FSLoader (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.persistence.Loader
- - ini.trakem2.persistence.FSLoader

```
public final class FSLoader
extends Loader
```
A class to rely on memory only; except images which are rolled from a folder or their original location and flushed when memory is needed for more. Ideally there would be a given folder for storing items temporarily of permanently as the "project folder", but I haven't implemented it.

Nested Class Summary
- Nested classes/interfaces inherited from class ini.trakem2.persistence.Loader
  Loader.ImageLoadingLock

Field Summary

Fields
Modifier and Type	Field and Description
`static Pattern`	`ABS_PATH`
`static ScheduledExecutorService`	`autosaver`
`static String[]`	`MIPMAP_FORMATS`
`static int`	`MIPMAP_JPEG`
`static int`	`MIPMAP_PNG`
`static int`	`MIPMAP_RAG`
`static int`	`MIPMAP_RAW`
`static int`	`MIPMAP_TIFF`
`static ExecutorService`	`repainter`

Fields inherited from class ini.trakem2.persistence.Loader
AREA_DOWNSAMPLING, changes, db_lock, DEFAULT_MIPMAPS_MODE, ERROR_PATH_NOT_FOUND, GAUSSIAN, GRAY_LUT, hs_unloadable, mawts, MAX_RETRIES, MIN_FREE_BYTES, MIPMAP_MODES, mipmaps_regen, NOT_FOUND, opener, PREPROCESSED, REGENERATING, RUNTIME, v_loaders

Constructor Summary

Constructors
Constructor and Description

FSLoader()
Used to open a project from an existing XML file.

FSLoader(String storage_folder)
Used to create a new project, NOT from an XML file.

