BMPFormat.java

/*
 * #%L
 * SCIFIO library for reading and converting scientific file formats.
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 * Copyright (C) 2011 - 2015 Board of Regents of the University of
 * Wisconsin-Madison
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package io.scif.formats;

import io.scif.AbstractChecker;
import io.scif.AbstractFormat;
import io.scif.AbstractMetadata;
import io.scif.AbstractParser;
import io.scif.ByteArrayPlane;
import io.scif.ByteArrayReader;
import io.scif.Format;
import io.scif.FormatException;
import io.scif.HasColorTable;
import io.scif.ImageMetadata;
import io.scif.MetaTable;
import io.scif.MetadataLevel;
import io.scif.UnsupportedCompressionException;
import io.scif.codec.BitBuffer;
import io.scif.config.SCIFIOConfig;
import io.scif.io.RandomAccessInputStream;
import io.scif.util.FormatTools;
import io.scif.util.ImageTools;

import java.io.IOException;

import net.imagej.axis.Axes;
import net.imglib2.display.ColorTable;
import net.imglib2.display.ColorTable8;

import org.scijava.plugin.Plugin;

/**
 * BMPReader is the file format reader for <a
 * href="https://en.wikipedia.org/wiki/BMP_file_format">Microsoft Bitmap
 * (BMP)</a> files.
 *
 * @author Mark Hiner
 */
@Plugin(type = Format.class, name = "Windows Bitmap")
public class BMPFormat extends AbstractFormat {

	// -- Constants --

	public static final String BMP_MAGIC_STRING = "BM";

	// -- Compression types --

	private static final int RAW = 0;

	private static final int RLE_8 = 1;

	private static final int RLE_4 = 2;

	private static final int RGB_MASK = 3;

	// -- AbstractFormat Methods --

	@Override
	protected String[] makeSuffixArray() {
		return new String[] { "bmp" };
	}

	// -- Nested Classes --

	public static class Metadata extends AbstractMetadata implements
		HasColorTable
	{

		// -- Fields --

		/** The palette for indexed color images. */
		private ColorTable8 palette;

		/** Compression type */
		private int compression;

		/** Offset to image data. */
		private long global;

		private boolean invertY = false;

		// -- Getters and Setters --

		public int getCompression() {
			return compression;
		}

		public void setCompression(final int compression) {
			this.compression = compression;
		}

		public long getGlobal() {
			return global;
		}

		public void setGlobal(final long global) {
			this.global = global;
		}

		public boolean isInvertY() {
			return invertY;
		}

		public void setInvertY(final boolean invertY) {
			this.invertY = invertY;
		}

		// -- Metadata API Methods --

		@Override
		public void populateImageMetadata() {
			log().info("Populating metadata");

			int bpp = get(0).getBitsPerPixel();
			final ImageMetadata iMeta = get(0);
			iMeta.setAxisTypes(Axes.X, Axes.Y);
			iMeta.setPlanarAxisCount(2);

			int sizeC = bpp != 24 ? 1 : 3;

			if (bpp == 32) sizeC = 4;
			if (bpp > 8) bpp /= sizeC;

			iMeta.setBitsPerPixel(bpp);

			switch (bpp) {
				case 16:
					iMeta.setPixelType(FormatTools.UINT16);
					break;
				case 32:
					iMeta.setPixelType(FormatTools.UINT32);
					break;
				default:
					iMeta.setPixelType(FormatTools.UINT8);
			}

			iMeta.setLittleEndian(true);

			iMeta.setMetadataComplete(true);
			iMeta.setIndexed(getColorTable(0, 0) != null);

			if (iMeta.isIndexed()) {
				sizeC = 1;
			}

			if (sizeC > 1 || iMeta.isIndexed()) {
				iMeta.addAxis(Axes.CHANNEL, sizeC);
				if (sizeC > 1) iMeta.setAxisTypes(Axes.CHANNEL, Axes.X, Axes.Y);
				iMeta.setPlanarAxisCount(3);
			}

			iMeta.setFalseColor(false);
		}

		// -- HasSource API Methods --

		@Override
		public void close(final boolean fileOnly) throws IOException {
			super.close(fileOnly);

			if (!fileOnly) {
				compression = 0;
				global = 0;
				palette = null;
				invertY = false;
			}
		}

