/*
* #%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.IOException;
import loci.common.DateTools;
import loci.common.RandomAccessInputStream;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
import ome.xml.model.primitives.PositiveFloat;
import ome.xml.model.primitives.Timestamp;
import ome.units.quantity.Length;
/**
* SpiderReader is the file format reader for SPIDER files.
*/
public class SpiderReader extends FormatReader {
// -- Constants --
private static final String DATE_FORMAT = "dd-MMM-yyyy HH:mm:ss";
// -- Fields --
private long headerSize = 0;
private boolean oneHeaderPerSlice = false;
// -- Constructor --
/** Constructs a new SPIDER reader. */
public SpiderReader() {
super("SPIDER", "spi");
domains = new String[] {FormatTools.EM_DOMAIN};
suffixSufficient = true;
suffixNecessary = false;
}
// -- IFormatReader API methods --
/**
* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream)
*/
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 104;
if (!FormatTools.validStream(stream, blockLen, true)) return false;
int size = (int) stream.readFloat() * 4;
stream.skipBytes(4);
size *= (int) stream.readFloat();
stream.seek(44);
int nsam = (int) stream.readFloat();
size *= nsam;
int headerSize = nsam * (int) stream.readFloat() * 4;
stream.skipBytes(48);
int slices = (int) stream.readFloat();
if (slices > 0) {
size *= slices;
}
return size + headerSize == stream.length();
}
/**
* @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);
long header = headerSize;
if (oneHeaderPerSlice) {
header += (no + 1) * headerSize;
}
in.seek(header + no * FormatTools.getPlaneSize(this));
readPlane(in, x, y, w, h, buf);
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
headerSize = 0;
oneHeaderPerSlice = false;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
CoreMetadata m = core.get(0);
m.littleEndian = true;
in.order(isLittleEndian());
int nSlice = (int) in.readFloat();
int nRow = (int) in.readFloat();
int irec = (int) in.readFloat();
in.skipBytes(4);
int iform = (int) in.readFloat();
int imami = (int) in.readFloat();
float fmax = in.readFloat();
float fmin = in.readFloat();
float average = in.readFloat();
float sig = in.readFloat();
in.skipBytes(4);
int nsam = (int) in.readFloat();
int labrec = (int) in.readFloat();
headerSize = (long) labrec * nsam * 4;
int iAngle = (int) in.readFloat();
float phi = in.readFloat();
float theta = in.readFloat();
float gamma = in.readFloat();
float xOff = in.readFloat();
float yOff = in.readFloat();
float zOff = in.readFloat();
float scale = in.readFloat();
int labbyte = (int) in.readFloat();
int lenbyte = (int) in.readFloat();
int istack = (int) in.readFloat();
in.skipBytes(4);
float maxim = in.readFloat();
float imgnum = in.readFloat();
float lastIndx = in.readFloat();
in.skipBytes(8);
float kAngle = in.readFloat();
float phi1 = in.readFloat();
float theta1 = in.readFloat();
float psi1 = in.readFloat();
float phi2 = in.readFloat();
float theta2 = in.readFloat();
float psi2 = in.readFloat();
float pixelSize = in.readFloat(); // in angstroms
float ev = in.readFloat();
in.skipBytes(4 * 61);
float psi3 = in.readFloat();
float theta3 = in.readFloat();
float phi3 = in.readFloat();
float lAngle = in.readFloat();
in.skipBytes(4 * 107);
String creationDate = in.readString(12).trim();
String creationTime = in.readString(8);
String title = in.readString(160);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
addGlobalMeta("NSLICE", nSlice);
addGlobalMeta("NROW", nRow);
addGlobalMeta("IREC", irec);
addGlobalMeta("IFORM", iform);
addGlobalMeta("IMAMI", imami);
addGlobalMeta("FMAX", fmax);
addGlobalMeta("FMIN", fmin);
addGlobalMeta("AV", average);
addGlobalMeta("SIG", sig);
addGlobalMeta("NSAM", nsam);
addGlobalMeta("LABREC", labrec);
addGlobalMeta("IANGLE", iAngle);
addGlobalMeta("PHI", phi);
addGlobalMeta("THETA", theta);
addGlobalMeta("GAMMA", gamma);
addGlobalMeta("XOFF", xOff);
addGlobalMeta("YOFF", yOff);
addGlobalMeta("ZOFF", zOff);
addGlobalMeta("SCALE", scale);
addGlobalMeta("LABBYT", labbyte);
addGlobalMeta("LENBYT", lenbyte);
addGlobalMeta("ISTACK/MAXINDX", istack);
addGlobalMeta("MAXIM", maxim);
addGlobalMeta("IMGNUM", imgnum);
addGlobalMeta("LASTINDX", lastIndx);
addGlobalMeta("KANGLE", kAngle);
addGlobalMeta("PHI1", phi1);
addGlobalMeta("THETA1", theta1);
addGlobalMeta("PSI1", psi1);
addGlobalMeta("PHI2", phi2);
addGlobalMeta("THETA2", theta2);
addGlobalMeta("PSI2", psi2);
addGlobalMeta("PIXSIZ", pixelSize);
addGlobalMeta("EV", ev);
addGlobalMeta("PHI3", phi3);
addGlobalMeta("THETA3", theta3);
addGlobalMeta("PSI3", psi3);
addGlobalMeta("LANGLE", lAngle);
addGlobalMeta("CDAT", creationDate);
addGlobalMeta("CTIM", creationTime);
addGlobalMeta("CTIT", title);
}
m.imageCount = (int) Math.max(nSlice, 1);
if (maxim > 0) {
m.imageCount *= maxim;
}
m.sizeZ = getImageCount();
m.sizeC = 1;
m.sizeT = 1;
m.sizeY = nRow;
m.sizeX = nsam;
m.pixelType = FormatTools.FLOAT;
m.dimensionOrder = "XYZCT";
m.rgb = false;
long planeSize = FormatTools.getPlaneSize(this);
oneHeaderPerSlice =
(irec * nsam * 4) != planeSize && ((irec - 1) * 4) != planeSize;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
store.setImageName(title, 0);
String date = creationDate + " " + creationTime;
date = DateTools.formatDate(date, DATE_FORMAT);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
Double size = new Double(pixelSize * 0.0001);
Length sizeX = FormatTools.getPhysicalSizeX(size);
Length sizeY = FormatTools.getPhysicalSizeY(size);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
}
}
}