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.
static final record	SpimDataUtils.N5Sources	Holds the sources produced by opening an N5 or OME-Zarr container via n5-ij/n5-universe/n5-viewer_fiji (see resolvePathToSource(String)).

Method Summary

Modifier and Type	Method	Description
static boolean	isRemoteUrl(String path)	Whether path is a remote URL (e.g.
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 SpimDataUtils.N5Sources	resolveN5Selection(org.janelia.saalfeldlab.n5.ui.DataSelection selection, String name)	Builds SpimDataUtils.N5Sources from a user-made DataSelection (e.g.
static Object	resolvePathToSource(String filePathOrUrl)	Resolves a file path to an AbstractSpimData (for .ims and .xml files), an SpimDataUtils.N5Sources (for .n5/.zarr containers), or an ImgPlus (fallback).
static String	restoreUrlScheme(String url)	Restores a URL's "://" scheme separator if File's path normalization collapsed it to a single slash (see isRemoteUrl(String)).
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 an AbstractSpimData (for .ims and .xml files), an SpimDataUtils.N5Sources (for .n5/.zarr containers), or an ImgPlus (fallback).

Parameters:

filePathOrUrl - path or URL to the image file

Returns:

an AbstractSpimData, SpimDataUtils.N5Sources, or ImgPlus

Throws:

IllegalArgumentException - if the file cannot be opened

isRemoteUrl

public static boolean isRemoteUrl(String path)

Whether path is a remote URL (e.g. https://.../dataset.ome.zarr, s3://bucket/key, gs://bucket/key) rather than a local filesystem path. Also recognizes the same URLs after their scheme separator has been collapsed from "://" to ":/" by File's own path normalization (see restoreUrlScheme(String)) -- this happens whenever a URL is round-tripped through a File-typed SciJava parameter, e.g. a user typing a URL into BigDataLoaderCmd's "Main volume" field. Neither Windows drive letters (C:\...) nor UNC paths (\\server\share) match either form, so local paths are never misidentified

restoreUrlScheme

public static String restoreUrlScheme(String url)

Restores a URL's "://" scheme separator if File's path normalization collapsed it to a single slash (see isRemoteUrl(String)). A no-op if the separator is already intact.

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

resolveN5Selection

public static SpimDataUtils.N5Sources resolveN5Selection(org.janelia.saalfeldlab.n5.ui.DataSelection selection,
 String name)

Builds SpimDataUtils.N5Sources from a user-made DataSelection (e.g. from an interactive DatasetSelectorDialog), reusing the same source-building logic as the automatic discovery in resolvePathToSource(String). Intended as a fallback UI for containers whose structure resolvePathToSource(String) could not resolve on its own.

Parameters:

selection - the user's dataset selection

name - display name for the resulting SpimDataUtils.N5Sources

Returns:

the resolved sources

Throws:

IllegalArgumentException - if no displayable sources are found

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