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.in |
Package containing Bio-Formats file format readers.
|
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.services | |
loci.plugins.util |
Utility classes and methods for the Bio-Formats plugins for ImageJ.
|
Modifier and Type | Field and Description |
---|---|
protected MetadataStore |
FormatReader.metadataStore
Current metadata store.
|
private MetadataStore |
Memoizer.replacementMetadataStore
MetadataStore created internally. |
private MetadataStore |
FileStitcher.store |
private MetadataStore |
Memoizer.userMetadataStore
MetadataStore set by the caller. |
Modifier and Type | Method and Description |
---|---|
MetadataStore |
Memoizer.getMetadataStore() |
MetadataStore |
FileStitcher.getMetadataStore() |
MetadataStore |
ReaderWrapper.getMetadataStore() |
MetadataStore |
ImageReader.getMetadataStore() |
MetadataStore |
IFormatReader.getMetadataStore()
Retrieves the current metadata store for this reader.
|
MetadataStore |
FormatReader.getMetadataStore() |
protected MetadataStore |
FormatReader.makeFilterMetadata()
Return a properly configured loci.formats.meta.FilterMetadata.
|
Modifier and Type | Method and Description |
---|---|
static void |
MetadataTools.populateMetadata(MetadataStore store,
int series,
java.lang.String imageName,
boolean littleEndian,
java.lang.String dimensionOrder,
java.lang.String pixelType,
int sizeX,
int sizeY,
int sizeZ,
int sizeC,
int sizeT,
int samplesPerPixel)
Populates the given
MetadataStore , for the specified series, using
the provided values. |
static void |
MetadataTools.populateMetadata(MetadataStore store,
int series,
java.lang.String imageName,
CoreMetadata coreMeta)
Populates the given
MetadataStore , for the specified series, using
the values from the provided CoreMetadata . |
static void |
MetadataTools.populateMetadata(MetadataStore store,
java.lang.String file,
int series,
java.lang.String imageName,
boolean littleEndian,
java.lang.String dimensionOrder,
java.lang.String pixelType,
int sizeX,
int sizeY,
int sizeZ,
int sizeC,
int sizeT,
int samplesPerPixel)
Populates the given
MetadataStore , for the specified series, using
the provided values. |
static void |
MetadataTools.populatePixels(MetadataStore store,
IFormatReader r)
Populates the Pixels element of the given metadata store, using core
metadata from the given reader.
|
static void |
MetadataTools.populatePixels(MetadataStore store,
IFormatReader r,
boolean doPlane)
Populates the Pixels element of the given metadata store, using core
metadata from the given reader.
|
static void |
MetadataTools.populatePixels(MetadataStore store,
IFormatReader r,
boolean doPlane,
boolean doImageName)
Populates the Pixels element of the given metadata store, using core
metadata from the given reader.
|
static void |
MetadataTools.populatePixelsOnly(MetadataStore store,
IFormatReader r) |
static void |
MetadataTools.populatePixelsOnly(MetadataStore store,
int series,
boolean littleEndian,
java.lang.String dimensionOrder,
java.lang.String pixelType,
int sizeX,
int sizeY,
int sizeZ,
int sizeC,
int sizeT,
int samplesPerPixel) |
static void |
MetadataTools.setDefaultCreationDate(MetadataStore store,
java.lang.String id,
int series)
Sets a default creation date.
|
void |
Memoizer.setMetadataStore(MetadataStore store) |
void |
FileStitcher.setMetadataStore(MetadataStore store) |
void |
ReaderWrapper.setMetadataStore(MetadataStore store) |
void |
ImageReader.setMetadataStore(MetadataStore store) |
void |
IFormatReader.setMetadataStore(MetadataStore store)
Sets the default metadata store for this reader.
|
void |
FormatReader.setMetadataStore(MetadataStore store) |
void |
DelegateReader.setMetadataStore(MetadataStore store) |
Modifier and Type | Field and Description |
---|---|
protected MetadataStore |
ImageViewer.omeMeta
Attached OME metadata store, if available.
|
Modifier and Type | Field and Description |
---|---|
private MetadataStore |
ZeissCZIReader.store |
private MetadataStore |
LeicaHandler.store |
private MetadataStore |
InCellReader.InCellHandler.store |
private MetadataStore |
FlexReader.FlexHandler.store |
private MetadataStore |
CellH5Reader.store |
Modifier and Type | Method and Description |
---|---|
MetadataStore |
FilePatternReader.getMetadataStore() |
MetadataStore |
OMETiffReader.getMetadataStoreForConversion()
Deprecated.
