Package net.preibisch.mvrecon.fiji.datasetmanager

Class StackList

java.lang.Object
net.preibisch.mvrecon.fiji.datasetmanager.StackList
All Implemented Interfaces:
MultiViewDatasetDefinition
Direct Known Subclasses:
StackListImageJ, StackListLOCI
public abstract class StackList extends Object implements MultiViewDatasetDefinition

  • Field Details

    • TIMEPOINT_PATTERN

      public static final char TIMEPOINT_PATTERN
      See Also:

    • CHANNEL_PATTERN

      public static final char CHANNEL_PATTERN
      See Also:

    • ILLUMINATION_PATTERN

      public static final char ILLUMINATION_PATTERN
      See Also:

    • ANGLE_PATTERN

      public static final char ANGLE_PATTERN
      See Also:

    • TILE_PATTERN

      public static final char TILE_PATTERN
      See Also:

    • dimensionChoiceTimePointsTrue

      protected String[] dimensionChoiceTimePointsTrue

    • dimensionChoiceTimePointsFalse

      protected String[] dimensionChoiceTimePointsFalse

    • dimensionChoiceChannelsTrue

      protected String[] dimensionChoiceChannelsTrue

    • dimensionChoiceChannelsFalse

      protected String[] dimensionChoiceChannelsFalse

    • dimensionChoiceIlluminationsTrue

      protected String[] dimensionChoiceIlluminationsTrue

    • dimensionChoiceIlluminationsFalse

      protected String[] dimensionChoiceIlluminationsFalse

    • dimensionChoiceAnglesTrue

      protected String[] dimensionChoiceAnglesTrue

    • dimensionChoiceAnglesFalse

      protected String[] dimensionChoiceAnglesFalse

    • dimensionChoiceTilesTrue

      protected String[] dimensionChoiceTilesTrue

    • dimensionChoiceTilesFalse

      protected String[] dimensionChoiceTilesFalse

    • hasMultipleAngles

      protected int hasMultipleAngles

    • hasMultipleTimePoints

      protected int hasMultipleTimePoints

    • hasMultipleChannels

      protected int hasMultipleChannels

    • hasMultipleIlluminations

      protected int hasMultipleIlluminations

    • hasMultipleTiles

      protected int hasMultipleTiles

    • showDebugFileNames

      public static boolean showDebugFileNames

    • defaultTimepoints

      public static String defaultTimepoints

    • defaultChannels

      public static String defaultChannels

    • defaultIlluminations

      public static String defaultIlluminations

    • defaultAngles

      public static String defaultAngles

    • defaultTiles

      public static String defaultTiles

    • timepoints

      protected String timepoints

    • channels

      protected String channels

    • illuminations

      protected String illuminations

    • angles

      protected String angles

    • tiles

      protected String tiles

    • timepointNameList

      protected ArrayList<String> timepointNameList

    • channelNameList

      protected ArrayList<String> channelNameList

    • illuminationsNameList

      protected ArrayList<String> illuminationsNameList

    • angleNameList

      protected ArrayList<String> angleNameList

    • tileNameList

      protected ArrayList<String> tileNameList

    • replaceTimepoints

      protected String replaceTimepoints

    • replaceChannels

      protected String replaceChannels

    • replaceIlluminations

      protected String replaceIlluminations

    • replaceAngles

      protected String replaceAngles

    • replaceTiles

      protected String replaceTiles

    • numDigitsTimepoints

      protected int numDigitsTimepoints

    • numDigitsChannels

      protected int numDigitsChannels

    • numDigitsIlluminations

      protected int numDigitsIlluminations

    • numDigitsAngles

      protected int numDigitsAngles

    • numDigitsTiles

      protected int numDigitsTiles

    • exceptionIds

      protected ArrayList<int[]> exceptionIds

    • calibrationChoice1

      protected String[] calibrationChoice1

    • calibrationChoice2

      protected String[] calibrationChoice2

    • defaultCalibration1

      public static int defaultCalibration1

    • defaultCalibration2

      public static int defaultCalibration2

    • calibration1

      public int calibration1

    • calibration2

      public int calibration2

    • calibrations

      protected HashMap<StackList.ViewSetupPrecursor,StackList.Calibration> calibrations

    • locations

      protected HashMap<StackList.ViewSetupPrecursor,double[]> locations

    • defaultDirectory

      public static String defaultDirectory

    • defaultFileNamePattern

      public static String defaultFileNamePattern

    • directory

      protected String directory

    • fileNamePattern

      protected String fileNamePattern

  • Constructor Details

    • StackList

      public StackList()

