org.janelia.saalfeldlab.n5.universe.metadata

Class MetadataUtils

java.lang.Object

org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils

public class MetadataUtils
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	DOWN_AVERAGE
static String	DOWN_SAMPLE

Constructor Summary

Constructors

Constructor and Description
MetadataUtils()

Method Summary

Modifier and Type	Method and Description
static N5CosemMetadata	buildCosemMetadata(String path, N5CosemMetadata baseMetadata, double[] absoluteResolution, double[] absoluteTranslation)
static N5SingleScaleMetadata	buildN5VMetadata(String path, N5SingleScaleMetadata baseMetadata, String downsampleMethod, double[] baseResolution, double[] downsamplingFactors)
static NgffSingleScaleAxesMetadata	buildNgffMetadata(String path, NgffSingleScaleAxesMetadata baseMetadata, double[] absoluteResolution, double[] absoluteTranslation)
static CoordinateTransformation<?>[]	buildScaleTranslationTransformList(double[] scale, double[] translation)
static String	canonicalPath(N5TreeNode parent, String child)
static String	canonicalPath(String parent, String child)
static net.imglib2.realtransform.ScaleAndTranslation	coordinateTransformToScaleAndTranslation(CoordinateTransformation<?> ct)
static long[]	downsamplingFactors(long factor, long[] dimensions, String[] types)
static String	getStringNullable(com.google.gson.JsonElement element) Gets a String from a JsonElement if possible, returning null if the element is JsonNull.
static <M extends N5DatasetMetadata> M	metadataForThisScale(String newPath, M baseMetadata, String downsampleMethod, double[] baseResolution, double[] absoluteDownsamplingFactors, double[] absoluteScale, double[] absoluteTranslation)
static double[]	mul(double[] a, double[] b)
static double[]	mul(double[] a, long[] b)
static String	normalizeGroupPath(String path)
static N5CosemMetadata	permuteCosemMetadata(N5CosemMetadata metadata, int[] axisPermutation)
static N5SingleScaleMetadata	permuteN5vMetadata(N5SingleScaleMetadata metadata, int[] axisPermutation)
static NgffSingleScaleAxesMetadata	permuteNgffMetadata(NgffSingleScaleAxesMetadata metadata, int[] axisPermutation)
static <M extends N5Metadata> M	permuteSpatialMetadata(M metadata, int[] axisPermutation)
static double[]	pow(double[] x, int d) Element-wise power.
static String	relativePath(String parent, String child) Returns a relative group path from the child absolute path group path child the parent absolute group path.
static com.google.gson.JsonArray	reversedCopy(com.google.gson.JsonArray array)
static <T> T[]	reversedCopy(T[] array) Creates a new array containing all elements of the input array in reversed order.
static double[][]	scalesAndTranslations(double[] baseScale, double[] downsamplingFactors, int numLevels)
static net.imglib2.realtransform.ScaleAndTranslation	scaleTranslationFromCoordinateTransformations(CoordinateTransformation<?>[] cts)
static net.imglib2.realtransform.AffineGet	scaleTranslationTransforms(double[] scale, double[] translation) Returns the most efficient transform given the input scale and translation parameters.
static N5SingleScaleMetadata	setDatasetAttributes(N5SingleScaleMetadata baseMetadata, N5DatasetMetadata datasetMetadata) Returns a new N5SingleScaleMetadata equal to the baseMetadata, but with DatasetAttributes coming from datasetMetadata.ew
static N5SingleScaleMetadata[]	updateChildrenDatasetAttributes(N5SingleScaleMetadata[] baseMetadata, N5DatasetMetadata[] datasetMetadata)
static void	updateChildrenMetadata(N5TreeNode parent, N5Metadata[] childrenMetadata, boolean relative)
static long[]	updateDownsamplingFactors(long factor, long[] baseFactors, long[] dimensions, String[] types)

Methods inherited from class java.lang.Object

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

Field Detail

DOWN_SAMPLE

public static final String DOWN_SAMPLE

See Also:

Constant Field Values

DOWN_AVERAGE

public static final String DOWN_AVERAGE

See Also:

Constant Field Values

Constructor Detail

MetadataUtils

public MetadataUtils()

