Re: importing Text Image files

Posted by Unruh, Jay-2 on Oct 13, 2009; 6:57pm
URL: http://imagej.273.s1.nabble.com/importing-Text-Image-files-tp3690802p3690805.html

Stephen,

Below is the source code for a version of text_reader.java that accepts commas instead of tabs.

Jay Unruh
Research Specialist
Stowers Institute for Medical Research

import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import ij.plugin.*;
import java.awt.image.*;
import java.io.*;
import ij.io.*;
import ij.util.Tools;
//here is a csv reader.  This is just a copy of text_reader.java with the tokenizer changed to accept commas as delimiters
//changes made 4/22/08 by Jay Unruh, Research Specialist, Stowers Institute for Medical Research


public class csv_reader_jru_v1 implements PlugIn {
    int words = 0, chars = 0, lines = 0, width=1;;
    String directory, name, path;
    boolean hideErrorMessages;
   
    public void run(String arg) {
        if (showDialog()) {
            IJ.showStatus("Opening: " + path);
            ImageProcessor ip = open(path);
            if (ip!=null)
                new ImagePlus(name, ip).show();
        }
    }
   
    boolean showDialog() {
        OpenDialog od = new OpenDialog("Open Text Image...", null);
        directory = od.getDirectory();
        name = od.getFileName();
        if (name!=null)
            path = directory + name;
        return name!=null;
    }
   
    /** Displays a file open dialog and opens the specified text file as a float image. */
    public ImageProcessor open(){
        if (showDialog())
            return open(path);
        else
            return null;
    }
   
    /** Opens the specified text file as a float image. */
    public ImageProcessor open(String path){
        ImageProcessor ip = null;
        try {
            words = chars = lines = 0;
            Reader r = new BufferedReader(new FileReader(path));
            countLines(r);
            r.close();
            r = new BufferedReader(new FileReader(path));
            //int width = words/lines;
            float[] pixels = new float[width*lines];
            ip = new FloatProcessor(width, lines, pixels, null);
            read(r, width*lines, pixels);
            r.close();
            ip.resetMinAndMax();
        }
        catch (IOException e) {
            String msg = e.getMessage();
            if (msg==null || msg.equals(""))
                msg = ""+e;
            if (!hideErrorMessages)
            IJ.error("TextReader", msg);
            ip = null;
        }
        return ip;
    }
   
    public void hideErrorMessages() {
        hideErrorMessages = true;
    }

    /** Returns the file name. */
    public String getName() {
        return name;
    }

    void countLines(Reader r) throws IOException {
        StreamTokenizer tok = new StreamTokenizer(r);
        int wordsPerLine=0, wordsInPreviousLine=0;

        tok.resetSyntax();
        tok.wordChars(46, 127);
        tok.whitespaceChars(0, 45);
        tok.whitespaceChars(128, 255);
        tok.eolIsSignificant(true);

        while (tok.nextToken() != StreamTokenizer.TT_EOF) {
            switch (tok.ttype) {
                case StreamTokenizer.TT_EOL:
                    lines++;
                    if (wordsPerLine==0)
                        lines--;  // ignore empty lines
                    if (lines==1)
                        width = wordsPerLine;
                    else if (wordsPerLine!=0 && wordsPerLine!=wordsInPreviousLine)
                         throw new IOException("Line "+lines+ " is not the same length as the first line.");
                    if (wordsPerLine!=0)
                        wordsInPreviousLine = wordsPerLine;
                    wordsPerLine = 0;
                    if (lines%20==0 && width>1 && lines<=width)
                        IJ.showProgress(((double)lines/width)/2.0);
                    break;
                case StreamTokenizer.TT_WORD:
                    words++;
                    wordsPerLine++;
                    break;
            }
        }
        if (wordsPerLine==width)
            lines++; // last line does not end with EOL
   }

    void read(Reader r, int size, float[] pixels) throws IOException {
        StreamTokenizer tok = new StreamTokenizer(r);
        tok.resetSyntax();
        //the next two lines were changed by JU to allow for comma delimiters
        tok.wordChars(46, 127);
        tok.whitespaceChars(0, 45);
        tok.whitespaceChars(128, 255);
        //tok.parseNumbers();

        int i = 0;
        int inc = size/20;
        if (inc<1)
            inc = 1;
        while (tok.nextToken() != StreamTokenizer.TT_EOF) {
            if (tok.ttype==StreamTokenizer.TT_WORD) {
                pixels[i++] = (float)Tools.parseDouble(tok.sval, 0.0);
                 if (i==size)
                     break;
                 if (i%inc==0)
                     IJ.showProgress(0.5+((double)i/size)/2.0);
            }
        }
        IJ.showProgress(1.0);
    }

}

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Chinn, Steve Dr CIV USA AMC
Sent: Tuesday, October 13, 2009 1:42 PM
To: [hidden email]
Subject: importing Text Image files

(1.43h, Win XP Pro, SP3)

The documentation says that Import-> Text Image works with tab-delimited text files. We have camera output that saves precise numerical data only in comma-delimited text format, which cannot be loaded into ImageJ without an intermediate format conversion step using another application (e.g. Excel, Igor Pro). I could not find an appropriate ImageJ plug-in on the web site. Does anyone have such a plug-in or simpler solution?
Could this be added to ImageJ as a Text Image option?

 

Stephen R. Chinn, Ph.D.
US Army RDECOM CERDEC
Night Vision and Electronic Sensors Directorate RDER-NVS-LT
10221 Burbeck Road
Fort Belvoir, VA 22060-5806
[phone]; FAX: [phone]
[hidden email] <mailto:[hidden email]>