixelType = in.readInt();
core.imageCount[0] = core.sizeZ[0] * core.sizeT[0];
addMeta("Width", new Long(core.sizeX[0]));
addMeta("Height", new Long(core.sizeY[0]));
addMeta("Channels", new Long(core.sizeC[0]));
addMeta("ZDepth", new Long(core.sizeZ[0]));
addMeta("TDepth", new Long(core.sizeT[0]));
String ptype;
bps = 1;
switch (filePixelType) {
case 0:
ptype = "8 bit unsigned";
core.pixelType[0] = FormatTools.UINT8;
bps = 1;
break;
case 1:
ptype = "16 bit signed short";
core.pixelType[0] = FormatTools.UINT16;
bps = 2;
break;
case 2:
ptype = "16 bit unsigned short";
core.pixelType[0] = FormatTools.UINT16;
bps = 2;
break;
case 3:
ptype = "32 bit signed long";
core.pixelType[0] = FormatTools.UINT32;
bps = 4;
break;
case 4:
ptype = "32 bit single-precision float";
core.pixelType[0] = FormatTools.FLOAT;
bps = 4;
break;
case 5:
ptype = "Color24";
core.pixelType[0] = FormatTools.UINT32;
bps = 1;
break;
case 6:
ptype = "Color48";
core.pixelType[0] = FormatTools.UINT16;
bps = 2;
break;
case 10:
ptype = "64 bit double-precision float";
core.pixelType[0] = FormatTools.DOUBLE;
bps = 8;
break;
default:
ptype = "reserved"; // for values 7-9
}
addMeta("PixelType", ptype);
in.skipBytes(dataSize);
core.currentOrder[0] = "XY";
if (core.sizeC[0] > 1) core.currentOrder[0] += "CZT";
else core.currentOrder[0] += "ZTC";
core.rgb[0] = core.sizeC[0] > 1;
core.interleaved[0] = false;
core.indexed[0] = false;
core.falseColor[0] = false;
core.metadataComplete[0] = true;
// The metadata store we're working with.
MetadataStore store = getMetadataStore();
store.setImage(currentId, null, null, null);
FormatTools.populatePixels(store, this);
for (int i=0; i<core.sizeC[0]; i++) {
store.setLogicalChannel(i, null, null, null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null, null, null, null,
null, null, null, null);
}
status("Reading tags");
String tag = in.readString(4);
while (!tag.equals("fini") && in.getFilePointer() < in.length() - 4) {
if (tag.equals("clut")) {
// read in Color Lookup Table
int size = in.readInt();
if (size == 8) {
// indexed lookup table
in.skipBytes(4);
int type = in.readInt();
String[] types = new String[] {
"monochrome", "reverse monochrome", "BGR", "classify", "rainbow",
"red", "green", "blue", "cyan", "magenta", "yellow",
"saturated pixels"
};
String clutType = (type >= 0 && type < types.length) ? types[type] :
"unknown";
addMeta("LUT type", clutType);
}
else {
// explicitly defined lookup table
// length is 772
in.skipBytes(772);
}
}
else if (tag.equals("norm")) {
// read in normalization information
int size = in.readInt();
// error checking
if (size != (44 * core.sizeC[0])) {
throw new FormatException("Bad normalization settings");
}
String[] types = new String[] {
"user", "plane", "sequence", "saturated plane",
"saturated sequence", "ROI"
};
for (int i=0; i<core.sizeC[0]; i++) {
int source = in.readInt();
String sourceType = (source >= 0 && source < types.length) ?
types[source] : "user";
addMeta("NormalizationSource" + i, sourceType);
double min = in.readDouble();
double max = in.readDouble();
double gamma = in.readDouble();
double black = in.readDouble();
double white = in.readDouble();
addMeta("NormalizationMin" + i, new Double(min));
addMeta("NormalizationMax" + i, new Double(max));
addMeta("NormalizationGamma" + i, new Double(gamma));
addMeta("NormalizationBlack" + i, new Double(black));
addMeta("NormalizationWhite" + i, new Double(white));
store = getMetadataStore();
store.setChannelGlobalMinMax(i, new Double(min),
new Double(max), null);
store.setDisplayChannel(new Integer(core.sizeC[0]), new Double(black),
new Double(white), new Float(gamma), null);
}
}
else if (tag.equals("head")) {
// read in header labels
int size = in.readInt();
for (int i=0; i<size / 22; i++) {
int num = in.readShort();
addMeta("Header" + num, in.readString(20));
}
}
else if (tag.equals("mmrc")) {
in.skipBytes(in.readInt());
}
else if (tag.equals("roi ")) {
// read in ROI information
in.skipBytes(8);
int roiLeft = in.readInt();
int roiTop = in.readInt();
int roiRight = in.readInt();
int roiBottom = in.readInt();
int numRoiPts = in.readInt();
Integer x0 = new Integer(roiLeft);
Integer x1 = new Integer(roiRight);
Integer y0 = new Integer(roiBottom);
Integer y1 = new Integer(roiTop);
store.setDisplayROI(x0, y0, null, x1, y1, null, null, null, null, null);
in.skipBytes(8 * numRoiPts);
}
else if (tag.equals("mask")) {
// read in Segmentation Mask
in.skipBytes(in.readInt());
}
else if (tag.equals("unit")) {
// read in units
in.skipBytes(4);
for (int i=0; i<4; i++) {
int xResStyle = in.readInt();
int unitsPerPixel = in.readInt();
int xUnitName = in.readInt();
addMeta("ResolutionStyle" + i, new Long(xResStyle));
addMeta("UnitsPerPixel" + i, new Long(unitsPerPixel));
if (i == 0) {
Float pixelSize = new Float(1 / (float) unitsPerPixel);
store.setDimensions(pixelSize, pixelSize, null, null, null, null);
}
addMeta("UnitName" + i, new Long(xUnitName));
}
}
else if (tag.equals("view")) {
// read in view
in.skipBytes(4);
}
else if (tag.equals("plot")) {
// read in plot
// skipping this field for the moment
in.skipBytes(2512);
}
else if (tag.equals("notes")) {
// read in notes (image info)
in.skipBytes(4);
String descriptor = in.readString(64);
String notes = in.readString(512);
addMeta("Descriptor", descriptor);
addMeta("Notes", notes);
store.setImage(currentId, null, notes, null);
}
if (in.getFilePointer() + 4 <= in.length()) {
tag = in.readString(4);
}
else {
tag = "fini";
}
if (in.getFilePointer() >= in.length() && !tag.equals("fini")) {
tag = "fini";
}
}
}
}