SlideSet (Slide Set: Batch Processing for ImageJ 1.6.1

java.lang.Object
- org.nanes.slideset.SlideSet

```
public class SlideSet
extends Object
```
Slide Set API documentation

Introduction
Slide Set is a framework for batch processing and analysis of image data using ImageJ. It consists of interconnected components at four levels:
1. A data model storing analysis inputs and results as a hierarchy of tables (SlideSet class);
2. Connections linking the data model to Slide Set-specific analysis commands and general ImageJ plugins (dm package);
3. A set of core Slide Set analysis commands (pi package); and
4. A graphical user interface wrapper (using Java Swing; ui package).
The Slide Set core provides a complete workflow for basic image analysis tasks repeated over multiple images and associated data, such as regions of interest and treatment group identifiers. However, Slide Set is also designed to be extensible, and can be leveraged to facilitate the automation and recording of custom image analysis tasks.

Extensions are possible at levels 2 through 4. Slide Set commands are discovered at run-time, and custom commands can be added using a simple variant of the ImageJ version 2 Command API. Many general ImageJ plugins developed using the version 2 API can also be used with Slide Set, provided appropriate ElementReaders and ElementWriters are available to link the data types of the plugins' input and output values to the Slide Set data model. If appropriate linkers are not available in the Slide Set core, custom ElementReaders and ElementWriters can be developed, and, as with custom Slide Set commands, loaded at run-time. Finally, the data model and plugins have no dependencies on the user interface, and can be used programmatically or wrapped with different user controls. The set of DataElements used in Slide Set tables is currently fixed, but dynamically loaded extensions may be possible in future releases.

The Slide Set data model

Slide Set projects organize data into tables, represented by the SlideSet class. Fields are represented as table columns, and entries are represented as table rows. Commands are run by matching table columns to the command inputs, then repeating the command with the inputs set to each row of values in the table. Command results are then stored in a new table, linked as a "child" to the input table "parent." Columns are therefore typed; each element in the column must represent the same kind of data.

SlideSet table elements are represented by descendants of the DataElement class. Each element contains "underlying" data, methods for converting the underlying data to and from a String (used to save Slide Set table data as XML and CSV files), and an additional parameter representing the data's MIME type. The underlying type and String conversion methods are determined by the DataElement class, while the MIME type String is independent. Thus, elements representing image files and ROI set files may use the same DataElement class, with an underlying data String containing the path to the relevant file, but they will have different values for their MIME type Strings. In order for two DataElements to be of the same overall data type (and therefore column-compatible), they must both be instances of the same DataElement class and have the same value set for their MIME type.

The underlying data is not passed directly to or from commands. Rather, it is interpreted through ElementReaders and ElementWriters which translate between the data representation in the table (ex.: an image file path String) and the actual data used by the command (ex.: a Dataset representing the actual image data). This data form used by commands is called the "processed" type to distinguish it from the DataElement's underlying data type. ElementReaders and ElementWriters contain annotations specifying the DataElement classes and MIME types with which they are compatible, allowing a relatively limited number of DataElement types to wrap many different kinds of information.

In addition to the DataElements, SlideSets contain metadata specifying the name, DataElement class, and MIME type associated with each column, the "working directory" of the table (used to resolve relative paths; generally the directory where the project XML file is saved), a list of parameters used to create the table (set only for tables which are created to store the results of commands), a table name, a reference to the parent table, and references to any child tables.
Further information
- Linking Slide Set tables to commands (DataTypeIDService)
- Slide Set commands (SlideSetPlugin)
- Managing command execution (SlideSetPluginLoader)
Author:

Benjamin Nanes

Field Summary

Fields
Modifier and Type	Field and Description
`private ArrayList<SlideSet>`	`children` Children of this `SlideSet`
`private ArrayList<LinkedHashMap<String,String>>`	`columnProperties` Index of column properties: elementClass - Name of DataElement subclass used mimeType - MIME type used name - Name associated with the column (required) defaultPath - Default relative path for this column (relevant for links only) defaultLinkPrefix - Prefix for generating default links (ex.
`private ArrayList<ArrayList<DataElement>>`	`columns` Columns in the SlideSet
`private CommandTemplate`	`commandTemplate` Command template data
`private LinkedHashMap<String,String>`	`creationParams` The input parameters used in the creation of this `SlideSet`
`private String`	`dir` Working directory of this `SlideSet`
`private DataTypeIDService`	`dtid` DataTypeIDService reference
`private net.imagej.ImageJ`	`ij` ImageJ context reference
`private boolean`	`locked` Is this `SlideSet` locked?
`private String`	`name` Name of this `SlideSet`
`private int`	`numRows` Number of rows in the SlideSet
`private SlideSet`	`parent` Parent of this `SlideSet`

