Modifier and Type | Method and Description |
---|---|
ImageMetadata |
FromStackReader.openFile(Path path,
StackReader defaultStackReader,
OperationContext context) |
abstract ImageMetadata |
ImageMetadataReader.openFile(Path path,
StackReader defaultStackReader,
OperationContext context)
Opens a file containing one or more images but does not read an image.
|
Modifier and Type | Method and Description |
---|---|
abstract OpenedImageFile |
StackReaderOrientationCorrection.openFile(Path path,
CalculateOrientationChange orientationCorrection,
ExecutionTimeRecorder executionTimeRecorder)
Opens a file containing one or more images but does not read an image.
|
abstract OpenedImageFile |
StackReader.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder)
Opens a file containing one or more images.
|
Stack |
StackReader.readStack(Path path,
OperationContext context)
Opens a file at
path that should contain only a single-stack. |
Modifier and Type | Method and Description |
---|---|
static <T extends StackWriter> |
WriterErrorMessageHelper.generalWriteException(Class<T> writerClass,
Path path,
Exception cause)
Creates a
ImageIOException with an error message that image-writing failed. |
Modifier and Type | Method and Description |
---|---|
ImageFileFormat |
OneOrThreeChannelsWriter.fileFormat(StackWriteOptions writeOptions) |
abstract ImageFileFormat |
StackWriter.fileFormat(StackWriteOptions writeOptions)
The file format that will be written by the generator.
|
ImageFileFormat |
StackWriter.fileFormatWarnUnexpected(StackWriteOptions writeOptions,
Optional<Logger> logger)
The file format that will be written by the generator, warning with a log message if
different to suggestion.
|
void |
OneOrThreeChannelsWriter.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
abstract void |
StackWriter.writeStack(Stack stack,
Path filePath,
StackWriteOptions options)
Writes a stack to the filesystem at a particular path.
|
protected abstract void |
OneOrThreeChannelsWriter.writeStackAfterCheck(Stack stack,
Path filePath)
Writes the
Stack to the file-system, after a check has already occurred that the
correct number of channels exist. |
Path |
StackWriter.writeStackWithExtension(Stack stack,
Path filePath,
StackWriteOptions options)
Writes a stack to the filesystem at a particular path with an extension appended to the path.
|
Modifier and Type | Method and Description |
---|---|
abstract int |
NamedChannelsInput.bitDepth(Logger logger)
Bit-depth of image.
|
abstract NamedChannelsMap |
NamedChannelsInput.createChannelsForSeries(int seriesIndex,
Logger logger)
Creates a
NamedChannelsMap representing the channels for a particular series in this
input. |
abstract Dimensions |
NamedChannelsInput.dimensions(int seriesIndex,
Logger logger)
Dimensions of a particular series.
|
abstract ImageMetadata |
NamedChannelsInput.metadata(int seriesIndex,
Logger logger)
The image-metadata associated with a particular series.
|
abstract int |
NamedChannelsInput.numberChannels(Logger logger)
Number of channels.
|
abstract int |
NamedChannelsInput.numberSeries()
Number of series that exist.
|
Modifier and Type | Method and Description |
---|---|
Dimensions |
OpenedNamedChannels.dimensions(Logger logger) |
Dimensions |
NamedChannelsConcatenate.dimensions(Logger logger) |
Dimensions |
NamedChannelsMap.dimensions(Logger logger)
The dimensions of each
Channel . |
boolean |
OpenedNamedChannels.isRGB(Logger logger) |
boolean |
NamedChannelsConcatenate.isRGB(Logger logger) |
boolean |
NamedChannelsMap.isRGB(Logger logger)
Whether the channels describe an RGB image.
|
int |
OpenedNamedChannels.sizeT(Logger logger) |
int |
NamedChannelsConcatenate.sizeT(Logger logger) |
int |
NamedChannelsMap.sizeT(Logger logger)
The number of frames along the time-axis.