Method Detail

mul

public static double[] mul(double[] a,
                           double[] b)

mul

public static double[] mul(double[] a,
                           long[] b)

scalesAndTranslations

public static double[][] scalesAndTranslations(double[] baseScale,
                                               double[] downsamplingFactors,
                                               int numLevels)

downsamplingFactors

public static long[] downsamplingFactors(long factor,
                                         long[] dimensions,
                                         String[] types)

updateDownsamplingFactors

public static long[] updateDownsamplingFactors(long factor,
                                               long[] baseFactors,
                                               long[] dimensions,
                                               String[] types)

buildScaleTranslationTransformList

public static CoordinateTransformation<?>[] buildScaleTranslationTransformList(double[] scale,
                                                                               double[] translation)

scaleTranslationFromCoordinateTransformations

public static net.imglib2.realtransform.ScaleAndTranslation scaleTranslationFromCoordinateTransformations(CoordinateTransformation<?>[] cts)

coordinateTransformToScaleAndTranslation

public static net.imglib2.realtransform.ScaleAndTranslation coordinateTransformToScaleAndTranslation(CoordinateTransformation<?> ct)

setDatasetAttributes

public static N5SingleScaleMetadata setDatasetAttributes(N5SingleScaleMetadata baseMetadata,
                                                         N5DatasetMetadata datasetMetadata)

Returns a new N5SingleScaleMetadata equal to the baseMetadata, but with DatasetAttributes coming from datasetMetadata.ew

Parameters:

baseMetadata - metadata

datasetMetadata - dataset metadata

Returns:

the single scale metadata

updateChildrenDatasetAttributes

public static N5SingleScaleMetadata[] updateChildrenDatasetAttributes(N5SingleScaleMetadata[] baseMetadata,
                                                                      N5DatasetMetadata[] datasetMetadata)

updateChildrenMetadata

public static void updateChildrenMetadata(N5TreeNode parent,
                                          N5Metadata[] childrenMetadata,
                                          boolean relative)

canonicalPath

public static String canonicalPath(N5TreeNode parent,
                                   String child)

canonicalPath

public static String canonicalPath(String parent,
                                   String child)

normalizeGroupPath

public static String normalizeGroupPath(String path)

relativePath

public static String relativePath(String parent,
                                  String child)

Returns a relative group path from the child absolute path group path child the parent absolute group path. If the child path is not a descendent of parent, child will be returned.

Parameters:

parent - an absolute path

child - an absolute path

Returns:

relative path from child to parent, if it exists.

pow

public static double[] pow(double[] x,
                           int d)

Element-wise power. Returns an array y such that y[i] = x[i] ^ d

Parameters:

x - array

d - exponent

Returns:

result

getStringNullable

public static String getStringNullable(com.google.gson.JsonElement element)

Gets a String from a JsonElement if possible, returning null if the element is JsonNull.

Parameters:

element - the json element

Returns:

a string

scaleTranslationTransforms

public static net.imglib2.realtransform.AffineGet scaleTranslationTransforms(double[] scale,
                                                                             double[] translation)

Returns the most efficient transform given the input scale and translation parameters. If both are null, this method will return null;

Parameters:

scale - the scale parameters

translation - the translation parameters

Returns:

an appropriate AffineGet

metadataForThisScale

public static <M extends N5DatasetMetadata> M metadataForThisScale(String newPath,
                                                                   M baseMetadata,
                                                                   String downsampleMethod,
                                                                   double[] baseResolution,
                                                                   double[] absoluteDownsamplingFactors,
                                                                   double[] absoluteScale,
                                                                   double[] absoluteTranslation)

buildN5VMetadata

public static N5SingleScaleMetadata buildN5VMetadata(String path,
                                                     N5SingleScaleMetadata baseMetadata,
                                                     String downsampleMethod,
                                                     double[] baseResolution,
                                                     double[] downsamplingFactors)

buildCosemMetadata

public static N5CosemMetadata buildCosemMetadata(String path,
                                                 N5CosemMetadata baseMetadata,
                                                 double[] absoluteResolution,
                                                 double[] absoluteTranslation)

buildNgffMetadata

public static NgffSingleScaleAxesMetadata buildNgffMetadata(String path,
                                                            NgffSingleScaleAxesMetadata baseMetadata,
                                                            double[] absoluteResolution,
                                                            double[] absoluteTranslation)

permuteSpatialMetadata

public static <M extends N5Metadata> M permuteSpatialMetadata(M metadata,
                                                              int[] axisPermutation)

permuteNgffMetadata

public static NgffSingleScaleAxesMetadata permuteNgffMetadata(NgffSingleScaleAxesMetadata metadata,
                                                              int[] axisPermutation)

permuteCosemMetadata

public static N5CosemMetadata permuteCosemMetadata(N5CosemMetadata metadata,
                                                   int[] axisPermutation)

permuteN5vMetadata

public static N5SingleScaleMetadata permuteN5vMetadata(N5SingleScaleMetadata metadata,
                                                       int[] axisPermutation)

reversedCopy

public static <T> T[] reversedCopy(T[] array)

Creates a new array containing all elements of the input array in reversed order.

Type Parameters:

T - the type of elements in the array

Parameters:

array - the input array to be reversed

Returns:

a new array with elements in reversed order compared to the input array

reversedCopy

public static com.google.gson.JsonArray reversedCopy(com.google.gson.JsonArray array)