Index

A B C D E F G H I K L M N O P Q R S T U V W X Y Z 
All Classes and Interfaces|All Packages|Constant Field Values

A

affiliation() - Method in record class qupath.bioimageio.spec.Author
Returns the value of the affiliation record component.
ANGSTROM - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
ATTOMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
ATTOSECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
Author - Record Class in qupath.bioimageio.spec
Author or maintainer.
Author(String, String, String, String) - Constructor for record class qupath.bioimageio.spec.Author
Creates an instance of a Author record class.
axes - Variable in class qupath.bioimageio.spec.tensor.BaseTensor
 
Axes - Class in qupath.bioimageio.spec.tensor.axes
Utility methods for Axis objects.
Axes() - Constructor for class qupath.bioimageio.spec.tensor.axes.Axes
 
Axis - Interface in qupath.bioimageio.spec.tensor.axes
Base axis class for 0.4 and 0.5 axes.
AxisType - Enum Class in qupath.bioimageio.spec.tensor.axes
The type of axis.

B

B - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.AxisType
 
Badge - Record Class in qupath.bioimageio.spec
Model or repository badge.
Badge(String, String, String) - Constructor for record class qupath.bioimageio.spec.Badge
Creates an instance of a Badge record class.
BaseTensor - Class in qupath.bioimageio.spec.tensor
The basic tensor representation for inputs and outputs.
BaseTensor() - Constructor for class qupath.bioimageio.spec.tensor.BaseTensor
 
BOOL - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
 

C

C - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.AxisType
 
CENTIMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
CENTISECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
CiteEntry - Record Class in qupath.bioimageio.spec
Citation entry.
CiteEntry(String, String, String) - Constructor for record class qupath.bioimageio.spec.CiteEntry
Creates an instance of a CiteEntry record class.
createShapeArray(String, Map<Character, Integer>, int) - Static method in class qupath.bioimageio.spec.tensor.Shape
Create a shape array for a given axes.

D

Dataset - Class in qupath.bioimageio.spec
Dataset spec.
Dataset() - Constructor for class qupath.bioimageio.spec.Dataset
 
DAY - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
DECIMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
DECISECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
deserializeField(JsonDeserializationContext, JsonObject, String, Type, boolean) - Static method in class qupath.bioimageio.spec.Model
Deserialize a field from a JSON object.
deserializeField(JsonDeserializationContext, JsonObject, String, Type, T) - Static method in class qupath.bioimageio.spec.Model
Deserialize a field from a JSON object.
deserializeSize(JsonDeserializationContext, JsonElement, JsonElement) - Static method in interface qupath.bioimageio.spec.tensor.sizes.Size
Deserialize a size object from JSON.
doi() - Method in record class qupath.bioimageio.spec.CiteEntry
Returns the value of the doi record component.

E

equals(Object) - Method in record class qupath.bioimageio.spec.Author
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class qupath.bioimageio.spec.Badge
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class qupath.bioimageio.spec.CiteEntry
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class qupath.bioimageio.spec.FileDescription
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class qupath.bioimageio.spec.ModelParent
Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class qupath.bioimageio.spec.tensor.sizes.FixedSize
Indicates whether some other object is "equal to" this one.
EXAMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
EXASECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 

F

FEMTOMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
FEMTOSECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
FileDescription - Record Class in qupath.bioimageio.spec
A file description (link and hash).
FileDescription(String, String) - Constructor for record class qupath.bioimageio.spec.FileDescription
Creates an instance of a FileDescription record class.
FIXED - Enum constant in enum class qupath.bioimageio.spec.tensor.Processing.ProcessingMode
 
FixedSize - Record Class in qupath.bioimageio.spec.tensor.sizes
A fixed axis size.
FixedSize(int) - Constructor for record class qupath.bioimageio.spec.tensor.sizes.FixedSize
Create a fixed size instance
FLOAT32 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
 