|
Modifier and Type | Method and Description |
---|---|
OrientationChange |
CalculateOrientationChange.calculateOrientationChange(Logger logger)
Calculates any needed orientation change.
|
Modifier and Type | Method and Description |
---|---|
int |
OpenedImageFile.bitDepth(Logger logger)
The bit-depth of the image voxels e.g.
|
Optional<List<String>> |
OpenedImageFile.channelNames(Logger logger)
The names of each channel, if they are known.
|
void |
OpenedImageFile.close()
Closes the opened image-file, removing any intermediate data-structures.
|
TimeSeries |
StackSequenceInput.createStackSequenceForSeries(int seriesIndex,
Logger logger)
Creates a supplier of a
TimeSeries of stacks for a particular series number. |
Dimensions |
OpenedImageFile.dimensionsForSeries(int seriesIndex,
Logger logger)
The
Dimensions associated with a particular series. |
boolean |
OpenedImageFile.isRGB(Logger logger)
Whether the image-file has RGB encoded voxels.
|
ImageMetadata |
ImageMetadataInput.metadata()
The associated image metadata.
|
default ImageMetadata |
OpenedImageFile.metadata(int seriesIndex,
Logger logger)
Extracts metadata about the image.
|
int |
OpenedImageFile.numberChannels(Logger logger)
The number of channels in the image-file e.g.
|
int |
OpenedImageFile.numberFrames(Logger logger)
The number of frames in the image-file i.e.
|
TimeSeries |
OpenedImageFile.open(int seriesIndex,
Logger logger)
Open when we don't have a specific-type.
|
default TimeSeries |
OpenedImageFile.open(Logger logger)
Open the first series when we don't have a specific-type.
|
default TimeSeries |
OpenedImageFile.openCheckType(int seriesIndex,
VoxelDataType channelDataType,
Logger logger)
Opens a time-series, and checks that it is a particular type.
|
static Mask |
MaskReader.openMask(StackReader stackReader,
Path path,
BinaryValuesInt binaryValues,
OperationContext context)
Utility functions for opening a single-channeled stack as a
Mask . |
Optional<ImagePyramidMetadata> |
OpenedImageFile.pyramid()
Metadata to describe an image-pyramid, if it exists for this opened-image.
|
ImageTimestampsAttributes |
OpenedImageFile.timestamps()
The timestamps and file-attributes associated with the image.
|
Constructor and Description |
---|
ImageMetadataInput(NamedFile file,
CheckedSupplier<ImageMetadata,ImageIOException> metadata)
Create for a particular file and metadata.
|
Modifier and Type | Method and Description |
---|---|
static String |
GeneratorOutputter.fileExtensionWriter(OutputWriteSettings settings,
StackWriteOptions writeOptions,
Optional<Logger> logger)
The file extension to use for the default
StackWriter , as returned by GeneratorOutputter.writer(OutputWriteSettings) . |
static StackWriter |
GeneratorOutputter.writer(OutputWriteSettings settings)
Gets the default
StackWriter . |
Modifier and Type | Method and Description |
---|---|
OpenedImageFile |
BioformatsReader.openFile(Path filePath,
CalculateOrientationChange orientationCorrection,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
BioformatsReader.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
byte[] |
ByteRepresentationForChannel.bytesForSlice(int sliceIndex)
The byte-representation of the voxels for a particular slice.
|
protected loci.formats.IFormatWriter |
OMETiff.createWriter() |
protected abstract loci.formats.IFormatWriter |
BioformatsWriter.createWriter()
Creates or gets an instance of
IFormatWriter which dictates the file format to use
for writing. |
protected loci.formats.IFormatWriter |
Tiff.createWriter() |
protected loci.formats.IFormatWriter |
OMEXML.createWriter() |
void |
BioformatsWriter.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
void |
Tiff.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
Modifier and Type | Method and Description |
---|---|
static Optional<OrientationChange> |
OrientationReader.determineOrientationCorrection(com.drew.metadata.Metadata metadata)
Determines the needed correction to orientation for the voxels if an EXIF orientation tag is
present.
