Examples with XMLOptions ini.trakem2.persistence.XMLOptions used on opensource projects

Example 1 with XMLOptions

use of ini.trakem2.persistence.XMLOptions in project TrakEM2 by trakem2.

the class Patch method exportXML.

/**
 * Opens and closes the tag and exports data. The image is saved in the directory provided in @param any as a String.
 */
@Override
public void exportXML(final StringBuilder sb_body, final String indent, final XMLOptions options) {
    // TODO the Loader should handle the saving of images, not this class.
    final String in = indent + "\t";
    String path = null;
    String path2 = null;
    if (options.export_images) {
        path = options.patches_dir + title;
        // save image without overwriting, and add proper extension (.zip)
        path2 = project.getLoader().exportImage(this, path, false);
    // path2 will be null if the file exists already
    }
    sb_body.append(indent).append("<t2_patch\n");
    String rel_path = null;
    if (null != path && path.equals(path2)) {
        // this happens when a DB project is exported. It may be a different path when it's a FS loader
        // Utils.log2("p id=" + id + "  path==path2");
        rel_path = path2;
        // TrakEM2 uses paths that always have '/' and never '\', so using java.io.File.separatorChar would be an error.
        int i_slash = rel_path.lastIndexOf('/');
        if (i_slash > 0) {
            i_slash = rel_path.lastIndexOf('/', i_slash - 1);
            if (-1 != i_slash) {
                rel_path = rel_path.substring(i_slash + 1);
            }
        }
    } else {
        // Utils.log2("Setting rel_path to " + path2);
        rel_path = path2;
    }
    // For FSLoader projects, saving a second time will save images as null unless calling it
    if (null == rel_path) {
        // Utils.log2("path2 was null");
        final Object ob = project.getLoader().getPath(this);
        path2 = null == ob ? null : (String) ob;
        if (null == path2) {
            // Utils.log2("ERROR: No path for Patch id=" + id + " and title: " + title);
            // at least some clue for recovery
            rel_path = title;
        } else {
            rel_path = path2;
        }
    }
    // Utils.log("Patch path is: " + rel_path);
    super.exportXML(sb_body, in, options);
    final String[] RGB = Utils.getHexRGBColor(color);
    int type = this.type;
    if (-1 == this.type) {
        Utils.log2("Retrieving type for p = " + this);
        final ImagePlus imp = project.getLoader().fetchImagePlus(this);
        if (null != imp)
            type = imp.getType();
    }
    sb_body.append(in).append("type=\"").append(type).append("\"\n").append(in).append("file_path=\"").append(rel_path).append("\"\n").append(in).append("style=\"fill-opacity:").append(alpha).append(";stroke:#").append(RGB[0]).append(RGB[1]).append(RGB[2]).append(";\"\n").append(in).append("o_width=\"").append(o_width).append("\"\n").append(in).append("o_height=\"").append(o_height).append("\"\n");
    if (null != original_path) {
        sb_body.append(in).append("original_path=\"").append(original_path).append("\"\n");
    }
    sb_body.append(in).append("min=\"").append(min).append("\"\n");
    sb_body.append(in).append("max=\"").append(max).append("\"\n");
    final String pps = getPreprocessorScriptPath();
    if (null != pps)
        sb_body.append(in).append("pps=\"").append(project.getLoader().makeRelativePath(pps)).append("\"\n");
    sb_body.append(in).append("mres=\"").append(meshResolution).append("\"\n");
    if (hasCoordinateTransform()) {
        sb_body.append(in).append("ct_id=\"").append(ct_id).append("\"\n");
    }
    if (hasAlphaMask()) {
        sb_body.append(in).append("alpha_mask_id=\"").append(alpha_mask_id).append("\"\n");
    }
    sb_body.append(indent).append(">\n");
    if (hasCoordinateTransform()) {
        if (options.include_coordinate_transform) {
            // Write an XML entry for the CoordinateTransform
            char[] ct_chars = null;
            try {
                ct_chars = readCoordinateTransformFile();
            } catch (final Exception e) {
                IJError.print(e);
            }
            if (null != ct_chars) {
                sb_body.append(ct_chars).append('\n');
            } else {
                Utils.log("ERROR: could not write the CoordinateTransform to the XML file!");
            }
        }
    }
    if (null != filters && filters.length > 0) {
        // specify their own line termination
        for (final IFilter f : filters) sb_body.append(f.toXML(in));
    }
    super.restXML(sb_body, in, options);
    sb_body.append(indent).append("</t2_patch>\n");
}

Example 2 with XMLOptions

use of ini.trakem2.persistence.XMLOptions in project TrakEM2 by trakem2.

the class FSLoader method saveAs.

/**
 * Meant for programmatic access, such as calls to project.saveAs(path, overwrite) which call exactly this method.
 */
@Override
public String saveAs(final String path, final XMLOptions options) {
    if (null == path) {
        Utils.log("Cannot save on null path.");
        return null;
    }
    String path2 = path;
    String extension = ".xml";
    if (// all fine
    path2.endsWith(extension)) // all fine
    {
    } else if (path2.endsWith(".xml.gz"))
        extension = ".xml.gz";
    else {
        // neither matches, add the default ".xml"
        path2 += extension;
    }
    File fxml = new File(path2);
    if (!fxml.canWrite()) {
        // write to storage folder instead
        String path3 = path2;
        path2 = getStorageFolder() + fxml.getName();
        Utils.logAll("WARNING can't write to " + path3 + "\n  --> will write instead to " + path2);
        fxml = new File(path2);
    }
    if (!options.overwriteXMLFile) {
        int i = 1;
        while (fxml.exists()) {
            String parent = fxml.getParent().replace('\\', '/');
            if (!parent.endsWith("/"))
                parent += "/";
            String name = fxml.getName();
            name = name.substring(0, name.length() - 4);
            path2 = parent + name + "-" + i + extension;
            fxml = new File(path2);
            i++;
        }
    }
    Project project = Project.findProject(this);
    path2 = super.saveAs(project, path2, options);
    if (null != path2) {
        project_file_path = path2;
        Utils.logAll("After saveAs, new xml path is: " + path2);
        ControlWindow.updateTitle(project);
        touched_mipmaps.clear();
    }
    return path2;
}

