DBLoader (Fiji Javadocs 0-SNAPSHOT API)

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

```
public class DBLoader
extends Loader
```

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

Field Summary
- 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

DBLoader()
Create and connect to the database.

Constructors
Constructor and Description
`DBLoader()` Create and connect to the database.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addCrossLink(long project_id, long id1, long id2)`
`boolean`	`addToDatabase(DBObject ob)`
`void`	`commitLargeUpdate()` Used in combination with startLargeUpdate()
`void`	`destroy()` Release all memory and unregister itself.
`void`	`disconnect()` Disconnect from the database.
`Area`	`fetchArea(long area_list_id, long layer_id)`
`ArrayList`	`fetchBallPoints(long id)`
`double[][][]`	`fetchBezierArrays(long id)` Get the bezier points from the database for the given profile but as a triple array of points, that is, three arrays with 2 arrays (x and y) each.
`ij.ImagePlus`	`fetchImagePlus(Patch p)`
`Object[]`	`fetchLabel(DLabel label)`
`ij.ImagePlus`	`fetchOriginal(Patch patch)` Used for the revert command.
`ArrayList`	`fetchPipePoints(long id)`
`long`	`getNextId()` Retrieve next id from a sequence for a new DBObject to be added.
`Project[]`	`getProjects()` Fetch all existing projects from the database.
`LayerThing`	`getRootLayerThing(Project project, ProjectThing project_thing, TemplateThing layer_set_tt, TemplateThing layer_tt)` Fetches the root LayerSet, fills it with children (recursively) and uses the profiles, pipes, etc., from the project_thing.
`ProjectThing`	`getRootProjectThing(Project project, TemplateThing root_tt, TemplateThing project_tt, HashMap<Long,Displayable> hs_d)` Get all the Thing objects, recursively, for the root, and their corresponding encapsulated objects.
`TemplateThing`	`getTemplateRoot(Project project)` Fetch the root of the TemplateThing tree from the database-stored hierarchy of TemplateThing objects defined in the original XML file .
`boolean`	`hasChanges()` Always returns false.
`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.
`boolean`	`isConnected()` Find out whether the connection is up.
`boolean`	`isIdenticalProjectSource(Loader loader)`
`boolean`	`isReady()` Check if settings are in.
`boolean`	`removeCrossLink(long id1, long id2)` Remove a link between two objects.
`boolean`	`removeFromDatabase(DBObject ob)`
`void`	`restoreNodesExpandedState(Project project)` Affects only those set to true; the rest are left untouched.
`void`	`rollback()` Used when errors ocurr during a large insertion.
`void`	`startLargeUpdate()` Used in combination with commitLargeUpdate()
`boolean`	`updateInDatabase(DBObject ob, Set<String> keys)`
`boolean`	`updateInDatabase(DBObject ob, String key)`

Methods inherited from class ini.trakem2.persistence.Loader
addedPatchFrom, addJob, addNewImage, addNewImage, adjustChannels, askForXMLTemplate, cache, cache, cacheAWT, cacheImagePlus, canReadAndWriteTo, checkMipMapFileExists, clearIntensityMap, computeDesirableMinFreeBytes, countObjects, createFlyThrough, createLazyFlyThrough, createZippedStream, debug, decache, decacheAWT, decacheImagePlus, decacheImagePlus, deleteStaleFiles, deserialize, destroyPreloader, doGUILater, doLater, embedAlpha, embedAlpha, embedAlphaPre, enhanceContrast, enhanceContrast, enoughFreeMemory, estimateImageFileSize, export, exportImage, exportImage, fetchAWTImage, fetchDataImage, fetchImage, fetchImage, fetchImageMask, fetchImagePlus, fetchImageProcessor, fetchMipMapAWT, flush, flushMipMaps, flushMipMaps, generateLayerMipMaps, generateMipMaps, generateMipMaps, generateMipMaps, getAbsolutePath, getCached, getCachedAWT, getCachedClosestAboveImage, getCachedClosestBelowImage, getCachedImagePlus, getClosestMipMapLevel, getCoordinateTransformsFolder, getCurrentMemory, getDimensions, getDimensions, getFileName, getFlatAWTImage, getFlatAWTImage, getFlatImage, getFlatImage, getFlatImage, getFlatImage, getFlatImage, getFlatImage, getHighestMipMapLevel, getHighestMipMapLevel, getImageFilePath, getImageStorageFolder, getInternalFileName, getJobsPopup, getMasksFolder, getMipMapFormat, getMipMapLevel, getMipMapModeIndex, getMipMapModeName, getMipMapsFolder, getMipMapsRegenerationEnabled, getNextBlobId, getNextTempId, getOrMakeImageLoadingLock, getOrMakeImageLoadingLock, getParentFolder, getPath, getPathsCopy, getPreprocessorScriptPath, getStorageFolder, getUNUId, getUNUIdFolder, handleCacheError, handlePathlessImage, importGrid, importGrid, importImage, importImage, importImage, importImages, importImages, importLabelsAsAreaLists, importLabelsAsAreaLists, importNextImage, importSequenceAsGrid, importSequenceAsGrid, importSequenceAsGrid, importStack, importStack, importStack, importStackAsPatches, insertXMLOptions, isAsynchronous, isCached, isImagePlusCached, isMipMapsRegenerationEnabled, isSignalImage, isSnapPaintable, isUnloadable, makeAllPathsRelativeTo, makeFlatImage, makeFlatImage, makeFlatImage, makeGrayLut, makePatchesDir, makePrescaledTiles, makeProjectName, makeRelativePath, mapIntensities, markStaleFileForDeletionUponSaving, maskBorders, maskBorders, maskBordersLayerWise, maxDim, measureSize, openImage, openImagePlus, openStack, preload, preload, preProcess, printCache, printCaches, printCacheStatus, printMemState, queueForMipmapRemoval, quitJob, recoverOOME, recreateBuckets, recreateBuckets, regenerateMipMaps, regenerateMipMaps, releaseAll, releaseAllCaches, releaseMemory, releaseMemory2, releaseToFit, releaseToFit, removeAlphaMask, removeCached, removeCached, removeFromUnloadable, removeImageLoadingLock, removeJob, removeMipMaps, restorePaths, save, saveAs, saveAs, saveAs, saveTask, scaleImage, scaleImage, serialize, setChanged, setDesirableMinFreeBytes, setHeapFraction, setImageFile, setMinAndMax, setMipMapFormat, setMipMapsRegeneration, setPreprocessorScriptPath, setPreprocessorScriptPathSilently, setupMenuItems, setupPreloader, setupPreloaderThreads, storeAlphaMask, tagForMipmapRemoval, unzipTiff, updateMipMapsFormat, usesMipMapsFolder, writeXMLTo