Constructor Summary

Constructors
Constructor and Description

SlideSet(net.imagej.ImageJ context, DataTypeIDService dtid)

Constructors
Constructor and Description
`SlideSet(net.imagej.ImageJ context, DataTypeIDService dtid)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addChild(SlideSet child)` Register a `SlideSet` as the child of this `SlideSet`
`int`	`addColumn(LinkedHashMap<String,String> properties)` Add an empty column
`int`	`addColumn(LinkedHashMap<String,String> properties, ArrayList<DataElement<?>> data)` Add a column with data
`int`	`addColumn(String name, Class<? extends DataElement> elementClass)` Add an empty column with no (`null`) MIME type.
`int`	`addColumn(String name, Class<? extends DataElement> elementClass, String mimeType)` Add an empty column.
`int`	`addColumn(String name, String elementClass)` Add an empty column with no (`null`) MIME type.
`int`	`addColumn(String name, String elementClass, String mimeType)` Add an empty column.
`int`	`addRow()` Add a row with default values
`int`	`addRow(List<DataElement> data)` Add a row from a `List` of `DataElement`s.
`private boolean`	`checkBounds(int column, int row)` Check validity of an index pair
`private boolean`	`checkColumnBounds(int index)` Check validity of a column index
`private boolean`	`checkColumnElementConsistency(int column)` Check if all the `DataElement`s in this column are of the same type and have the same MIME type set.
`private boolean`	`checkColumnLengths()` Check to make sure each column is of equal length
`private boolean`	`checkDataElementCompatibility(int column, DataElement<?> element)` Check if the class and MIME type of a `DataElement` match those of a column in this table.
`private boolean`	`checkRowBounds(int index)` Check validity of a row index
`private boolean`	`checkUnderlyingCompatability(int column, Object underlying)` Check if an object may be stored in a column directly using a `setUnderlying()` method (i.e.
`void`	`convertColumn(int index, Class<? extends DataElement<?>> elementType, String mimeType)` Convert the data type stored in a column.
`private String`	`generateDefaultLinkPath(int column, int row)` Generate a default link path for a specified cell.
`ArrayList<SlideSet>`	`getChildren()` Get a list of this `SlideSet`'s children
`String`	`getColumnDefaultPath(int index)` Get the default relative path associated with the column.
`private Class<? extends DataElement<?>>`	`getColumnElementClass(int index)`
`Class<? extends DataElement>`	`getColumnElementType(int index)` Get the `DataElement` type used in a column.
`int`	`getColumnIndex(String name)` Get the index of the first column with a matching name, or -1 if no such column
`String`	`getColumnMimeType(int index)` Get the column MIME type
`String`	`getColumnName(int index)` Get the name of a column
`LinkedHashMap<String,String>`	`getColumnProperties(int index)` Get the properties of a column
`String`	`getColumnTypeName(int index)` Get a human-readable name for the data type of a column.
`Class<?>`	`getColumnUnderlyingType(int index)` Get the underlying type used to store data in a column.
`CommandTemplate`	`getCommandTemplate()` Get the command template data for this `SlideSet`
`org.scijava.Context`	`getContext()` Get the SciJava application `Context`
`LinkedHashMap<String,String>`	`getCreationParams()` Get the creation parameters of this `SlideSet`
`DataElement`	`getDataElement(int column, int row)` Get a `DataElement`
`int`	`getDefaultLinkCount(int column)` Get the counter for default links for a column.
`String`	`getDefaultLinkExtension(int column)` Get the default link extension for a column.
`String`	`getDefaultLinkPrefix(int column)` Get the prefix for default links for a column.
`String`	`getItemText(int column, int row)` Get a text representation of an item, i.e.
`String`	`getName()` Get the name of this `SlideSet`
`private DataElement<?>`	`getNewColumnElement(int index)` Generate a new `DataElement` appropriate for the selected column.
`int`	`getNumCols()` Get the number of columns
`int`	`getNumRows()` Get the number of rows
`SlideSet`	`getParent()` Get the parent of this `SlideSet`
`Object`	`getUnderlying(int column, int row)` Get an item as the underlying data object, i.e.
`String`	`getWorkingDirectory()` Get the working directory of this `SlideSet`
`boolean`	`isLocked()` Is the read-only flag set on this `SlideSet`?
`void`	`makeDefaultLink(int column, int row)` Set a cell to an auto-generated link
`void`	`removeChild(SlideSet child)` Remove a `SlideSet` as a child of this `SlideSet`
`void`	`removeColumn(int index)` Remove a column
`void`	`removeRow(int index)` Remove a row
`String`	`resolvePath(String path)` Resolve a possibly abstract path using this `SlideSet`'s working directory.
`void`	`setColumnDefaultPath(int index, String path)` Set the default relative path associated with the column.
`void`	`setColumnMimeType(int index, String type)` Set the column MIME type
`void`	`setColumnName(int index, String name)` Set the name of a column
`void`	`setCommandTemplate(CommandTemplate ct)` Set the command template data for this `SlideSet`
`void`	`setCreationParams(LinkedHashMap parameters)` Set the creation parameters of this `SlideSet`
`void`	`setDefaultLinkCount(int column, int counter)` Set the counter for default links for a column.
`void`	`setDefaultLinkExtension(int column, String extension)` Set the default link extension for a column.
`void`	`setDefaultLinkPrefix(int column, String prefix)` Set the prefix for default links for a column.
`void`	`setLock(boolean lock)` Set the read-only flag for this `SlideSet`.
`void`	`setName(String name)` Set the name of this `SlideSet`
`void`	`setParent(SlideSet parent)` Register a `SlideSet` as the parent of this `SlideSet`
`void`	`setUnderlying(int column, int row, Object underlying)` Change the underlying table-stored value of an item.
`void`	`setWorkingDirectory(String path)` Set the working directory of this `SlideSet`
`String`	`toString()` Get the name of this `SlideSet`

