StackList (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- spim.fiji.datasetmanager.StackList

All Implemented Interfaces:

MultiViewDatasetDefinition

Direct Known Subclasses:

StackListImageJ, StackListLOCI
```
public abstract class StackList
extends Object
implements MultiViewDatasetDefinition
```

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

protected class StackList.Calibration

protected class StackList.ViewSetupPrecursor

Nested Classes
Modifier and Type	Class and Description
`protected class`	`StackList.Calibration`
`protected class`	`StackList.ViewSetupPrecursor`

Field Summary

Fields
Modifier and Type	Field and Description
`static char`	`ANGLE_PATTERN`
`protected ArrayList<String>`	`angleNameList`
`protected String`	`angles`
`int`	`calibration1`
`int`	`calibration2`
`protected String[]`	`calibrationChoice1`
`protected String[]`	`calibrationChoice2`
`protected HashMap<StackList.ViewSetupPrecursor,StackList.Calibration>`	`calibrations`
`static char`	`CHANNEL_PATTERN`
`protected ArrayList<String>`	`channelNameList`
`protected String`	`channels`
`static String`	`defaultAngles`
`static int`	`defaultCalibration1`
`static int`	`defaultCalibration2`
`static String`	`defaultChannels`
`static int`	`defaultContainer`
`static String`	`defaultDirectory`
`static String`	`defaultFileNamePattern`
`static String`	`defaultIlluminations`
`static String`	`defaultTimepoints`
`protected String[]`	`dimensionChoiceAnglesFalse`
`protected String[]`	`dimensionChoiceAnglesTrue`
`protected String[]`	`dimensionChoiceChannelsFalse`
`protected String[]`	`dimensionChoiceChannelsTrue`
`protected String[]`	`dimensionChoiceIlluminationsFalse`
`protected String[]`	`dimensionChoiceIlluminationsTrue`
`protected String[]`	`dimensionChoiceTimePointsFalse`
`protected String[]`	`dimensionChoiceTimePointsTrue`
`protected String`	`directory`
`protected ArrayList<int[]>`	`exceptionIds`
`protected String`	`fileNamePattern`
`protected int`	`hasMultipleAngles`
`protected int`	`hasMultipleChannels`
`protected int`	`hasMultipleIlluminations`
`protected int`	`hasMultipleTimePoints`
`static char`	`ILLUMINATION_PATTERN`
`protected String`	`illuminations`
`protected ArrayList<String>`	`illuminationsNameList`
`ImgFactory<? extends NativeType<?>>`	`imgFactory`
`static String[]`	`imglib2Container`
`protected int`	`numDigitsAngles`
`protected int`	`numDigitsChannels`
`protected int`	`numDigitsIlluminations`
`protected int`	`numDigitsTimepoints`
`protected String`	`replaceAngles`
`protected String`	`replaceChannels`
`protected String`	`replaceIlluminations`
`protected String`	`replaceTimepoints`
`static boolean`	`showDebugFileNames`
`static char`	`TIMEPOINT_PATTERN`
`protected ArrayList<String>`	`timepointNameList`
`protected String`	`timepoints`

Constructor Summary

Constructors
Constructor and Description

StackList()