		// -- HasColorTable API Methods --

		@Override
		public ColorTable
			getColorTable(final int imageIndex, final long planeIndex)
		{
			return palette;
		}
	}

	public static class Checker extends AbstractChecker {

		@Override
		public boolean isFormat(final RandomAccessInputStream stream)
			throws IOException
		{
			final int blockLen = 2;
			if (!FormatTools.validStream(stream, blockLen, false)) return false;
			return stream.readString(blockLen).startsWith(BMP_MAGIC_STRING);
		}
	}

	public static class Parser extends AbstractParser<Metadata> {

		@Override
		protected void typedParse(final RandomAccessInputStream stream,
			final Metadata meta, final SCIFIOConfig config) throws IOException,
			FormatException
		{
			meta.createImageMetadata(1);

			final ImageMetadata iMeta = meta.get(0);
			final MetaTable globalTable = meta.getTable();

			stream.order(true);

			// read the first header - 14 bytes

			globalTable.put("Magic identifier", getSource().readString(2));

			globalTable.put("File size (in bytes)", getSource().readInt());
			getSource().skipBytes(4);

			meta.setGlobal(getSource().readInt());

			// read the second header - 40 bytes

			getSource().skipBytes(4);

			int sizeX = 0, sizeY = 0;

			// get the dimensions

			sizeX = getSource().readInt();
			sizeY = getSource().readInt();

			iMeta.addAxis(Axes.X, sizeX);
			iMeta.addAxis(Axes.Y, sizeY);

			if (sizeX < 1) {
				log().trace("Invalid width: " + sizeX + "; using the absolute value");
				sizeX = Math.abs(sizeX);
			}
			if (sizeY < 1) {
				log().trace("Invalid height: " + sizeY + "; using the absolute value");
				sizeY = Math.abs(sizeY);
				meta.setInvertY(true);
			}

			globalTable.put("Color planes", getSource().readShort());

			final short bpp = getSource().readShort();

			iMeta.setBitsPerPixel(bpp);

			meta.setCompression(getSource().readInt());

			getSource().skipBytes(4);
			final int pixelSizeX = getSource().readInt();
			final int pixelSizeY = getSource().readInt();
			int nColors = getSource().readInt();
			if (nColors == 0 && bpp != 32 && bpp != 24) {
				nColors = bpp < 8 ? 1 << bpp : 256;
			}
			getSource().skipBytes(4);

			// read the palette, if it exists

			if (nColors != 0 && bpp == 8) {
				final byte[][] palette = new byte[3][256];

				for (int i = 0; i < nColors; i++) {
					for (int j = palette.length - 1; j >= 0; j--) {
						palette[j][i] = getSource().readByte();
					}
					getSource().skipBytes(1);
				}

				meta.palette = new ColorTable8(palette);
			}
			else if (nColors != 0) getSource().skipBytes(nColors * 4);

			if (config.parserGetLevel() != MetadataLevel.MINIMUM) {
				globalTable.put("Indexed color", meta.getColorTable(0, 0) != null);
				globalTable.put("Image width", sizeX);
				globalTable.put("Image height", sizeY);
				globalTable.put("Bits per pixel", bpp);
				String comp = "invalid";

				switch (meta.getCompression()) {
					case RAW:
						comp = "None";
						break;
					case RLE_8:
						comp = "8 bit run length encoding";
						break;
					case RLE_4:
						comp = "4 bit run length encoding";
						break;
					case RGB_MASK:
						comp = "RGB bitmap with mask";
						break;
				}

				globalTable.put("Compression type", comp);
				globalTable.put("X resolution", pixelSizeX);
				globalTable.put("Y resolution", pixelSizeY);
			}
		}
	}

	public static class Reader extends ByteArrayReader<Metadata> {

		// -- AbstractReader API Methods --

		@Override
		protected String[] createDomainArray() {
			return new String[] { FormatTools.GRAPHICS_DOMAIN };
		}

