| Modifier and Type | Method and Description |
|---|---|
protected static boolean |
ExportSpimSequencePlugIn.init(SPIMConfiguration conf)
Deprecated.
|
protected boolean |
ExportSpimFusionPlugIn.updateProposedMipmaps(String fusionDirectory,
SPIMConfiguration conf)
Deprecated.
|
| Constructor and Description |
|---|
Parameters(SPIMConfiguration conf,
boolean setMipmapManual,
int[][] resolutions,
int[][] subdivisions,
File seqFile,
File hdf5File,
boolean deflate,
boolean split,
int timepointsPerPartition,
int setupsPerPartition) |
Parameters(SPIMConfiguration conf,
int[][] resolutions,
int[][] subdivisions,
int cropOffsetX,
int cropOffsetY,
int cropOffsetZ,
int scale,
String fusionDirectory,
String filenamePattern,
int numSlices,
double sliceValueMin,
double sliceValueMax,
File seqFile,
File hdf5File,
boolean appendToExistingFile,
boolean deflate,
boolean split,
int timepointsPerPartition,
int setupsPerPartition) |
| Modifier and Type | Method and Description |
|---|---|
SPIMConfiguration |
SpimRegistrationSequence.getConf()
Deprecated.
|
protected static SPIMConfiguration |
SpimRegistrationSequence.initExperimentConfiguration(String inputDirectory,
String inputFilePattern,
String angles,
String timepoints,
int referenceTimePoint,
boolean overrideImageZStretching,
double zStretching)
Deprecated.
Instantiate the SPIM configuration only with the necessary parameters
|
protected static SPIMConfiguration |
SpimRegistrationSequence.initExperimentConfiguration(String inputDirectory,
String inputFilePattern,
String channels,
String angles,
String timepoints,
int referenceTimePoint,
boolean overrideImageZStretching,
double zStretching)
Deprecated.
Instantiate the SPIM configuration only with the necessary parameters
|
| Modifier and Type | Method and Description |
|---|---|
protected static BasicImgLoader |
SpimRegistrationSequence.createImageLoader(SPIMConfiguration conf,
ArrayList<ViewSetup> setups)
Deprecated.
|
protected static TimePoints |
SpimRegistrationSequence.createTimePoints(SPIMConfiguration conf)
Deprecated.
|
protected static ViewRegistrations |
SpimRegistrationSequence.createViewRegistrations(SPIMConfiguration conf,
ArrayList<ViewSetup> setups)
Deprecated.
|
protected static ArrayList<ViewSetup> |
SpimRegistrationSequence.createViewSetups(SPIMConfiguration conf)
Deprecated.
|
protected static RealInterval |
SpimRegistrationSequence.getFusionBoundingBox(SPIMConfiguration conf,
int timepointId)
Deprecated.
|
| Constructor and Description |
|---|
SpimRegistrationSequence(SPIMConfiguration conf)
Deprecated.
|
| Modifier and Type | Method and Description |
|---|---|
protected SPIMConfiguration |
Multi_View_Deconvolution.getParameters() |
protected SPIMConfiguration |
Apply_External_Transformation.getParameters() |
protected SPIMConfiguration |
Multi_View_Fusion.getParameters(boolean multichannel) |
SPIMConfiguration |
Bead_Registration.multiChannel(int choiceType) |
SPIMConfiguration |
Bead_Registration.singleChannel(int choiceType) |
| Modifier and Type | Method and Description |
|---|---|
void |
Multi_View_Deconvolution.deconvolve(ViewStructure viewStructure,
SPIMConfiguration conf,
int timePoint) |
protected static boolean |
Bead_Registration.init(SPIMConfiguration conf) |
| Modifier and Type | Method and Description |
|---|---|
static ArrayList<RegistrationStatistics> |
TimeLapseDisplay.loadData(SPIMConfiguration conf) |
| Modifier and Type | Field and Description |
|---|---|
protected SPIMConfiguration |
Reconstruction.conf |
| Modifier and Type | Method and Description |
|---|---|
SPIMConfiguration |
Reconstruction.getSPIMConfiguration() |
| Modifier and Type | Method and Description |
|---|---|
protected void |
Reconstruction.processIndividualViewStructure(SPIMConfiguration conf) |
protected void |
Reconstruction.processTimeLapse(SPIMConfiguration conf) |
| Constructor and Description |
|---|
Reconstruction(SPIMConfiguration conf) |
| Modifier and Type | Field and Description |
|---|---|
protected SPIMConfiguration |
SPIMImageFusion.conf |
| Modifier and Type | Method and Description |
|---|---|
static SPIMConfiguration |
IOFunctions.initSPIMProcessing() |
static SPIMConfiguration |
IOFunctions.initSPIMProcessing(String configFile,
String spimConfigFile) |
static SPIMConfiguration |
ConfigurationParserSPIM.parseFile(String confFileName) |
| Modifier and Type | Method and Description |
|---|---|
static boolean |
IOFunctions.readSegmentation(ViewDataBeads view,
String directory,
SPIMConfiguration conf) |
static void |
ConfigurationParserSPIM.testDirectories(SPIMConfiguration conf) |
| Constructor and Description |
|---|
ExtractPSF(SPIMConfiguration config) |
| Modifier and Type | Field and Description |
|---|---|
protected SPIMConfiguration |
ViewStructure.conf
The configuration of the current SPIM registration
|
| Modifier and Type | Method and Description |
|---|---|
SPIMConfiguration |
ViewStructure.getSPIMConfiguration()
Return the current SPIMConfiguration
|
| Modifier and Type | Method and Description |
|---|---|
static <M extends AbstractAffineModel3D<M>> |
ViewStructure.initViewStructure(SPIMConfiguration conf,
int timePointIndex,
M model,
String id,
int debugLevel)
This static methods creates an instance of
ViewStructure with all ViewDataBeads completely instantiated. |
| Constructor and Description |
|---|
ViewStructure(ArrayList<ViewDataBeads> views,
SPIMConfiguration conf,
String id,
int timePoint,
int numChannels) |
ViewStructure(ArrayList<ViewDataBeads> views,
SPIMConfiguration conf,
String id,
int timePoint,
int numChannels,
int debugLevel) |
| Modifier and Type | Method and Description |
|---|---|
protected BeadStructure |
BeadSegmentation.extractBeadsDOM(ViewDataBeads view,
SPIMConfiguration conf)
Computes potential beads based on the difference-of-mean (DOM).
|
protected BeadStructure |
BeadSegmentation.extractBeadsLaPlaceImgLib(ViewDataBeads view,
SPIMConfiguration conf) |
void |
BeadSegmentation.segment(SPIMConfiguration conf,
ArrayList<ViewDataBeads> views) |
| Constructor and Description |
|---|
VisualizeBeads(SPIMConfiguration config) |
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