|
static Optional<OrientationChange> |
OrientationReader.determineOrientationCorrection(Path path)
Determines the needed correction to orientation for the voxels if an EXIF orientation tag is
present.
|
static ImageTimestampsAttributes |
ImageTimestampsAttributesFactory.fromPath(Path path)
Reads
ImageTimestampsAttributes from a path, trying to infer the acquisition-date
from metadata headers. |
static Optional<java.time.ZonedDateTime> |
AcquisitionDateReader.readAcquisitionDate(Path path)
Reads an image acquisition-date from a file identified by path, based on the present of EXIF
data.
|
static Optional<Extent> |
ReadMetadataUtilities.readFromWidthHeightTags(com.drew.metadata.Directory directory,
int tagWidth,
int tagHeight)
Reads two metadata entries, representing width and height, and use them to form a
Extent . |
static <T extends com.drew.metadata.Directory> |
ReadMetadataUtilities.readFromWidthHeightTags(com.drew.metadata.Metadata metadata,
Class<T> directoryType,
int tagWidth,
int tagHeight)
Reads two metadata entries, representing width and height, and use them to form a
Extent . |
static Optional<com.drew.metadata.Metadata> |
ReadMetadataUtilities.readMetadata(Path path)
Reads metadata, if it exists, from an image.
|
Modifier and Type | Method and Description |
---|---|
protected abstract boolean |
ImageJRasterWriter.writeRaster(ij.io.FileSaver fileSaver,
String path,
boolean asStack)
Writes an annotation to the filesystem at
outPath . |
protected boolean |
PNG.writeRaster(ij.io.FileSaver fileSaver,
String path,
boolean asStack) |
void |
ImageJRasterWriter.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
protected void |
ImageJRasterWriter.writeStackTime(Stack stack,
Path path,
boolean makeRGB)
Writes a stack as a time-sequence (many images together in a single file.).
|
Modifier and Type | Method and Description |
---|---|
TimeSeries |
ConvertNamedChannelsInputToStack.createStackSequenceForSeries(int seriesIndex,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
Optional<ImageMetadata> |
HeaderFormat.populateFrom(Path path)
Creates a
ImageMetadata , if possible, from the metadata at path . |
protected Optional<ImageMetadata> |
JPEG.populateFromMetadata(com.drew.metadata.Metadata metadata,
ImageFileAttributes attributes) |
protected abstract Optional<ImageMetadata> |
HeaderFormat.populateFromMetadata(com.drew.metadata.Metadata metadata,
ImageFileAttributes attributes)
Creates a
ImageMetadata , if possible, from metadata . |
protected Optional<ImageMetadata> |
PNG.populateFromMetadata(com.drew.metadata.Metadata metadata,
ImageFileAttributes attributes) |
protected Optional<ImageMetadata> |
BMP.populateFromMetadata(com.drew.metadata.Metadata metadata,
ImageFileAttributes attributes) |
Modifier and Type | Method and Description |
---|---|
ImageMetadata |
AlwaysReject.openFile(Path path,
StackReader defaultStackReader,
OperationContext context) |
ImageMetadata |
InferFromHeader.openFile(Path path,
StackReader defaultStackReader,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
OpenedImageFile |
RotateImageToMatchEXIFOrientation.openFile(Path path,
CalculateOrientationChange orientationCorrection,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
BranchExtension.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
FlattenAsChannel.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
RejectIfConditionXYResolution.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
ImposeResolution.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
RotateImageToMatchEXIFOrientation.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
MultiFileReader.openFile(Path filePath,
ExecutionTimeRecorder executionTimeRecorder) |
OpenedImageFile |
ReadVoxelExtentXml.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
static Optional<Resolution> |
ReadVoxelExtentXml.readMetadata(Path filePath,
boolean acceptNoResolution)
Looks for a metadata file describing the resolution
