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Merge branch 'feature/depict'
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@egonw
egonw committed Sep 19, 2015
2 parents 6be33e7 + b305bb3 commit 5be3cb1
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66 changes: 66 additions & 0 deletions app/depict/pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!--
~ Copyright (c) 2015. NextMove Software Ltd
-->

<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>cdk-app</artifactId>
<groupId>org.openscience.cdk</groupId>
<version>1.5.12-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

<artifactId>cdk-depict</artifactId>

<dependencies>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-renderextra</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-renderawt</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-renderbasic</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-smiles</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-smarts</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-sdg</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-silent</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.freehep</groupId>
<artifactId>freehep-graphicsio-svg</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>org.freehep</groupId>
<artifactId>freehep-graphicsio-pdf</artifactId>
<version>2.4</version>
</dependency>
</dependencies>

</project>
323 changes: 323 additions & 0 deletions app/depict/src/main/java/org/openscience/cdk/depict/Depiction.java
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/* Copyright (C) 2015 The Chemistry Development Kit (CDK) project
*
* Contact: cdk-devel@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk.depict;

import com.google.common.base.Charsets;
import org.openscience.cdk.renderer.RendererModel;
import org.openscience.cdk.renderer.elements.Bounds;
import org.openscience.cdk.renderer.font.AWTFontManager;
import org.openscience.cdk.renderer.generators.BasicSceneGenerator;
import org.openscience.cdk.renderer.visitor.IDrawVisitor;

import javax.imageio.ImageIO;
import java.awt.geom.AffineTransform;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Locale;

import static org.openscience.cdk.depict.DepictionGenerator.AUTOMATIC;

/**
* Base class of a pre-rendered depiction. The class allows introspection of
* depiction size (decided at generation time) and serialization to raster
* and vector graphic formats.
*
* @author John May
*/
@SuppressWarnings("PMD.ShortVariable")
public abstract class Depiction {

/**
* Structured Vector Graphics (SVG) format key.
*/
public static final String SVG_FMT = "svg";

/**
* PostScript (PS) format key.
*/
public static final String PS_FMT = "ps";

/**
* Portable Document Format (PDF) format key.
*/
public static final String PDF_FMT = "pdf";

/**
* Joint Photographic Experts Group (JPG) format key.
*/
public static final String JPG_FMT = "jpg";

/**
* Portable Network Graphics (PNG) format key.
*/
public static final String PNG_FMT = "png";

/**
* Graphics Interchange Format (GIF) format key.
*/
public static final String GIF_FMT = "gif";

static final double ACS_1996_BOND_LENGTH_MM = 5.08;

private static final char DOT = '.';

private final RendererModel model;

/**
* Internal method passes in the rendering model parameters.
*
* @param model parameters
*/
Depiction(RendererModel model) {
this.model = model;
}

/**
* Render the depiction to a Java AWT {@link BufferedImage}.
*
* @return AWT buffered image
*/
public abstract BufferedImage toImg();

/**
* Render the image to an SVG image.
*
* @return svg XML content
*/
public final String toSvgStr() {
return toVecStr(SVG_FMT);
}

/**
* Render the image to an EPS format string.
*
* @return eps content
*/
public final String toEpsStr() {
return toVecStr(PS_FMT);
}

/**
* Render the image to an PDF format string.
*
* @return pdf content
*/
public final String toPdfStr() {
return toVecStr(PDF_FMT);
}

/**
* Access the specified padding value or fallback to a provided
* default.
*
* @param defaultPadding default value if the parameter is 'automatic'
* @return padding
*/
double getPaddingValue(double defaultPadding) {
double padding = model.get(RendererModel.Padding.class);
if (padding == AUTOMATIC)
padding = defaultPadding;
return padding;
}

/**
* Access the specified margin value or fallback to a provided
* default.
*
* @param defaultMargin default value if the parameter is 'automatic'
* @return margin
*/
double getMarginValue(final double defaultMargin) {
double margin = model.get(BasicSceneGenerator.Margin.class);
if (margin == AUTOMATIC)
margin = defaultMargin;
return margin;
}

/**
* Internal - implementations should overload this method for vector graphics
* rendering.
*
* @param fmt the vector graphics format
* @return the vector graphics format string
*/
abstract String toVecStr(String fmt);

/**
* List the available formats that can be rendered.
*
* @return supported formats
*/
public final List<String> listFormats() {
final List<String> formats = new ArrayList<>();
formats.add(SVG_FMT);
formats.add(SVG_FMT.toUpperCase(Locale.ROOT));
formats.add(PS_FMT);
formats.add(PS_FMT.toUpperCase(Locale.ROOT));
formats.add(PDF_FMT);
formats.add(PDF_FMT.toUpperCase(Locale.ROOT));
formats.addAll(Arrays.asList(ImageIO.getWriterFormatNames()));
return formats;
}

