| Package | Description |
|---|---|
| ini.trakem2 | |
| ini.trakem2.analysis | |
| ini.trakem2.display | |
| ini.trakem2.imaging | |
| ini.trakem2.persistence | |
| ini.trakem2.tree | |
| ini.trakem2.utils | |
| lenscorrection | |
| lineage | |
| mpicbg.trakem2.align |
| Modifier and Type | Method and Description |
|---|---|
Bureaucrat |
Project.saveTask(String command) |
| Modifier and Type | Method and Description |
|---|---|
static Bureaucrat |
Compare.compareAllToAll(boolean to_file,
String regex,
String[] ignore,
Project[] projects) |
static Bureaucrat |
Compare.compareAllToAll(boolean to_file,
String regex,
String[] ignore,
Project[] projects,
boolean crop,
boolean from_end,
int max_n_elements,
String outgroup)
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.
|
static Bureaucrat |
Compare.reliabilityAnalysis(String[] ignore)
Reliability analysis of pipe comparisons: compares all to all,
recording the score position of homonimous pipes in other projects.
|
static Bureaucrat |
Compare.reliabilityAnalysis(String[] ignore,
boolean output_arff,
boolean weka_classify,
boolean show_dialog,
double delta,
double wi,
double wd,
double wm) |
static Bureaucrat |
Compare.reliabilityAnalysisSpaceExploration(String[] ignore) |
static Bureaucrat |
Compare.variabilityAnalysis(Project reference_project,
String regex,
String[] ignore,
boolean show_cata_dialog,
boolean generate_plots,
boolean show_plots,
String plot_dir_,
boolean show_3D,
boolean show_condensed_3D,
boolean show_sources_3D,
Map<Project,Color> sources_color_table,
boolean show_envelope_3D,
float envelope_alpha,
double delta_envelope,
int envelope_type,
boolean show_axes_3D,
boolean heat_map,
Map<String,VectorString3D> map_condensed,
Project[] projects) |
| Modifier and Type | Method and Description |
|---|---|
Bureaucrat |
Display.applyPatchTask(List<Patch> patches,
String taskTitle,
Operation<Boolean,Patch> task,
Filter<Patch> filter)
Meant for tasks that require setting an undo and regenerating mipmaps.
|
static Bureaucrat |
TreeConnectorsView.create(Tree<?> tree) |
Bureaucrat |
Tree.generateAllReviewStacks() |
Bureaucrat |
Tree.generateReviewStackForSlab(float x,
float y,
Layer layer,
double magnification) |
Bureaucrat |
Tree.generateReviewStackForSlab(Node<T> node)
Generate a review stack from the previous branch node or root, to the next branch node or end node.
|
Bureaucrat |
Tree.generateSubtreeReviewStacks(int x,
int y,
Layer layer,
double magnification) |
Bureaucrat |
Tree.generateSubtreeReviewStacks(Node<T> root) |
protected Bureaucrat |
Display.importImage() |
protected Bureaucrat |
Display.importNextImage() |
static Bureaucrat |
Display.openLater()
After reloading a project from the database, open the Displays that the project had.
|
static Bureaucrat |
Display.removeAlphaMasks(Collection<Patch> patches) |
Bureaucrat |
Display.removeCoordinateTransforms(List<Patch> patches) |
Bureaucrat |
Tree.removeReviews() |
Bureaucrat |
Display.removeScalingRotationShear(List<Patch> patches) |
Bureaucrat |
Display.setCoordinateTransform(List<Patch> patches,
CoordinateTransform ct,
boolean append)
Deprecated.
Use
Display.setCoordinateTransform(List, CoordinateTransform, int) instead which implements pre-appending as a third mode. |
Bureaucrat |
Display.setCoordinateTransform(List<Patch> patches,
CoordinateTransform ct,
int existingTransform) |
Bureaucrat |
Display.setMeshResolution(List<Patch> patches,
int meshResolution) |
static Bureaucrat |
Display.snap(Patch patch)
Snap a Patch to the most overlapping Patch, if any.
|
| Modifier and Type | Method and Description |
|---|---|
static Bureaucrat |
Blending.blend(List<Layer> layers,
boolean respect_current_mask,
Filter<Patch> filter) |
static Bureaucrat |
Blending.blend(Set<Patch> patches,
boolean respect_current_mask)
For each file, find the weight for the alpha mask according to
wether the pixel overlaps with other images (weighted alpha
dependent on the distante to the image border and of that on
the other images) or not (full alpha).