Constructors
Constructor and Description
`FSLoader()` Used to open a project from an existing XML file.
`FSLoader(String storage_folder)` Used to create a new project, NOT from an XML file.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addedPatchFrom(String path, Patch patch)` All backslashes are converted to slashes to avoid havoc in MSWindows.
`boolean`	`addToDatabase(DBObject ob)`
`static String`	`asSafePath(String name)` Takes a String and returns a copy with the following conversions: / to -, space to _, and \ to -.
`boolean`	`checkMipMapFileExists(Patch p, double magnification)` Checks if the mipmap file for the Patch and closest upper level to the desired magnification exists.
`boolean`	`clearIntensityMap(Patch p)` Clear the intensity map coefficients for a patch.
`static String`	`createIdPath(String sid, String filename, String ext)` For sid=12345 creates 12/34/5.${filename}.jpg Will be fine with other filename-valid chars in sid.
`static String`	`createMipMapRelPath(Patch p, String ext)` For Patch id=12345 creates 12/34/5.${filename}.jpg
`boolean`	`deleteStaleFiles(boolean coordinate_transforms, boolean alpha_masks)` Delete stale files under the `unuid` folder.
`void`	`destroy()` Release all memory and unregister itself.
`long`	`estimateImageFileSize(Patch p, int level)` Compute the number of bytes that the ImagePlus of a Patch will take.
`Area`	`fetchArea(long area_list_id, long layer_id)` Loaded in full from XML file
`ArrayList<?>`	`fetchBallPoints(long id)` Loaded in full from XML file
`double[][][]`	`fetchBezierArrays(long id)` Loaded in full from XML file
`MipMapImage`	`fetchDataImage(Patch p, double mag)` Waits until a proper image of the desired size or larger can be returned, which is never the Loader.REGENERATING image.
`Object`	`fetchImage(Patch p, int format)` So far accepts Layer.IMAGEPLUS and Layer.IMAGEPROCESSOR as format.
`ij.process.ByteProcessor`	`fetchImageMask(Patch p)` Returns the alpha mask image from a file, or null if none stored.
`ij.ImagePlus`	`fetchImagePlus(Patch p)`
`ij.ImagePlus`	`fetchImagePlus(Stack stack)`
`ij.process.ImageProcessor`	`fetchImageProcessor(Patch p)` Fetch the ImageProcessor in a synchronized manner, so that there are no conflicts in retrieving the ImageProcessor for a specific stack slice, for example.
`Object[]`	`fetchLabel(DLabel label)` Loaded in full from XML file
`MipMapImage`	`fetchMipMap(Patch patch, int level, long n_bytes)` Does the actual fetching of the file.
`protected MipMapImage`	`fetchMipMapAWT(Patch patch, int level, long n_bytes)` Loads the file containing the scaled image corresponding to the given level (or the maximum possible level, if too large) and returns it as an awt.Image, or null if not found.
`ij.ImagePlus`	`fetchOriginal(Patch patch)` Loads and returns the original image, which is not cached, or returns null if it's not different than the working image.
`ArrayList<?>`	`fetchPipePoints(long id)` Loaded in full from XML file
`boolean`	`fixStorageFolders()` Convert old-style storage folders to new style.
`void`	`flushMipMaps(boolean forget_dir_mipmaps)` Remove all mipmap images from the cache, and optionally set the dir_mipmaps to null.
`void`	`flushMipMaps(long id)` Remove from the cache all images of level larger than zero corresponding to the given patch id.
`Bureaucrat`	`generateMipMaps(Collection<Displayable> patches, boolean overwrite)` Generate image pyramids and store them into files under the dir_mipmaps for each Patch object in the Project.
`protected boolean`	`generateMipMaps(Patch patch)` Given an image and its source file name (without directory prepended), generate a pyramid of images until reaching an image not smaller than 32x32 pixels.
`String`	`getAbsolutePath(Patch patch)` With slice info appended at the end; only if it exists, otherwise null.
`String`	`getAbsolutePath(String path)` Return an absolute path made from path: if it's already absolute, retursn itself; otherwise, the parent folder of all relative paths of this Loader is prepended.
`int`	`getClosestMipMapLevel(Patch patch, int level, int max_level)` Return the closest level to `level` that exists as a file.
`String`	`getCoordinateTransformsFolder()` Returns null unless overriden.
`String`	`getImageFilePath(Patch p)` Returns null unless overriden.
`String`	`getImageStorageFolder()` Returns a folder proven to be writable for images can be stored into.
`String`	`getMasksFolder()` Returns null unless override.
`int`	`getMipMapFormat()` Any of: `MIPMAP_JPEG`, `MIPMAP_PNG`, `MIPMAP_TIFF`, `MIPMAP_RAW`, `MIPMAP_RAG`.
`String`	`getMipMapsFolder()` Returns the path to the directory hosting the file image pyramids.
`long`	`getNextBlobId()` Get the next unique id to be used for the `Patch`'s `CoordinateTransform` or alpha mask.
