Package | Description |
---|---|
org.anchoranalysis.experiment.bean.io |
Generic experiments that handle input and output in structured ways.
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org.anchoranalysis.experiment.bean.processor |
How a task is executed on multiple inputs.
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org.anchoranalysis.experiment.bean.task |
Defines a task,
which is a set of operations run on an input, that may or may not generate an output.
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org.anchoranalysis.experiment.io |
Interfaces for replacing attributes of an experiment: input, output, task etc.
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org.anchoranalysis.experiment.task.processor |
Non-bean classes related to
JobProcessor . |
org.anchoranalysis.launcher.run.tasks |
Loading and displaying pre-defined tasks.
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org.anchoranalysis.plugin.annotation.bean.aggregate |
Beans to combine two or more annotations.
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org.anchoranalysis.plugin.annotation.bean.comparison |
Task to compare a set of annotations to a segmentation or another set of annotations.
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org.anchoranalysis.plugin.image.task.bean |
A parent package for many different kinds of tasks.
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org.anchoranalysis.plugin.image.task.bean.combine |
Combining multiple images together into a single image.
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org.anchoranalysis.plugin.image.task.bean.feature |
Tasks pertaining to
Feature s. |
org.anchoranalysis.plugin.image.task.bean.format |
Tasks for converting image-formats.
|
org.anchoranalysis.plugin.image.task.bean.grouped |
Tasks that involved stacks (usually each channel from an image) that are somehow
grouped-together.
|
org.anchoranalysis.plugin.image.task.bean.grouped.histogram |
Task(s) to export histograms of intensity values.
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org.anchoranalysis.plugin.image.task.bean.labeller |
Associating labels with images.
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org.anchoranalysis.plugin.image.task.bean.scale |
Tasks to scale an image.
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org.anchoranalysis.plugin.image.task.bean.segment |
Tasks to segment an image.
|
org.anchoranalysis.plugin.image.task.bean.slice |
Tasks that process on one or more slices from a z-stack.
|
org.anchoranalysis.plugin.io.bean.task |
Implementations of
Task related to file-system
I/O. |
org.anchoranalysis.plugin.mpp.experiment.bean.convert |
Converting from
NamedChannelsInput to the
input-type expected by a Task . |
org.anchoranalysis.plugin.mpp.experiment.bean.define |
Tasks that use a
DefineOutputter or related
classes. |
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task |
Tasks that calculate and export
ReportFeature s. |
org.anchoranalysis.plugin.mpp.experiment.bean.objects |
Tasks involving
ObjectMask s. |
org.anchoranalysis.plugin.mpp.experiment.bean.segment |
Tasks that segment an image to produce a
MarkCollection . |
org.anchoranalysis.plugin.quick.bean.experiment |
Quickly defining experiments via several assumptions, including particular file-paths.
|
org.anchoranalysis.plugin.quick.bean.structure |
Specifying a structure of subdirectories and filenames when quickly defining an experiment.
|
org.anchoranalysis.test.experiment.task |
Helper classes to execute
Task s in tests. |
Modifier and Type | Method and Description |
---|---|
void |
InputOutputExperiment.replaceTask(Task<T,S> taskToReplace) |
Modifier and Type | Method and Description |
---|---|
Task<T,S> |
JobProcessor.getTask()
The task to be applied to inputs.
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Modifier and Type | Method and Description |
---|---|
void |
JobProcessor.replaceTask(Task<T,S> taskToReplace) |
void |
JobProcessor.setTask(Task<T,S> task)
The task to be applied to inputs.
|
Modifier and Type | Class and Description |
---|---|
class |
TaskWithoutSharedState<T extends InputFromManager>
A particular type of task that doesn't share-state between running jobs
|
Modifier and Type | Method and Description |
---|---|
void |
ReplaceTask.replaceTask(Task<T,S> taskToReplace)
Replace the currently-assigned
Task with another. |
Constructor and Description |
---|
CallableJob(Task<T,S> task,
ParametersUnbound<T,S> parametersUnbound,
JobStateMonitor stateMonitor,
JobDescription jobDescription,
ConcurrentJobMonitor monitor,
Optional<MessageLogger> loggerMonitor,
int showOngoingJobsLessThan)
Constructor.
|
Modifier and Type | Class and Description |
---|---|
class |
HelloWorld<S extends InputFromManager>
A dummy task that simply writes a message to all log files, specifically: 1.
|
Modifier and Type | Class and Description |
---|---|
class |
AggregateAnnotations<S extends AnnotatorStrategy>
Aggregates many per-image annotations together in form of a CSV file.
|
Modifier and Type | Class and Description |
---|---|
class |
CompareAnnotations<T extends Assignment<ObjectMask>>
Task to compare a set of annotations to a segmentation or another set of annotations.
|
Modifier and Type | Class and Description |
---|---|
class |
RasterTask<S,U>
An experiment that takes (primarily) a series of raster images as an input.