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

Constructor Detail
- DBLoader
```
public DBLoader()
```
  Create and connect to the database.

Method Detail

isReady
```
public boolean isReady()
```
Check if settings are in.

destroy
```
public void destroy()
```
Release all memory and unregister itself.

Overrides:

destroy in class Loader

startLargeUpdate
```
public void startLargeUpdate()
```
Used in combination with commitLargeUpdate()

Overrides:

startLargeUpdate in class Loader

commitLargeUpdate
```
public void commitLargeUpdate()
```
Used in combination with startLargeUpdate()

Overrides:

commitLargeUpdate in class Loader

rollback
```
public void rollback()
```
Used when errors ocurr during a large insertion.

Overrides:

rollback in class Loader

isConnected
```
public boolean isConnected()
```
Find out whether the connection is up.

disconnect
```
public void disconnect()
```
Disconnect from the database.

getNextId
```
public long getNextId()
```
Retrieve next id from a sequence for a new DBObject to be added.

Specified by:

getNextId in class Loader

getTemplateRoot
```
public TemplateThing getTemplateRoot(Project project)
```
Fetch the root of the TemplateThing tree from the database-stored hierarchy of TemplateThing objects defined in the original XML file .

getProjects
```
public Project[] getProjects()
```
Fetch all existing projects from the database.

getRootProjectThing

public ProjectThing getRootProjectThing(Project project,
                                        TemplateThing root_tt,
                                        TemplateThing project_tt,
                                        HashMap<Long,Displayable> hs_d)

Get all the Thing objects, recursively, for the root, and their corresponding encapsulated objects. Also, fills in the given ArrayList with all loaded Displayable objects.

getRootLayerThing

public LayerThing getRootLayerThing(Project project,
                                    ProjectThing project_thing,
                                    TemplateThing layer_set_tt,
                                    TemplateThing layer_tt)

Fetches the root LayerSet, fills it with children (recursively) and uses the profiles, pipes, etc., from the project_thing. Will reconnect the links and open Displays for the layers that have one.

fetchBezierArrays
```
public double[][][] fetchBezierArrays(long id)
```
Get the bezier points from the database for the given profile but as a triple array of points, that is, three arrays with 2 arrays (x and y) each.

Specified by:

fetchBezierArrays in class Loader

fetchArea

public Area fetchArea(long area_list_id,
                      long layer_id)

Specified by:: fetchArea in class Loader

fetchPipePoints
```
public ArrayList fetchPipePoints(long id)
```
Specified by:

fetchPipePoints in class Loader

fetchBallPoints
```
public ArrayList fetchBallPoints(long id)
```
Specified by:

fetchBallPoints 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

addCrossLink

public void addCrossLink(long project_id,
                         long id1,
                         long id2)

Overrides:: addCrossLink in class Loader

removeCrossLink
```
public boolean removeCrossLink(long id1,
                               long id2)
```
Remove a link between two objects.

Overrides:

removeCrossLink in class Loader

fetchImagePlus
```
public ij.ImagePlus fetchImagePlus(Patch p)
```
Specified by:

fetchImagePlus in class Loader

fetchLabel

public Object[] fetchLabel(DLabel label)

Specified by:: fetchLabel in class Loader

fetchOriginal
```
public ij.ImagePlus fetchOriginal(Patch patch)
```
Description copied from class: Loader

Used for the revert command.

Specified by:

fetchOriginal in class Loader

hasChanges
```
public boolean hasChanges()
```
Always returns false.

Overrides:

hasChanges in class Loader

isIdenticalProjectSource

public boolean isIdenticalProjectSource(Loader loader)

restoreNodesExpandedState
```
public void restoreNodesExpandedState(Project project)
```
Affects only those set to true; the rest are left untouched.

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

Class DBLoader

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

Constructor Detail

DBLoader

Method Detail

isReady

destroy

startLargeUpdate

commitLargeUpdate

rollback

isConnected

disconnect

getNextId

getTemplateRoot

getProjects

getRootProjectThing

getRootLayerThing

fetchBezierArrays

fetchArea

fetchPipePoints

fetchBallPoints

addToDatabase

updateInDatabase

updateInDatabase

removeFromDatabase

addCrossLink

removeCrossLink

fetchImagePlus

fetchLabel

fetchOriginal

hasChanges

isIdenticalProjectSource

restoreNodesExpandedState

importStackAsPatches