`long`	`getNextId()` Get the next unique id, not shared by any other object within the same project.
`static Project`	`getOpenProject(String project_file_path)`
`String`	`getParentFolder()` Return the path to the folder containing the project XML file.
`String`	`getPath(Patch patch)` Returns the stored path for the given Patch image, which may be relative and may contain slice information appended.
`protected Map<Long,String>`	`getPathsCopy()`
`String`	`getProjectXMLPath()`
`String`	`getStorageFolder()` Return the folder selected by a user to store files into; it's also the parent folder of the UNUId folder, and the recommended folder to store the XML file into.
`String`	`getUNUId()` Get the Universal Near-Unique Id for the project hosted by this loader.
`String`	`getUNUIdFolder()` Returns the near-unique folder for the project hosted by this FSLoader.
`static Object`	`grabPixels(BufferedImage bi)` Returns the array of pixels, whose type depends on the bi.getType(); for example, for a BufferedImage.TYPE_BYTE_INDEXED, returns a byte[].
`String`	`handlePathlessImage(ij.ImagePlus imp)` Returns the path where the imp is saved to: the storage folder plus a name.
`protected Patch`	`importStackAsPatches(Project project, Layer first_layer, double x, double y, ij.ImagePlus imp_stack, boolean as_copy, String filepath)` Returns the last Patch.
`void`	`insertXMLOptions(StringBuilder sb_body, String indent)` Specific options for the Loader which exist as attributes to the Project XML node.
`static boolean`	`isRelativePath(String path)`
`static boolean`	`isURL(String path)`
`protected void`	`makeAllPathsRelativeTo(String xml_path, Project project)` Try to make all paths in ht_paths be relative to the given xml_path.
`String`	`makeProjectName()`
`String`	`makeRelativePath(String path)` Takes the given path and tries to makes it relative to this instance's project_file_path, if possible.
`protected boolean`	`mapIntensities(Patch p, ij.ImagePlus imp)`
`static int`	`nStaticServiceThreads()`
`Object[]`	`openFSProject(String path, boolean open_displays)` Returns TMLHandler.getProjectData() .
`void`	`parseXMLOptions(HashMap<String,String> ht_attributes)` Specific options for the Loader which exist as attributes to the Project XML node.
`void`	`queueForMipmapRemoval(Patch p, boolean yes)` Queue/unqueue for mipmap removal on shutdown without saving; the `yes`, when true, makes the `p` be queued, and when false, be removed from the queue.
`Bureaucrat`	`regenerateMipMaps(Collection<? extends Displayable> patches)` Order the regeneration of all mipmaps for the Patch instances in `patches`, setting up a task that blocks input until all completed.
`Future<Boolean>`	`regenerateMipMaps(Patch patch)` Queue the regeneration of mipmaps for the Patch; returns immediately, having submitted the job to an executor queue; returns a Future if the task was submitted, null if not.
`boolean`	`removeFromDatabase(DBObject ob)`
`Future<Boolean>`	`removeMipMaps(Patch p)` Gets data from the Patch and queues a new task to do the file removal in a separate task manager thread.
`boolean`	`removeSerializedFeatures(Patch patch)` Remove the file, if it exists, with serialized features for patch.
`boolean`	`removeSerializedPointMatches(Patch patch)` Remove the file, if it exists, with serialized point matches for patch.
`static void`	`restartMipMapThreads(int n_threads)` Restart the ExecutorService for mipmaps with `n_threads`.
`protected void`	`restorePaths(Map<Long,String> copy, String mipmaps_folder, String storage_folder)`
`String`	`save(Project project, XMLOptions options)` Overwrites the XML file.
`String`	`saveAs(Project project, XMLOptions options)` The saveAs called from menus via saveTask.
`String`	`saveAs(String path, XMLOptions options)` Meant for programmatic access, such as calls to project.saveAs(path, overwrite) which call exactly this method.
`String`	`setImageFile(Patch p, ij.ImagePlus imp)` Returns the absolute path to a file that contains the given ImagePlus image - which may be the path as described in the ImagePlus FileInfo object itself, or a totally new file.
`boolean`	`setMipMapFormat(int format)` Does nothing unless overriden.
`void`	`setMipMapsRegeneration(boolean b)`
`void`	`setupMenuItems(JMenu menu, Project project)` Adds a "Save" and "Save as" menu items.
`void`	`tagForMipmapRemoval(Patch p, boolean yes)` Queue/unqueue for mipmap removal on shutdown without saving; the `yes`, when true, makes the `p` be queued, and when false, be removed from the queue.
`boolean`	`updateInDatabase(DBObject ob, Set<String> keys)`
`boolean`	`updateInDatabase(DBObject ob, String key)`
`Bureaucrat`	`updateMipMapsFormat(int old_format, int new_format)` Removes all mipmap files and recreates them with the currently set mipmaps format.
`boolean`	`usesMipMapsFolder()` Does nothing and returns false unless overriden.