FLOAT32 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
 
FLOAT64 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
 
FLOAT64 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
 
FOOT - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 

G

getAttachments() - Method in class qupath.bioimageio.spec.Resource
file and other attachments
getAttachments() - Method in class qupath.bioimageio.spec.Weights.ModelWeights
Attachments that are specific to this weights entry
getAuthors() - Method in class qupath.bioimageio.spec.Resource
The authors are the creators of the model RDF and the primary points of contact.
getAuthors() - Method in class qupath.bioimageio.spec.Weights.ModelWeights
Either the person(s) that have trained this model resulting in the original weights file.
getAxes() - Method in class qupath.bioimageio.spec.tensor.BaseTensor
Get the axes of the tensor.
getAxes() - Method in class qupath.bioimageio.spec.tensor.Processing.ProcessingWithMode
The subset of axes to scale jointly.
getAxes() - Method in class qupath.bioimageio.spec.tensor.Processing.ScaleLinear
Get the axes this applies to.
getAxesString(Axis[]) - Static method in class qupath.bioimageio.spec.tensor.axes.Axes
Get the old "bcyx" style axis representation of an Axis array.
getBadges() - Method in class qupath.bioimageio.spec.Resource
Get the badges for the resource.
getBaseURI() - Method in class qupath.bioimageio.spec.Model
Get the base URI, providing the location of the model.
getCite() - Method in class qupath.bioimageio.spec.Resource
Get the citations for the resource.
getConfig() - Method in class qupath.bioimageio.spec.Model
A field for custom configuration that can contain any keys not present in the RDF spec.
getCovers() - Method in class qupath.bioimageio.spec.Resource
Cover images.
getDataDescription() - Method in class qupath.bioimageio.spec.tensor.BaseTensor
get the data description object.
getDataRange() - Method in class qupath.bioimageio.spec.tensor.BaseTensor
Tuple `(minimum, maximum)` specifying the allowed range of the data in this tensor.
getDataType() - Method in class qupath.bioimageio.spec.tensor.BaseTensor
Get the data type of the tensor.
getDescription() - Method in class qupath.bioimageio.spec.Resource
Get the resource description
getDeserializers() - Static method in class qupath.bioimageio.spec.tensor.axes.Axes
Get any type adapters/deserializers needed for axis objects.
getDeserializers() - Static method in class qupath.bioimageio.spec.tensor.Processing
Get the type adapters/deserializers necessary for any Processing objects.
getDeserializers() - Static method in class qupath.bioimageio.spec.tensor.Tensors
Get the type adapters/deserializers for all classes in the tensor sub-package.
getDocumentation() - Method in class qupath.bioimageio.spec.Resource
URL or relative path to a markdown file with additional documentation.
getEps() - Method in class qupath.bioimageio.spec.tensor.Processing.ProcessingWithMode
Epsilon for numeric stability: out = (tensor - mean) / (std + eps) * (ref_std + eps) + ref_mean.
getFormatVersion() - Method in class qupath.bioimageio.spec.Resource
Get the version of the bioimage format used for this resource.
getGain() - Method in class qupath.bioimageio.spec.tensor.Processing.ScaleLinear
Get the multiplicative scaling factor
getGitRepo() - Method in class qupath.bioimageio.spec.Resource
Get a link to the git repository for this resource
getHalo() - Method in interface qupath.bioimageio.spec.tensor.axes.WithHalo
Get the size of the halo for this axis.
getHalo() - Method in class qupath.bioimageio.spec.tensor.OutputTensor
The "halo" that should be cropped from the output tensor to avoid boundary effects.
getIcon() - Method in class qupath.bioimageio.spec.Resource
Get the relative path to the resource icon
getId() - Method in class qupath.bioimageio.spec.tensor.BaseTensor
Get the ID of the tensor.
getID() - Method in class qupath.bioimageio.spec.Resource
bioimage.io-wide unique resource identifier assigned by bioimage.io; version **un**specific.
getID() - Method in interface qupath.bioimageio.spec.tensor.axes.Axis
Get the axis ID.
getInputs() - Method in class qupath.bioimageio.spec.Model
Get the input tensors
getKwargs() - Method in class qupath.bioimageio.spec.tensor.Processing
Get the keyword arguments for the operation
getLength() - Method in class qupath.bioimageio.spec.tensor.Shape
Get the number of elements in the shape array.
getLicense() - Method in class qupath.bioimageio.spec.Resource
getLinks() - Method in class qupath.bioimageio.spec.Resource
IDs of other bioimage.io resources
getMaintainers() - Method in class qupath.bioimageio.spec.Resource
Maintainers of this resource.
getMax() - Method in class qupath.bioimageio.spec.tensor.Processing.Clip
The maximum value
getMaxPercentile() - Method in class qupath.bioimageio.spec.tensor.Processing.ScaleRange
The maximum percentile.
getMean() - Method in class qupath.bioimageio.spec.tensor.Processing.ZeroMeanUnitVariance
The mean value(s) to use for `mode: fixed`.
getMin() - Method in class qupath.bioimageio.spec.tensor.Processing.Clip
The minimum value
getMin() - Method in record class qupath.bioimageio.spec.tensor.sizes.FixedSize
 