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

- Field Detail
  - columns
```
private ArrayList<ArrayList<DataElement>> columns
```
    Columns in the SlideSet
  - columnProperties
```
private ArrayList<LinkedHashMap<String,String>> columnProperties
```
    Index of column properties:
    - elementClass - Name of DataElement subclass used
    - mimeType - MIME type used
    - name - Name associated with the column (required)
    - defaultPath - Default relative path for this column (relevant for links only)
    - defaultLinkPrefix - Prefix for generating default links (ex. file-01.xml)
    - defaultLinkCount - Index counter for generating default links (ex. file-01.xml)
    - defaultLinkExtension - Extension for generating default links (ex. file-01.xml)
  - numRows
```
private int numRows
```
    Number of rows in the SlideSet
  - parent
```
private SlideSet parent
```
    Parent of this SlideSet
  - children
```
private ArrayList<SlideSet> children
```
    Children of this SlideSet
  - creationParams
```
private LinkedHashMap<String,String> creationParams
```
    The input parameters used in the creation of this SlideSet
  - name
```
private String name
```
    Name of this SlideSet
  - dir
```
private String dir
```
    Working directory of this SlideSet
  - locked
```
private boolean locked
```
    Is this SlideSet locked?
  - commandTemplate
```
private CommandTemplate commandTemplate
```
    Command template data
  - ij
```
private net.imagej.ImageJ ij
```
    ImageJ context reference
  - dtid
```
private DataTypeIDService dtid
```
    DataTypeIDService reference
- Constructor Detail
  - SlideSet
```
public SlideSet(net.imagej.ImageJ context,
                DataTypeIDService dtid)
```
- Method Detail
  - getNumCols
```
public int getNumCols()
```
    Get the number of columns
  - getNumRows
```
public int getNumRows()
```
    Get the number of rows
  - getDataElement
```
public DataElement getDataElement(int column,
                                  int row)
```
    Get a DataElement
  - getUnderlying
```
public Object getUnderlying(int column,
                            int row)
```
    Get an item as the underlying data object, i.e. for editing in a table
  - getItemText
```
public String getItemText(int column,
                          int row)
```
    Get a text representation of an item, i.e. for writing to a file
  - getColumnProperties
```
public LinkedHashMap<String,String> getColumnProperties(int index)
```
    Get the properties of a column
  - getColumnName
```
public String getColumnName(int index)
```
    Get the name of a column
  - setColumnName
```
public void setColumnName(int index,
                          String name)
```
    Set the name of a column
  - getColumnMimeType
```
public String getColumnMimeType(int index)
```
    Get the column MIME type
  - setColumnMimeType
```
public void setColumnMimeType(int index,
                              String type)
```
    Set the column MIME type
  - getColumnTypeName
```
public String getColumnTypeName(int index)
```
    Get a human-readable name for the data type of a column.
  - getColumnUnderlyingType
```
public Class<?> getColumnUnderlyingType(int index)
                                 throws SlideSetException
```
    Get the underlying type used to store data in a column.
    