Use the general
FormatReader.getMetadataStore() method. |
MetadataStore |
OMETiffReader.getMetadataStoreForDisplay()
Deprecated.
Use the general
FormatReader.getMetadataStore() method. |
Modifier and Type | Method and Description |
---|---|
private void |
FakeReader.fillAcquisitionDate(MetadataStore store,
java.lang.String date,
int imageIndex) |
private void |
FakeReader.fillAnnotations(MetadataStore store,
int imageIndex) |
private void |
FakeReader.fillExposureTime(MetadataStore store) |
protected void |
ZeissZVIReader.fillMetadataPass1(MetadataStore store) |
protected void |
ZeissTIFFReader.fillMetadataPass1(MetadataStore store) |
protected void |
BaseZeissReader.fillMetadataPass1(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
ZeissTIFFReader.fillMetadataPass2(MetadataStore store) |
protected void |
BaseZeissReader.fillMetadataPass2(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
ZeissZVIReader.fillMetadataPass3(MetadataStore store) |
protected void |
BaseZeissReader.fillMetadataPass3(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
BaseZeissReader.fillMetadataPass4(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
ZeissZVIReader.fillMetadataPass5(MetadataStore store) |
protected void |
ZeissTIFFReader.fillMetadataPass5(MetadataStore store) |
protected void |
BaseZeissReader.fillMetadataPass5(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
BaseZeissReader.fillMetadataPass6(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
BaseZeissReader.fillMetadataPass7(MetadataStore store)
Store basic dimensions in model
|
private void |
FakeReader.fillPhysicalSizes(MetadataStore store) |
private void |
FakeReader.fillRegions(MetadataStore store,
int imageIndex) |
private void |
FlexReader.groupFiles(java.lang.String[] fileList,
MetadataStore store) |
private void |
DeltavisionReader.parseDeconvolutionLog(MetadataStore store)
Parse deconvolution output, if it exists.
|
private void |
FlexReader.parseFlexFile(int currentWell,
int wellRow,
int wellCol,
int field,
boolean firstFile,
MetadataStore store)
Parses XML metadata from the Flex file corresponding to the given well.
|
private void |
LeicaReader.parseInstrumentData(MetadataStore store,
int blockNum) |
private boolean |
DeltavisionReader.parseLogFile(MetadataStore store)
Extract metadata from associated log file, if it exists.
|
(package private) void |
BaseZeissReader.parseMainTags(int image,
MetadataStore store,
java.util.ArrayList<BaseZeissReader.Tag> tags) |
void |
MIASReader.parseMasks(MetadataStore overlayStore)
Parse masks into a separate overlay-specific MetadataStore.
|
private int |
MIASReader.parseMasks(MetadataStore store,
int series,
int roi,
java.lang.String overlayTiff)
Parse Mask ROIs from the given TIFF and place them in the given
MetadataStore.
|
private boolean |
BioRadReader.parseNotes(MetadataStore store) |
protected void |
ZeissLSMReader.parseOverlays(int series,
long data,
java.lang.String suffix,
MetadataStore store)
Parses overlay-related fields.
|
private int |
FV1000Reader.parseROIFile(java.lang.String filename,
MetadataStore store,
int nextROI,
int plane) |
private void |
ZeissZVIReader.parseROIs(int imageNum,
java.lang.String name,
MetadataStore store)
Parse ROI data from the given RandomAccessInputStream and store it in the
given MetadataStore.
|
private void |
TrestleReader.parseROIs(MetadataStore store) |
private void |
BDReader.parseROIs(MetadataStore store) |
private void |
ZeissZVIReader.parseTags(int image,
java.lang.String file,
MetadataStore store)
Parse all of the tags in a stream.
|
private void |
IPLabReader.parseTags(MetadataStore store) |
private void |
MIASReader.parseTemplateFile(MetadataStore store)
Parse metadata from the Nugenesistemplate.txt file.
|
private void |
CellWorxReader.parseWellLogFile(int wellIndex,
MetadataStore store)
Parse metadata from a well log file.
|
boolean |
MIASReader.populateMaskPixels(int imageIndex,
int roiIndex,
int shapeIndex,
MetadataStore store)
Populate the MaskPixels.BinData attribute for the Mask identified by the
given Image index, ROI index, and Shape index.
|
private void |
FlexReader.populateMetadataStore(MetadataStore store) |
private void |
FV1000Reader.populateMetadataStore(MetadataStore store,
java.lang.String path) |
protected void |
ZeissLSMReader.populateMetadataStore(ZeissLSMReader.SubBlock block,
MetadataStore store,
int series) |
private void |
TiffReader.populateMetadataStoreImageJ(MetadataStore store)
Checks the original metadata table for ImageJ-specific information
to propagate into the metadata store.