getMin() - Method in class qupath.bioimageio.spec.tensor.sizes.ParameterizedSize
 
getMin() - Method in class qupath.bioimageio.spec.tensor.sizes.ReferencedSize
 
getMin() - Method in interface qupath.bioimageio.spec.tensor.sizes.Size
Gets the minimum shape for this axis.
getMinPercentile() - Method in class qupath.bioimageio.spec.tensor.Processing.ScaleRange
The minimum percentile.
getMode() - Method in class qupath.bioimageio.spec.tensor.Processing.ProcessingWithMode
Mode for computing processing.
getName() - Method in class qupath.bioimageio.spec.Resource
A human-readable name of this model.
getName() - Method in class qupath.bioimageio.spec.tensor.BaseTensor
Get the tensor name
getName() - Method in class qupath.bioimageio.spec.tensor.Processing
Get the name of this operation
getOffset() - Method in class qupath.bioimageio.spec.tensor.Processing.ScaleLinear
Get the additive offset
getOffset() - Method in class qupath.bioimageio.spec.tensor.Shape
Get the shape scale, useful for implicit shapes.
getOffset() - Method in class qupath.bioimageio.spec.tensor.Shape.ImplicitOutputShape
 
getOffset() - Method in class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDataDescription
Offset for data on a ratio scale.
getOutputs() - Method in class qupath.bioimageio.spec.Model
Get the output tensors
getParent() - Method in class qupath.bioimageio.spec.Model
The model from which this model is derived, e.g.
getParent() - Method in class qupath.bioimageio.spec.Weights.ModelWeights
The source weights these weights were converted from.
getPostprocessing() - Method in class qupath.bioimageio.spec.tensor.OutputTensor
Get the post-processing steps for this output tensor.
getPreprocessing() - Method in class qupath.bioimageio.spec.tensor.InputTensor
Get the pre-processing steps for this tensor.
getRange() - Method in class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDataDescription
Get the range (if present)
getReferenceTensor() - Method in class qupath.bioimageio.spec.tensor.Processing.ScaleMeanVariance
The tensor to match mean and variance to.
getReferenceTensor() - Method in class qupath.bioimageio.spec.tensor.Processing.ScaleRange
The reference tensor, which we use for range scaling.
getReferenceTensor() - Method in class qupath.bioimageio.spec.tensor.Shape.ImplicitOutputShape
Get the reference tensor used to define this tensor shape.
getSampleInputs() - Method in class qupath.bioimageio.spec.Model
URLs/relative paths to sample outputs corresponding to the `sample_inputs`.
getSampleOutputs() - Method in class qupath.bioimageio.spec.Model
URLs/relative paths to sample outputs corresponding to the `sample_outputs`.
getSampleTensor() - Method in class qupath.bioimageio.spec.tensor.BaseTensor
A sample tensor to illustrate a possible input/output for the model, The sample image primarily serves to inform a human user about an example use case and is typically stored as .hdf5, .png or .tiff.
getScale() - Method in interface qupath.bioimageio.spec.tensor.axes.ScaledAxis
Get the scale of this axis.
getScale() - Method in class qupath.bioimageio.spec.tensor.Shape
Get the shape scale, useful for implicit shapes.
getScale() - Method in class qupath.bioimageio.spec.tensor.Shape.ImplicitOutputShape
 
