Package | Description |
---|---|
org.anchoranalysis.image.bean.displayer | |
org.anchoranalysis.image.bean.nonbean |
Classes that are used elsewhere in this package but which aren't themselves AnchorBeans.
|
org.anchoranalysis.image.core.channel |
The
Channel core data-class and related operations
and converters. |
org.anchoranalysis.image.core.channel.convert |
Converts a channel to other data-types.
|
org.anchoranalysis.image.core.channel.factory |
Factory classes for creating
Channel for various
voxel data-types. |
org.anchoranalysis.image.core.stack |
Defines the key data object,
Stack , and related
classes. |
org.anchoranalysis.image.io.stack.input |
Non-bean classes for reading a
Stack from the
filesystem. |
org.anchoranalysis.image.io.stack.time |
A time-sequence of
Stack s. |
org.anchoranalysis.image.voxel |
Data-structures to store and manipulate image raster-data or voxels.
|
org.anchoranalysis.image.voxel.binary |
The
BinaryVoxels class and related operations. |
org.anchoranalysis.image.voxel.buffer |
A buffer of voxel-values, usually corresponding to a single z-slice in
Voxels . |
org.anchoranalysis.image.voxel.datatype |
The different data-types that can be used to represent voxels.
|
org.anchoranalysis.image.voxel.factory |
Creates new instances of
Voxels and VoxelsUntyped with specific data-types. |
org.anchoranalysis.image.voxel.projection |
Classes for calculating differnet kind of projections of voxel values across multiple buffers.
|
org.anchoranalysis.image.voxel.projection.extrema |
Classes for performing both a Maximum Intensity
Projection and a minimum projection.
|
org.anchoranalysis.io.bioformats.copyconvert |
Converts the byte stream opened by Bioformats into channels of particular data-type.
|
org.anchoranalysis.plugin.image.bean.channel.aggregator |
Implementations of
ConvertChannelTo and ConvertChannelToWithHistogram . |
org.anchoranalysis.plugin.image.bean.channel.provider.intensity |
Implementations of
ChannelProvider that manipulate
the intensity-values of the voxels of a Channel 's
voxels. |
org.anchoranalysis.plugin.image.bean.stack.provider.color |
Implementations of
StackProvider that color
portions of an image. |
org.anchoranalysis.plugin.io.multifile.buffer |
Buffers used in
org.anchoranalysis.plugin.io.multifile . |
org.anchoranalysis.test.image |
Testing utilities and fixtures with no greater downstream dependency than anchor-image-io
or anchor-io-bioformats or anchor-imagej.
|
org.anchoranalysis.test.image.stackwriter |
Fixtures for testing
StackWriter and
related classes. |
Modifier and Type | Method and Description |
---|---|
protected abstract ChannelConverterAttached<Channel,UnsignedByteBuffer> |
StackDisplayer.createConverterFor(VoxelDataType dataType)
Determines what kind of converter to use for a particular channel, to map it to an unsigned
8-bit channel.
|
protected ChannelConverterAttached<Channel,UnsignedByteBuffer> |
IntensityQuantiles.createConverterFor(VoxelDataType dataType) |
Modifier and Type | Method and Description |
---|---|
VoxelDataType |
ConsistentChannelChecker.getVoxelDataType()
The voxel-data-type that is consistent across all channels.
|
Modifier and Type | Method and Description |
---|---|
VoxelDataType |
Channel.getVoxelDataType()
The underlying data-type of the voxels in the channel, represented by a
VoxelDataType
instance. |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelConverterMulti.convert(Channel channel,
VoxelDataType outputVoxelType)
Converts a
Channel 's voxels to another type. |
Constructor and Description |
---|
ChannelConverter(VoxelDataType targetDataType,
VoxelsConverter<T> voxelsConverter,
VoxelsFactoryTypeBound<T> voxelsFactory) |
Modifier and Type | Method and Description |
---|---|
VoxelDataType |
ChannelFactorySingleType.dataType() |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelFactory.create(Dimensions dimensions,
VoxelDataType channelDataType)
Creates an empty initialized channel for a particular data-type.
|
Channel |
ChannelFactory.createUninitialised(Dimensions dimensions,
VoxelDataType channelDataType)
Create a
Channel without initialization with voxel-buffers. |
Constructor and Description |
---|
ChannelFactorySingleType(VoxelDataType dataType,
VoxelsFactoryTypeBound<?> factory) |
Modifier and Type | Method and Description |
---|---|
Optional<VoxelDataType> |
DisplayStack.unconvertedDataType()
The data-type of the underlying voxels before they are converted to 8-bit.
|
Modifier and Type | Method and Description |
---|---|
boolean |
RGBStack.allChannelsHaveType(VoxelDataType channelDataType)
Determines if all channels have a specific data-type.
|
boolean |
Stack.allChannelsHaveType(VoxelDataType voxelDataType)
Determines if all channels have a specific data-type.
