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PDFWriter.java
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PDFWriter.java
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/*-
* #%L
* Fiji's plugin for colocalization analysis.
* %%
* Copyright (C) 2009 - 2017 Fiji developers.
* %%
* 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 3 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-3.0.html>.
* #L%
*/
package sc.fiji.coloc.results;
import com.itextpdf.text.BadElementException;
import com.itextpdf.text.Document;
import com.itextpdf.text.DocumentException;
import com.itextpdf.text.PageSize;
import com.itextpdf.text.Paragraph;
import com.itextpdf.text.pdf.PdfContentByte;
import com.itextpdf.text.pdf.PdfWriter;
import ij.IJ;
import ij.ImagePlus;
import ij.io.SaveDialog;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.algorithm.math.ImageStatistics;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.LongType;
import sc.fiji.coloc.algorithms.Histogram2D;
import sc.fiji.coloc.gadgets.DataContainer;
import sc.fiji.coloc.gadgets.DataContainer.MaskType;
public class PDFWriter<T extends RealType<T>> implements ResultHandler<T> {
// indicates if we want to produce US letter or A4 size
boolean isLetter = false;
// indicates if the content is the first item on the page
boolean isFirst = true;
// show the name of the image
static boolean showName=true;
// a static counter for this sessions created PDFs
static int succeededPrints = 0;
// show the size in pixels of the image
static boolean showSize=true;
// a reference to the data container
DataContainer<T> container;
PdfWriter writer;
Document document;
// a list of the available result images, no matter what specific kinds
protected List<com.itextpdf.text.Image> listOfPDFImages
= new ArrayList<com.itextpdf.text.Image>();
protected List<Paragraph> listOfPDFTexts
= new ArrayList<Paragraph>();
// a list of PDF warnings
protected List<Paragraph> PDFwarnings = new ArrayList<Paragraph>();
/**
* Creates a new PDFWriter that can access the container.
*
* @param container The data container for source image data
*/
public PDFWriter(DataContainer<T> container) {
this.container = container;
}
@Override
public void handleImage(RandomAccessibleInterval<T> image, String name) {
ImagePlus imp = ImageJFunctions.wrapFloat( image, name );
// set the display range
double max = ImageStatistics.getImageMax(image).getRealDouble();
imp.setDisplayRange(0.0, max);
addImageToList(imp, name);
}
/**
* Handles a histogram the following way: create snapshot, log data, reset the
* display range, apply the Fire LUT and finally store it as an iText PDF image.
* Afterwards the image is reset to its orignal state again
*/
@Override
public void handleHistogram(Histogram2D<T> histogram, String name) {
RandomAccessibleInterval<LongType> image = histogram.getPlotImage();
ImagePlus imp = ImageJFunctions.wrapFloat( image, name );
// make a snapshot to be able to reset after modifications
imp.getProcessor().snapshot();
imp.getProcessor().log();
imp.updateAndDraw();
imp.getProcessor().resetMinAndMax();
IJ.run(imp,"Fire", null);
addImageToList(imp, name);
// reset the imp from the log scaling we applied earlier
imp.getProcessor().reset();
}
protected void addImageToList(ImagePlus imp, String name) {
java.awt.Image awtImage = imp.getImage();
try {
com.itextpdf.text.Image pdfImage = com.itextpdf.text.Image.getInstance(awtImage, null);
pdfImage.setAlt(name); // iText-1.3 setMarkupAttribute("name", name);
listOfPDFImages.add(pdfImage);
}
catch (BadElementException e) {
IJ.log("Could not convert image to correct format for PDF generation");
IJ.handleException(e);
}
catch (IOException e) {
IJ.log("Could not convert image to correct format for PDF generation");
IJ.handleException(e);
}
}
@Override
public void handleWarning(Warning warning) {
PDFwarnings.add(new Paragraph("Warning! " + warning.getShortMessage() + " - " + warning.getLongMessage()));
}
@Override
public void handleValue(String name, String value) {
listOfPDFTexts.add(new Paragraph(name + ": " + value));
}
@Override
public void handleValue(String name, double value) {
handleValue(name, value, 3);
}
@Override
public void handleValue(String name, double value, int decimals) {
listOfPDFTexts.add(new Paragraph(name + ": " + IJ.d2s(value, decimals)));
}
/**
* Prints an image into the opened PDF.
* @param image The image to print.
*/
protected void addImage(com.itextpdf.text.Image image)
throws DocumentException, IOException {
if (! isFirst) {
document.add(new Paragraph("\n"));
float vertPos = writer.getVerticalPosition(true);
if (vertPos - document.bottom() < image.getHeight()) {
document.newPage();
} else {
PdfContentByte cb = writer.getDirectContent();
cb.setLineWidth(1f);
if (isLetter) {
cb.moveTo(PageSize.LETTER.getLeft(50), vertPos);
cb.lineTo(PageSize.LETTER.getRight(50), vertPos);
} else {
cb.moveTo(PageSize.A4.getLeft(50), vertPos);
cb.lineTo(PageSize.A4.getRight(50), vertPos);
}
cb.stroke();
}
}
if (showName) {
Paragraph paragraph = new Paragraph(image.getAlt()); // iText-1.3: getMarkupAttribute("name"));
paragraph.setAlignment(Paragraph.ALIGN_CENTER);
document.add(paragraph);
//spcNm = 40;
}
if (showSize) {
Paragraph paragraph = new Paragraph(image.getWidth() + " x " + image.getHeight());
paragraph.setAlignment(Paragraph.ALIGN_CENTER);
document.add(paragraph);
//spcSz = 40;
}
image.setAlignment(com.itextpdf.text.Image.ALIGN_CENTER);
document.add(image);
isFirst = false;
}
@Override
public void process() {
try {
// Use the getJobName() in DataContainer for the job name.
String jobName = container.getJobName();
/* If a mask is in use, add a counter
* information to the jobName.
*/
if (container.getMaskType() != MaskType.None) {
// maskHash is now used as the mask or ROI unique ID in the
// jobName but we can still increment and use succeededPrints at
// the end of the filename for PDFs when there is a mask.
jobName += (succeededPrints + 1);
}
// get the path to the file we are about to create
SaveDialog sd = new SaveDialog("Save as PDF", jobName, ".pdf");
// update jobName if the user changes it in the save file dialog.
jobName = sd.getFileName();
String directory = sd.getDirectory();
// make sure we have what we need next
if ((jobName == null) || (directory == null)) {
return;
}
String path = directory+jobName;
// create a new iText Document and add date and title
document = new Document(isLetter ? PageSize.LETTER : PageSize.A4);
document.addCreationDate();
document.addTitle(jobName);
// get a writer object to do the actual output
writer = PdfWriter.getInstance(document, new FileOutputStream(path));
document.open();
// write job name at the top of the PDF file as a title
Paragraph titlePara = new Paragraph(jobName);
document.add(titlePara);
// iterate over all produced images
for (com.itextpdf.text.Image img : listOfPDFImages) {
addImage(img);
}
//iterate over all produced PDFwarnings
for (Paragraph p : PDFwarnings) {
document.add(p);
}
//iterate over all produced text objects
for (Paragraph p : listOfPDFTexts) {
document.add(p);
}
} catch(DocumentException de) {
IJ.showMessage("PDF Writer", de.getMessage());
} catch(IOException ioe) {
IJ.showMessage("PDF Writer", ioe.getMessage());
} finally {
if (document !=null) {
document.close();
succeededPrints++;
}
}
}
}

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