getScale() - Method in class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDataDescription
Scale for data on an interval (or ratio) scale.
getSha256() - Method in class qupath.bioimageio.spec.Weights.ModelWeights
Get the SHA of the source file.
getShape() - Method in class qupath.bioimageio.spec.tensor.BaseTensor
Get the shape of the tensor.
getShape() - Method in class qupath.bioimageio.spec.tensor.Shape
Get the shape, if this is defined explicitly.
getShape() - Method in class qupath.bioimageio.spec.tensor.Shape.SizesShape
 
getShapeMin() - Method in class qupath.bioimageio.spec.tensor.Shape
Get the minimum shape; useful for parameterized shapes.
getShapeMin() - Method in class qupath.bioimageio.spec.tensor.Shape.ParameterizedInputShape
 
getShapeMin() - Method in class qupath.bioimageio.spec.tensor.Shape.SizesShape
 
getShapeStep() - Method in class qupath.bioimageio.spec.tensor.Shape
Get the shape step (increment), useful for parameterized shapes.
getShapeStep() - Method in class qupath.bioimageio.spec.tensor.Shape.ParameterizedInputShape
 
getShapeStep() - Method in class qupath.bioimageio.spec.tensor.Shape.SizesShape
 
getSize() - Method in interface qupath.bioimageio.spec.tensor.axes.Axis
Get the size of this axis.
getSize() - Method in interface qupath.bioimageio.spec.tensor.axes.ScaledAxis
Get the size of this axis.
getSource() - Method in class qupath.bioimageio.spec.Resource
Get the source file for the resource
getSource() - Method in class qupath.bioimageio.spec.Weights.ModelWeights
Get the source file or link (http etc.)
getStd() - Method in class qupath.bioimageio.spec.tensor.Processing.ZeroMeanUnitVariance
The standard deviation values to use for `mode: fixed`.
getStep() - Method in record class qupath.bioimageio.spec.tensor.sizes.FixedSize
 
getStep() - Method in class qupath.bioimageio.spec.tensor.sizes.ParameterizedSize
 
getStep() - Method in class qupath.bioimageio.spec.tensor.sizes.ReferencedSize
 
getStep() - Method in interface qupath.bioimageio.spec.tensor.sizes.Size
Get the step size of this axis size.
getTags() - Method in class qupath.bioimageio.spec.Resource
Associated tage
getTargetShape(int...) - Method in class qupath.bioimageio.spec.tensor.Shape
Get a compatible shape given the specified target.
getTargetShape(int...) - Method in class qupath.bioimageio.spec.tensor.Shape.ImplicitOutputShape
Get the output shape for the given input.
getTargetShape(int...) - Method in class qupath.bioimageio.spec.tensor.Shape.ParameterizedInputShape
 
getTargetShape(int[]) - Method in class qupath.bioimageio.spec.tensor.Shape.SizesShape
 
getTargetSize(int) - Method in record class qupath.bioimageio.spec.tensor.sizes.FixedSize
 
getTargetSize(int) - Method in class qupath.bioimageio.spec.tensor.sizes.ParameterizedSize
 
getTargetSize(int) - Method in class qupath.bioimageio.spec.tensor.sizes.ReferencedSize
 
getTargetSize(int) - Method in interface qupath.bioimageio.spec.tensor.sizes.Size
Get a size as close as possible to a target.
getTestInputs() - Method in class qupath.bioimageio.spec.Model
Test input tensors compatible with the `inputs` description for a **single test case**.
getTestOutputs() - Method in class qupath.bioimageio.spec.Model
Test output tensors compatible with the `output` description for a **single test case**.
getTestTensor() - Method in class qupath.bioimageio.spec.tensor.BaseTensor
An example tensor to use for testing.
getThreshold() - Method in class qupath.bioimageio.spec.tensor.Processing.Binarize
Get the threshold for binarization
getTimestamp() - Method in class qupath.bioimageio.spec.Model
Timestamp in #ISO 8601) format with a few restrictions listed in the python docs).
getType() - Method in interface qupath.bioimageio.spec.tensor.axes.Axis
Get the type of this axis, see AxisType.
getType() - Method in class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDataDescription
Get the data type of the ratio
getType() - Method in class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDataDescription
The data type of the underlying tensor.
getUnit() - Method in class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDataDescription
Get the unit of the ratio
getUnit(String) - Static method in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
Get the SpaceUnit corresponding to a String value.
getUnit(String) - Static method in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
Get the TimeUnit corresponding to a String value.
getURI() - Method in class qupath.bioimageio.spec.Model
Get the URI providing the location of the model.
getValues() - Method in class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDataDescription
Get the possible values for the described tensor to which numeric dtype values relate to.
getVersion() - Method in class qupath.bioimageio.spec.Resource
Get the version of the resource.
getWeights() - Method in class qupath.bioimageio.spec.Model
Get a map view of the weights.
getWeights(String) - Method in class qupath.bioimageio.spec.Model
Alternative to Model.getWeights()} using a string key.
getWeights(Weights.WeightsEntry) - Method in class qupath.bioimageio.spec.Model
Alternative to Model.getWeights() that corrects for keys that have been renamed.
GIGAMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
GIGASECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
githubUser() - Method in record class qupath.bioimageio.spec.Author
Returns the value of the githubUser record component.