  • Method Details

    • getDefaultMultipleAngles

      protected abstract int getDefaultMultipleAngles()

    • getDefaultMultipleTimepoints

      protected abstract int getDefaultMultipleTimepoints()

    • getDefaultMultipleChannels

      protected abstract int getDefaultMultipleChannels()

    • getDefaultMultipleIlluminations

      protected abstract int getDefaultMultipleIlluminations()

    • getDefaultMultipleTiles

      protected abstract int getDefaultMultipleTiles()

    • setDefaultMultipleAngles

      protected abstract void setDefaultMultipleAngles(int defaultAngleChoice)

    • setDefaultMultipleTimepoints

      protected abstract void setDefaultMultipleTimepoints(int defaultTimepointChoice)

    • setDefaultMultipleChannels

      protected abstract void setDefaultMultipleChannels(int defaultChannelChoice)

    • setDefaultMultipleIlluminations

      protected abstract void setDefaultMultipleIlluminations(int defaultIlluminationChoice)

    • setDefaultMultipleTiles

      protected abstract void setDefaultMultipleTiles(int defaultTileChoice)

    • supportsMultipleTimepointsPerFile

      protected abstract boolean supportsMultipleTimepointsPerFile()

    • supportsMultipleChannelsPerFile

      protected abstract boolean supportsMultipleChannelsPerFile()

    • supportsMultipleAnglesPerFile

      protected abstract boolean supportsMultipleAnglesPerFile()

    • supportsMultipleIlluminationsPerFile

      protected abstract boolean supportsMultipleIlluminationsPerFile()

    • supportsMultipleTilesPerFile

      protected abstract boolean supportsMultipleTilesPerFile()

    • canLoadTileLocationFromMeta

      protected abstract boolean canLoadTileLocationFromMeta()

    • loadTileLocationFromMetaData

      protected abstract double[] loadTileLocationFromMetaData(File file, int seriesOffset)

    • loadAllTileLocations

      protected boolean loadAllTileLocations()

    • queryInformation

      protected boolean queryInformation()

    • createAndInitImgLoader

      protected abstract StackImgLoader createAndInitImgLoader(String path, File basePath, mpicbg.spim.data.sequence.SequenceDescription sequenceDescription)

    • createDataset

      public SpimData2 createDataset(String xmlFileName)
      Description copied from interface: MultiViewDatasetDefinition
      This method is supposed to (interactively, ideally ImageJ-macroscriptable) query all necessary data from the user to build up a SpimData object and save it as an XML file.
      Specified by:
      createDataset in interface MultiViewDatasetDefinition
      Parameters:
      xmlFileName - - the filename of the XML that was selected (no path!)
      Returns:
      - the saved SpimData2 object

    • createMissingViews

      protected mpicbg.spim.data.sequence.MissingViews createMissingViews()

    • createViewSetups

      protected ArrayList<mpicbg.spim.data.sequence.ViewSetup> createViewSetups()

    • createTimePoints

      protected mpicbg.spim.data.sequence.TimePoints createTimePoints()

    • queryDetails

      protected boolean queryDetails()

    • debugShowFiles

      protected boolean debugShowFiles()

    • queryNames

      protected boolean queryNames() throws ParseException
      Throws:
      ParseException

    • convertIntegerList

      public static ArrayList<String> convertIntegerList(List<Integer> list)

    • getFileNameFor

      protected String getFileNameFor(int tpID, int chID, int illID, int angleID, int tileID)

    • getFileNamesFor

      public static String[] getFileNamesFor(String fileNames, String replaceTimepoints, String replaceChannels, String replaceIlluminations, String replaceAngles, String replaceTiles, String tpName, String chName, String illName, String angleName, String tileName, int numDigitsTP, int numDigitsCh, int numDigitsIll, int numDigitsAngle, int numDigitsTile)

    • leadingZeros

      public static String leadingZeros(String s, int numDigits)

    • loadFirstCalibration

      protected boolean loadFirstCalibration()

    • loadAllCalibrations

      protected boolean loadAllCalibrations()

    • loadCalibration

      protected abstract StackList.Calibration loadCalibration(File file)

    • assembleDefaultPattern

      protected String assembleDefaultPattern()

    • queryGeneralInformation

      protected boolean queryGeneralInformation()