		// -- Reader API Methods --

		@Override
		public ByteArrayPlane openPlane(final int imageIndex,
			final long planeIndex, final ByteArrayPlane plane, final long[] planeMin,
			final long[] planeMax, final SCIFIOConfig config) throws FormatException,
			IOException
		{
			final Metadata meta = getMetadata();
			final int xIndex = meta.get(imageIndex).getAxisIndex(Axes.X);
			final int yIndex = meta.get(imageIndex).getAxisIndex(Axes.Y);
			final int x = (int) planeMin[xIndex], y = (int) planeMin[yIndex], w =
				(int) planeMax[xIndex], h = (int) planeMax[yIndex];

			final byte[] buf = plane.getData();
			final int compression = meta.getCompression();
			final int bpp = meta.get(imageIndex).getBitsPerPixel();
			final int sizeX = (int) meta.get(imageIndex).getAxisLength(Axes.X);
			final int sizeY = (int) meta.get(imageIndex).getAxisLength(Axes.Y);
			final int sizeC = (int) meta.get(imageIndex).getAxisLength(Axes.CHANNEL);

			FormatTools.checkPlaneForReading(meta, imageIndex, planeIndex,
				buf.length, planeMin, planeMax);

			if (compression != RAW &&
				getStream().length() < FormatTools.getPlaneSize(this, imageIndex))
			{
				throw new UnsupportedCompressionException(compression +
					" not supported");
			}

			final int rowsToSkip = meta.isInvertY() ? y : sizeY - (h + y);
			final int rowLength =
				sizeX * (meta.get(imageIndex).isIndexed() ? 1 : sizeC);
			getStream().seek(meta.getGlobal() + rowsToSkip * rowLength);

			int pad = ((rowLength * bpp) / 8) % 2;
			if (pad == 0) pad = ((rowLength * bpp) / 8) % 4;
			else pad *= sizeC;
			int planeSize = sizeX * sizeC * h;
			if (bpp >= 8) planeSize *= (bpp / 8);
			else planeSize /= (8 / bpp);
			planeSize += pad * h;
			if (planeSize + getStream().getFilePointer() > getStream().length()) {
				planeSize -= (pad * h);

				// sometimes we have RGB images with a single padding byte
				if (planeSize + sizeY + getStream().getFilePointer() <= getStream()
					.length())
				{
					pad = 1;
					planeSize += h;
				}
				else {
					pad = 0;
				}
			}

			getStream().skipBytes(rowsToSkip * pad);

			final byte[] rawPlane = new byte[planeSize];
			getStream().read(rawPlane);

			final BitBuffer bb = new BitBuffer(rawPlane);

			final ColorTable palette = meta.getColorTable(0, 0);
			plane.setColorTable(palette);

			final int effectiveC =
				palette != null && palette.getLength() > 0 ? 1 : sizeC;
			for (int row = h - 1; row >= 0; row--) {
				final int rowIndex = meta.isInvertY() ? h - 1 - row : row;
				bb.skipBits(x * bpp * effectiveC);
				for (int i = 0; i < w * effectiveC; i++) {
					if (bpp <= 8) {
						buf[rowIndex * w * effectiveC + i] =
							(byte) (bb.getBits(bpp) & 0xff);
					}
					else {
						for (int b = 0; b < bpp / 8; b++) {
							buf[(bpp / 8) * (rowIndex * w * effectiveC + i) + b] =
								(byte) (bb.getBits(8) & 0xff);
						}
					}
				}
				if (row > 0) {
					bb.skipBits((sizeX - w - x) * bpp * effectiveC + pad * 8);
				}
			}

			if (meta.get(imageIndex).getAxisLength(Axes.CHANNEL) > 1) {
				ImageTools.bgrToRgb(buf,
					meta.get(imageIndex).getInterleavedAxisCount() > 0, 1, (int) meta
						.get(imageIndex).getAxisLength(Axes.CHANNEL));
			}
			return plane;
		}

	}
}