Package sc.fiji.snt.io

Class SpimDataUtils

java.lang.Object

sc.fiji.snt.io.SpimDataUtils

public class SpimDataUtils
extends Object

Utilities for working with AbstractSpimData and BigDataViewer XML descriptors.

Author:

Tiago Ferreira

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SpimDataUtils.CalibratedSource<T extends net.imglib2.type.numeric.NumericType<T>>	Wraps a RandomAccessibleIntervalSource and overrides SpimDataUtils.CalibratedSource.getVoxelDimensions() to carry the physical unit (e.g.

Method Summary

Modifier and Type	Method	Description
static void	patchImsXml(String xmlPath, String base)	Patches an IMS XML sidecar file, replacing all "(name not specified)" placeholders with sequential channel names derived from the base name.
static Object	resolvePathToSource(String filePathOrUrl)	Resolves a file path to either an AbstractSpimData (for .ims and .xml files) or an ImgPlus (fallback).
static void	writeBdvN5Xml(File xmlFile, String n5DirName, long[][] levelDims, double[] voxelSize, String unit, int nTimepoints, String setupName)	Writes a BDV-compatible XML descriptor for an N5 dataset.
static void	writeBdvN5Xml(File xmlFile, String n5DirName, long[][] levelDims, double[] voxelSize, String unit, int nTimepoints, String setupName, int nChannels)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

resolvePathToSource

public static Object resolvePathToSource(String filePathOrUrl)

Resolves a file path to either an AbstractSpimData (for .ims and .xml files) or an ImgPlus (fallback).

Parameters:

filePathOrUrl - path or URL to the image file

Returns:

an AbstractSpimData or ImgPlus

Throws:

IllegalArgumentException - if the file cannot be opened

patchImsXml

public static void patchImsXml(String xmlPath,
 String base)
                        throws IOException

Patches an IMS XML sidecar file, replacing all "(name not specified)" placeholders with sequential channel names derived from the base name.

Parameters:

xmlPath - path to the XML sidecar

base - base name to use (typically the IMS filename without extension)

Throws:

IOException - if the file cannot be read or written

writeBdvN5Xml

public static void writeBdvN5Xml(File xmlFile,
 String n5DirName,
 long[][] levelDims,
 double[] voxelSize,
 String unit,
 int nTimepoints,
 String setupName)
                          throws IOException

Writes a BDV-compatible XML descriptor for an N5 dataset. The resulting XML can be opened by BigDataViewer, BigVolumeViewer, or any BDV-based tool via XmlIoSpimDataMinimal.load().

The descriptor references the N5 container using a relative path (assumes the XML sits next to the N5 directory). A single ViewSetup (id 0) is created with the supplied voxel size and calibration unit.

Parameters:

xmlFile - the XML file to write (will be overwritten if it exists)

n5DirName - name of the N5 container directory (relative to the XML file's parent; e.g., "dataset_unmixed")

levelDims - per-level dimensions: levelDims[level] = {x, y, z}

voxelSize - physical voxel size at level 0: {sx, sy, sz}

unit - calibration unit (e.g., "um", "pixel")

nTimepoints - number of timepoints in the dataset

setupName - display name for the single ViewSetup (e.g., "unmixed")

Throws:

IOException - if the file cannot be written

writeBdvN5Xml

public static void writeBdvN5Xml(File xmlFile,
 String n5DirName,
 long[][] levelDims,
 double[] voxelSize,
 String unit,
 int nTimepoints,
 String setupName,
 int nChannels)
                          throws IOException

Throws:

IOException