|
Modifier and Type | Method and Description |
---|---|
ImageFileFormat |
StackWriterDelegateBase.fileFormat(StackWriteOptions writeOptions) |
ImageFileFormat |
WriteResolutionXml.fileFormat(StackWriteOptions writeOptions) |
protected abstract StackWriter |
StackWriterDelegateBase.selectDelegate(StackWriteOptions writeOptions)
Selects a
StackWriter to use as a delegate. |
protected StackWriter |
BranchSuggestedFormat.selectDelegate(StackWriteOptions writeOptions) |
void |
StackWriterDelegateBase.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
void |
WriteResolutionXml.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
protected void |
ImageIOWriter.writeStackAfterCheck(Stack stack,
Path filePath) |
Modifier and Type | Method and Description |
---|---|
protected Integer |
NumberChannels.extractKey(ImageMetadataInput element) |
protected Integer |
BitDepth.extractKey(ImageMetadataInput element) |
protected abstract T |
SummarizerImageMetadataSimple.extractKey(ImageMetadataInput element) |
Modifier and Type | Method and Description |
---|---|
int |
OpenedMultiFile.bitDepth(Logger logger) |
void |
OpenedMultiFile.close() |
Dimensions |
OpenedMultiFile.dimensionsForSeries(int seriesIndex,
Logger logger) |
boolean |
OpenedMultiFile.isRGB(Logger logger) |
int |
OpenedMultiFile.numberChannels(Logger logger) |
int |
OpenedMultiFile.numberFrames(Logger logger) |
TimeSeries |
OpenedMultiFile.open(int seriesIndex,
Logger logger) |
Optional<ImagePyramidMetadata> |
OpenedMultiFile.pyramid() |
ImageTimestampsAttributes |
OpenedMultiFile.timestamps() |
Modifier and Type | Method and Description |
---|---|
static Resolution |
ResolutionAsXml.readResolutionXml(File file)
Retrieves resolution from a XML file previously written by
ResolutionAsXml.writeResolutionXml(Resolution, Path) . |
static void |
ResolutionAsXml.writeResolutionXml(Resolution resolution,
Path path)
Writes a XML metadata file describing the image-resolution.
|
Modifier and Type | Method and Description |
---|---|
OpenedImageFile |
OpenCVReader.openFile(Path path,
ExecutionTimeRecorder executionTimeRecorder) |
protected void |
OpenCVWriter.writeStackAfterCheck(Stack stack,
Path filePath) |
Modifier and Type | Method and Description |
---|---|
void |
StackTester.performTest(ChannelSpecification channels,
Optional<ImageComparer> comparer) |
void |
StackTester.performTest(ChannelSpecification channels,
Optional<VoxelDataType> forceFirstChannel,
Optional<ImageComparer> comparer) |
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()
Tests a stack with four-channels of unsigned 8-bit data type.
|
void |
FourChannelStackTester.testFourChannels(VoxelDataType[] channelVoxelTypes)
Tests a stack with four-channels of specified types
|
void |
FourChannelStackTester.testSingleChannel()
Tests the creation of a single-channel stack of unsigned 8-bit data type with the RGB flag
off.
|
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.testSingleChannelRGB()
Tests the creation of a single-channel stack of unsigned 8-bit data type with the RGB flag
on, which should typically produce an exception.
|
void |
FourChannelStackTester.testThreeChannelsHeterogeneous()
Tests the creation of a three-channel stack of heterogeneous channel types.
|
void |
FourChannelStackTester.testThreeChannelsRGB()
Tests the creation of a three-channel stack of unsigned 8-bit data type with the rgb-flag set
to true.
|
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()
Tests the creation of a three-channel stack of unsigned 8-bit data type with the rgb-flag set
to false.
|
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()
Tests the creation of a two-channel stack of unsigned 8-bit data type.
|
void |
FourChannelStackTester.testTwoChannels(VoxelDataType[] channelVoxelTypes)
Tests the creation of a two-channel stack of specified data types.
|
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.