Package sc.fiji.snt.analysis

Class SNTTable

java.lang.Object

java.util.AbstractCollection<org.scijava.table.Column<? extends Object>>

java.util.AbstractList<org.scijava.table.Column<? extends Object>>

java.util.ArrayList<org.scijava.table.Column<? extends Object>>

org.scijava.util.SizableArrayList<org.scijava.table.Column<? extends Object>>

org.scijava.table.AbstractTable<org.scijava.table.Column<? extends Object>,Object>

org.scijava.table.DefaultGenericTable

sc.fiji.snt.analysis.SNTTable

All Implemented Interfaces:

Serializable, Cloneable, Iterable<org.scijava.table.Column<? extends Object>>, Collection<org.scijava.table.Column<? extends Object>>, List<org.scijava.table.Column<? extends Object>>, RandomAccess, SequencedCollection<org.scijava.table.Column<? extends Object>>, org.scijava.table.GenericTable, org.scijava.table.Table<org.scijava.table.Column<? extends Object>,Object>, org.scijava.util.Sizable

Direct Known Subclasses:

ShollTable

public class SNTTable
extends org.scijava.table.DefaultGenericTable

Extension of DefaultGenericTable with (minor) scripting conveniences.

Author:

Tiago Ferreira

See Also:

• Serialized Form

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor	Description
SNTTable()
SNTTable(String filePath)
SNTTable(String filePath, char columDelimiter)
SNTTable(Map<String,Collection<Number>> values)

Method Summary

Modifier and Type	Method	Description
void	addColumn(String colHeader, double[] array)
void	addColumn(String colHeader, Collection<Double> array)
void	addGenericColumn(String colHeader, Collection<?> collection)
void	appendToLastRow(String colHeader, Object value)	Appends a value to the last row in the specified column.
void	clear()
void	createOrUpdateDisplay()	Creates a new display or updates an existing one.
void	fillEmptyCells(Object value)	Fills all empty cells in the table with the specified value.
static SNTTable	fromFile(String filePathOrURL)	Script-friendly method for loading CSV data from a file/URL.
static SNTTable	fromFile(String filePathOrURL, String delimiter)	Script-friendly method for loading tabular data from a file/URL.
static SNTTable	fromGenericTable(org.scijava.table.GenericTable source)
org.apache.commons.math3.stat.descriptive.SummaryStatistics	geColumnStats(int columnIndex, int startRowIndex, int endRowIndex)
org.apache.commons.math3.stat.descriptive.SummaryStatistics	geColumnStats(String colHeader, int startRowIndex, int endRowIndex)
org.apache.commons.math3.stat.descriptive.SummaryStatistics	geRowStats(int rowIndex, int startColumnIndex, int endColumnIndex)
org.apache.commons.math3.stat.descriptive.SummaryStatistics	geRowStats(String rowHeader, int startColumnIndex, int endColumnIndex)
List<String>	getColumnHeaders()
List<String>	getColumnHeaders(String pattern)
int	getSummaryRow()
String	getTitle()	Gets the title of the table.
boolean	hasUnsavedData()	Checks if the table has unsaved data.
int	insertRow(String header)
boolean	isSummarized()	Checks if the table contains summary statistics.
org.scijava.table.Column<?>	removeColumn(String header)
void	removeSummary()	Removes summary statistics from the table.
void	replace(String columnHeadersPattern, double originalValue, double replacementValue)
void	save(File outputFile)
boolean	save(String filePath)
static void	save(org.scijava.table.Table<?,?> table, char columnSep, boolean saveColHeaders, boolean saveRowHeaders, File outputFile)
void	set(int col, int row, Object value)
void	set(String colHeader, int row, Object value)
void	set(String colHeader, String rowHeader, Object value)
void	setContext(org.scijava.Context context)	Sets a SciJava context to this table.
void	setTitle(String title)	Sets the title of the table.
void	show()	Displays the table in a window.
void	show(String windowTitle)
void	summarize()
static String	toString(org.scijava.table.GenericTable table)
static String	toString(org.scijava.table.GenericTable table, int firstRow, int lastRow)
void	updateDisplay()	Updates the existing table display.
protected void	validate()

