Package net.preibisch.mvrecon.fiji.datasetmanager

Class FileListDatasetDefinitionUtil

java.lang.Object

net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

public class FileListDatasetDefinitionUtil
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	FileListDatasetDefinitionUtil.AngleInfo
static class	FileListDatasetDefinitionUtil.ChannelInfo
static class	FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo
static enum	FileListDatasetDefinitionUtil.CheckResult
static class	FileListDatasetDefinitionUtil.TileInfo
static class	FileListDatasetDefinitionUtil.TileOrAngleInfo

Constructor Summary

Constructors

Constructor	Description
FileListDatasetDefinitionUtil()

Method Summary

Modifier and Type	Method	Description
static FileListDatasetDefinitionUtil.CheckResult	checkMultipleTimepoints(Map<Integer,List<net.imglib2.util.Pair<Integer,Integer>>> tpMap)
static <T, S> FileListDatasetDefinitionUtil.CheckResult	checkMultiplicity(Map<T,List<S>> map)
static void	detectDimensionsInFile(File file, Map<FileMapEntry,net.imglib2.util.Pair<net.imglib2.Dimensions,mpicbg.spim.data.sequence.VoxelDimensions>> dimensionMaps, loci.formats.ImageReader reader)
static void	detectViewsInFile(File file, Map<File,Map<Class<? extends mpicbg.spim.data.generic.base.Entity>,FileListDatasetDefinitionUtil.CheckResult>> multiplicityMap, FileListViewDetectionState state, List<String> usedFiles, loci.formats.ImageReader reader)
static void	detectViewsInFiles(List<File> files, FileListViewDetectionState state)
static void	expandAccumulatedViewInfos(Map<Class<? extends mpicbg.spim.data.generic.base.Entity>,List<Integer>> fileVariableToUse, FilenamePatternDetector patternDetector, FileListViewDetectionState state)
static <T> Map<Integer,List<FileMapEntry>>	expandMapIndexed(Map<T,List<FileMapEntry>> map, boolean useSeries)
static <T> net.imglib2.util.Pair<Map<Integer,T>,Map<Integer,List<FileMapEntry>>>	expandMapSingleFromFile(Map<T,List<FileMapEntry>> map, FilenamePatternDetector det, List<Integer> patternIdx)
static <T> net.imglib2.util.Pair<Map<Integer,T>,Map<Integer,List<FileMapEntry>>>	expandMapSingleFromFileGroupedFormat(Map<T,List<FileMapEntry>> map, FilenamePatternDetector det, List<Integer> patternIdx, Map<String,net.imglib2.util.Pair<File,Integer>> groupUsageMap)
static <T> Map<Integer,List<FileMapEntry>>	expandTimePointMapIndexed(Map<T,List<FileMapEntry>> map)
protected static HashSet<Integer>	extractFullResSeries(loci.formats.IFormatReader r, int nSeries)
static String	getPatternFile(FilenamePatternDetector patternDetector, List<Integer> variableIdxes, List<Integer> invariants, List<List<Integer>> variables)
static void	groupZPlanes(FileListViewDetectionState state, FilenamePatternDetector patternDetector, List<Integer> variablesToUse)
static <T> SortedMap<FileMapEntry,T>	invertMapSortValue(Map<T,List<FileMapEntry>> map)
static <T> List<T>	listIntersect(List<T> a, List<T> b)
static void	main(String[] args)
static net.imglib2.util.Pair<Map<FileListDatasetDefinitionUtil.TileInfo,List<net.imglib2.util.Pair<Integer,Integer>>>,Map<FileListDatasetDefinitionUtil.AngleInfo,List<net.imglib2.util.Pair<Integer,Integer>>>>	mapTilesAndAnglesToSeries(List<FileListDatasetDefinitionUtil.TileOrAngleInfo> infos)
static net.imglib2.util.Pair<Map<Integer,List<net.imglib2.util.Pair<Integer,Integer>>>,net.imglib2.util.Pair<Map<FileListDatasetDefinitionUtil.ChannelInfo,List<net.imglib2.util.Pair<Integer,Integer>>>,Map<Integer,List<net.imglib2.util.Pair<Integer,Integer>>>>>	mapTimepointsChannelsAndIlluminations(List<net.imglib2.util.Pair<Integer,List<FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo>>> infos)
static List<FileListDatasetDefinitionUtil.TileOrAngleInfo>	predictTilesAndAngles(loci.formats.IFormatReader r)
static List<net.imglib2.util.Pair<Integer,List<FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo>>>	predictTimepointsChannelsAndIllums(loci.formats.IFormatReader r)
static void	resolveAmbiguity(Map<Class<? extends mpicbg.spim.data.generic.base.Entity>,FileListDatasetDefinitionUtil.CheckResult> checkResults, boolean channelIllumAmbiguous, boolean preferChannel, boolean angleTileAmbiguous, boolean preferTile)
static <T> net.imglib2.util.Pair<Map<Integer,T>,Map<Integer,List<FileMapEntry>>>	resortMapNamed(Map<T,List<FileMapEntry>> map)

Methods inherited from class java.lang.Object

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

Constructor Details

FileListDatasetDefinitionUtil

public FileListDatasetDefinitionUtil()

