SCIFIOConfig (SCIFIO Core 0.48.0 API)

java.lang.Object
- java.util.AbstractMap<K,V>
- - java.util.HashMap<String,Object>
  - - io.scif.config.SCIFIOConfig

All Implemented Interfaces:

Serializable, Cloneable, Map<String,Object>
```
public class SCIFIOConfig
extends HashMap<String,Object>
```
Configuration class for all SCIFIO components. Similar to a Context, this class is effectively a container for state. However, its intended scope is per method call stack, and not through a complete application. If any object in a call stack has behavior that can be modified through this class, a complete method chain accepting SCIFIOConfig instances should be available - even if the intermediate classes do not require configuration (the need for configuration is, effectively contagious).
Note that each getter and setter method signature in this class is prefixed by the component it affects.

Author:

Mark Hiner

See Also:

Checker, Parser, Writer, Groupable, ImgOpener, ImgSaver, Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class SCIFIOConfig.ImgMode
Access type options for opening datasets.
- Nested classes/interfaces inherited from class java.util.AbstractMap
  AbstractMap.SimpleEntry<K,V>, AbstractMap.SimpleImmutableEntry<K,V>
- Nested classes/interfaces inherited from interface java.util.Map
  Map.Entry<K,V>

Nested Classes
Modifier and Type	Class and Description
`static class`	`SCIFIOConfig.ImgMode` Access type options for opening datasets.

Constructor Summary

Constructors
Constructor and Description
`SCIFIOConfig()` Zero-param constructor.
`SCIFIOConfig(org.scijava.Context context)` Context-injecting constructor.
`SCIFIOConfig(SCIFIOConfig config)` Copying constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`bufferedReadingEnabled()`
`boolean`	`checkerIsOpen()`
`SCIFIOConfig`	`checkerSetOpen(boolean open)`
`SCIFIOConfig`	`clone()`
`SCIFIOConfig`	`enableBufferedReading(boolean enabled)`
`boolean`	`groupableIsGroupFiles()`
`SCIFIOConfig`	`groupableSetGroupFiles(boolean groupFiles)`
`ImgFactoryHeuristic`	`imgOpenerGetImgFactoryHeuristic()`
`SCIFIOConfig.ImgMode[]`	`imgOpenerGetImgModes()`
`PlaneConverter`	`imgOpenerGetPlaneConverter()`
`Range`	`imgOpenerGetRange()`
`ImageRegion`	`imgOpenerGetRegion()` Returns a `ImageRegion` specifying dimension constraints.
`boolean`	`imgOpenerIsComputeMinMax()`
`boolean`	`imgOpenerIsOpenAllImages()`
`SCIFIOConfig`	`imgOpenerSetComputeMinMax(boolean computeMinMax)`
`SCIFIOConfig`	`imgOpenerSetImgFactoryHeuristic(ImgFactoryHeuristic imgFactoryHeuristic)`
`SCIFIOConfig`	`imgOpenerSetImgModes(SCIFIOConfig.ImgMode... imgModes)`
`SCIFIOConfig`	`imgOpenerSetIndex(int index)`
`SCIFIOConfig`	`imgOpenerSetOpenAllImages(boolean openAll)`
`SCIFIOConfig`	`imgOpenerSetPlaneConverter(PlaneConverter planeConverter)`
`SCIFIOConfig`	`imgOpenerSetRange(Range range)`
`SCIFIOConfig`	`imgOpenerSetRange(String range)`
`SCIFIOConfig`	`imgOpenerSetRegion(ImageRegion region)`
`boolean`	`imgSaverGetWriteRGB()`
`SCIFIOConfig`	`imgSaverSetWriteRGB(boolean rgb)`
`MetadataLevel`	`parserGetLevel()`
`boolean`	`parserIsFiltered()`
`boolean`	`parserIsSaveOriginalMetadata()`
`SCIFIOConfig`	`parserSetFiltered(boolean filterMetadata)`
`SCIFIOConfig`	`parserSetLevel(MetadataLevel level)`
`SCIFIOConfig`	`parserSetSaveOriginalMetadata(boolean saveOriginalMetadata)`
`CodecOptions`	`writerGetCodecOptions()`
`ColorModel`	`writerGetColorModel()`
`String`	`writerGetCompression()`
`boolean`	`writerGetFailIfOverwriting()`
`int`	`writerGetFramesPerSecond()`
`boolean`	`writerIsSequential()`
`SCIFIOConfig`	`writerSetCodecOptions(CodecOptions options)`
`SCIFIOConfig`	`writerSetColorModel(ColorModel cm)`
`SCIFIOConfig`	`writerSetCompression(CompressionType compressType)`
`SCIFIOConfig`	`writerSetCompression(String compress)`
`SCIFIOConfig`	`writerSetFailIfOverwriting(boolean failIfOverwriting)` Warning: "overwriting" behavior is format-specific and not guaranteed to result in a valid image.
`SCIFIOConfig`	`writerSetFramesPerSecond(int rate)`
`SCIFIOConfig`	`writerSetSequential(boolean sequential)` Sets whether or not we know that planes will be written sequentially.

