| Modifier and Type | Method and Description |
|---|---|
static BigDataViewer |
BigDataViewer.open(String xmlFilename,
String windowTitle,
ProgressWriter progressWriter,
ViewerOptions options) |
| Modifier and Type | Method and Description |
|---|---|
static void |
ExportSpimFusionPlugIn.appendToExistingFile(ExportSpimFusionPlugIn.Parameters params)
Deprecated.
|
static void |
ExportSpimFusionPlugIn.saveAsNewFile(ExportSpimFusionPlugIn.Parameters params)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
FixAbsolutePathsInHdf5Partitions.fix(String xmlFilename)
Deprecated.
|
void |
Scripting.PartitionedSequenceWriter.writeXmlAndLinks() |
| Modifier and Type | Method and Description |
|---|---|
SpimDataMinimal |
XmlIoSpimDataMinimal.load(String xmlFilename) |
| Modifier and Type | Method and Description |
|---|---|
static void |
MergeExample.mergeHdf5ViewsSetups(List<String> inputFilenames,
List<ViewTransform> transforms,
String outputXmlFilename)
Merge multiple HDF5 datasets, where each dataset contains the same
timepoints but different views.
|
static void |
MergeExample.mergeHdf5ViewsTimepoints(List<String> inputFilenames,
String outputXmlFilename)
Append multiple HDF5 datasets, where each dataset contains the same
setups but different timepoints.
|
| Modifier and Type | Method and Description |
|---|---|
void |
CropDialog.cropGlobal(int minTimepointIndex,
int maxTimepointIndex,
File hdf5File,
File xmlFile) |
| Modifier and Type | Method and Description |
|---|---|
static void |
PrintSequenceMipmapInfo.printSequenceMipmapInfo(String xmlFilename) |
| Constructor and Description |
|---|
BigWarp(BigWarp.BigWarpData<T> data,
String windowTitle,
BigWarpViewerOptions options,
ProgressWriter progressWriter) |
BigWarp(BigWarp.BigWarpData<T> data,
String windowTitle,
ProgressWriter progressWriter) |
| Modifier and Type | Class and Description |
|---|---|
class |
SpimDataInstantiationException
This exception is thrown when SpimData entities cannot be constructed (while
loading).
|
class |
SpimDataIOException
This exception is thrown when an IO error occurs while reading or writing an
XML file.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
SpimDataExample2.exampleSequenceDescription() |
static void |
SpimDataExample2.exampleTimePoints() |
static void |
SpimDataExample2.exampleViewRegistrations() |
static void |
SpimDataExample2.exampleViewSetups() |
static void |
SpimDataExample2.main(String[] args) |
| Modifier and Type | Method and Description |
|---|---|
T |
XmlIoAbstractSpimData.fromXml(org.jdom2.Element root,
File xmlFile)
TODO
|
T |
XmlIoAbstractSpimData.load(String xmlFilename) |
void |
XmlIoAbstractSpimData.save(T spimData,
String xmlFilename) |
org.jdom2.Element |
XmlIoAbstractSpimData.toXml(T spimData,
File xmlFileDirectory)
TODO
|
| Modifier and Type | Method and Description |
|---|---|
protected T |
XmlIoSingleton.fromXml(org.jdom2.Element elem)
Create an object from the given element.
|
T |
XmlIoNamedEntity.fromXml(org.jdom2.Element elem) |
HashMap<Integer,T> |
XmlIoEntityMap.fromXml(org.jdom2.Element elem) |
T |
XmlIoEntity.fromXml(org.jdom2.Element elem)
Create an object from the given element.
|
org.jdom2.Element |
XmlIoEntityMap.toXml(Collection<T> values)
Add the values to a new
XmlIoSingleton.getTag() element (in the iteration order of the collection). |
org.jdom2.Element |
XmlIoEntityMap.toXml(Map<Integer,? extends T> map)
Sort the
values in the entity map by id and add them
to a new XmlIoSingleton.getTag() element. |
| Modifier and Type | Method and Description |
|---|---|
HashMap<Integer,T> |
XmlIoBasicViewSetups.fromXml(org.jdom2.Element elem) |
T |
XmlIoBasicViewSetup.fromXml(org.jdom2.Element elem) |
T |
XmlIoAbstractSequenceDescription.fromXml(org.jdom2.Element elem,
File basePath) |
org.jdom2.Element |
XmlIoBasicViewSetups.toXml(Collection<T> setups) |
org.jdom2.Element |
XmlIoAbstractSequenceDescription.toXml(T sequenceDescription,
File basePath) |
| Modifier and Type | Method and Description |
|---|---|
ViewRegistrations |
XmlIoViewRegistrations.fromXml(org.jdom2.Element elem)
Load
ViewRegistrations from the given DOM element. |
| Modifier and Type | Method and Description |
|---|---|
TimePoints |
XmlIoTimePoints.fromXml(org.jdom2.Element elem) |
Tile |
XmlIoTile.fromXml(org.jdom2.Element elem) |
MissingViews |
XmlIoMissingViews.fromXml(org.jdom2.Element elem) |
Angle |
XmlIoAngle.fromXml(org.jdom2.Element elem) |
protected void |
XmlIoTimePoints.fromXmlList(TimePoints timepoints,
org.jdom2.Element elem)
Create
TimePointsPattern from <
> element of type |
| Modifier and Type | Method and Description |
|---|---|
static void |
MergeClusterJobs.merge(List<File> xmls,
File output)
This performs a merge of attributes of the different xml's only assuming the same instances of viewsetups and timepoints
are present in all instances.
|
| Modifier and Type | Method and Description |
|---|---|
protected AS |
GenericLoadParseQueryXML.parseXML(String xmlFilename) |
| Modifier and Type | Method and Description |
|---|---|
static <T extends AbstractSpimData<A>,A extends AbstractSequenceDescription<?,?,? super ImgLoader>> |
Generic_Resave_HDF5.writeXML(T spimData,
XmlIoAbstractSpimData<A,T> io,
Generic_Resave_HDF5.Parameters params,
ProgressWriter progressWriter) |
| Modifier and Type | Method and Description |
|---|---|
SpimData2 |
XmlIoSpimData2.fromXml(org.jdom2.Element root,
File xmlFile) |
void |
XmlIoSpimData2.save(SpimData2 spimData,
String xmlFilename) |
org.jdom2.Element |
XmlIoSpimData2.toXml(SpimData2 spimData,
File xmlFileDirectory) |
| Modifier and Type | Method and Description |
|---|---|
BoundingBoxes |
XmlIoBoundingBoxes.fromXml(org.jdom2.Element allBoundingBoxes) |
| Modifier and Type | Method and Description |
|---|---|
ViewInterestPoints |
XmlIoViewInterestPoints.fromXml(org.jdom2.Element allInterestPointLists,
File basePath,
Map<ViewId,ViewDescription> viewDescriptions) |
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