Examples with Section com.lowagie.text.Section used on opensource projects

Example 11 with Section

use of com.lowagie.text.Section in project vcell by virtualcell.

the class ITextWriter method writeGeometry.

// for now, the preferences for a geometry is a dummy.
public void writeGeometry(Geometry geom, FileOutputStream fos, PageFormat pageFormat, PublishPreferences preferences) throws Exception {
    if (geom == null || fos == null || pageFormat == null || preferences == null) {
        throw new IllegalArgumentException("One or more null params while publishing Geometry.");
    }
    try {
        createDocument(pageFormat);
        createDocWriter(fos);
        // Add metadata before you open the document...
        String name = geom.getName().trim();
        String userName = "Unknown";
        if (geom.getVersion() != null) {
            userName = geom.getVersion().getOwner().getName();
        }
        document.addTitle(name + "[owned by " + userName + "]");
        document.addCreator("Virtual Cell");
        document.addCreationDate();
        // writeWatermark(document, pageFormat);
        writeHeaderFooter("Geometry: " + name);
        document.open();
        // 
        Section introSection = null;
        int chapterNum = 1;
        Chapter geomChapter = new Chapter("Geometry", chapterNum++);
        introSection = geomChapter.addSection("General Info", geomChapter.numberDepth() + 1);
        writeMetadata(introSection, name, geom.getDescription(), userName, "Geometry");
        // title?
        Section geomSection = geomChapter.addSection("Geometry", geomChapter.numberDepth() + 1);
        writeGeom(geomSection, geom, null);
        document.add(geomChapter);
        document.close();
    } catch (DocumentException e) {
        System.err.println("Unable to publish BioModel.");
        e.printStackTrace();
        throw e;
    }
}

Example 12 with Section

use of com.lowagie.text.Section in project vcell by virtualcell.

the class ITextWriter method writeMathDescAsImages.

// container can be a chapter or a section of a chapter.
// MathDescription.description ignored.
// currently not used.
protected void writeMathDescAsImages(Section container, MathDescription mathDesc) throws DocumentException {
    if (mathDesc == null) {
        return;
    }
    Section mathDescSection = container.addSection("Math Description: " + mathDesc.getName(), container.depth() + 1);
    Section mathDescSubSection = null;
    Expression[] expArray = null;
    BufferedImage dummy = new BufferedImage(500, 50, BufferedImage.TYPE_3BYTE_BGR);
    int scale = 1;
    int viewableWidth = (int) (document.getPageSize().width() - document.leftMargin() - document.rightMargin());
    // add Constants
    Enumeration<Constant> constantsList = mathDesc.getConstants();
    while (constantsList.hasMoreElements()) {
        Constant constant = constantsList.nextElement();
        Expression exp = constant.getExpression();
        try {
            expArray = new Expression[] { Expression.assign(new Expression(constant.getName()), exp.flatten()) };
        } catch (ExpressionException ee) {
            System.err.println("Unable to process constant " + constant.getName() + " for publishing");
            ee.printStackTrace();
            continue;
        }
        try {
            Dimension dim = ExpressionCanvas.getExpressionImageSize(expArray, (Graphics2D) dummy.getGraphics());
            BufferedImage bufferedImage = new BufferedImage((int) dim.getWidth() * scale, (int) dim.getHeight() * scale, BufferedImage.TYPE_3BYTE_BGR);
            ExpressionCanvas.getExpressionAsImage(expArray, bufferedImage, scale);
            com.lowagie.text.Image expImage = com.lowagie.text.Image.getInstance(bufferedImage, null);
            expImage.setAlignment(com.lowagie.text.Image.ALIGN_LEFT);
            if (mathDescSubSection == null) {
                mathDescSubSection = mathDescSection.addSection("Constants", mathDescSection.depth() + 1);
            }
            if (viewableWidth < Math.floor(expImage.scaledWidth())) {
                expImage.scaleToFit(viewableWidth, expImage.plainHeight());
                System.out.println("Constant After scaling: " + expImage.scaledWidth());
            }
            mathDescSubSection.add(expImage);
        } catch (Exception e) {
            System.err.println("Unable to add structure mapping image to report.");
            e.printStackTrace();
        }
    }
    mathDescSubSection = null;
    // add functions
    Enumeration<Function> functionsList = mathDesc.getFunctions();
    while (functionsList.hasMoreElements()) {
        Function function = functionsList.nextElement();
        Expression exp = function.getExpression();
        try {
            expArray = new Expression[] { Expression.assign(new Expression(function.getName()), exp.flatten()) };
        } catch (ExpressionException ee) {
            System.err.println("Unable to process function " + function.getName() + " for publishing");
            ee.printStackTrace();
            continue;
        }
        try {
            Dimension dim = ExpressionCanvas.getExpressionImageSize(expArray, (Graphics2D) dummy.getGraphics());
            BufferedImage bufferedImage = new BufferedImage((int) dim.getWidth() * scale, (int) dim.getHeight() * scale, BufferedImage.TYPE_3BYTE_BGR);
            ExpressionCanvas.getExpressionAsImage(expArray, bufferedImage, scale);
            com.lowagie.text.Image expImage = com.lowagie.text.Image.getInstance(bufferedImage, null);
            expImage.setAlignment(com.lowagie.text.Image.ALIGN_LEFT);
            if (mathDescSubSection == null) {
                mathDescSubSection = mathDescSection.addSection("Functions", mathDescSection.depth() + 1);
            }
            if (viewableWidth < Math.floor(expImage.scaledWidth())) {
                expImage.scaleToFit(viewableWidth, expImage.height());
                System.out.println("Function After scaling: " + expImage.scaledWidth());
            }
            mathDescSubSection.add(expImage);
        } catch (Exception e) {
            System.err.println("Unable to add structure mapping image to report.");
            e.printStackTrace();
        }
    }
    writeSubDomainsEquationsAsImages(mathDescSection, mathDesc);
}