|
static Bureaucrat |
Segmentation.fastMarching(AreaWrapper aw,
Layer layer,
Rectangle srcRect,
int x_p_w,
int y_p_w,
List<Runnable> post_tasks) |
static Bureaucrat |
Segmentation.fastMarching(AreaWrapper aw,
Layer layer,
Rectangle srcRect,
int x_p_w,
int y_p_w,
Runnable post_task) |
static Bureaucrat |
Segmentation.magicWand(AreaWrapper aw,
Layer layer,
Rectangle srcRect,
int x_p_w,
int y_p_w,
List<Runnable> post_tasks,
boolean inverse,
boolean subtract) |
static Bureaucrat |
Segmentation.magicWand(AreaWrapper aw,
Layer layer,
Rectangle srcRect,
int x_p_w,
int y_p_w,
Runnable post_task,
boolean inverse,
boolean subtract) |
static Bureaucrat |
StitchingTEM.montageWithPhaseCorrelationTask(Collection<Patch> col)
For each Patch, find who overlaps with it and perform a phase correlation or cross-correlation with it;
then consider all successful correlations as links and run the optimizer on it all.
|
static Bureaucrat |
StitchingTEM.montageWithPhaseCorrelationTask(List<Layer> layers) |
| Modifier and Type | Method and Description |
|---|---|
Bureaucrat |
Loader.enhanceContrast(Collection<Displayable> patches,
Patch reference)
Homogenize contrast for all patches, optionally using the @param reference Patch (can be null).
|
Bureaucrat |
Loader.enhanceContrast(Collection<Layer> layers)
Homogenize contrast layer-wise, for all given layers.
|
Bureaucrat |
Loader.generateLayerMipMaps(Layer[] la,
int starting_level)
Does nothing unless overriden.
|
Bureaucrat |
Loader.generateMipMaps(ArrayList<Displayable> al)
Returns generateMipMaps(al, false).
|
Bureaucrat |
Loader.generateMipMaps(ArrayList<Displayable> al,
boolean overwrite)
Does nothing and returns null unless overriden.
|
Bureaucrat |
FSLoader.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.
|
Bureaucrat |
Loader.importGrid(Layer layer) |
Bureaucrat |
Loader.importGrid(Layer layer,
String dir)
Import a grid of images and put them in the layer.
|
Bureaucrat |
Loader.importImage(Layer layer,
double x,
double y,
String path,
boolean synch_mipmap_generation)
Import an image into the given layer, in a separate task thread.
|
Bureaucrat |
Loader.importImages(Layer ref_layer) |
Bureaucrat |
Loader.importImages(Layer ref_layer,
String abs_text_file_path_,
String column_separator_,
double layer_thickness_,
double calibration_,
boolean homogenize_contrast_,
float scale_,
int border_width_)
Import images from the given text file, which is expected to contain 4 columns or optionally 9 columns:
|
Bureaucrat |
Loader.importLabelsAsAreaLists(Layer layer) |
Bureaucrat |
Loader.importLabelsAsAreaLists(Layer first_layer,
String path_,
double base_x_,
double base_y_,
float alpha_,
boolean add_background_)
If base_x or base_y are Double.MAX_VALUE, then those values are asked for in a GenericDialog.
|
Bureaucrat |
Loader.importSequenceAsGrid(Layer layer) |
Bureaucrat |
Loader.importSequenceAsGrid(Layer layer,
String dir) |
Bureaucrat |
Loader.importSequenceAsGrid(Layer first_layer,
String dir,
String[] image_file_names)
Import a sequence of images as a grid, and put them in the layer.
|
Bureaucrat |
Loader.importStack(Layer first_layer,
double x,
double y,
ij.ImagePlus imp_stack_,
boolean ask_for_data,
String filepath_,
boolean one_patch_per_layer_)
Imports an image stack from a multitiff file and places each slice in the proper layer, creating new layers as it goes.
|
Bureaucrat |
Loader.importStack(Layer first_layer,
ij.ImagePlus imp_stack_,
boolean ask_for_data) |
Bureaucrat |
Loader.importStack(Layer first_layer,
ij.ImagePlus imp_stack_,
boolean ask_for_data,
String filepath_) |
Bureaucrat |
Loader.makeFlatImage(Layer[] layer,
Rectangle srcRect,
double scale,
int c_alphas,
int type,
boolean force_to_file,
boolean quality) |
Bureaucrat |
Loader.makeFlatImage(Layer[] layer,
Rectangle srcRect,
double scale,
int c_alphas,
int type,
boolean force_to_file,
boolean quality,
Color background) |
Bureaucrat |
Loader.makeFlatImage(Layer[] layer,
Rectangle srcRect,
double scale,
int c_alphas,
int type,
boolean force_to_file,
String format,
boolean quality,
Color background)
If the srcRect is null, makes a flat 8-bit or RGB image of the entire layer.