H

hashCode() - Method in record class qupath.bioimageio.spec.Author
Returns a hash code value for this object.
hashCode() - Method in record class qupath.bioimageio.spec.Badge
Returns a hash code value for this object.
hashCode() - Method in record class qupath.bioimageio.spec.CiteEntry
Returns a hash code value for this object.
hashCode() - Method in record class qupath.bioimageio.spec.FileDescription
Returns a hash code value for this object.
hashCode() - Method in record class qupath.bioimageio.spec.ModelParent
Returns a hash code value for this object.
hashCode() - Method in record class qupath.bioimageio.spec.tensor.sizes.FixedSize
Returns a hash code value for this object.
hashSha256() - Method in record class qupath.bioimageio.spec.FileDescription
Returns the value of the hashSha256 record component.
HECTOMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
HECTOSECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
HOUR - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 

I

I - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.AxisType
 
icon() - Method in record class qupath.bioimageio.spec.Badge
Returns the value of the icon record component.
id() - Method in record class qupath.bioimageio.spec.ModelParent
Returns the value of the id record component.
ImplicitOutputShape() - Constructor for class qupath.bioimageio.spec.tensor.Shape.ImplicitOutputShape
 
INCH - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
IndexAxes - Class in qupath.bioimageio.spec.tensor.axes
Axes that relate to indexes rather than space/time/channel/batch, for example lists of objects.
IndexAxes() - Constructor for class qupath.bioimageio.spec.tensor.axes.IndexAxes
 
InputTensor - Class in qupath.bioimageio.spec.tensor
Model input, including shape, axes, datatype and preprocessing.
InputTensor() - Constructor for class qupath.bioimageio.spec.tensor.InputTensor
 
INT16 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
 
INT16 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
 
INT32 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
 
INT32 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
 
INT64 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
 
INT64 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
 
INT8 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
 
INT8 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
 
io.github.qupath.bioimageio.spec - module io.github.qupath.bioimageio.spec
 
isFormatNewerThan(String) - Method in class qupath.bioimageio.spec.Resource
Compare a resource's format version to a semantic version

K

KERAS_HDF5 - Enum constant in enum class qupath.bioimageio.spec.Weights.WeightsEntry
 
KILOMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
KILOSECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 

L

label() - Method in record class qupath.bioimageio.spec.Badge
Returns the value of the label record component.

M

MEGAMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
MEGASECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
METER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
MICROMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
MICROSECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
MILE - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
MILLIMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
MILLISECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
MINUTE - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
Model - Class in qupath.bioimageio.spec
Resource based on the main model spec.
Model() - Constructor for class qupath.bioimageio.spec.Model
 
ModelParent - Record Class in qupath.bioimageio.spec
Model parent.
ModelParent(String, String, String) - Constructor for record class qupath.bioimageio.spec.ModelParent
Creates an instance of a ModelParent record class.
ModelWeights() - Constructor for class qupath.bioimageio.spec.Weights.ModelWeights
 