Example 13 with Section

use of com.lowagie.text.Section in project vcell by virtualcell.

the class ITextWriter method writeGeom.

// Section used can be a chapter or a section of one, based on the document type.
protected void writeGeom(Section container, Geometry geom, GeometryContext geomCont) throws Exception {
    try {
        Section geomSection = container.addSection("Geometry: " + geom.getName(), container.numberDepth() + 1);
        if (geom.getDimension() == 0) {
            Paragraph p = new Paragraph(new Phrase("Non spatial geometry."));
            p.setAlignment(Paragraph.ALIGN_CENTER);
            geomSection.add(p);
            return;
        }
        ByteArrayOutputStream bos = generateGeometryImage(geom);
        com.lowagie.text.Image geomImage = com.lowagie.text.Image.getInstance(java.awt.Toolkit.getDefaultToolkit().createImage(bos.toByteArray()), null);
        geomImage.setAlignment(Table.ALIGN_LEFT);
        geomSection.add(geomImage);
        // addImage(geomSection, bos);
        Table geomTable = getTable(2, 50, 1, 2, 2);
        geomTable.setAlignment(Table.ALIGN_LEFT);
        Extent extent = geom.getExtent();
        String extentStr = "(" + extent.getX() + ", " + extent.getY() + ", " + extent.getZ() + ")";
        Origin origin = geom.getOrigin();
        String originStr = "(" + origin.getX() + ", " + origin.getY() + ", " + origin.getZ() + ")";
        geomTable.addCell(createCell("Size", getFont()));
        geomTable.addCell(createCell(extentStr, getFont()));
        geomTable.addCell(createCell("Origin", getFont()));
        geomTable.addCell(createCell(originStr, getFont()));
        geomSection.add(geomTable);
    } catch (Exception e) {
        System.err.println("Unable to add geometry image to report.");
        e.printStackTrace();
    }
}

Example 14 with Section

use of com.lowagie.text.Section in project vcell by virtualcell.

the class ITextWriter method writeStructureMapping.

// boundary types ignored.
protected void writeStructureMapping(Section simContextSection, SimulationContext sc) throws DocumentException {
    GeometryContext gc = sc.getGeometryContext();
    if (gc == null) {
        return;
    }
    Section structMappSection = null;
    /*try {
			ByteArrayOutputStream bos = generateStructureMappingImage(sc);
			com.lowagie.text.Image structMapImage = com.lowagie.text.Image.getInstance(Toolkit.getDefaultToolkit().createImage(bos.toByteArray()), null);
			structMappSection = simContextSection.addSection("Structure Mapping For " + sc.getName(), simContextSection.numberDepth() + 1);
			structMappSection.add(structMapImage);
		} catch (Exception e) {
			System.err.println("Unable to add structure mapping image to report.");
			e.printStackTrace();
		}*/
    StructureMapping[] structMap = gc.getStructureMappings();
    Table structMapTable = null;
    ModelUnitSystem modelUnitSystem = sc.getModel().getUnitSystem();
    for (int i = 0; i < structMap.length; i++) {
        if (!(structMap[i] instanceof FeatureMapping)) {
            continue;
        }
        if (i == 0) {
            structMapTable = getTable(5, 100, 1, 3, 3);
            structMapTable.addCell(createCell("Structure Mapping", getBold(DEF_HEADER_FONT_SIZE), 5, 1, Element.ALIGN_CENTER, true));
            structMapTable.addCell(createHeaderCell("Structure", getBold(), 1));
            structMapTable.addCell(createHeaderCell("Subdomain", getBold(), 1));
            structMapTable.addCell(createHeaderCell("Resolved (T/F)", getBold(), 1));
            structMapTable.addCell(createHeaderCell("Surf/Vol", getBold(), 1));
            structMapTable.addCell(createHeaderCell("VolFract", getBold(), 1));
            structMapTable.endHeaders();
        }
        String structName = structMap[i].getStructure().getName();
        SubVolume subVol = (SubVolume) ((FeatureMapping) structMap[i]).getGeometryClass();
        String subDomain = "";
        if (subVol != null) {
            subDomain = subVol.getName();
        }
        // ((FeatureMapping)structMap[i]).getResolved();
        boolean isResolved = false;
        String surfVolStr = "", volFractStr = "";
        MembraneMapping mm = (MembraneMapping) gc.getStructureMapping(sc.getModel().getStructureTopology().getParentStructure(structMap[i].getStructure()));
        if (mm != null) {
            StructureMapping.StructureMappingParameter smp = mm.getSurfaceToVolumeParameter();
            if (smp != null) {
                Expression tempExp = smp.getExpression();
                VCUnitDefinition tempUnit = smp.getUnitDefinition();
                if (tempExp != null) {
                    surfVolStr = tempExp.infix();
                    if (tempUnit != null && !modelUnitSystem.getInstance_DIMENSIONLESS().compareEqual(tempUnit)) {
                        // no need to add '1' for dimensionless unit
                        surfVolStr += " " + tempUnit.getSymbolUnicode();
                    }
                }
            }
            smp = mm.getVolumeFractionParameter();
            if (smp != null) {
                Expression tempExp = smp.getExpression();
                VCUnitDefinition tempUnit = smp.getUnitDefinition();
                if (tempExp != null) {
                    volFractStr = tempExp.infix();
                    if (tempUnit != null && !modelUnitSystem.getInstance_DIMENSIONLESS().compareEqual(tempUnit)) {
                        volFractStr += " " + tempUnit.getSymbolUnicode();
                    }
                }
            }
        }
        structMapTable.addCell(createCell(structName, getFont()));
        structMapTable.addCell(createCell(subDomain, getFont()));
        structMapTable.addCell(createCell((isResolved ? " T " : " F "), getFont()));
        structMapTable.addCell(createCell(surfVolStr, getFont()));
        structMapTable.addCell(createCell(volFractStr, getFont()));
    }
    if (structMapTable != null) {
        if (structMappSection == null) {
            structMappSection = simContextSection.addSection("Structure Mapping For " + sc.getName(), simContextSection.numberDepth() + 1);
        }
        structMappSection.add(structMapTable);
    }
}