|
Constructor and Description |
---|
DisplayStack(Stack stack,
boolean eventuallyThree,
java.util.function.Function<VoxelDataType,ChannelConverterAttached<Channel,UnsignedByteBuffer>> createConverter)
Create for a particular
Stack that may needed to be converted. |
Modifier and Type | Method and Description |
---|---|
default TimeSeries |
OpenedImageFile.openCheckType(int seriesIndex,
VoxelDataType channelDataType,
Logger logger)
Opens a time-series, and checks that it is a particular type.
|
Modifier and Type | Method and Description |
---|---|
boolean |
TimeSeries.allChannelsHaveType(VoxelDataType voxelDataType)
Whether all
Channel s in all frames in the times-series have a particular voxel-data
type? |
Modifier and Type | Method and Description |
---|---|
VoxelDataType |
Voxels.dataType()
The underlying data-type of the voxels, represented by a
VoxelDataType instance. |
VoxelDataType |
VoxelsUntyped.getVoxelDataType()
The underlying data-type of the voxels, represented by a
VoxelDataType instance. |
Modifier and Type | Method and Description |
---|---|
Voxels<?> |
VoxelsUntyped.checkIdenticalDataType(VoxelDataType match)
Do the voxels have a data-type that is equal to
match ? |
Modifier and Type | Method and Description |
---|---|
static BinaryVoxels<?> |
BinaryVoxelsFactory.createEmptyOff(Extent extent,
VoxelDataType dataType)
Creates an empty binary-voxels of a particular data-type with all voxels initialized to
off.
|
Modifier and Type | Method and Description |
---|---|
abstract VoxelDataType |
VoxelBuffer.dataType()
Data-type of each voxel in the buffer.
|
Modifier and Type | Class and Description |
---|---|
class |
FloatVoxelType
A 32-bit voxel data-type representing floating-point numbers, as per the Java primitive
float type.
|
class |
SignedShortVoxelType
A 16-bit voxel data-type representing signed-short numbers.
|
class |
SignedVoxelType
Base class for voxel-data-types that are signed and integral.
|
class |
UnsignedByteVoxelType
A 8-bit voxel data-type representing unsigned-byte numbers.
|
class |
UnsignedIntVoxelType
A 32-bit voxel data-type representing unsigned-int numbers.
|
class |
UnsignedShortVoxelType
A 16-bit voxel data-type representing unsigned-short numbers.
|
class |
UnsignedVoxelType
Base class for voxel-data-types that are unsigned and integral.
|
Modifier and Type | Method and Description |
---|---|
static VoxelDataType |
CombineTypes.combineTypes(VoxelDataType type1,
VoxelDataType type2)
What data-type to use to represent voxels of both
type1 and type2 ? |
static VoxelDataType |
FindCommonVoxelType.commonType(VoxelDataType first,
VoxelDataType second)
Finds a common type to represent (ideally without loss of precision} both
first and
second . |
Modifier and Type | Method and Description |
---|---|
static Optional<VoxelDataType> |
FindCommonVoxelType.commonType(java.util.stream.Stream<VoxelDataType> stream)
Finds a common type to represent (ideally without loss of precision} of a stream of types.
|
Modifier and Type | Method and Description |
---|---|
static VoxelDataType |
CombineTypes.combineTypes(VoxelDataType type1,
VoxelDataType type2)
What data-type to use to represent voxels of both
type1 and type2 ? |
static VoxelDataType |
FindCommonVoxelType.commonType(VoxelDataType first,
VoxelDataType second)
Finds a common type to represent (ideally without loss of precision} both
first and
second . |
T |
VoxelDataTypeFactoryMultiplexer.get(VoxelDataType dataType)
Multiplexes one of the factories according to data-type
|
Modifier and Type | Method and Description |
---|---|
static Optional<VoxelDataType> |
FindCommonVoxelType.commonType(java.util.stream.Stream<VoxelDataType> stream)
Finds a common type to represent (ideally without loss of precision} of a stream of types.
|
Modifier and Type | Method and Description |
---|---|
VoxelDataType |
VoxelsFactoryTypeBound.dataType()
The data-type of the voxels, as created by this factory.
|
Modifier and Type | Method and Description |
---|---|
VoxelsUntyped |
VoxelsFactory.createEmpty(Extent extent,
VoxelDataType dataType)
Creates empty voxels to match a particular size.
|
<T> VoxelsUntyped |
VoxelsFactory.createFrom(SliceBufferIndex<T> buffer,
VoxelDataType dataType)
Creates voxels from a particular
SliceBufferIndex with specified type. |
Modifier and Type | Method and Description |
---|---|
static <T> ProjectableBuffer<T> |
MeanIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a mean-intensity projection for unsigned byte voxels.
|
static <T> ProjectableBuffer<T> |
StandardDeviationIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a standard-deviation projection for unsigned byte voxels.