/**
* Write the depiction to the provided output stream.
*
* @param fmt format
* @param out output stream
* @throws IOException depiction could not be written, low level IO problem
* @see #listFormats()
*/
public final void writeTo(String fmt, OutputStream out) throws IOException {
if (fmt.equalsIgnoreCase(SVG_FMT)) {
out.write(toSvgStr().getBytes(Charsets.UTF_8));
} else if (fmt.equalsIgnoreCase(PS_FMT)) {
out.write(toEpsStr().getBytes(Charsets.UTF_8));
} else if (fmt.equalsIgnoreCase(PDF_FMT)) {
out.write(toPdfStr().getBytes(Charsets.UTF_8));
} else {
ImageIO.write(toImg(), fmt, out);
}
}

/**
* Write the depiction to the provided output stream.
*
* @param fmt format
* @param file output destination
* @throws IOException depiction could not be written, low level IO problem
* @see #listFormats()
*/
public final void writeTo(String fmt, File file) throws IOException {
try (FileOutputStream out = new FileOutputStream(file)) {
writeTo(fmt, out);
}
}

/**
* Write the depiction to the provided file path.
*
* @param fmt format
* @param path output destination path
* @throws IOException depiction could not be written, low level IO problem
* @see #listFormats()
*/
public final void writeTo(String fmt, String path) throws IOException {
writeTo(fmt, new File(replaceTildaWithHomeDir(ensureSuffix(path, fmt))));
}

/**
* Write the depiction to the provided file path, the format is determined
* by the path suffix.
*
* @param path output destination path
* @throws IOException depiction could not be written, low level IO problem
* @see #listFormats()
*/
public final void writeTo(String path) throws IOException {
final int i = path.lastIndexOf(DOT);
if (i < 0 || i + 1 == path.length())
throw new IOException("Cannot find suffix in provided path: " + path);
final String fmt = path.substring(i + 1);
writeTo(fmt, path);
}

/**
* Utility for resolving paths on unix systems that contain tilda for
* the home directory.
*
* @param path the file system path
* @return normalised path
*/
private static String replaceTildaWithHomeDir(String path) {
if (path.startsWith("~/"))
return System.getProperty("user.home") + path.substring(1);
return path;
}

/**
* Ensures a suffix on a file output if the path doesn't
* currently end with it. For example calling
* {@code writeTo(SVG_FMT, "~/chemical")} would create a file
* {@code ~/chemical.svg}.
*
* @param path the file system path
* @param suffix the format suffix
* @return path with correct suffix
*/
private static String ensureSuffix(String path, String suffix) {
if (path.endsWith(DOT + suffix))
return path;
return path + DOT + suffix;
}

/**
* Low-level draw method used by other rendering methods.
*
* @param visitor the draw visitor
* @param bounds a bound rendering element
* @param zoom if the diagram is zoomed at all
* @param viewBounds the view bounds - the root will be centered in the bounds
*/
protected final void draw(IDrawVisitor visitor, double zoom, Bounds bounds, Rectangle2D viewBounds) {

double modelScale = zoom * model.get(BasicSceneGenerator.Scale.class);
double zoomToFit = Math.min(viewBounds.getWidth() / (bounds.width() * modelScale),
viewBounds.getHeight() / (bounds.height() * modelScale));

AffineTransform transform = new AffineTransform();
transform.translate(viewBounds.getCenterX(), viewBounds.getCenterY());
transform.scale(modelScale, -modelScale);

// default is shrink only unless specified
if (model.get(BasicSceneGenerator.FitToScreen.class) || zoomToFit < 1)
transform.scale(zoomToFit, zoomToFit);

transform.translate(-(bounds.minX + bounds.maxX) / 2,
-(bounds.minY + bounds.maxY) / 2);

// not always needed
AWTFontManager fontManager = new AWTFontManager();
fontManager.setFontForZoom(zoomToFit);

visitor.setRendererModel(model);
visitor.setFontManager(fontManager);
visitor.setTransform(transform);

// setup up transform
visitor.visit(bounds.root());
}

/**
* Utility method for recalling a depiction in pixels to one in millimeters.
*
* @param bondLength the desired bond length (mm)
* @return the scaling factor
*/
final double rescaleForBondLength(double bondLength) {
return bondLength / model.get(BasicSceneGenerator.BondLength.class);
}
}

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