Method Details

checkMultipleTimepoints

public static FileListDatasetDefinitionUtil.CheckResult checkMultipleTimepoints(Map<Integer,List<net.imglib2.util.Pair<Integer,Integer>>> tpMap)

checkMultiplicity

public static <T,
S>
FileListDatasetDefinitionUtil.CheckResult checkMultiplicity(Map<T,List<S>> map)

extractFullResSeries

protected static HashSet<Integer> extractFullResSeries(loci.formats.IFormatReader r,
 int nSeries)

predictTilesAndAngles

public static List<FileListDatasetDefinitionUtil.TileOrAngleInfo> predictTilesAndAngles(loci.formats.IFormatReader r)

predictTimepointsChannelsAndIllums

public static List<net.imglib2.util.Pair<Integer,List<FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo>>> predictTimepointsChannelsAndIllums(loci.formats.IFormatReader r)

mapTilesAndAnglesToSeries

public static net.imglib2.util.Pair<Map<FileListDatasetDefinitionUtil.TileInfo,List<net.imglib2.util.Pair<Integer,Integer>>>,Map<FileListDatasetDefinitionUtil.AngleInfo,List<net.imglib2.util.Pair<Integer,Integer>>>> mapTilesAndAnglesToSeries(List<FileListDatasetDefinitionUtil.TileOrAngleInfo> infos)

mapTimepointsChannelsAndIlluminations

public static net.imglib2.util.Pair<Map<Integer,List<net.imglib2.util.Pair<Integer,Integer>>>,net.imglib2.util.Pair<Map<FileListDatasetDefinitionUtil.ChannelInfo,List<net.imglib2.util.Pair<Integer,Integer>>>,Map<Integer,List<net.imglib2.util.Pair<Integer,Integer>>>>> mapTimepointsChannelsAndIlluminations(List<net.imglib2.util.Pair<Integer,List<FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo>>> infos)

listIntersect

public static <T> List<T> listIntersect(List<T> a,
 List<T> b)

resolveAmbiguity

public static void resolveAmbiguity(Map<Class<? extends mpicbg.spim.data.generic.base.Entity>,FileListDatasetDefinitionUtil.CheckResult> checkResults,
 boolean channelIllumAmbiguous,
 boolean preferChannel,
 boolean angleTileAmbiguous,
 boolean preferTile)

groupZPlanes

public static void groupZPlanes(FileListViewDetectionState state,
 FilenamePatternDetector patternDetector,
 List<Integer> variablesToUse)

getPatternFile

public static String getPatternFile(FilenamePatternDetector patternDetector,
 List<Integer> variableIdxes,
 List<Integer> invariants,
 List<List<Integer>> variables)

expandAccumulatedViewInfos

public static void expandAccumulatedViewInfos(Map<Class<? extends mpicbg.spim.data.generic.base.Entity>,List<Integer>> fileVariableToUse,
 FilenamePatternDetector patternDetector,
 FileListViewDetectionState state)

expandMapSingleFromFile

public static <T>
net.imglib2.util.Pair<Map<Integer,T>,Map<Integer,List<FileMapEntry>>> expandMapSingleFromFile(Map<T,List<FileMapEntry>> map,
 FilenamePatternDetector det,
 List<Integer> patternIdx)

expandMapSingleFromFileGroupedFormat

public static <T>
net.imglib2.util.Pair<Map<Integer,T>,Map<Integer,List<FileMapEntry>>> expandMapSingleFromFileGroupedFormat(Map<T,List<FileMapEntry>> map,
 FilenamePatternDetector det,
 List<Integer> patternIdx,
 Map<String,net.imglib2.util.Pair<File,Integer>> groupUsageMap)

resortMapNamed

public static <T>
net.imglib2.util.Pair<Map<Integer,T>,Map<Integer,List<FileMapEntry>>> resortMapNamed(Map<T,List<FileMapEntry>> map)

expandMapIndexed

public static <T> Map<Integer,List<FileMapEntry>> expandMapIndexed(Map<T,List<FileMapEntry>> map,
 boolean useSeries)

expandTimePointMapIndexed

public static <T> Map<Integer,List<FileMapEntry>> expandTimePointMapIndexed(Map<T,List<FileMapEntry>> map)

invertMapSortValue

public static <T> SortedMap<FileMapEntry,T> invertMapSortValue(Map<T,List<FileMapEntry>> map)

detectDimensionsInFile

public static void detectDimensionsInFile(File file,
 Map<FileMapEntry,net.imglib2.util.Pair<net.imglib2.Dimensions,mpicbg.spim.data.sequence.VoxelDimensions>> dimensionMaps,
 loci.formats.ImageReader reader)

detectViewsInFiles

public static void detectViewsInFiles(List<File> files,
 FileListViewDetectionState state)

detectViewsInFile

public static void detectViewsInFile(File file,
 Map<File,Map<Class<? extends mpicbg.spim.data.generic.base.Entity>,FileListDatasetDefinitionUtil.CheckResult>> multiplicityMap,
 FileListViewDetectionState state,
 List<String> usedFiles,
 loci.formats.ImageReader reader)

main

public static void main(String[] args)