Package | Description |
---|---|
loci.formats |
Bio-Formats: a library for reading and writing popular microscopy file
formats.
|
loci.formats.gui |
Package containing Bio-Formats graphical user interface code.
|
loci.formats.meta |
Package containing core Bio-Formats metadata interfaces for the OME data model.
|
loci.formats.ome |
Package containing Bio-Formats OME-related logic for
OME-XML metadata, and database import, upload and download.
|
loci.formats.out |
Package containing Bio-Formats file format writers.
|
loci.formats.services |
Modifier and Type | Field and Description |
---|---|
protected MetadataRetrieve |
FormatWriter.metadataRetrieve
Current metadata retrieval object.
|
Modifier and Type | Method and Description |
---|---|
MetadataRetrieve |
ImageWriter.getMetadataRetrieve() |
MetadataRetrieve |
IFormatWriter.getMetadataRetrieve()
Retrieves the current metadata retrieval object for this writer.
|
MetadataRetrieve |
FormatWriter.getMetadataRetrieve() |
MetadataRetrieve |
WriterWrapper.getMetadataRetrieve() |
Modifier and Type | Method and Description |
---|---|
static String |
FormatTools.getFilename(int series,
int image,
MetadataRetrieve retrieve,
String pattern,
boolean padded) |
void |
ImageWriter.setMetadataRetrieve(MetadataRetrieve r) |
void |
IFormatWriter.setMetadataRetrieve(MetadataRetrieve r)
Sets the metadata retrieval object from
which to retrieve standardized metadata.
|
void |
FormatWriter.setMetadataRetrieve(MetadataRetrieve retrieve) |
void |
WriterWrapper.setMetadataRetrieve(MetadataRetrieve r) |
static void |
MetadataTools.verifyMinimumPopulated(MetadataRetrieve src)
Checks whether the given metadata object has the minimum metadata
populated to successfully describe an Image.
|
static void |
MetadataTools.verifyMinimumPopulated(MetadataRetrieve src,
int n)
Checks whether the given metadata object has the minimum metadata
populated to successfully describe the nth Image.
|
Modifier and Type | Method and Description |
---|---|
static BufferedImage |
AWTImageTools.makeImage(byte[] data,
boolean interleaved,
MetadataRetrieve meta,
int series)
Creates an image from the given raw byte array, obtaining the
dimensional parameters from the specified metadata object.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IMetadata |
Modifier and Type | Method and Description |
---|---|
private static void |
MetadataConverter.convertBooleanAnnotations(MetadataRetrieve src,
MetadataStore dest)
Convert all BooleanAnnotation attributes.
|
private static void |
MetadataConverter.convertCommentAnnotations(MetadataRetrieve src,
MetadataStore dest)
Convert all CommentAnnotation attributes.
|
private static void |
MetadataConverter.convertDatasets(MetadataRetrieve src,
MetadataStore dest)
Convert all Dataset attributes.
|
private static void |
MetadataConverter.convertDoubleAnnotations(MetadataRetrieve src,
MetadataStore dest)
Convert all DoubleAnnotation attributes.
|
private static void |
MetadataConverter.convertExperimenterGroups(MetadataRetrieve src,
MetadataStore dest)
Convert all ExperimenterGroup attributes.
|
private static void |
MetadataConverter.convertExperimenters(MetadataRetrieve src,
MetadataStore dest)
Convert all Experimenter attributes.
|
private static void |
MetadataConverter.convertExperiments(MetadataRetrieve src,
MetadataStore dest)
Convert all Experiment attributes.
|
private static void |
MetadataConverter.convertFileAnnotations(MetadataRetrieve src,
MetadataStore dest)
Convert all FileAnnotation attributes.
|
private static void |
MetadataConverter.convertFolders(MetadataRetrieve src,
MetadataStore dest)
Convert all Folder attributes.
|
private static void |
MetadataConverter.convertImages(MetadataRetrieve src,
MetadataStore dest,
List<String> lightSourceIds)
Convert all Image attributes.
|
private static List<String> |
MetadataConverter.convertInstruments(MetadataRetrieve src,
MetadataStore dest)
Convert all Instrument attributes.
