Examples with SaveDialog ij.io.SaveDialog used on opensource projects

Example 6 with SaveDialog

use of ij.io.SaveDialog in project imagej1 by imagej.

the class TextPanel method saveAs.

/**
 * Saves all the text in this TextPanel to a file. Set
 *		'path' to "" to display a save as dialog. Returns
 *		'false' if the user cancels the save as dialog.
 */
public boolean saveAs(String path) {
    boolean isResults = IJ.isResultsWindow() && IJ.getTextPanel() == this;
    boolean summarized = false;
    if (isResults) {
        String lastLine = iRowCount >= 2 ? getLine(iRowCount - 2) : null;
        summarized = lastLine != null && lastLine.startsWith("Max");
    }
    String fileName = null;
    if (rt != null && rt.getCounter() != 0 && !summarized) {
        if (path == null || path.equals("")) {
            IJ.wait(10);
            String name = isResults ? "Results" : title;
            SaveDialog sd = new SaveDialog("Save Results", name, Prefs.defaultResultsExtension());
            fileName = sd.getFileName();
            if (fileName == null)
                return false;
            path = sd.getDirectory() + fileName;
        }
        rt.save(path);
        TextWindow tw = getTextWindow();
        if (fileName != null && tw != null && !"Results".equals(title)) {
            tw.setTitle(fileName);
            title = fileName;
        }
    } else {
        if (path.equals("")) {
            IJ.wait(10);
            boolean hasHeadings = !getColumnHeadings().equals("");
            String ext = isResults || hasHeadings ? Prefs.defaultResultsExtension() : ".txt";
            SaveDialog sd = new SaveDialog("Save as Text", title, ext);
            String file = sd.getFileName();
            if (file == null)
                return false;
            path = sd.getDirectory() + file;
        }
        PrintWriter pw = null;
        try {
            FileOutputStream fos = new FileOutputStream(path);
            BufferedOutputStream bos = new BufferedOutputStream(fos);
            pw = new PrintWriter(bos);
        } catch (IOException e) {
            IJ.error("Save As>Text", e.getMessage());
            return true;
        }
        saveAsCSV = path.endsWith(".csv");
        save(pw);
        saveAsCSV = false;
        pw.close();
    }
    if (isResults) {
        Analyzer.setUnsavedMeasurements(false);
        if (Recorder.record && !IJ.isMacro())
            Recorder.record("saveAs", "Results", path);
    } else if (rt != null) {
        if (Recorder.record && !IJ.isMacro())
            Recorder.record("saveAs", "Results", path);
    } else {
        if (Recorder.record && !IJ.isMacro())
            Recorder.record("saveAs", "Text", path);
    }
    IJ.showStatus("");
    return true;
}

Example 7 with SaveDialog

use of ij.io.SaveDialog in project TrakEM2 by trakem2.

the class Compare method compareAllToAll.

/**
 * Gets pipes for all open projects, and generates a matrix of dissimilarities, which gets passed on to the Worker thread and also to a file, if desired.
 *
 * @param to_file Whether to save the results to a file and popup a save dialog for it or not. In any case the results are stored in the worker's load, which you can retrieve like:
 * <pre>
 * Bureaucrat bu = Compare.compareAllToAll(true, null, null);
 * Object result = bu.getWorker().getResult();
 * float[][] scores = (float[][])result[0];
 * ArrayList&lt;Compare.Chain&gt; chains = (ArrayList&lt;Compare.Chain&gt;)result[1];
 * </pre>
 */
public static Bureaucrat compareAllToAll(final boolean to_file, final String regex, final String[] ignore, final Project[] projects, final boolean crop, final boolean from_end, final int max_n_elements, final String outgroup) {
    // gather all open projects
    final Project[] p = null == projects ? Project.getProjects().toArray(new Project[0]) : projects;
    final Worker worker = new Worker("Comparing all to all") {