    Throws:
    
    SlideSetException
  - getColumnElementType
```
public Class<? extends DataElement> getColumnElementType(int index)
                                                  throws SlideSetException
```
    Get the DataElement type used in a column.
    
    Throws:
    
    SlideSetException
  - getColumnIndex
```
public int getColumnIndex(String name)
```
    Get the index of the first column with a matching name, or -1 if no such column
  - getColumnDefaultPath
```
public String getColumnDefaultPath(int index)
```
    Get the default relative path associated with the column. May be null.
    This property is used for auto-generating new links. Not relevant for columns in which the data is stored directly (i.e. String, int, etc.).
  - setColumnDefaultPath
```
public void setColumnDefaultPath(int index,
                                 String path)
```
    Set the default relative path associated with the column. May be null.
    This property is used for auto-generating new links. Not relevant for columns in which the data is stored directly (i.e. String, int, etc.).
  - setUnderlying
```
public void setUnderlying(int column,
                          int row,
                          Object underlying)
                   throws SlideSetException
```
    Change the underlying table-stored value of an item. Can use Object of matching class.
    
    Throws:
    
    SlideSetException
  - addColumn
```
public int addColumn(LinkedHashMap<String,String> properties)
              throws SlideSetException
```
    Add an empty column
    
    Parameters:
    
    properties - Column properties
    
    Returns:
    
    The column index of the new column
    
    Throws:
    
    SlideSetException
  - addColumn
```
public int addColumn(String name,
                     String elementClass)
              throws SlideSetException
```
    Add an empty column with no (null) MIME type.
    
    Parameters:
    
    name - Label for the column
    
    elementClass - Name of the DataElement type to use for this column
    
    Returns:
    
    Index of the newly created column
    
    Throws:
    
    SlideSetException
  - addColumn
```
public int addColumn(String name,
                     Class<? extends DataElement> elementClass)
              throws SlideSetException
```
    Add an empty column with no (null) MIME type.
    
    Parameters:
    
    name - Label for the column
    
    elementClass - DataElement type to use for this column
    
    Returns:
    
    Index of the newly created column
    
    Throws:
    
    SlideSetException
  - addColumn
```
public int addColumn(String name,
                     String elementClass,
                     String mimeType)
              throws SlideSetException
```
    Add an empty column.
    
    Parameters:
    
    name - Label for the column
    
    elementClass - Name of the DataElement type to use for this column
    
    mimeType - MIME type to associate with the column
    
    Returns:
    
    Index of the newly created column
    
    Throws:
    
    SlideSetException
  - addColumn
```
public int addColumn(String name,
                     Class<? extends DataElement> elementClass,
                     String mimeType)
              throws SlideSetException
```
    Add an empty column.
    