|
private void |
DeltavisionReader.populateObjective(MetadataStore store,
int lensID)
Populate an Objective based upon the lens ID.
|
private void |
HitachiReader.populateOMEMetadata(loci.common.IniTable image,
MetadataStore store) |
private void |
MIASReader.populateROI(java.util.List<java.lang.String> columns,
java.lang.String[] data,
int series,
int roi,
int time,
int z,
MetadataStore store) |
private void |
SPEReader.populateRoiMetaData(MetadataStore store)
Reads and populates ROI Meta Data values.
|
void |
ND2Handler.populateROIs(MetadataStore store) |
private int |
FakeReader.populateSPW(MetadataStore store,
int screens,
int plates,
int rows,
int cols,
int fields,
int acqs,
boolean withMicrobeam) |
private void |
KodakReader.readExtraMetadata(MetadataStore store) |
private void |
KodakReader.readFileInfoMetadata(MetadataStore store) |
private void |
DeltavisionReader.readWavelength(int channel,
MetadataStore store) |
void |
FilePatternReader.setMetadataStore(MetadataStore store) |
void |
LeicaHandler.ROI.storeROI(MetadataStore store,
int series,
int roi) |
void |
LIFReader.ROI.storeROI(MetadataStore store,
int series,
int roi,
int roiIndex) |
protected void |
BaseZeissReader.storeROIs(MetadataStore store)
Store basic dimensions in model
|
Constructor and Description |
---|
FlexHandler(java.util.List<java.lang.String> names,
java.util.List<java.lang.String> factors,
MetadataStore store,
boolean populateCore,
int well,
int thisField) |
InCellHandler(MetadataStore store) |
LeicaHandler(MetadataStore store,
MetadataLevel level) |
Modifier and Type | Interface and Description |
---|---|
interface |
IMetadata |
Constructor and Description |
---|
FilterMetadata(MetadataStore store,
boolean filter) |
Modifier and Type | Interface and Description |
---|---|
interface |
OMEXMLMetadata |
Modifier and Type | Method and Description |
---|---|
MetadataStore |
OMEXMLServiceImpl.asStore(MetadataRetrieve meta) |
MetadataStore |
OMEXMLService.asStore(MetadataRetrieve meta)
Gets the given
MetadataRetrieve object as a MetadataStore . |
Modifier and Type | Method and Description |
---|---|
MetadataRetrieve |
OMEXMLServiceImpl.asRetrieve(MetadataStore meta) |
MetadataRetrieve |
OMEXMLService.asRetrieve(MetadataStore meta)
Gets the given
MetadataStore object as a MetadataRetrieve . |
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).
|
void |
OMEXMLServiceImpl.convertMetadata(java.lang.String xml,
MetadataStore dest) |
void |
OMEXMLService.convertMetadata(java.lang.String xml,
MetadataStore dest)
Converts information from an OME-XML string (source)
into a metadata store (destination).
|
Modifier and Type | Method and Description |
---|---|
static void |
ROIHandler.saveROIs(MetadataStore store)
Save ROIs in the ROI manager to the given MetadataStore.
|
private static void |
ROIHandler.storeLine(ij.gui.Line roi,
MetadataStore store,
int roiNum,
int shape,
int c,
int z,
int t)
Stores the Line ROI into the specified metadata store.
|
private static void |
ROIHandler.storeOval(ij.gui.OvalRoi roi,
MetadataStore store,
int roiNum,
int shape,
int c,
int z,
int t)
Stores the Oval ROI into the specified metadata store.
|
private static void |
ROIHandler.storePoint(ij.gui.PointRoi roi,
MetadataStore store,
int roiNum,
int shape,
int c,
int z,
int t)
Stores the Point ROI into the specified metadata store.
|
private static void |
ROIHandler.storePolygon(ij.gui.PolygonRoi roi,
MetadataStore store,
int roiNum,
int shape,
int c,
int z,
int t)
Stores the Polygon ROI into the specified metadata store.
|
private static void |
ROIHandler.storeRectangle(ij.gui.Roi roi,
MetadataStore store,
int roiNum,
int shape,
int c,
int z,
int t)
Stores the Rectangle ROI into the specified metadata store.
|
private static void |
ROIHandler.storeText(ij.gui.TextRoi roi,
MetadataStore store,
int roiNum,
int shape,
int c,
int z,
int t)
Stores the text ROI into the metadata stored.
|
Copyright © 2018 Open Microscopy Environment