<commit_before>package edu.emory.cellbio.svg;

import ij.IJ;

import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.Iterator;

import java.awt.image.BufferedImage;
import javax.imageio.ImageIO;
import javax.imageio.ImageWriteParam;
import javax.imageio.ImageWriter;
import javax.imageio.stream.ImageOutputStream;
import javax.swing.JFileChooser;
import javax.swing.JOptionPane;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;

import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.apache.commons.codec.binary.Base64OutputStream;

/**
 * 
 * @author <NAME>
 */
public class EmbedAndCrop 
{
     
     // -- Fields --
     
     private String imgFileType = "png";
     private float compQual = 0.8f;
     
     // -- Methods --
     
     public void runInkscapeExtension(String[] args) {
          File input = null;
          if(args == null || args.length<1) {
               System.err.println("Missing command line arguments");
               input = openDialog();
          }
          try {
               getOutputParams();
               if(input == null && args != null)
                    input = new File(args[0]);
               if(input == null || !input.canRead())
                    throw new EmbedAndCropException("Can't read temporary input file "
                         + input != null ? input.getPath() : "<null>");
               Document dom = readSVG(input);
               process(dom);
               SVGToStream(dom, System.out);
          } catch(Throwable t) {
               t.printStackTrace();
               JOptionPane.showMessageDialog(null, t.getMessage(), "Error", JOptionPane.ERROR_MESSAGE);
               System.exit(1);
          }
          System.exit(0);
     }
     
     // -- Helper methods --
     
     /** Process an SVG DOM */
     private void process(Document dom) throws EmbedAndCropException {
          NodeList images = dom.getElementsByTagName("image");
          for(int i=0; i<images.getLength(); i++) {
               Node img = images.item(i);
               if(img.getNodeType() == Node.ELEMENT_NODE) {
                    Element clip = getClipPath((Element)img, dom);
                    if(clip != null) {
                         processImg((Element)img, clip);
                    }
                    else
                         processImg((Element)img, null);<commit_msg>Added command flags for automation<commit_after>package edu.emory.cellbio.svg;

import ij.IJ;

import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.Iterator;

import java.awt.image.BufferedImage;
import javax.imageio.ImageIO;
import javax.imageio.ImageWriteParam;
import javax.imageio.ImageWriter;
import javax.imageio.stream.ImageOutputStream;
import javax.swing.JFileChooser;
import javax.swing.JOptionPane;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;

import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.apache.commons.codec.binary.Base64OutputStream;

/**
 * 
 * @author <NAME>
 */
public class EmbedAndCrop 
{
     
     // -- Fields --
     
     private String imgFileType = "png";
     private float compQual = 0.8f;
     
     // -- Methods --
     
     /**
      * Run the extension
      * @param args
      *   <br>- The first argument should be the path of the
      *   source svg file
      *   <br>- The second (optional) command should be the image file type
      *   <br>- The third (optional, but required if a file type is given)
      *        command should be the compression quality.
      *   <br><br>Example: "file.svg" "jpeg" "0.95" or "file.svg" "png" "1"
      */
     public void runInkscapeExtension(String[] args) {
          File input = null;
          if(args == null || args.length<1) {
               System.err.println("Missing command line arguments");
               input = openDialog();
          }
          try {
               if(input == null && args != null)
                    input = new File(args[0]);
               if(args != null && !(args.length < 3)) {
                    imgFileType = args[1];
                    try{ compQual = Float.parseFloat(args[2]); }
                    catch(NumberFormatException e){ throw new EmbedAndCropException(e.toString()); }
               }
               else getOutputParams();
               if(input == null || !input.canRead())
                    throw new EmbedAndCropException("Can't read temporary input file "
                         + input != null ? input.getPath() : "<null>");
               Document dom = readSVG(input);
               process(dom);
               SVGToStream(dom, System.out);
          } catch(Throwable t) {
               t.printStackTrace();
               JOptionPane.showMessageDialog(null, t.getMessage(), "Error", JOptionPane.ERROR_MESSAGE);
               System.exit(1);
          }
          System.exit(0);
     }
     
     // -- Helper methods --
     
     /** Process an SVG DOM */
     private void process(Document dom) throws EmbedAndCropException {
          NodeList images = dom.getElementsByTagName("image");
          for(int i=0; i<images.getLength(); i++) {
               Node img = images.item(i);
               if(img.getNodeType() == Node.ELEMENT_NODE) {
                    Element clip = getClipPath((Element)img, dom);
                    if(clip != null) {
                         processImg((Element)img, clip);
                    }
                    else
                         processImg((Element)img, null);
{'fraction_non_alphanumeric': 0.11455735660847881, 'fraction_numerical': 0.005143391521197007, 'mean_word_length': 2.102998065764023, 'pattern_counts': {'":': 0, '<': 17, '<?xml version=': 0, '>': 12, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 16}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '368374', 'n_tokens_mistral': 1810, 'n_tokens_neox': 1767, 'n_words': 393}