    Parameters:
    
    name - Label for the column
    
    elementClass - DataElement type to use for this column
    
    mimeType - MIME type to associate with the column
    
    Returns:
    
    Index of the newly created column
    
    Throws:
    
    SlideSetException
  - addColumn
```
public int addColumn(LinkedHashMap<String,String> properties,
                     ArrayList<DataElement<?>> data)
              throws SlideSetException
```
    Add a column with data
    
    Parameters:
    
    properties - Column properties
    
    data - An ArrayList of the DataElements in the column
    
    Returns:
    
    The column index of the new column
    
    Throws:
    
    SlideSetException
  - removeColumn
```
public void removeColumn(int index)
```
    Remove a column
    Note that columns are re-indexed after a deletion, so if this function is called repeatedly, indeces should be given from high to low.
  - convertColumn
```
public void convertColumn(int index,
                          Class<? extends DataElement<?>> elementType,
                          String mimeType)
                   throws SlideSetException
```
    Convert the data type stored in a column. If the column contains any DataElements, they are converted through String intermediates.
    
    Parameters:
    
    index - Column to convert
    
    elementType - Target DataElement
    
    mimeType - Target MIME type
    
    Throws:
    
    SlideSetException - If the conversion is aborted, usually because the target data type is not compatible with pre-existing data.
    
    See Also:
    
    DataElement.getUnderlyingText(), DataElement.setUnderlyingText(java.lang.String)
  - addRow
```
public int addRow()
           throws SlideSetException
```
    Add a row with default values
    
    Returns:
    
    The row index of the new row
    
    Throws:
    
    SlideSetException
  - addRow
```
public int addRow(List<DataElement> data)
           throws SlideSetException
```
    Add a row from a List of DataElements. The DataElement types must match the column types.
    
    Returns:
    
    The row index of the new row
    
    Throws:
    
    SlideSetException
    
    See Also:
    
    checkUnderlyingCompatability(int, java.lang.Object)
  - removeRow
```
public void removeRow(int index)
```
    Remove a row
    Note that rows are re-indexed after a deletion, so if this function is called repeatedly, indeces should be given from hight to low.
  - getParent
```
public SlideSet getParent()
```
    Get the parent of this SlideSet
  - setParent
```
public void setParent(SlideSet parent)
```
    Register a SlideSet as the parent of this SlideSet
  - getChildren
```
public ArrayList<SlideSet> getChildren()
```
    Get a list of this SlideSet's children
  - addChild
```
public void addChild(SlideSet child)
```
    Register a SlideSet as the child of this SlideSet
  - removeChild
```
public void removeChild(SlideSet child)
                 throws SlideSetException
```
    Remove a SlideSet as a child of this SlideSet
    
    Throws:
    
    SlideSetException
  - getName
```
public String getName()
```
    Get the name of this SlideSet
  - toString
```
public String toString()
```
    Get the name of this SlideSet
    
    Overrides:
    
    toString in class Object
  - setName
```
public void setName(String name)
```
    Set the name of this SlideSet
  - getCreationParams
```
public LinkedHashMap<String,String> getCreationParams()
```
    Get the creation parameters of this SlideSet
  - setCreationParams
```
public void setCreationParams(LinkedHashMap parameters)
```
    Set the creation parameters of this SlideSet
  - getCommandTemplate
```
public CommandTemplate getCommandTemplate()
```
    Get the command template data for this SlideSet
  - setCommandTemplate
```
public void setCommandTemplate(CommandTemplate ct)
```
    Set the command template data for this SlideSet
  - getWorkingDirectory
```
public String getWorkingDirectory()
```
    Get the working directory of this SlideSet
  - setWorkingDirectory
```
public void setWorkingDirectory(String path)
```
    Set the working directory of this SlideSet
  - getContext
```
public org.scijava.Context getContext()
```
    Get the SciJava application Context
  - getDefaultLinkPrefix
```
public String getDefaultLinkPrefix(int column)
```
    Get the prefix for default links for a column. null if unset.
    ex. file-01.xml
  - setDefaultLinkPrefix
```
public void setDefaultLinkPrefix(int column,
                                 String prefix)
```
    Set the prefix for default links for a column.
    ex. file-01.xml
  - getDefaultLinkCount
```
public int getDefaultLinkCount(int column)
```
    Get the counter for default links for a column. null if unset.
    ex. file-01.xml
  - setDefaultLinkCount
```
public void setDefaultLinkCount(int column,
                                int counter)
```
    Set the counter for default links for a column.
    ex. file-01.xml
  - getDefaultLinkExtension
```
public String getDefaultLinkExtension(int column)
```
    Get the default link extension for a column. null if unset.
    ex. file-01.xml
  - setDefaultLinkExtension
```
public void setDefaultLinkExtension(int column,
                                    String extension)
```
    Set the default link extension for a column.
    ex. file-01.xml
  - resolvePath
```
public String resolvePath(String path)
```
    Resolve a possibly abstract path using this SlideSet's working directory.
  - makeDefaultLink
```
public void makeDefaultLink(int column,
                            int row)
                     throws SlideSetException
```
    Set a cell to an auto-generated link
    