N

name() - Method in record class qupath.bioimageio.spec.Author
Returns the value of the name record component.
NANOMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
NANOSECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
NO_SIZE - Static variable in interface qupath.bioimageio.spec.tensor.sizes.Size
Constant to indicate that this element has no meaningful size for some context.
NO_UNIT - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
NO_UNIT - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 

O

ONNX - Enum constant in enum class qupath.bioimageio.spec.Weights.WeightsEntry
 
orcid() - Method in record class qupath.bioimageio.spec.Author
Returns the value of the orcid record component.
OutputTensor - Class in qupath.bioimageio.spec.tensor
Model output, including shape, axes, halo, datatype and postprocessing.
OutputTensor() - Constructor for class qupath.bioimageio.spec.tensor.OutputTensor
 

P

ParameterizedInputShape() - Constructor for class qupath.bioimageio.spec.tensor.Shape.ParameterizedInputShape
 
ParameterizedSize - Class in qupath.bioimageio.spec.tensor.sizes
Describes a range of valid tensor axis sizes as `size = min + n*step`.
parse(File) - Static method in class qupath.bioimageio.spec.Model
Parse a model from a file or directory.
parse(InputStream) - Static method in class qupath.bioimageio.spec.Model
Parse a model from an input stream.
parse(Path) - Static method in class qupath.bioimageio.spec.Model
Parse a model from a path.
PARSEC - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
PER_DATASET - Enum constant in enum class qupath.bioimageio.spec.tensor.Processing.ProcessingMode
 
PER_SAMPLE - Enum constant in enum class qupath.bioimageio.spec.tensor.Processing.ProcessingMode
 
PETAMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
PETASECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
PICOMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
PICOSECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
Processing - Class in qupath.bioimageio.spec.tensor
Base class for pre- and post-processing operations.
Processing.Binarize - Class in qupath.bioimageio.spec.tensor
A binarize operation.
Processing.Clip - Class in qupath.bioimageio.spec.tensor
A clipping operation.
Processing.ProcessingMode - Enum Class in qupath.bioimageio.spec.tensor
Requested mode for pre- or post-processing.
Processing.ProcessingWithMode - Class in qupath.bioimageio.spec.tensor
A processing mode that operates optionally on different sets of data.
Processing.ScaleLinear - Class in qupath.bioimageio.spec.tensor
A linear scaling operation.
Processing.ScaleMeanVariance - Class in qupath.bioimageio.spec.tensor
A scaling operation to the mean and variance of a reference tensor.
Processing.ScaleRange - Class in qupath.bioimageio.spec.tensor
A scaling operation to a reference tensor.
Processing.Sigmoid - Class in qupath.bioimageio.spec.tensor
A sigmoid transofmration.
Processing.ZeroMeanUnitVariance - Class in qupath.bioimageio.spec.tensor
A scaling operation to zero mean and unit variqnce.
PYTORCH_STATE_DICT - Enum constant in enum class qupath.bioimageio.spec.Weights.WeightsEntry
 

Q

qupath.bioimageio.spec - package qupath.bioimageio.spec
Support for parsing the model spec for the BioImage Model Zoo at https://bioimage.io.
qupath.bioimageio.spec.tensor - package qupath.bioimageio.spec.tensor
 
qupath.bioimageio.spec.tensor.axes - package qupath.bioimageio.spec.tensor.axes
 
qupath.bioimageio.spec.tensor.sizes - package qupath.bioimageio.spec.tensor.sizes
 

R

ReferencedSize - Class in qupath.bioimageio.spec.tensor.sizes
A tensor axis size (extent in pixels/frames) defined in relation to a reference axis.
Resource - Class in qupath.bioimageio.spec
General resource, based upon the RDF.
Resource() - Constructor for class qupath.bioimageio.spec.Resource
 

S

ScaledAxis - Interface in qupath.bioimageio.spec.tensor.axes
Axes that have both size and scale.
SECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
setBaseURI(URI) - Method in class qupath.bioimageio.spec.Model
 
setUri(URI) - Method in class qupath.bioimageio.spec.Model
 
sha256() - Method in record class qupath.bioimageio.spec.ModelParent
Returns the value of the sha256 record component.
shape - Variable in class qupath.bioimageio.spec.tensor.Shape
 