|
Modifier and Type | Class and Description |
---|---|
class |
AggregateChannelTask
Creates a an aggregated-image for each group, where each voxel-value is aggregated across each
channel in each image in the group.
|
class |
Montage
Creates a montage of images, by tiling them side-by-side.
|
Modifier and Type | Class and Description |
---|---|
class |
ExportFeatures<T extends InputFromManager,S,U extends FeatureInput>
Calculates features and exports them as a CSV file.
|
Modifier and Type | Class and Description |
---|---|
class |
ConvertImageFormat
Converts each input-image to an output format, optionally changing the bit depth.
|
Modifier and Type | Class and Description |
---|---|
class |
GroupedStackBase<S,T>
Base class for stacks (usually each channel from an image) that are somehow grouped-together.
|
Modifier and Type | Class and Description |
---|---|
class |
ExportImageHistograms
Exports a histogram of voxel intensities as a CSV file for each channel of an image.
|
Modifier and Type | Class and Description |
---|---|
class |
ImageAssignLabel<T>
Assigns a label to each image and copies into subdirectories for each label, and creates a
labelling CSV.
|
Modifier and Type | Class and Description |
---|---|
class |
ScaleImage<S>
Base class for tasks whose primary aim is to scale (resize) an image.
|
class |
ScaleImageCommonSize
Creates a scaled copy of images, ensuring all images have identical output size.
|
class |
ScaleImageIndependently
Creates a scaled copy of images, treating each image independently, and without any padding or
alignment.
|
Modifier and Type | Class and Description |
---|---|
class |
SegmentInstanceWithModel<T extends InferenceModel>
Using a model-pool, performs instance segmentation on an image producing zero, one or more
objects per image.
|
Modifier and Type | Class and Description |
---|---|
class |
ExtractSlice
Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice.
|
Modifier and Type | Class and Description |
---|---|
class |
CombineCSV
Combines multiple CSV files into a single CSV file.
|
class |
CopyFiles<T>
Copy files to the output-directory, possibly changing the name or performing other operations
like compression in the process.
|
class |
SummarizeBase<T extends InputFromManager,S> |
class |
SummarizeInputs<T extends InputFromManager> |
Modifier and Type | Class and Description |
---|---|
class |
ConvertNamedChannels<T extends NamedChannelsInput,S,U extends InputFromManager>
Converts
NamedChannelsInput to a variety of others to match a delegate task. |
Modifier and Type | Method and Description |
---|---|
Task<U,S> |
ConvertNamedChannels.getTask()
The underlying task that will be called, perhaps with a different input-type.
|
Modifier and Type | Method and Description |
---|---|
void |
ConvertNamedChannels.replaceTask(Task<U,S> taskToReplace) |
void |
ConvertNamedChannels.setTask(Task<U,S> task)
The underlying task that will be called, perhaps with a different input-type.
|
Modifier and Type | Class and Description |
---|---|
class |
Develop
Derives various types of outputs (images, histograms etc.) from
MultiInput s. |
Modifier and Type | Class and Description |
---|---|
class |
ExportReportFeatures
Creates a report of feature values from a
DefineOutputter and a MultiInput . |
Modifier and Type | Class and Description |
---|---|
class |
ExportObjectsAsCroppedImages
Exports a cropped image for each object-mask showing its context within an image
|
class |
ExportObjectsBase<T extends InputFromManager,S> |
class |
ExportObjectsFromCSV
Given a CSV with a point representing one or more object-masks, these object-masks are extracted
from a segmentation.
|
Modifier and Type | Class and Description |
---|---|
class |
SegmentMarksFromImage
Segments an image into a collection of
Mark s. |
Modifier and Type | Method and Description |
---|---|
Task<MultiInput,S> |
QuickExperiment.getTask() |
Task<T,S> |
QuickMultiDatasetExperiment.getTask() |
Modifier and Type | Method and Description |
---|---|
void |
QuickExperiment.setTask(Task<MultiInput,S> task) |
void |
QuickMultiDatasetExperiment.setTask(Task<T,S> task) |
Modifier and Type | Method and Description |
---|---|
Task<T,S> |
QuickMultiDatasetStructuredExperiment.getTask() |
Modifier and Type | Method and Description |
---|---|
void |
QuickMultiDatasetStructuredExperiment.setTask(Task<T,S> task) |
Modifier and Type | Method and Description |
---|---|
<T extends InputFromManager,S,V extends Task<T,S>> |
ExecuteTaskHelper.assertExpectedTaskOutputs(List<T> inputs,
V task,
Path pathDirectoryOutput,
String pathDirectorySaved,
Iterable<String> pathsFileToCompare)
Executes a task on a multiple inputs and asserts expected outputs - with task arguments.
|
<T extends InputFromManager,S,V extends Task<T,S>> |
ExecuteTaskHelper.assertExpectedTaskOutputs(T input,
V task,
Path pathDirectoryOutput,
String pathDirectorySaved,
Iterable<String> pathsFileToCompare)
Executes a task on a single-input.
|
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.