Methods inherited from class ini.trakem2.persistence.Loader
addCrossLink, addJob, addNewImage, addNewImage, adjustChannels, askForXMLTemplate, cache, cache, cacheAWT, cacheImagePlus, canReadAndWriteTo, commitLargeUpdate, computeDesirableMinFreeBytes, countObjects, createFlyThrough, createLazyFlyThrough, createZippedStream, debug, decache, decacheAWT, decacheImagePlus, decacheImagePlus, deserialize, destroyPreloader, doGUILater, doLater, embedAlpha, embedAlpha, embedAlphaPre, enhanceContrast, enhanceContrast, enoughFreeMemory, export, exportImage, exportImage, fetchAWTImage, fetchImage, fetchImage, flush, generateLayerMipMaps, generateMipMaps, generateMipMaps, getCached, getCachedAWT, getCachedClosestAboveImage, getCachedClosestBelowImage, getCachedImagePlus, getCurrentMemory, getDimensions, getDimensions, getFileName, getFlatAWTImage, getFlatAWTImage, getFlatImage, getFlatImage, getFlatImage, getFlatImage, getFlatImage, getFlatImage, getHighestMipMapLevel, getHighestMipMapLevel, getInternalFileName, getJobsPopup, getMipMapLevel, getMipMapModeIndex, getMipMapModeName, getMipMapsRegenerationEnabled, getNextTempId, getOrMakeImageLoadingLock, getOrMakeImageLoadingLock, getPreprocessorScriptPath, handleCacheError, hasChanges, importGrid, importGrid, importImage, importImage, importImage, importImages, importImages, importLabelsAsAreaLists, importLabelsAsAreaLists, importNextImage, importSequenceAsGrid, importSequenceAsGrid, importSequenceAsGrid, importStack, importStack, importStack, importStackAsPatches, isAsynchronous, isCached, isImagePlusCached, isMipMapsRegenerationEnabled, isSignalImage, isSnapPaintable, isUnloadable, makeFlatImage, makeFlatImage, makeFlatImage, makeGrayLut, makePatchesDir, makePrescaledTiles, markStaleFileForDeletionUponSaving, maskBorders, maskBorders, maskBordersLayerWise, maxDim, measureSize, openImage, openImagePlus, openStack, preload, preload, preProcess, printCache, printCaches, printCacheStatus, printMemState, quitJob, recoverOOME, recreateBuckets, recreateBuckets, releaseAll, releaseAllCaches, releaseMemory, releaseMemory2, releaseToFit, releaseToFit, removeAlphaMask, removeCached, removeCached, removeCrossLink, removeFromUnloadable, removeImageLoadingLock, removeJob, rollback, saveAs, saveTask, scaleImage, scaleImage, serialize, setChanged, setDesirableMinFreeBytes, setHeapFraction, setMinAndMax, setPreprocessorScriptPath, setPreprocessorScriptPathSilently, setupPreloader, setupPreloaderThreads, startLargeUpdate, storeAlphaMask, unzipTiff, writeXMLTo