        @Override
        public void run() {
            startedWorking();
            try {
                final CATAParameters cp = new CATAParameters();
                if (!cp.setup(to_file, regex, false, false)) {
                    finishedWorking();
                    return;
                }
                String filename = null, dir = null;
                if (to_file) {
                    final SaveDialog sd = new SaveDialog("Save matrix", OpenDialog.getDefaultDirectory(), null, ".csv");
                    filename = sd.getFileName();
                    if (null == filename) {
                        finishedWorking();
                        return;
                    }
                    dir = sd.getDirectory().replace('\\', '/');
                    if (!dir.endsWith("/"))
                        dir += "/";
                }
                Object[] ob = gatherChains(p, cp, ignore);
                final ArrayList<Chain> chains = (ArrayList<Chain>) ob[0];
                // to keep track of each project's chains
                final ArrayList[] p_chains = (ArrayList[]) ob[1];
                ob = null;
                if (null == chains) {
                    finishedWorking();
                    return;
                }
                final int n_chains = chains.size();
                // crop chains if desired
                if (crop) {
                    for (final Chain chain : chains) {
                        if (from_end) {
                            final int start = chain.vs.length() - max_n_elements;
                            if (start > 0) {
                                chain.vs = chain.vs.substring(start, chain.vs.length());
                                // BEFORE making it relative
                                chain.vs.resample(cp.delta, cp.with_source);
                            }
                        } else {
                            if (max_n_elements < chain.vs.length()) {
                                chain.vs = chain.vs.substring(0, max_n_elements);
                                // BEFORE making it relative
                                chain.vs.resample(cp.delta, cp.with_source);
                            }
                        }
                    }
                }
                // compare all to all
                final VectorString3D[] vs = new VectorString3D[n_chains];
                for (int i = 0; i < n_chains; i++) vs[i] = chains.get(i).vs;
                final float[][] scores = Compare.scoreAllToAll(vs, cp.distance_type, cp.delta, cp.skip_ends, cp.max_mut, cp.min_chunk, cp.direct, cp.substring_matching, this);
                if (null == scores) {
                    finishedWorking();
                    return;
                }
                // store matrix and chains into the worker
                this.result = new Object[] { scores, chains };
                // write to file
                if (!to_file) {
                    finishedWorking();
                    return;
                }
                final File f = new File(dir + filename);
                // encoding in Latin 1 (for macosx not to mess around
                final OutputStreamWriter dos = new OutputStreamWriter(new BufferedOutputStream(new FileOutputStream(f)), "8859_1");
                // Normalize matrix to largest value of 1.0
                if (cp.normalize) {
                    float max = 0;
                    for (int i = 0; i < scores.length; i++) {
                        // traverse half matrix ony: it's mirrored
                        for (int j = i; j < scores[0].length; j++) {
                            if (scores[i][j] > max)
                                max = scores[i][j];
                        }
                    }
                    for (int i = 0; i < scores.length; i++) {
                        for (int j = i; j < scores[0].length; j++) {
                            scores[i][j] = scores[j][i] /= max;
                        }
                    }
                }
                // write chain titles, with project prefix
                if (cp.format.equals(cp.formats[0])) {
                    // as csv:
                    try {
                        final StringBuffer[] titles = new StringBuffer[n_chains];
                        int next = 0;
                        for (int i = 0; i < p.length; i++) {
                            final String prefix = Utils.getCharacter(i + 1);
                            // empty upper left corner
                            dos.write("\"\"");
                            for (final Chain chain : (ArrayList<Chain>) p_chains[i]) {
                                dos.write(",");
                                titles[next] = new StringBuffer().append('\"').append(prefix).append(' ').append(chain.getCellTitle()).append('\"');
                                dos.write(titles[next].toString());
                                next++;
                            }
                        }
                        dos.write("\n");
                        for (int i = 0; i < n_chains; i++) {
                            final StringBuffer line = new StringBuffer();
                            line.append(titles[i]);
                            for (int j = 0; j < n_chains; j++) line.append(',').append(scores[i][j]);
                            line.append('\n');
                            dos.write(line.toString());
                        }
                        dos.flush();
                    } catch (final Exception e) {
                        e.printStackTrace();
                    }
                } else if (cp.format.equals(cp.formats[1])) {
                    // as XML:
                    try {
                        final StringBuffer sb = new StringBuffer("<?xml version=\"1.0\"?>\n<!DOCTYPE ggobidata SYSTEM \"ggobi.dtd\">\n");
                        sb.append("<ggobidata count=\"2\">\n");
                        sb.append("<data name=\"Pipe Chains\">\n");
                        sb.append("<description />\n");
                        // ggobi: what a crappy XML parser it has
                        sb.append("<variables count=\"0\">\n</variables>\n");
                        sb.append("<records count=\"").append(chains.size()).append("\" glyph=\"fr 1\" color=\"3\">\n");
