| 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 | 
WriterWrapper.getMetadataRetrieve()  | 
MetadataRetrieve | 
ImageWriter.getMetadataRetrieve()  | 
MetadataRetrieve | 
IFormatWriter.getMetadataRetrieve()
Retrieves the current metadata retrieval object for this writer. 
 | 
MetadataRetrieve | 
FormatWriter.getMetadataRetrieve()  | 
| Modifier and Type | Method and Description | 
|---|---|
static java.lang.String | 
FormatTools.getFilename(int series,
           int image,
           MetadataRetrieve retrieve,
           java.lang.String pattern,
           boolean padded)  | 
void | 
WriterWrapper.setMetadataRetrieve(MetadataRetrieve r)  | 
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)  | 
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 java.awt.image.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 | Interface and Description | 
|---|---|
interface  | 
OMEXMLMetadata  | 
| Modifier and Type | Method and Description | 
|---|---|
private int[] | 
ICSWriter.overwriteDimensions(MetadataRetrieve meta)  | 
| Modifier and Type | Method and Description | 
|---|---|
MetadataRetrieve | 
OMEXMLServiceImpl.asRetrieve(MetadataStore meta)  | 
MetadataRetrieve | 
OMEXMLService.asRetrieve(MetadataStore meta)
Gets the given  
MetadataStore object as a MetadataRetrieve. | 
| Modifier and Type | Method and Description | 
|---|---|
MetadataStore | 
OMEXMLServiceImpl.asStore(MetadataRetrieve meta)  | 
MetadataStore | 
OMEXMLService.asStore(MetadataRetrieve meta)
Gets the given  
MetadataRetrieve object as a MetadataStore. | 
void | 
OMEXMLServiceImpl.convertMetadata(MetadataRetrieve src,
               MetadataStore dest)  | 
void | 
OMEXMLService.convertMetadata(MetadataRetrieve src,
               MetadataStore dest)
Copies information from a metadata retrieval object
 (source) into a metadata store (destination). 
 | 
OMEXMLMetadata | 
OMEXMLServiceImpl.getOMEMetadata(MetadataRetrieve src)  | 
OMEXMLMetadata | 
OMEXMLService.getOMEMetadata(MetadataRetrieve src)
Returns a  
OMEXMLMetadata object with the same
 contents as the given MetadataRetrieve, converting it if necessary. | 
java.lang.String | 
OMEXMLServiceImpl.getOMEXML(MetadataRetrieve src)  | 
java.lang.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. 
 | 
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