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - ABS_PATH
```
public static final Pattern ABS_PATH
```
  - repainter
```
public static ExecutorService repainter
```
  - autosaver
```
public static ScheduledExecutorService autosaver
```
  - MIPMAP_FORMATS
```
public static final String[] MIPMAP_FORMATS
```
  - MIPMAP_JPEG
```
public static final int MIPMAP_JPEG
```
    See Also:
    
    Constant Field Values
  - MIPMAP_PNG
```
public static final int MIPMAP_PNG
```
    See Also:
    
    Constant Field Values
  - MIPMAP_TIFF
```
public static final int MIPMAP_TIFF
```
    See Also:
    
    Constant Field Values
  - MIPMAP_RAW
```
public static final int MIPMAP_RAW
```
    See Also:
    
    Constant Field Values
  - MIPMAP_RAG
```
public static final int MIPMAP_RAG
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - FSLoader
```
public FSLoader()
```
    Used to open a project from an existing XML file.
  - FSLoader
```
public FSLoader(String storage_folder)
         throws Exception
```
    Used to create a new project, NOT from an XML file. Throws an Exception if the loader cannot read and write to the storage folder.
    
    Throws:
    
    Exception
- Method Detail
  - getProjectXMLPath
```
public String getProjectXMLPath()
```
  - getStorageFolder
```
public String getStorageFolder()
```
    Return the folder selected by a user to store files into; it's also the parent folder of the UNUId folder, and the recommended folder to store the XML file into.
    
    Overrides:
    
    getStorageFolder in class Loader
  - getImageStorageFolder
```
public String getImageStorageFolder()
```
    Returns a folder proven to be writable for images can be stored into.
    
    Overrides:
    
    getImageStorageFolder in class Loader
  - openFSProject
```
public Object[] openFSProject(String path,
                              boolean open_displays)
```
    Returns TMLHandler.getProjectData() . If the path is null it'll be asked for.
  - getOpenProject
```
public static final Project getOpenProject(String project_file_path)
```
  - nStaticServiceThreads
```
public static final int nStaticServiceThreads()
```
  - restartMipMapThreads
```
public static final void restartMipMapThreads(int n_threads)
```
    Restart the ExecutorService for mipmaps with n_threads.
  - destroy
```
public void destroy()
```
    Description copied from class: Loader
    
    Release all memory and unregister itself. Child Loader classes should call this method in their destroy() methods.
    
    Overrides:
    
    destroy in class Loader
  - getNextId
```
public long getNextId()
```
    Get the next unique id, not shared by any other object within the same project.
    
    Specified by:
    
    getNextId in class Loader
  - getNextBlobId
```
public long getNextBlobId()
```
    Get the next unique id to be used for the Patch's CoordinateTransform or alpha mask.
    
    Overrides:
    
    getNextBlobId in class Loader
  - fetchBezierArrays
```
public double[][][] fetchBezierArrays(long id)
```
    Loaded in full from XML file
    
    Specified by:
    
    fetchBezierArrays in class Loader
  - fetchPipePoints
```
public ArrayList<?> fetchPipePoints(long id)
```
    Loaded in full from XML file
    
    Specified by:
    
    fetchPipePoints in class Loader
  - fetchBallPoints
```
public ArrayList<?> fetchBallPoints(long id)
```
    Loaded in full from XML file
    
    Specified by:
    
    fetchBallPoints in class Loader
  - fetchArea
```
public Area fetchArea(long area_list_id,
                      long layer_id)
```
    Loaded in full from XML file
    
    Specified by:
    
    fetchArea in class Loader
  - fetchImagePlus
```
public ij.ImagePlus fetchImagePlus(Patch p)
```
    Specified by:
    
    fetchImagePlus in class Loader
  - fetchImageProcessor
```
public ij.process.ImageProcessor fetchImageProcessor(Patch p)
```
    Fetch the ImageProcessor in a synchronized manner, so that there are no conflicts in retrieving the ImageProcessor for a specific stack slice, for example. Note that the min and max is not set -- it's your burden to call setMinAndMax(p.getMin(), p.getMax()) on the returned ImageProcessor.
    
    Overrides:
    
    fetchImageProcessor in class Loader
  - fetchImage
```
public Object fetchImage(Patch p,
                         int format)
```
    So far accepts Layer.IMAGEPLUS and Layer.IMAGEPROCESSOR as format.
  - fetchImageMask
```
public ij.process.ByteProcessor fetchImageMask(Patch p)
```
    Returns the alpha mask image from a file, or null if none stored.
    
    Overrides:
    
    fetchImageMask in class Loader
    
    See Also:
    
    Patch.getAlphaMask()
  - getMasksFolder
```
public final String getMasksFolder()
```
    Description copied from class: Loader
    
    Returns null unless override.
    
    Overrides:
    
    getMasksFolder in class Loader
  - getCoordinateTransformsFolder
```
public final String getCoordinateTransformsFolder()
```
    Description copied from class: Loader
    
    Returns null unless overriden.
    
    Overrides:
    
    getCoordinateTransformsFolder in class Loader
  - fetchLabel
```
public Object[] fetchLabel(DLabel label)
```
    Loaded in full from XML file
    
    Specified by:
    
    fetchLabel in class Loader
  - fetchOriginal
```
public ij.ImagePlus fetchOriginal(Patch patch)
```
    Loads and returns the original image, which is not cached, or returns null if it's not different than the working image.
    
    Specified by:
    
    fetchOriginal in class Loader
  - addToDatabase
```
public boolean addToDatabase(DBObject ob)
```
    Specified by:
    
    addToDatabase in class Loader
  - updateInDatabase
```
public boolean updateInDatabase(DBObject ob,