|
Modifier and Type | Method and Description |
---|---|
static <T> ProjectableBuffer<T> |
MaxIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a maximum-intensity projection for unsigned byte voxels.
|
static <T> ProjectableBuffer<T> |
MinIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a minimum-intensity projection for unsigned byte voxels.
|
Modifier and Type | Method and Description |
---|---|
static ConvertTo<?> |
ConvertToFactory.create(loci.formats.IFormatReader reader,
VoxelDataType targetDataType,
int effectiveBitsPerPixel) |
Modifier and Type | Method and Description |
---|---|
protected abstract ProjectableBuffer<T> |
ProjectableBufferAggregator.create(VoxelDataType dataType,
Extent extent)
Creates the
ProjectableBuffer used for aggregation. |
protected ProjectableBuffer<T> |
MeanProjection.create(VoxelDataType dataType,
Extent extent) |
protected ProjectableBuffer<T> |
MinProjection.create(VoxelDataType dataType,
Extent extent) |
protected ProjectableBuffer<T> |
MaxProjection.create(VoxelDataType dataType,
Extent extent) |
protected ProjectableBuffer<T> |
StandardDeviationProjection.create(VoxelDataType dataType,
Extent extent) |
Modifier and Type | Method and Description |
---|---|
static Channel |
IfVoxelZero.mergeViaZeroCheck(Channel channel,
Channel channelIfPixelZero,
VoxelDataType combinedType,
double multiplierIfNonZero)
Creates a new channel which is a merged version of two input channels according to rules.
|
Modifier and Type | Method and Description |
---|---|
static Stack |
ThreeChannels.createRGBStack(Channel channelRed,
Channel channelGreen,
Channel channelBlue,
VoxelDataType outputType) |
Modifier and Type | Method and Description |
---|---|
TimeSeries |
MultiBufferSized.createSequence(VoxelDataType dataType) |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelFixture.createChannel(Extent extent,
ChannelFixture.IntensityFunction createIntensity,
VoxelDataType channelVoxelType) |
Constructor and Description |
---|
StackFixture(Optional<VoxelDataType> firstChannelVoxelType)
Create with a voxel-type for the first channel.
|
Modifier and Type | Field and Description |
---|---|
protected static VoxelDataType[] |
StackWriterTestBase.ALL_SUPPORTED_VOXEL_TYPES
All possible voxel types that can be supported.
|
protected static VoxelDataType[] |
PNGTestBase.ALL_SUPPORTED_VOXEL_TYPES
All possible voxel types that can be supported.
|
Modifier and Type | Method and Description |
---|---|
VoxelDataType |
ChannelSpecification.getChannelVoxelType()
Default data-type for all channels in the stack if not otherwise specified.
|
Modifier and Type | Method and Description |
---|---|
void |
StackTester.performTest(VoxelDataType[] channelVoxelTypes,
int numberChannels,
boolean makeRGB,
Optional<ImageComparer> comparer) |
void |
StackTester.performTest(VoxelDataType[] channelVoxelTypes,
int numberChannels,
boolean makeRGB,
Optional<VoxelDataType> forceFirstChannel,
Optional<ImageComparer> comparer) |
void |
FourChannelStackTester.testFourChannels(VoxelDataType[] channelVoxelTypes)
Tests a stack with four-channels of specified types
|
void |
FourChannelStackTester.testSingleChannel(VoxelDataType channelVoxelType)
Tests the creation of a single-channel stack of specified data type with the RGB flag off.
|
void |
FourChannelStackTester.testSingleChannel(VoxelDataType[] channelVoxelTypes)
Tests the creation of a single-channel stack of specified data types with the RGB flag off.
|
void |
FourChannelStackTester.testThreeChannelsRGB(VoxelDataType channelVoxelType)
Tests the creation of a three-channel stack of specified data type with the rgb-flag set to
true.
|
void |
FourChannelStackTester.testThreeChannelsRGB(VoxelDataType[] channelVoxelTypes)
Tests the creation of a three-channel stack of specified data types with the rgb-flag set to
true.
|
void |
FourChannelStackTester.testThreeChannelsSeparate(VoxelDataType[] channelVoxelTypes)
Tests the creation of a three-channel stack of specified data types with the rgb-flag set to
false.
|
void |
FourChannelStackTester.testTwoChannels(VoxelDataType[] channelVoxelTypes)
Tests the creation of a two-channel stack of specified data types.
|
Modifier and Type | Method and Description |
---|---|
void |
StackTester.performTest(ChannelSpecification channels,
Optional<VoxelDataType> forceFirstChannel,
Optional<ImageComparer> comparer) |
void |
StackTester.performTest(VoxelDataType[] channelVoxelTypes,
int numberChannels,
boolean makeRGB,
Optional<VoxelDataType> forceFirstChannel,
Optional<ImageComparer> comparer) |
Constructor and Description |
---|
ChannelSpecification(VoxelDataType channelVoxelType,
int numberChannels,
boolean makeRGB) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.