|
private static void |
MetadataConverter.convertLightSources(MetadataRetrieve src,
MetadataStore dest,
int instrumentIndex,
List<String> lightSourceIds)
Convert all LightSource attributes for the given instrument.
|
private static void |
MetadataConverter.convertListAnnotations(MetadataRetrieve src,
MetadataStore dest)
Convert all ListAnnotation attributes.
|
private static void |
MetadataConverter.convertLongAnnotations(MetadataRetrieve src,
MetadataStore dest)
Convert all LongAnnotation attributes.
|
private static void |
MetadataConverter.convertMapAnnotations(MetadataRetrieve src,
MetadataStore dest)
Convert all MapAnnotation attributes.
|
static void |
MetadataConverter.convertMetadata(MetadataRetrieve src,
MetadataStore dest)
Copies information from a metadata retrieval object
(source) into a metadata store (destination).
|
private static void |
MetadataConverter.convertPlates(MetadataRetrieve src,
MetadataStore dest)
Convert all Plate attributes.
|
private static void |
MetadataConverter.convertProjects(MetadataRetrieve src,
MetadataStore dest)
Convert all Project attributes.
|
private static void |
MetadataConverter.convertROIs(MetadataRetrieve src,
MetadataStore dest)
Convert all ROI attributes.
|
private static void |
MetadataConverter.convertRootAttributes(MetadataRetrieve src,
MetadataStore dest)
Convert all top-level attributes.
|
private static void |
MetadataConverter.convertScreens(MetadataRetrieve src,
MetadataStore dest)
Convert all Screen attributes.
|
private static void |
MetadataConverter.convertTagAnnotations(MetadataRetrieve src,
MetadataStore dest)
Convert all TagAnnotation attributes.
|
private static void |
MetadataConverter.convertTermAnnotations(MetadataRetrieve src,
MetadataStore dest)
Convert all TermAnnotation attributes.
|
private static void |
MetadataConverter.convertTimestampAnnotations(MetadataRetrieve src,
MetadataStore dest)
Convert all TimestampAnnotation attributes.
|
private static void |
MetadataConverter.convertXMLAnnotations(MetadataRetrieve src,
MetadataStore dest)
Convert all XMLAnnotation attributes.
|
Modifier and Type | Interface and Description |
---|---|
interface |
OMEXMLMetadata |
Modifier and Type | Method and Description |
---|---|
private int[] |
ICSWriter.overwriteDimensions(MetadataRetrieve meta) |
Modifier and Type | Method and Description |
---|---|
MetadataRetrieve |
OMEXMLService.asRetrieve(MetadataStore meta)
Gets the given
MetadataStore object as a MetadataRetrieve . |
MetadataRetrieve |
OMEXMLServiceImpl.asRetrieve(MetadataStore meta) |
Modifier and Type | Method and Description |
---|---|
MetadataStore |
OMEXMLService.asStore(MetadataRetrieve meta)
Gets the given
MetadataRetrieve object as a MetadataStore . |
MetadataStore |
OMEXMLServiceImpl.asStore(MetadataRetrieve meta) |
void |
OMEXMLService.convertMetadata(MetadataRetrieve src,
MetadataStore dest)
Copies information from a metadata retrieval object
(source) into a metadata store (destination).
|
void |
OMEXMLServiceImpl.convertMetadata(MetadataRetrieve src,
MetadataStore dest) |
OMEXMLMetadata |
OMEXMLService.getOMEMetadata(MetadataRetrieve src)
Returns a
OMEXMLMetadata object with the same
contents as the given MetadataRetrieve, converting it if necessary. |
OMEXMLMetadata |
OMEXMLServiceImpl.getOMEMetadata(MetadataRetrieve src) |
String |
OMEXMLService.getOMEXML(MetadataRetrieve src)
Extracts an OME-XML metadata string from the given metadata object,
by converting to an OME-XML metadata object if necessary.
|
String |
OMEXMLServiceImpl.getOMEXML(MetadataRetrieve src) |
Copyright © 2016 Open Microscopy Environment