                                String key)
```
    Specified by:
    
    updateInDatabase in class Loader
  - updateInDatabase
```
public boolean updateInDatabase(DBObject ob,
                                Set<String> keys)
```
    Specified by:
    
    updateInDatabase in class Loader
  - removeFromDatabase
```
public boolean removeFromDatabase(DBObject ob)
```
    Specified by:
    
    removeFromDatabase in class Loader
  - setImageFile
```
public String setImageFile(Patch p,
                           ij.ImagePlus imp)
```
    Returns the absolute path to a file that contains the given ImagePlus image - which may be the path as described in the ImagePlus FileInfo object itself, or a totally new file. If the Patch p current image path is different than its original image path, then the file is overwritten if it exists already.
    
    Overrides:
    
    setImageFile in class Loader
  - getAbsolutePath
```
public String getAbsolutePath(Patch patch)
```
    With slice info appended at the end; only if it exists, otherwise null.
    
    Overrides:
    
    getAbsolutePath in class Loader
  - getAbsolutePath
```
public String getAbsolutePath(String path)
```
    Return an absolute path made from path: if it's already absolute, retursn itself; otherwise, the parent folder of all relative paths of this Loader is prepended.
  - getImageFilePath
```
public final String getImageFilePath(Patch p)
```
    Description copied from class: Loader
    
    Returns null unless overriden. This is intended for FSLoader projects.
    
    Overrides:
    
    getImageFilePath in class Loader
  - isURL
```
public static final boolean isURL(String path)
```
  - isRelativePath
```
public static final boolean isRelativePath(String path)
```
  - addedPatchFrom
```
public void addedPatchFrom(String path,
                           Patch patch)
```
    All backslashes are converted to slashes to avoid havoc in MSWindows.
    
    Overrides:
    
    addedPatchFrom in class Loader
  - asSafePath
```
public static String asSafePath(String name)
```
    Takes a String and returns a copy with the following conversions: / to -, space to _, and \ to -.
  - save
```
public String save(Project project,
                   XMLOptions options)
```
    Overwrites the XML file. If some images do not exist in the file system, a directory with the same name of the XML file plus an "_images" tag appended will be created and images saved there.
    
    Overrides:
    
    save in class Loader
    
    options - TODO
  - saveAs
```
public String saveAs(Project project,
                     XMLOptions options)
```
    The saveAs called from menus via saveTask.
    
    Overrides:
    
    saveAs in class Loader
  - saveAs
```
public String saveAs(String path,
                     XMLOptions options)
```
    Meant for programmatic access, such as calls to project.saveAs(path, overwrite) which call exactly this method.
    
    Overrides:
    
    saveAs in class Loader
  - getPath
```
public String getPath(Patch patch)
```
    Returns the stored path for the given Patch image, which may be relative and may contain slice information appended.
    
    Overrides:
    
    getPath in class Loader
  - getPathsCopy
```
protected Map<Long,String> getPathsCopy()
```
    Overrides:
    
    getPathsCopy in class Loader
  - makeAllPathsRelativeTo
```
protected void makeAllPathsRelativeTo(String xml_path,
                                      Project project)
```
    Try to make all paths in ht_paths be relative to the given xml_path. This is intended for making all paths relative when saving to XML for the first time. dir_storage and dir_mipmaps remain untouched--otherwise, after a saveAs, images would not be found.
    
    Overrides:
    
    makeAllPathsRelativeTo in class Loader
  - restorePaths
```
protected void restorePaths(Map<Long,String> copy,
                            String mipmaps_folder,
                            String storage_folder)
```
    Overrides:
    
    restorePaths in class Loader
  - makeRelativePath
```
public String makeRelativePath(String path)
```
    Takes the given path and tries to makes it relative to this instance's project_file_path, if possible. Otherwise returns the argument as is.
    
    Overrides:
    
    makeRelativePath in class Loader
  - setupMenuItems
```
public void setupMenuItems(JMenu menu,
                           Project project)
```
    Adds a "Save" and "Save as" menu items.
    
    Overrides:
    
    setupMenuItems in class Loader
  - importStackAsPatches
```
protected Patch importStackAsPatches(Project project,
                                     Layer first_layer,
                                     double x,
                                     double y,
                                     ij.ImagePlus imp_stack,
                                     boolean as_copy,
                                     String filepath)
```
    Returns the last Patch.
    
    Specified by:
    
    importStackAsPatches in class Loader
  - parseXMLOptions
```
public void parseXMLOptions(HashMap<String,String> ht_attributes)
```
    Specific options for the Loader which exist as attributes to the Project XML node.
  - regenerateMipMaps
```
public Bureaucrat regenerateMipMaps(Collection<? extends Displayable> patches)
```
    Order the regeneration of all mipmaps for the Patch instances in patches, setting up a task that blocks input until all completed.
    
    Overrides:
    
    regenerateMipMaps in class Loader
  - insertXMLOptions
```
public void insertXMLOptions(StringBuilder sb_body,
                             String indent)
```
    Specific options for the Loader which exist as attributes to the Project XML node.
    
    Overrides:
    