Methods inherited from class java.util.HashMap
clear, compute, computeIfAbsent, computeIfPresent, containsKey, containsValue, entrySet, forEach, get, getOrDefault, isEmpty, keySet, merge, put, putAll, putIfAbsent, remove, remove, replace, replace, replaceAll, size, values

Methods inherited from class java.util.AbstractMap
equals, hashCode, toString

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map
equals, hashCode

- Constructor Detail
  - SCIFIOConfig
```
public SCIFIOConfig()
```
    Zero-param constructor. Creates an empty configuration.
  - SCIFIOConfig
```
public SCIFIOConfig(org.scijava.Context context)
```
    Context-injecting constructor. Injects context into the given SCIFIOConfig.
    
    Parameters:
    
    context - Context to inject
  - SCIFIOConfig
```
public SCIFIOConfig(SCIFIOConfig config)
```
    Copying constructor. Returns a copy of the given SCIFIOConfig.
    
    Parameters:
    
    config - Configuration to copy.
- Method Detail
  - enableBufferedReading
```
public SCIFIOConfig enableBufferedReading(boolean enabled)
```
  - bufferedReadingEnabled
```
public boolean bufferedReadingEnabled()
```
  - checkerSetOpen
```
public SCIFIOConfig checkerSetOpen(boolean open)
```
  - checkerIsOpen
```
public boolean checkerIsOpen()
```
  - parserGetLevel
```
public MetadataLevel parserGetLevel()
```
    Returns:
    
    MetadataLevel desired for parsing.
  - parserSetLevel
```
public SCIFIOConfig parserSetLevel(MetadataLevel level)
```
    Parameters:
    
    level - Desired metadata level for parsing.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - parserIsFiltered
```
public boolean parserIsFiltered()
```
    Returns:
    
    True if parsers should filter parsed metadata.
  - parserSetFiltered
```
public SCIFIOConfig parserSetFiltered(boolean filterMetadata)
```
    Parameters:
    
    filterMetadata - Desired filtering behavior for parsing.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - parserIsSaveOriginalMetadata
```
public boolean parserIsSaveOriginalMetadata()
```
    Returns:
    
    True if parsers should save original metadata.
  - parserSetSaveOriginalMetadata
```
public SCIFIOConfig parserSetSaveOriginalMetadata(boolean saveOriginalMetadata)
```
    Parameters:
    
    saveOriginalMetadata - Desired metadata saving behavior for parsing.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - writerSetFailIfOverwriting
```
public SCIFIOConfig writerSetFailIfOverwriting(boolean failIfOverwriting)
```
    Warning: "overwriting" behavior is format-specific and not guaranteed to result in a valid image.
    
    Parameters:
    
    failIfOverwriting - Whether or not an exception should be raised if the writer's destination already exists. Default: true
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - writerGetFailIfOverwriting
```
public boolean writerGetFailIfOverwriting()
```
    Returns:
    
    Whether or not an exception should be raised if the writer's destination already exists.
  - writerSetSequential
```
public SCIFIOConfig writerSetSequential(boolean sequential)
```
    Sets whether or not we know that planes will be written sequentially. If planes are written sequentially and this flag is set, then performance will be slightly improved.
    