Example 3 with XMLOptions

use of ini.trakem2.persistence.XMLOptions in project TrakEM2 by trakem2.

the class Project method saveTask.

public Bureaucrat saveTask(final String command) {
    return Bureaucrat.createAndStart(new Worker.Task("Saving") {

        public void exec() {
            if (command.equals("Save")) {
                save();
            } else if (command.equals("Save as...")) {
                XMLOptions options = new XMLOptions();
                options.overwriteXMLFile = false;
                options.export_images = false;
                options.include_coordinate_transform = true;
                options.patches_dir = null;
                // Will open a file dialog
                loader.saveAs(project, options);
                restartAutosaving();
            // 
            } else if (command.equals("Save as... without coordinate transforms")) {
                YesNoDialog yn = new YesNoDialog("WARNING", "You are about to save an XML file that lacks the information for the coordinate transforms of each image.\n" + "These transforms are referred to with the attribute 'ct_id' of each 't2_patch' entry in the XML document,\n" + "and the data for the transform is stored in an individual file under the folder 'trakem2.cts/'.\n" + " \n" + "It is advised to keep a complete XML file with all coordinate transforms included along with this new copy.\n" + "Please check NOW that you have such a complete XML copy.\n" + " \n" + "Proceed?");
                if (!yn.yesPressed())
                    return;
                saveWithoutCoordinateTransforms();
            // 
            } else if (command.equals("Delete stale files...")) {
                setTaskName("Deleting stale files");
                GenericDialog gd = new GenericDialog("Delete stale files");
                gd.addMessage("You are about to remove all files under the folder 'trakem2.cts/' which are not referred to from the\n" + "currently loaded project. If you have sibling XML files whose 't2_patch' entries (the images) refer,\n" + "via 'ct_id' attributes, to coordinate transforms in 'trakem2.cts/' that this current XML doesn't,\n" + "they may be LOST FOREVER. Unless you have a version of the XML file with the coordinate transforms\n" + "written in it, as can be obtained by using the 'Project - Save' command.\n" + " \n" + "The same is true for the .zip files that store alpha masks, under folder 'trakem2.masks/'\n" + "and which are referred to from the 'alpha_mask_id' attribute of 't2_patch' entries.\n" + " \n" + "Do you have such complete XML file? Check *NOW*.\n" + " \n" + "Proceed with deleting:");
                gd.addCheckbox("Delete stale coordinate transform files", true);
                gd.addCheckbox("Delete stale alpha mask files", true);
                gd.showDialog();
                if (gd.wasCanceled())
                    return;
                project.getLoader().deleteStaleFiles(gd.getNextBoolean(), gd.getNextBoolean());
            }
        }
    }, project);
}

Example 4 with XMLOptions

use of ini.trakem2.persistence.XMLOptions in project TrakEM2 by trakem2.

the class Project method saveWithoutCoordinateTransforms.

/**
 * Save an XML file that is stripped of coordinate transforms,
 * and merely refers to them by the 'ct_id' attribute of each 't2_patch' element;
 * this method will NOT overwrite the XML file but save into a new one,
 * which is chosen from a file dialog.
 */
public String saveWithoutCoordinateTransforms() {
    XMLOptions options = new XMLOptions();
    options.overwriteXMLFile = false;
    options.export_images = false;
    options.include_coordinate_transform = false;
    options.patches_dir = null;
    return loader.saveAs(this, options);
}

Example 5 with XMLOptions

use of ini.trakem2.persistence.XMLOptions in project TrakEM2 by trakem2.

the class Layer method exportXML.

@Override
public void exportXML(final StringBuilder sb_body, final String indent, final XMLOptions options) {
    final String in = indent + "\t";
    // 1 - open tag
    sb_body.append(indent).append("<t2_layer oid=\"").append(id).append("\"\n").append(in).append(" thickness=\"").append(thickness).append("\"\n").append(in).append(" z=\"").append(z).append("\"\n");
    // TODO this search is linear!
    final LayerThing lt = project.findLayerThing(this);
    String title;
    if (null == lt)
        title = null;
    else
        title = lt.getTitle();
    if (null == title)
        title = "";
    // TODO 'title' should be a property of the Layer, not the LayerThing. Also, the LayerThing should not exist: LayerSet and Layer should be directly presentable in a tree. They are not Things as in "objects of the sample", but rather, structural necessities such as Patch.
    sb_body.append(in).append(" title=\"").append(title).append("\"\n");
    sb_body.append(indent).append(">\n");
    // 2 - export children
    if (null != al_displayables) {
        for (final Displayable d : al_displayables) {
            d.exportXML(sb_body, in, options);
        }
    }
    // 3 - close tag
    sb_body.append(indent).append("</t2_layer>\n");
}