    insertXMLOptions in class Loader
  - getParentFolder
```
public final String getParentFolder()
```
    Return the path to the folder containing the project XML file.
    
    Overrides:
    
    getParentFolder in class Loader
  - getMipMapsFolder
```
public String getMipMapsFolder()
```
    Returns the path to the directory hosting the file image pyramids.
    
    Overrides:
    
    getMipMapsFolder in class Loader
  - grabPixels
```
public static final Object grabPixels(BufferedImage bi)
```
    Returns the array of pixels, whose type depends on the bi.getType(); for example, for a BufferedImage.TYPE_BYTE_INDEXED, returns a byte[].
  - queueForMipmapRemoval
```
public void queueForMipmapRemoval(Patch p,
                                  boolean yes)
```
    Queue/unqueue for mipmap removal on shutdown without saving; the yes, when true, makes the p be queued, and when false, be removed from the queue.
    
    Overrides:
    
    queueForMipmapRemoval in class Loader
  - tagForMipmapRemoval
```
public void tagForMipmapRemoval(Patch p,
                                boolean yes)
```
    Queue/unqueue for mipmap removal on shutdown without saving; the yes, when true, makes the p be queued, and when false, be removed from the queue.
    
    Overrides:
    
    tagForMipmapRemoval in class Loader
  - generateMipMaps
```
protected boolean generateMipMaps(Patch patch)
```
    Given an image and its source file name (without directory prepended), generate a pyramid of images until reaching an image not smaller than 32x32 pixels.
    Such images are stored as jpeg 85% quality in a folder named trakem2.mipmaps.
    
    The Patch id and the right extension will be appended to the filename in all cases.
    
    Any equally named files will be overwritten.
    
    Overrides:
    
    generateMipMaps in class Loader
  - removeSerializedFeatures
```
public boolean removeSerializedFeatures(Patch patch)
```
    Remove the file, if it exists, with serialized features for patch. Returns true when no such file or on success; false otherwise.
  - removeSerializedPointMatches
```
public boolean removeSerializedPointMatches(Patch patch)
```
    Remove the file, if it exists, with serialized point matches for patch. Returns true when no such file or on success; false otherwise.
  - generateMipMaps
```
public Bureaucrat generateMipMaps(Collection<Displayable> patches,
                                  boolean overwrite)
```
    Generate image pyramids and store them into files under the dir_mipmaps for each Patch object in the Project. The method is multithreaded, using as many processors as available to the JVM.
    
    Parameters:
    
    patches - : the list of Patch instances to generate mipmaps for.
    
    overwrite - : whether to overwrite any existing mipmaps, or save only those that don't exist yet for whatever reason. This flag provides the means for minimal effort mipmap regeneration.)
  - getUNUIdFolder
```
public String getUNUIdFolder()
```
    Returns the near-unique folder for the project hosted by this FSLoader.
    
    Overrides:
    
    getUNUIdFolder in class Loader
  - setMipMapsRegeneration
```
public void setMipMapsRegeneration(boolean b)
```
    Overrides:
    
    setMipMapsRegeneration in class Loader
  - flushMipMaps
```
public void flushMipMaps(boolean forget_dir_mipmaps)
```
    Remove all mipmap images from the cache, and optionally set the dir_mipmaps to null.
    
    Overrides:
    
    flushMipMaps in class Loader
  - flushMipMaps
```
public void flushMipMaps(long id)
```
    Remove from the cache all images of level larger than zero corresponding to the given patch id.
    
    Overrides:
    
    flushMipMaps in class Loader
  - removeMipMaps
```
public Future<Boolean> removeMipMaps(Patch p)
```
    Gets data from the Patch and queues a new task to do the file removal in a separate task manager thread.
    
    Overrides:
    
    removeMipMaps in class Loader
  - usesMipMapsFolder
```
public boolean usesMipMapsFolder()
```
    Description copied from class: Loader
    
    Does nothing and returns false unless overriden.
    
    Overrides:
    
    usesMipMapsFolder in class Loader
  - getClosestMipMapLevel
```
public int getClosestMipMapLevel(Patch patch,
                                 int level,
                                 int max_level)
```
    Return the closest level to level that exists as a file. If no valid path is found for the patch, returns ERROR_PATH_NOT_FOUND.
    
    Overrides:
    
    getClosestMipMapLevel in class Loader
  - checkMipMapFileExists
```
public boolean checkMipMapFileExists(Patch p,
                                     double magnification)
```
    Checks if the mipmap file for the Patch and closest upper level to the desired magnification exists.
    
    Overrides:
    
    checkMipMapFileExists in class Loader
  - fetchMipMapAWT
```
protected MipMapImage fetchMipMapAWT(Patch patch,
                                     int level,
                                     long n_bytes)
```
    Loads the file containing the scaled image corresponding to the given level (or the maximum possible level, if too large) and returns it as an awt.Image, or null if not found. Will also regenerate the mipmaps, i.e. recreate the pre-scaled jpeg images if they are missing. Does NOT release memory, avoiding locking on the db_lock.
    
    Overrides:
    
    fetchMipMapAWT in class Loader
  - fetchMipMap
```
public final MipMapImage fetchMipMap(Patch patch,
                                     int level,
                                     long n_bytes)
```
    Does the actual fetching of the file. Returns null if the file does not exist. Does NOT pre-release memory from the cache; call releaseToFit to do that.