    Parameters:
    
    sequential - Flag for writing sequential planes.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - writerIsSequential
```
public boolean writerIsSequential()
```
    Returns:
    
    True if writers should write image planes sequentially.
  - writerSetColorModel
```
public SCIFIOConfig writerSetColorModel(ColorModel cm)
```
    Parameters:
    
    cm - ColorModel to use for writing.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - writerGetColorModel
```
public ColorModel writerGetColorModel()
```
    Returns:
    
    The ColorModel to use when writing.
  - writerSetFramesPerSecond
```
public SCIFIOConfig writerSetFramesPerSecond(int rate)
```
    Parameters:
    
    rate - Desired frames per second to use when writing.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - writerGetFramesPerSecond
```
public int writerGetFramesPerSecond()
```
    Returns:
    
    The number of frames per second to use when writing.
  - writerSetCompression
```
public SCIFIOConfig writerSetCompression(String compress)
```
    Parameters:
    
    compress - Desired compression type to use when writing.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - writerSetCompression
```
public SCIFIOConfig writerSetCompression(CompressionType compressType)
```
    Parameters:
    
    compressType -
    
    Returns:
  - writerGetCompression
```
public String writerGetCompression()
```
    Returns:
    
    The compression type writers will use when writing.
  - writerSetCodecOptions
```
public SCIFIOConfig writerSetCodecOptions(CodecOptions options)
```
    Parameters:
    
    options - Desired CodecOptions to use for writing.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - writerGetCodecOptions
```
public CodecOptions writerGetCodecOptions()
```
    Returns:
    
    The CodecOptions that writers will use when writing.
  - groupableSetGroupFiles
```
public SCIFIOConfig groupableSetGroupFiles(boolean groupFiles)
```
    Parameters:
    
    groupFiles - Desired behavior for grouping potential multi-file datasets. If true, these will be grouped into one single dataset.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - groupableIsGroupFiles
```
public boolean groupableIsGroupFiles()
```
    Returns:
    
    Whether or not Groupable classes should group similar files when operating on them.
  - imgOpenerGetImgModes
```
public SCIFIOConfig.ImgMode[] imgOpenerGetImgModes()
```
    Returns:
    
    The access type to attempt to open the dataset with. Default: imgMode.AUTO, which allows the calling program to decide.
  - imgOpenerSetImgModes
```
public SCIFIOConfig imgOpenerSetImgModes(SCIFIOConfig.ImgMode... imgModes)
```
    Parameters:
    
    imgModes - A list of ImgMode access types. How these are interpreted is up to the ImgFactoryHeuristic, but it is reasonable to expect modes listed earlier to be preferred.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - imgOpenerIsComputeMinMax
```
public boolean imgOpenerIsComputeMinMax()
```
    Returns:
    
    True if the image should be scaled to its min and max intensities. Default: false
  - imgOpenerSetComputeMinMax
```
public SCIFIOConfig imgOpenerSetComputeMinMax(boolean computeMinMax)
```
    Parameters:
    
    computeMinMax - Whether or not images should be scaled to min/max intensities.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - imgOpenerGetRegion
```
public ImageRegion imgOpenerGetRegion()
```
    Returns a ImageRegion specifying dimension constraints. This may be of a different dimensionality than the underlying image, in which case the lengths are assume to be in the natural ordering of the image.
    
    Returns:
    
    A Subregion specifying dimension offsets and lengths. Default: null
  - imgOpenerSetRegion
```
public SCIFIOConfig imgOpenerSetRegion(ImageRegion region)
```
    Parameters:
    
    region - Region constraints for any image to open
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - imgOpenerGetPlaneConverter
```
public PlaneConverter imgOpenerGetPlaneConverter()
```
    Returns:
    
    A custom plane converter. Default: null
  - imgOpenerSetPlaneConverter
```
public SCIFIOConfig imgOpenerSetPlaneConverter(PlaneConverter planeConverter)
```
    Parameters:
    
    planeConverter - Sets a PlaneConverter to use when opening datasets. This is useful when using a custom Img type.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - imgOpenerGetImgFactoryHeuristic
```
public ImgFactoryHeuristic imgOpenerGetImgFactoryHeuristic()
```
    Returns:
    