Shape - Class in qupath.bioimageio.spec.tensor
Shape of input or output tensor.
Shape() - Constructor for class qupath.bioimageio.spec.tensor.Shape
 
Shape.ImplicitOutputShape - Class in qupath.bioimageio.spec.tensor
A shape that is determined based on the shape of another tensor.
Shape.ParameterizedInputShape - Class in qupath.bioimageio.spec.tensor
A shape that is determined based on a minimum and a step size.
Shape.SizesShape - Class in qupath.bioimageio.spec.tensor
A Shape that wraps tensor Size objects from the 0.5 spec.
size() - Method in record class qupath.bioimageio.spec.tensor.sizes.FixedSize
Returns the value of the size record component.
size() - Method in class qupath.bioimageio.spec.tensor.sizes.ParameterizedSize
 
size() - Method in class qupath.bioimageio.spec.tensor.sizes.ReferencedSize
 
size() - Method in interface qupath.bioimageio.spec.tensor.sizes.Size
Get the default size of this axis.
Size - Interface in qupath.bioimageio.spec.tensor.sizes
An axis size.
source() - Method in record class qupath.bioimageio.spec.FileDescription
Returns the value of the source record component.
SpaceAxes - Class in qupath.bioimageio.spec.tensor.axes
Axes relating to physical space.
SpaceAxes() - Constructor for class qupath.bioimageio.spec.tensor.axes.SpaceAxes
 
SpaceAxes.SpaceUnit - Enum Class in qupath.bioimageio.spec.tensor.axes
Possible SI and imperial units for distance in physical space.

T

T - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.AxisType
 
TensorDataDescription - Interface in qupath.bioimageio.spec.tensor
Descriptions of tensor data types, primarily ratio types or nominal/ordinal types represented by int-like numeric values.
TENSORFLOW_JS - Enum constant in enum class qupath.bioimageio.spec.Weights.WeightsEntry
 
TENSORFLOW_SAVED_MODEL_BUNDLE - Enum constant in enum class qupath.bioimageio.spec.Weights.WeightsEntry
 
Tensors - Class in qupath.bioimageio.spec.tensor
 
Tensors() - Constructor for class qupath.bioimageio.spec.tensor.Tensors
 
Tensors.IntervalOrRatioDataDescription - Class in qupath.bioimageio.spec.tensor
A description of the possible ratio data values in a tensor.
Tensors.IntervalOrRatioDType - Enum Class in qupath.bioimageio.spec.tensor
Data type of ratio data.
Tensors.NominalOrOrdinalDataDescription - Class in qupath.bioimageio.spec.tensor
A description of the possible discrete data values in a tensor.
Tensors.NominalOrOrdinalDType - Enum Class in qupath.bioimageio.spec.tensor
Data type of nominal or ordinal data.
TERAMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
TERASECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
text() - Method in record class qupath.bioimageio.spec.CiteEntry
Returns the value of the text record component.
TimeAxes - Class in qupath.bioimageio.spec.tensor.axes
Axes relating to physical time.
TimeAxes() - Constructor for class qupath.bioimageio.spec.tensor.axes.TimeAxes
 
TimeAxes.TimeUnit - Enum Class in qupath.bioimageio.spec.tensor.axes
Possible units for time.
TORCHSCRIPT - Enum constant in enum class qupath.bioimageio.spec.Weights.WeightsEntry
 
toString() - Method in record class qupath.bioimageio.spec.Author
Returns a string representation of this record class.
toString() - Method in record class qupath.bioimageio.spec.Badge
Returns a string representation of this record class.
toString() - Method in record class qupath.bioimageio.spec.CiteEntry
Returns a string representation of this record class.
toString() - Method in record class qupath.bioimageio.spec.FileDescription
Returns a string representation of this record class.
toString() - Method in record class qupath.bioimageio.spec.ModelParent
Returns a string representation of this record class.
toString() - Method in enum class qupath.bioimageio.spec.tensor.axes.AxisType
 
toString() - Method in class qupath.bioimageio.spec.tensor.InputTensor
 
toString() - Method in class qupath.bioimageio.spec.tensor.OutputTensor
 
toString() - Method in class qupath.bioimageio.spec.tensor.Shape.ImplicitOutputShape
 