Constructors
Constructor and Description
`StackList()`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`protected String`	`assembleDefaultPattern()`
`static ArrayList<String>`	`convertIntegerList(List<Integer> list)`
`protected abstract StackImgLoader`	`createAndInitImgLoader(String path, File basePath, ImgFactory<? extends NativeType<?>> imgFactory, SequenceDescription sequenceDescription)` Instantiate the `ImgLoader`
`SpimData2`	`createDataset()` 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.
`protected MissingViews`	`createMissingViews()` Assembles the list of missing view instances, i.e.
`protected TimePoints`	`createTimePoints()` Creates the `TimePoints` for the `SpimData` object
`protected static ViewRegistrations`	`createViewRegistrations(Map<ViewId,ViewDescription> viewDescriptionList, double minResolution)` Assembles the `ViewRegistration` object consisting of a list of `ViewRegistration`s for all `ViewDescription`s that are present
`protected ArrayList<ViewSetup>`	`createViewSetups()` Creates the List of `ViewSetup` for the `SpimData` object.
`protected boolean`	`debugShowFiles()`
`protected abstract int`	`getDefaultMultipleAngles()`
`protected abstract int`	`getDefaultMultipleChannels()`
`protected abstract int`	`getDefaultMultipleIlluminations()`
`protected abstract int`	`getDefaultMultipleTimepoints()`
`protected String`	`getFileNameFor(int tpID, int chID, int illID, int angleID)` Assemble the filename for the corresponding file based on the indices for time, channel, illumination and angle If the fileNamePattern is separated by ';', it will return multiple solutions for each filenamepattern
`static String[]`	`getFileNamesFor(String fileNames, String replaceTimepoints, String replaceChannels, String replaceIlluminations, String replaceAngles, String tpName, String chName, String illName, String angleName, int numDigitsTP, int numDigitsCh, int numDigitsIll, int numDigitsAngle)` Assemble the filename for the corresponding file based on the indices for time, channel, illumination and angle If the fileNamePattern is separated by ';', it will return multiple solutions for each filenamepattern
`static String`	`leadingZeros(String s, int numDigits)`
`protected boolean`	`loadAllCalibrations()` populates the fields calX, calY, calZ from the first file of the series
`protected abstract StackList.Calibration`	`loadCalibration(File file)` Loads the calibration stored in a specific file and closes it afterwards.
`protected boolean`	`loadFirstCalibration()` populates the fields calX, calY, calZ from the first file of the series
`protected boolean`	`queryDetails()`
`protected boolean`	`queryGeneralInformation()`
`protected boolean`	`queryInformation()`
`protected boolean`	`queryNames()`
`protected abstract void`	`setDefaultMultipleAngles(int defaultAngleChoice)`
`protected abstract void`	`setDefaultMultipleChannels(int defaultChannelChoice)`
`protected abstract void`	`setDefaultMultipleIlluminations(int defaultIlluminationChoice)`
`protected abstract void`	`setDefaultMultipleTimepoints(int defaultTimepointChoice)`
`protected abstract boolean`	`supportsMultipleAnglesPerFile()`
`protected abstract boolean`	`supportsMultipleChannelsPerFile()`
`protected abstract boolean`	`supportsMultipleIlluminationsPerFile()`
`protected abstract boolean`	`supportsMultipleTimepointsPerFile()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface spim.fiji.datasetmanager.MultiViewDatasetDefinition
getExtendedDescription, getTitle, newInstance

Field Detail

TIMEPOINT_PATTERN
```
public static final char TIMEPOINT_PATTERN
```
See Also:

Constant Field Values

CHANNEL_PATTERN
```
public static final char CHANNEL_PATTERN
```
See Also:

Constant Field Values

ILLUMINATION_PATTERN
```
public static final char ILLUMINATION_PATTERN
```
See Also:

Constant Field Values

ANGLE_PATTERN
```
public static final char ANGLE_PATTERN
```
See Also:

Constant Field Values

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

hasMultipleAngles
```
protected int hasMultipleAngles
```

hasMultipleTimePoints
```
protected int hasMultipleTimePoints
```

hasMultipleChannels
```
protected int hasMultipleChannels
```

hasMultipleIlluminations
```
protected int hasMultipleIlluminations
```

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
```

timepoints
```
protected String timepoints
```

channels
```
protected String channels
```

illuminations
```
protected String illuminations
```

angles
```
protected String angles
```

timepointNameList

protected ArrayList<String> timepointNameList

channelNameList

protected ArrayList<String> channelNameList

illuminationsNameList

protected ArrayList<String> illuminationsNameList

angleNameList

protected ArrayList<String> angleNameList

replaceTimepoints
```
protected String replaceTimepoints
```

replaceChannels
```
protected String replaceChannels
```

replaceIlluminations
```
protected String replaceIlluminations
```

replaceAngles
```
protected String replaceAngles
```

numDigitsTimepoints
```
protected int numDigitsTimepoints
```

numDigitsChannels
```
protected int numDigitsChannels
```

numDigitsIlluminations
```
protected int numDigitsIlluminations
```

numDigitsAngles
```
protected int numDigitsAngles
```

exceptionIds

protected ArrayList<int[]> exceptionIds

calibrationChoice1
```
protected String[] calibrationChoice1
```

calibrationChoice2
```
protected String[] calibrationChoice2
```

imglib2Container

public static String[] imglib2Container

defaultContainer
```
public static int defaultContainer
```

imgFactory

public ImgFactory<? extends NativeType<?>> imgFactory

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

defaultDirectory
```
public static String defaultDirectory
```

defaultFileNamePattern

public static String defaultFileNamePattern

directory
```
protected String directory
```

fileNamePattern
```
protected String fileNamePattern
```

Constructor Detail
- StackList
```
public StackList()
```

Method Detail

getDefaultMultipleAngles

protected abstract int getDefaultMultipleAngles()

getDefaultMultipleTimepoints

protected abstract int getDefaultMultipleTimepoints()

getDefaultMultipleChannels

protected abstract int getDefaultMultipleChannels()

getDefaultMultipleIlluminations

protected abstract int getDefaultMultipleIlluminations()

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)

supportsMultipleTimepointsPerFile

protected abstract boolean supportsMultipleTimepointsPerFile()

supportsMultipleChannelsPerFile

protected abstract boolean supportsMultipleChannelsPerFile()

supportsMultipleAnglesPerFile

protected abstract boolean supportsMultipleAnglesPerFile()

supportsMultipleIlluminationsPerFile

protected abstract boolean supportsMultipleIlluminationsPerFile()

queryInformation
```
protected boolean queryInformation()
```

createAndInitImgLoader

protected abstract StackImgLoader createAndInitImgLoader(String path,
                                                         File basePath,
                                                         ImgFactory<? extends NativeType<?>> imgFactory,
                                                         SequenceDescription sequenceDescription)

Instantiate the ImgLoader

Parameters:: path - - The path relative to the basepath; basePath - - The base path, where XML will be and the image stack are; sequenceDescription -
Returns:

createDataset
```
public SpimData2 createDataset()
```
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

Returns:

- the saved SpimData object

createViewRegistrations
```
protected static ViewRegistrations createViewRegistrations(Map<ViewId,ViewDescription> viewDescriptionList,
                                                           double minResolution)
```
Assembles the ViewRegistration object consisting of a list of ViewRegistrations for all ViewDescriptions that are present

Parameters:

viewDescriptionList -

minResolution - - the smallest resolution in any dimension (distance between two pixels in the output image will be that wide)

Returns:

createMissingViews
```
protected MissingViews createMissingViews()
```
Assembles the list of missing view instances, i.e. ViewSetup that are missing at certain TimePoints.

Returns:

createViewSetups
```
protected ArrayList<ViewSetup> createViewSetups()
```
Creates the List of ViewSetup for the SpimData object. The ViewSetup are defined independent of the TimePoint, each TimePoint should have the same ViewSetups. The MissingViews class defines if some of them are missing for some of the TimePoints

Returns:

createTimePoints
```
protected TimePoints createTimePoints()
```
Creates the TimePoints for the SpimData object

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)
```
Assemble the filename for the corresponding file based on the indices for time, channel, illumination and angle If the fileNamePattern is separated by ';', it will return multiple solutions for each filenamepattern