Example 15 with Section

use of com.lowagie.text.Section in project vcell by virtualcell.

the class ITextWriter method writeMathModel.

public void writeMathModel(MathModel mathModel, FileOutputStream fos, PageFormat pageFormat, PublishPreferences preferences) throws Exception {
    if (mathModel == null || fos == null || pageFormat == null || preferences == null) {
        throw new IllegalArgumentException("One or more null params while publishing MathModel.");
    }
    try {
        createDocument(pageFormat);
        createDocWriter(fos);
        // Add metadata before you open the document...
        String name = mathModel.getName().trim();
        String userName = "Unknown";
        if (mathModel.getVersion() != null) {
            userName = mathModel.getVersion().getOwner().getName();
        }
        document.addTitle(name + "[owned by " + userName + "]");
        document.addCreator("Virtual Cell");
        document.addCreationDate();
        // writeWatermark(document, pageFormat);
        writeHeaderFooter("MathModel: " + name);
        document.open();
        // 
        int chapterNum = 1;
        Section introSection = null;
        if (preferences.includeMathDesc()) {
            MathDescription mathDesc = mathModel.getMathDescription();
            Chapter mathDescChapter = new Chapter("Math Description", chapterNum++);
            introSection = mathDescChapter.addSection("General Info", mathDescChapter.numberDepth() + 1);
            writeMetadata(introSection, name, mathModel.getDescription(), userName, "MathModel");
            writeMathDescAsText(mathDescChapter, mathDesc);
            document.add(mathDescChapter);
        }
        if (preferences.includeSim()) {
            // unlike biomodels, simulations are chapters, not chapter sections.
            Simulation[] sims = mathModel.getSimulations();
            if (sims != null) {
                Chapter simChapter = new Chapter("Simulations", chapterNum++);
                if (introSection == null) {
                    introSection = simChapter.addSection("General Info", simChapter.numberDepth() + 1);
                    writeMetadata(introSection, name, mathModel.getDescription(), userName, "MathModel");
                }
                for (int i = 0; i < sims.length; i++) {
                    writeSimulation(simChapter, sims[i]);
                }
                document.add(simChapter);
            } else {
                System.err.println("Bad Request: No simulations to publish for Mathmodel: " + name);
            }
        }
        if (preferences.includeGeom()) {
            // unlike biomodels, geometry is a chapter, not a chapter section.
            Geometry geom = mathModel.getMathDescription().getGeometry();
            if (geom != null) {
                Chapter geomChapter = new Chapter("Geometry", chapterNum++);
                if (introSection == null) {
                    introSection = geomChapter.addSection("General Info", geomChapter.numberDepth() + 1);
                    writeMetadata(introSection, name, mathModel.getDescription(), userName, "MathModel");
                }
                writeGeom(geomChapter, geom, null);
                document.add(geomChapter);
            } else {
                System.err.println("Bad Request: No geometry to publish for Mathmodel: " + name);
            }
        }
        document.close();
    } catch (DocumentException e) {
        System.err.println("Unable to publish MathModel.");
        e.printStackTrace();
        throw e;
    }
}