|
Bureaucrat |
Loader.makePrescaledTiles(Layer[] layers,
Class<?> clazz,
Rectangle srcRect,
int c_alphas,
int type,
String target_dir,
int strategy,
Saver saver,
int tileSide,
int directory_structure_type,
boolean skip_empty_tiles,
boolean use_layer_indices,
int n_threads) |
static Bureaucrat |
ExportMultilevelTiles.makePrescaledTiles(Layer[] layers,
Class<?> clazz,
Rectangle srcRect,
int c_alphas,
int type,
String target_dir,
int strategy,
Saver saver,
int tileSide,
int directory_structure_type,
boolean skip_empty_tiles,
boolean use_layer_indices,
int n_threads)
Generate e.g.
|
Bureaucrat |
Loader.maskBorders(Collection<Displayable> patches,
int left,
int top,
int right,
int bottom)
Make the border have an alpha of zero.
|
Bureaucrat |
Loader.maskBordersLayerWise(Collection<Layer> layers,
int left,
int top,
int right,
int bottom)
Make the border have an alpha of zero.
|
Bureaucrat |
Loader.regenerateMipMaps(Collection<? extends Displayable> patches)
Does nothing and returns null unless overriden.
|
Bureaucrat |
FSLoader.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. |
Bureaucrat |
Loader.saveTask(Project project,
String command)
Run save or saveAs in a Bureaucract that blocks user input to the project being saved.
|
Bureaucrat |
Loader.setMinAndMax(Collection<? extends Displayable> patches,
double min,
double max) |
Bureaucrat |
Loader.updateMipMapsFormat(int old_format,
int new_format)
Does nothing unless overriden.
|
Bureaucrat |
FSLoader.updateMipMapsFormat(int old_format,
int new_format)
Removes all mipmap files and recreates them with the currently set mipmaps format.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Loader.addJob(Bureaucrat burro)
Adds a new job to monitor.
|
void |
Loader.removeJob(Bureaucrat burro) |
| Modifier and Type | Method and Description |
|---|---|
Bureaucrat |
ProjectTree.sendToSiblingProjectTask(DefaultMutableTreeNode node) |
| Modifier and Type | Method and Description |
|---|---|
static Bureaucrat |
Bureaucrat.create(Worker worker,
Project project)
Creates but does not start the Bureaucrat thread.
|
static Bureaucrat |
Bureaucrat.create(Worker worker,
Project[] project)
Creates but does not start the Bureaucrat thread.
|
static Bureaucrat |
Bureaucrat.createAndStart(Worker worker,
Project project)
Creates and start the Bureaucrat thread.
|
static Bureaucrat |
Bureaucrat.createAndStart(Worker worker,
Project[] project)
Creates and start the Bureaucrat thread.
|
static Bureaucrat |
Utils.launchTPlugIn(KeyEvent ke,
String menu,
Project project,
Displayable active)
Returns null if no plugin was launched.
|
| Modifier and Type | Method and Description |
|---|---|
static Bureaucrat |
DistortionCorrectionTask.correctDistortionFromSelection(Selection selection) |
static Bureaucrat |
DistortionCorrectionTask.correctDistortionFromSelectionTask(Selection selection) |
| Modifier and Type | Method and Description |
|---|---|
Bureaucrat |
Identify.identify(Line3D pipe) |
| Modifier and Type | Method and Description |
|---|---|
static Bureaucrat |
AlignLayersTask.alignLayersTask(Layer l) |
static Bureaucrat |
AlignLayersTask.alignLayersTask(Layer l,
Rectangle fov) |
static Bureaucrat |
AlignTask.alignMultiLayerMosaicTask(Layer l) |
static Bureaucrat |
AlignTask.alignMultiLayerMosaicTask(Layer l,
Patch nail) |
static Bureaucrat |
AlignTask.alignPatchesTask(List<Patch> patches,
Set<Patch> fixedPatches) |
static Bureaucrat |
AlignTask.alignSelectionTask(Selection selection) |
static Bureaucrat |
AlignTask.montageLayersTask(List<Layer> layers)
Montage each layer independently.
|
static Bureaucrat |
AlignTask.registerStackSlices(Patch slice) |
static Bureaucrat |
AlignTask.snap(Patch patch,
Align.ParamOptimize p_snapIn,
boolean setup)
Find the most overlapping image to @param patch in the same layer where @param patch sits, and snap @param patch and all its linked Displayable objects.
|
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