Parameters:

tpID -

chID -

illID -

angleID -

Returns:

getFileNamesFor

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

Assemble the filename for the corresponding file based on the indices for time, channel, illumination and angle If the fileNamePattern is separated by ';', it will return multiple solutions for each filenamepattern

Parameters:: fileNames -; replaceTimepoints -; replaceChannels -; replaceIlluminations -; replaceAngles -; tpName -; chName -; illName -; angleName -; numDigitsTP -; numDigitsCh -; numDigitsIll -; numDigitsAngle -
Returns:

leadingZeros

public static String leadingZeros(String s,
                                  int numDigits)

loadFirstCalibration
```
protected boolean loadFirstCalibration()
```
populates the fields calX, calY, calZ from the first file of the series

Returns:

- true if successful

loadAllCalibrations
```
protected boolean loadAllCalibrations()
```
populates the fields calX, calY, calZ from the first file of the series

Returns:

- true if successful

loadCalibration
```
protected abstract StackList.Calibration loadCalibration(File file)
```
Loads the calibration stored in a specific file and closes it afterwards. Depends on the type of opener that is used.

Parameters:

file -

Returns:

- the Calibration or null if it could not be loaded for some reason

assembleDefaultPattern

protected String assembleDefaultPattern()

queryGeneralInformation

protected boolean queryGeneralInformation()

Class StackList

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface spim.fiji.datasetmanager.MultiViewDatasetDefinition

Field Detail

TIMEPOINT_PATTERN

CHANNEL_PATTERN

ILLUMINATION_PATTERN

ANGLE_PATTERN

dimensionChoiceTimePointsTrue

dimensionChoiceTimePointsFalse

dimensionChoiceChannelsTrue

dimensionChoiceChannelsFalse

dimensionChoiceIlluminationsTrue

dimensionChoiceIlluminationsFalse

dimensionChoiceAnglesTrue

dimensionChoiceAnglesFalse

hasMultipleAngles

hasMultipleTimePoints

hasMultipleChannels

hasMultipleIlluminations

showDebugFileNames

defaultTimepoints

defaultChannels

defaultIlluminations

defaultAngles

timepoints

channels

illuminations

angles

timepointNameList

channelNameList

illuminationsNameList

angleNameList

replaceTimepoints

replaceChannels

replaceIlluminations

replaceAngles

numDigitsTimepoints

numDigitsChannels

numDigitsIlluminations

numDigitsAngles

exceptionIds

calibrationChoice1

calibrationChoice2

imglib2Container

defaultContainer

imgFactory

defaultCalibration1

defaultCalibration2

calibration1

calibration2

calibrations

defaultDirectory

defaultFileNamePattern

directory

fileNamePattern

Constructor Detail

StackList