                        int next = 0;
                        for (int i = 0; i < p.length; i++) {
                            final String prefix = Utils.getCharacter(i + 1);
                            final String color = new StringBuffer("color=\"").append(i + 1).append('\"').toString();
                            for (final Chain chain : (ArrayList<Chain>) p_chains[i]) {
                                sb.append("<record id=\"").append(next + 1).append("\" label=\"").append(prefix).append(' ').append(chain.getCellTitle()).append("\" ").append(color).append("></record>\n");
                                next++;
                            }
                        }
                        sb.append("</records>\n</data>\n");
                        sb.append("<data name=\"distances\">\n");
                        sb.append("<description />\n");
                        sb.append("<variables count=\"1\">\n<realvariable name=\"D\" />\n</variables>\n");
                        sb.append("<records count=\"").append(n_chains * (n_chains - 1)).append("\" glyph=\"fr 1\" color=\"0\">\n");
                        for (int i = 0; i < n_chains; i++) {
                            for (int j = 0; j < n_chains; j++) {
                                if (i == j)
                                    continue;
                                sb.append("<record source=\"").append(i + 1).append("\" destination=\"").append(j + 1).append("\">").append(scores[i][j]).append("</record>\n");
                            }
                        }
                        sb.append("</records>\n</data>\n");
                        sb.append("</ggobidata>");
                        dos.write(sb.toString());
                        dos.flush();
                    } catch (final Exception e) {
                        e.printStackTrace();
                    }
                } else if (cp.format.equals(cp.formats[2])) {
                    // as Phylip .dis
                    try {
                        // collect different projects
                        final ArrayList<Project> projects = new ArrayList<Project>();
                        for (final Chain chain : chains) {
                            final Project p = chain.getRoot().getProject();
                            if (!projects.contains(p))
                                projects.add(p);
                        }
                        final HashSet names = new HashSet();
                        final StringBuffer sb = new StringBuffer();
                        sb.append(scores.length).append('\n');
                        dos.write(sb.toString());
                        // unique ids, since phylip cannot handle long names
                        final AtomicInteger ids = new AtomicInteger(0);
                        final File ftags = new File(dir + filename + ".tags");
                        // encoding in Latin 1 (for macosx not to mess around
                        final OutputStreamWriter dostags = new OutputStreamWriter(new BufferedOutputStream(new FileOutputStream(ftags)), "8859_1");
                        for (int i = 0; i < scores.length; i++) {
                            sb.setLength(0);
                            // String title = chains.get(i).getShortCellTitle().replace(' ', '_').replace('\t', '_').replace('[', '-').replace(']', '-');
                            final int id = ids.incrementAndGet();
                            final String sid = Utils.getCharacter(id);
                            String name = chains.get(i).getShortCellTitle();
                            // If sid.length() > 10 chars, trouble!
                            if (sid.length() > 10) {
                                Utils.log2("Ignoring " + name + " : id longer than 10 chars: " + id);
                                continue;
                            }
                            final int k = 1;
                            // Prepend a project char identifier to the name
                            String project_name = "";
                            if (projects.size() > 1) {
                                project_name = Utils.getCharacter(projects.indexOf(chains.get(i).getRoot().getProject()) + 1).toLowerCase();
                                name = project_name + name;
                            }
                            dostags.write(new StringBuilder().append(sid).append('\t').append(name).append('\n').toString());
                            if (null != outgroup && -1 != name.indexOf(outgroup)) {
                                Utils.logAll("Outgroup 0-based index is " + id + ", with id " + sid + ", with name " + name);
                            }
                            // 
                            final int len = 12;
                            sb.append(sid);
                            // pad with spaces up to len
                            for (int j = len - sid.length(); j > 0; j--) sb.append(' ');
                            int count = 0;
                            for (int j = 0; j < scores[0].length; j++) {
                                sb.append(' ').append(scores[i][j]);
                                count++;
                                if (7 == count && j < scores[0].length - 1) {
                                    sb.append('\n');
                                    count = 0;
                                    while (++count < len) sb.append(' ');
                                    sb.append(' ');
                                    count = 0;
                                }
                            }
                            sb.append('\n');
                            dos.write(sb.toString());
                        }
                        dos.flush();
                        dostags.flush();
                        dostags.close();
                    } catch (final Exception e) {
                        e.printStackTrace();
                    }
                }
                dos.close();
            } catch (final Exception e) {
                e.printStackTrace();
            } finally {
                finishedWorking();
            }
        }
    };
    return Bureaucrat.createAndStart(worker, p);
}