    The ImgFactoryHeuristic to use when selecting an ImgFactory. Default: null
  - imgOpenerSetImgFactoryHeuristic
```
public SCIFIOConfig imgOpenerSetImgFactoryHeuristic(ImgFactoryHeuristic imgFactoryHeuristic)
```
    Parameters:
    
    imgFactoryHeuristic - Heuristic to use when selecting an ImgFactory. Will not be used if an ImgFactory is provided to the ImgOpener.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - imgOpenerIsOpenAllImages
```
public boolean imgOpenerIsOpenAllImages()
```
    Returns:
    
    True if all available images should be opened. Useful if the actual range of available images is not known.
  - imgOpenerSetOpenAllImages
```
public SCIFIOConfig imgOpenerSetOpenAllImages(boolean openAll)
```
    Parameters:
    
    openAll - Whether or not all available images should be opened. Default: false.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - imgOpenerGetRange
```
public Range imgOpenerGetRange()
```
    Returns:
    
    The image range to be opened. Default: [0]
  - imgOpenerSetIndex
```
public SCIFIOConfig imgOpenerSetIndex(int index)
```
    Parameters:
    
    index - Image index within the dataset to open
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - imgOpenerSetRange
```
public SCIFIOConfig imgOpenerSetRange(String range)
```
    Parameters:
    
    range - Range of image indices to open.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
    
    Throws:
    
    IllegalArgumentException - If a valid Range can not be parsed.
  - imgOpenerSetRange
```
public SCIFIOConfig imgOpenerSetRange(Range range)
```
    Parameters:
    
    range - Image index to open.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
    
    Throws:
    
    IllegalArgumentException - If index < 0
  - imgSaverGetWriteRGB
```
public boolean imgSaverGetWriteRGB()
```
    Returns:
    
    True if channels should be composited during ImgSaver operation.
  - imgSaverSetWriteRGB
```
public SCIFIOConfig imgSaverSetWriteRGB(boolean rgb)
```
    Parameters:
    
    rgb - Whether or not the ImgSaver should composite channels when writing.
    
    Returns:
    
    This SCIFIOConfig for method chaining.
  - clone
```
public SCIFIOConfig clone()
```
    Overrides:
    
    clone in class HashMap<String,Object>

Class SCIFIOConfig

Nested Class Summary

Nested classes/interfaces inherited from class java.util.AbstractMap

Nested classes/interfaces inherited from interface java.util.Map

Constructor Summary

Method Summary

Methods inherited from class java.util.HashMap

Methods inherited from class java.util.AbstractMap

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Map

Constructor Detail

SCIFIOConfig

SCIFIOConfig

SCIFIOConfig

Method Detail

enableBufferedReading

bufferedReadingEnabled

checkerSetOpen

checkerIsOpen

parserGetLevel

parserSetLevel

parserIsFiltered

parserSetFiltered

parserIsSaveOriginalMetadata

parserSetSaveOriginalMetadata

writerSetFailIfOverwriting

writerGetFailIfOverwriting

writerSetSequential

writerIsSequential

writerSetColorModel

writerGetColorModel

writerSetFramesPerSecond

writerGetFramesPerSecond

writerSetCompression

writerSetCompression

writerGetCompression

writerSetCodecOptions

writerGetCodecOptions

groupableSetGroupFiles

groupableIsGroupFiles

imgOpenerGetImgModes

imgOpenerSetImgModes

imgOpenerIsComputeMinMax

imgOpenerSetComputeMinMax

imgOpenerGetRegion

imgOpenerSetRegion

imgOpenerGetPlaneConverter

imgOpenerSetPlaneConverter

imgOpenerGetImgFactoryHeuristic

imgOpenerSetImgFactoryHeuristic

imgOpenerIsOpenAllImages

imgOpenerSetOpenAllImages

imgOpenerGetRange

imgOpenerSetIndex

imgOpenerSetRange

imgOpenerSetRange

imgSaverGetWriteRGB

imgSaverSetWriteRGB

clone