    Parameters:
    
    column -
    
    row -
    
    Throws:
    
    DefaultPathNotSetException
    
    SlideSetException
  - isLocked
```
public boolean isLocked()
```
    Is the read-only flag set on this SlideSet?
  - setLock
```
public void setLock(boolean lock)
```
    Set the read-only flag for this SlideSet. Note that setting the flag will not actually prevent changes to the table, but it intended to be used as a signal for the UI.
  - checkColumnBounds
```
private boolean checkColumnBounds(int index)
```
    Check validity of a column index
  - checkRowBounds
```
private boolean checkRowBounds(int index)
```
    Check validity of a row index
  - checkBounds
```
private boolean checkBounds(int column,
                            int row)
```
    Check validity of an index pair
  - checkColumnLengths
```
private boolean checkColumnLengths()
```
    Check to make sure each column is of equal length
  - generateDefaultLinkPath
```
private String generateDefaultLinkPath(int column,
                                       int row)
                                throws DefaultPathNotSetException
```
    Generate a default link path for a specified cell.
    
    Throws:
    
    DefaultPathNotSetException
  - getColumnElementClass
```
private Class<? extends DataElement<?>> getColumnElementClass(int index)
                                                       throws SlideSetException
```
    Throws:
    
    SlideSetException
  - getNewColumnElement
```
private DataElement<?> getNewColumnElement(int index)
                                    throws SlideSetException
```
    Generate a new DataElement appropriate for the selected column. The element is initialized with the type's default value.
    
    Throws:
    
    SlideSetException
  - checkUnderlyingCompatability
```
private boolean checkUnderlyingCompatability(int column,
                                             Object underlying)
                                      throws SlideSetException
```
    Check if an object may be stored in a column directly using a setUnderlying() method (i.e. without using an ElementWriter).
    
    Throws:
    
    SlideSetException
  - checkDataElementCompatibility
```
private boolean checkDataElementCompatibility(int column,
                                              DataElement<?> element)
                                       throws SlideSetException
```
    Check if the class and MIME type of a DataElement match those of a column in this table.
    
    Throws:
    
    SlideSetException
  - checkColumnElementConsistency
```
private boolean checkColumnElementConsistency(int column)
                                       throws SlideSetException
```
    Check if all the DataElements in this column are of the same type and have the same MIME type set.
    
    Throws:
    
    SlideSetException

Class SlideSet

Slide Set API documentation

Introduction

The Slide Set data model

Further information

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

columns

columnProperties

numRows

parent

children

creationParams

name

dir

locked

commandTemplate

ij

dtid

Constructor Detail

SlideSet

Method Detail

getNumCols

getNumRows

getDataElement

getUnderlying

getItemText

getColumnProperties

getColumnName

setColumnName

getColumnMimeType

setColumnMimeType

getColumnTypeName

getColumnUnderlyingType

getColumnElementType

getColumnIndex

getColumnDefaultPath

setColumnDefaultPath

setUnderlying

addColumn

addColumn

addColumn

addColumn

addColumn

addColumn

removeColumn

convertColumn

addRow

addRow

removeRow

getParent

setParent

getChildren

addChild

removeChild

getName

toString

setName

getCreationParams

setCreationParams

getCommandTemplate

setCommandTemplate

getWorkingDirectory

setWorkingDirectory

getContext

getDefaultLinkPrefix

setDefaultLinkPrefix

getDefaultLinkCount

setDefaultLinkCount

getDefaultLinkExtension

setDefaultLinkExtension

resolvePath

makeDefaultLink

isLocked

setLock

checkColumnBounds

checkRowBounds