  - regenerateMipMaps
```
public final Future<Boolean> regenerateMipMaps(Patch patch)
```
    Queue the regeneration of mipmaps for the Patch; returns immediately, having submitted the job to an executor queue; returns a Future if the task was submitted, null if not.
    
    Overrides:
    
    regenerateMipMaps in class Loader
  - estimateImageFileSize
```
public long estimateImageFileSize(Patch p,
                                  int level)
```
    Compute the number of bytes that the ImagePlus of a Patch will take. Assumes a large header of 1024 bytes. If the image is saved as a grayscale jpeg the returned bytes will be 5 times as expected, because jpeg images are opened as int[] and then copied to a byte[] if all channels have the same values for all pixels.
    
    Overrides:
    
    estimateImageFileSize in class Loader
  - makeProjectName
```
public String makeProjectName()
```
    Overrides:
    
    makeProjectName in class Loader
  - handlePathlessImage
```
public String handlePathlessImage(ij.ImagePlus imp)
```
    Returns the path where the imp is saved to: the storage folder plus a name.
    
    Overrides:
    
    handlePathlessImage in class Loader
  - fixStorageFolders
```
public boolean fixStorageFolders()
```
    Convert old-style storage folders to new style.
  - createMipMapRelPath
```
public static final String createMipMapRelPath(Patch p,
                                               String ext)
```
    For Patch id=12345 creates 12/34/5.${filename}.jpg
  - createIdPath
```
public static final String createIdPath(String sid,
                                        String filename,
                                        String ext)
```
    For sid=12345 creates 12/34/5.${filename}.jpg Will be fine with other filename-valid chars in sid.
  - getUNUId
```
public String getUNUId()
```
    Description copied from class: Loader
    
    Get the Universal Near-Unique Id for the project hosted by this loader.
    
    Overrides:
    
    getUNUId in class Loader
  - fetchDataImage
```
public MipMapImage fetchDataImage(Patch p,
                                  double mag)
```
    Waits until a proper image of the desired size or larger can be returned, which is never the Loader.REGENERATING image. If no image can be loaded, returns Loader.NOT_FOUND. If the Patch is undergoing mipmap regeneration, it waits until done.
    
    Overrides:
    
    fetchDataImage in class Loader
  - fetchImagePlus
```
public ij.ImagePlus fetchImagePlus(Stack stack)
```
    Overrides:
    
    fetchImagePlus in class Loader
  - deleteStaleFiles
```
public boolean deleteStaleFiles(boolean coordinate_transforms,
                                boolean alpha_masks)
```
    Delete stale files under the unuid folder. These include "*.ct" files (for CoordinateTransform) and "*.zip" files (for alpha mask images) that are not referenced from any Patch.
    
    Overrides:
    
    deleteStaleFiles in class Loader
  - getMipMapFormat
```
public final int getMipMapFormat()
```
    Any of: MIPMAP_JPEG, MIPMAP_PNG, MIPMAP_TIFF, MIPMAP_RAW, MIPMAP_RAG.
    
    Overrides:
    
    getMipMapFormat in class Loader
  - setMipMapFormat
```
public final boolean setMipMapFormat(int format)
```
    Description copied from class: Loader
    
    Does nothing unless overriden.
    
    Overrides:
    
    setMipMapFormat in class Loader
  - updateMipMapsFormat
```
public Bureaucrat updateMipMapsFormat(int old_format,
                                      int new_format)
```
    Removes all mipmap files and recreates them with the currently set mipmaps format.
    
    Overrides:
    
    updateMipMapsFormat in class Loader
    
    Parameters:
    
    old_format - Any of MIPMAP_JPEG, MIPMAP_PNG in which files were saved before.
  - mapIntensities
```
protected boolean mapIntensities(Patch p,
                                 ij.ImagePlus imp)
```
    Overrides:
    
    mapIntensities in class Loader
  - clearIntensityMap
```
public boolean clearIntensityMap(Patch p)
```
    Description copied from class: Loader
    
    Clear the intensity map coefficients for a patch.
    
    Overrides:
    
    clearIntensityMap in class Loader
    
    Returns:
    
    true if a coefficient map did exist and was successfully deleted

Class FSLoader

Nested Class Summary

Nested classes/interfaces inherited from class ini.trakem2.persistence.Loader

Field Summary

Fields inherited from class ini.trakem2.persistence.Loader

Constructor Summary

Method Summary

Methods inherited from class ini.trakem2.persistence.Loader

Methods inherited from class java.lang.Object

Field Detail

ABS_PATH

repainter

autosaver

MIPMAP_FORMATS

MIPMAP_JPEG

MIPMAP_PNG

MIPMAP_TIFF

MIPMAP_RAW

MIPMAP_RAG

Constructor Detail

FSLoader

FSLoader

Method Detail

getProjectXMLPath

getStorageFolder

getImageStorageFolder

openFSProject

getOpenProject

nStaticServiceThreads

restartMipMapThreads

destroy

getNextId

getNextBlobId

fetchBezierArrays

fetchPipePoints

fetchBallPoints

fetchArea

fetchImagePlus

fetchImageProcessor

fetchImage

fetchImageMask

getMasksFolder

getCoordinateTransformsFolder

fetchLabel

fetchOriginal

addToDatabase

updateInDatabase

updateInDatabase

removeFromDatabase

setImageFile

getAbsolutePath

getAbsolutePath

getImageFilePath

isURL

isRelativePath

addedPatchFrom

asSafePath

save

saveAs

saveAs

getPath

getPathsCopy

makeAllPathsRelativeTo

restorePaths

makeRelativePath

setupMenuItems

importStackAsPatches

parseXMLOptions

regenerateMipMaps

insertXMLOptions

getParentFolder

getMipMapsFolder

grabPixels

queueForMipmapRemoval

tagForMipmapRemoval

generateMipMaps

removeSerializedFeatures

removeSerializedPointMatches

generateMipMaps

getUNUIdFolder