toString() - Method in class qupath.bioimageio.spec.tensor.Shape.ParameterizedInputShape
 
toString() - Method in class qupath.bioimageio.spec.tensor.Shape
 
toString() - Method in record class qupath.bioimageio.spec.tensor.sizes.FixedSize
Returns a string representation of this record class.
toString() - Method in class qupath.bioimageio.spec.Weights.ModelWeights
 
toString() - Method in enum class qupath.bioimageio.spec.Weights.WeightsEntry
 
toUnmodifiableList(List<T>) - Static method in class qupath.bioimageio.spec.Model
Ensure the input is an unmodifiable list, or empty list if null.

U

UINT16 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
 
UINT16 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
 
UINT32 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
 
UINT32 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
 
UINT64 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
 
UINT64 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
 
UINT8 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
 
UINT8 - Enum constant in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
 
uri() - Method in record class qupath.bioimageio.spec.ModelParent
Returns the value of the uri record component.
url() - Method in record class qupath.bioimageio.spec.Badge
Returns the value of the url record component.
url() - Method in record class qupath.bioimageio.spec.CiteEntry
Returns the value of the url record component.

V

validate(List<? extends BaseTensor>) - Method in interface qupath.bioimageio.spec.tensor.axes.Axis
Ensure the parameters of the axis are valid, possibly resolving references to other tensors and/or axes.
validate(List<? extends BaseTensor>) - Method in class qupath.bioimageio.spec.tensor.BaseTensor
Validate a tensor by resolving links between tensors and other parameter settings.
validate(List<? extends BaseTensor>) - Method in record class qupath.bioimageio.spec.tensor.sizes.FixedSize
 
validate(List<? extends BaseTensor>) - Method in class qupath.bioimageio.spec.tensor.sizes.ParameterizedSize
 
validate(List<? extends BaseTensor>) - Method in class qupath.bioimageio.spec.tensor.sizes.ReferencedSize
 
validate(List<? extends BaseTensor>) - Method in interface qupath.bioimageio.spec.tensor.sizes.Size
Validate a tensor's size, ensuring that all internal fields are valid and resolving links between tensor objects.
valueOf(String) - Static method in enum class qupath.bioimageio.spec.tensor.axes.AxisType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.bioimageio.spec.tensor.Processing.ProcessingMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.bioimageio.spec.Weights.WeightsEntry
Returns the enum constant of this class with the specified name.
values() - Static method in enum class qupath.bioimageio.spec.tensor.axes.AxisType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.bioimageio.spec.tensor.Processing.ProcessingMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.bioimageio.spec.tensor.Tensors.IntervalOrRatioDType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.bioimageio.spec.tensor.Tensors.NominalOrOrdinalDType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.bioimageio.spec.Weights.WeightsEntry
Returns an array containing the constants of this enum class, in the order they are declared.

W

Weights - Class in qupath.bioimageio.spec
Model weights and model weights accessories.
Weights() - Constructor for class qupath.bioimageio.spec.Weights
 
Weights.ModelWeights - Class in qupath.bioimageio.spec
Model weights information for a specific format.
Weights.WeightsEntry - Enum Class in qupath.bioimageio.spec
Enum representing supported model weights.
Weights.WeightsMap - Class in qupath.bioimageio.spec
A map of weights types (e.g., TensorFlow, ONNX, PyTorch) to model weights.
WeightsMap() - Constructor for class qupath.bioimageio.spec.Weights.WeightsMap
 
WithHalo - Interface in qupath.bioimageio.spec.tensor.axes
An axis with a halo.
withStringKeys() - Method in class qupath.bioimageio.spec.Weights.WeightsMap
Convert to a map with String keys.

X

X - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.AxisType
 

Y

Y - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.AxisType
 
YARD - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
YOCTOMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
YOCTOSECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
YOTTAMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
YOTTASECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 

Z

Z - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.AxisType
 
ZEPTOMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
ZEPTOSECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
ZETTAMETER - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.SpaceAxes.SpaceUnit
 
ZETTASECOND - Enum constant in enum class qupath.bioimageio.spec.tensor.axes.TimeAxes.TimeUnit
 
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