Example 8 with SaveDialog

use of ij.io.SaveDialog in project TrakEM2 by trakem2.

the class Render method exportSVG.

// ///////////////////////
// SVG format//
public static void exportSVG(ProjectThing thing, double z_scale) {
    StringBuffer data = new StringBuffer();
    data.append("<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n").append("<svg\n").append("\txmlns:dc=\"http://purl.org/dc/elements/1.1/\"\n").append("\txmlns:cc=\"http://web.resource.org/cc/\"\n").append("\txmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\n").append("\txmlns:svg=\"http://www.w3.org/2000/svg\"\n").append("\txmlns=\"http://www.w3.org/2000/svg\"\n").append("\tid=\"").append(thing.getProject().toString()).append("\">\n");
    // traverse the tree at node 'thing'
    thing.exportSVG(data, z_scale, "\t");
    data.append("</svg>");
    // save the file
    final SaveDialog sd = new SaveDialog("Save .svg", OpenDialog.getDefaultDirectory(), "svg");
    String dir = sd.getDirectory();
    if (null == dir)
        return;
    if (IJ.isWindows())
        dir = dir.replace('\\', '/');
    if (!dir.endsWith("/"))
        dir += "/";
    String file_name = sd.getFileName();
    String file_path = dir + file_name;
    File f = new File(file_path);
    if (f.exists()) {
        YesNoCancelDialog d = new YesNoCancelDialog(IJ.getInstance(), "Overwrite?", "File " + file_name + " exists! Overwrite?");
        if (!d.yesPressed()) {
            return;
        }
    }
    String contents = data.toString();
    try {
        DataOutputStream dos = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(f), data.length()));
        dos.writeBytes(contents);
        dos.flush();
    } catch (Exception e) {
        IJError.print(e);
        Utils.log("ERROR: Most likely did NOT save your file.");
    }
}

Example 9 with SaveDialog

use of ij.io.SaveDialog in project TrakEM2 by trakem2.

the class Utils method chooseFile.

/**
 * Select a file from the file system, for saving purposes. Prompts for overwritting if the file exists, unless the ControlWindow.isGUIEnabled() returns false (i.e. there is no GUI).
 */
public static final File chooseFile(final String default_dir, final String name, final String extension) {
    try {
        return new TaskOnEDT<File>(new Callable<File>() {

            @Override
            public File call() {
                // using ImageJ's JFileChooser or internal FileDialog, according to user preferences.
                String name2 = null;
                if (null != name && null != extension)
                    name2 = name + extension;
                else if (null != name)
                    name2 = name;
                else if (null != extension)
                    name2 = "untitled" + extension;
                if (null != default_dir) {
                    OpenDialog.setDefaultDirectory(default_dir);
                }
                final SaveDialog sd = new SaveDialog("Save", OpenDialog.getDefaultDirectory(), name2, extension);
                final String filename = sd.getFileName();
                if (null == filename || filename.toLowerCase().startsWith("null"))
                    return null;
                String dir = sd.getDirectory();
                if (IJ.isWindows())
                    dir = dir.replace('\\', '/');
                if (!dir.endsWith("/"))
                    dir += "/";
                final File f = new File(dir + filename);
                if (f.exists() && ControlWindow.isGUIEnabled()) {
                    final YesNoCancelDialog d = new YesNoCancelDialog(IJ.getInstance(), "Overwrite?", "File " + filename + " exists! Overwrite?");
                    if (d.cancelPressed()) {
                        return null;
                    } else if (!d.yesPressed()) {
                        return chooseFile(name, extension);
                    }
                // else if yes pressed, overwrite.
                }
                return f;
            }
        }).get();
    } catch (final Throwable t) {
        IJError.print(t);
        return null;
    }
}