Methods inherited from class org.scijava.table.DefaultGenericTable

createColumn

Methods inherited from class org.scijava.table.AbstractTable

add, add, addAll, addAll, getRowCount, getRowHeader, insertColumns, removeRows, setColumnCount, setRowCount, setRowHeader

Methods inherited from class org.scijava.util.SizableArrayList

ensureCapacity, setSize

Methods inherited from class java.util.ArrayList

addFirst, addLast, clone, contains, equals, forEach, get, getFirst, getLast, hashCode, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeFirst, removeIf, removeLast, removeRange, replaceAll, retainAll, set, size, sort, spliterator, subList, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractCollection

containsAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream, toArray

Methods inherited from interface java.lang.Iterable

forEach

Methods inherited from interface java.util.List

addFirst, addLast, equals, getFirst, getLast, hashCode, removeFirst, removeLast, replaceAll, reversed, sort, spliterator

Methods inherited from interface org.scijava.util.Sizable

size

Methods inherited from interface org.scijava.table.Table

add, add, addAll, addAll, appendColumn, appendColumn, appendColumns, appendColumns, appendRow, appendRow, appendRows, appendRows, contains, containsAll, get, get, get, get, getColumnCount, getColumnHeader, getColumnIndex, getRowCount, getRowHeader, getRowIndex, indexOf, insertColumn, insertColumn, insertColumns, insertColumns, insertRow, insertRow, insertRows, insertRows, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeColumn, removeColumns, removeColumns, removeRow, removeRow, removeRows, removeRows, retainAll, set, setColumnCount, setColumnHeader, setDimensions, setRowCount, setRowHeader, size, subList, toArray, toArray

Constructor Details

SNTTable

public SNTTable()

SNTTable

public SNTTable(Map<String,Collection<Number>> values)

SNTTable

public SNTTable(String filePath)
         throws IOException

Throws:

IOException

SNTTable

public SNTTable(String filePath,
 char columDelimiter)
         throws IOException

Throws:

IOException

Method Details

validate

protected void validate()

fillEmptyCells

public void fillEmptyCells(Object value)

Fills all empty cells in the table with the specified value.

Iterates through all cells in the table and replaces null values with the provided replacement value.

Parameters:

value - the value to use for filling empty cells

replace

public void replace(String columnHeadersPattern,
 double originalValue,
 double replacementValue)

hasUnsavedData

public boolean hasUnsavedData()

Checks if the table has unsaved data.

Returns true if the table contains data and has been modified since the last save operation.

Returns:

true if there is unsaved data, false otherwise

appendToLastRow

public void appendToLastRow(String colHeader,
 Object value)

Appends a value to the last row in the specified column.

If the table is empty, a new row is created first. The value is then set in the specified column of the last row.

Parameters:

colHeader - the column header

value - the value to append

addColumn

public void addColumn(String colHeader,
 double[] array)

set

public void set(String colHeader,
 String rowHeader,
 Object value)

clear

public void clear()

Specified by:

clear in interface Collection<org.scijava.table.Column<? extends Object>>

Specified by:

clear in interface List<org.scijava.table.Column<? extends Object>>

Specified by:

clear in interface org.scijava.table.Table<org.scijava.table.Column<? extends Object>,Object>

Overrides:

clear in class ArrayList<org.scijava.table.Column<? extends Object>>

addColumn

public void addColumn(String colHeader,
 Collection<Double> array)

addGenericColumn

public void addGenericColumn(String colHeader,
 Collection<?> collection)

insertRow

public int insertRow(String header)

set

public void set(String colHeader,
 int row,
 Object value)

Specified by:

set in interface org.scijava.table.Table<org.scijava.table.Column<? extends Object>,Object>

Overrides:

set in class org.scijava.table.AbstractTable<org.scijava.table.Column<? extends Object>,Object>

set

public void set(int col,
 int row,
 Object value)

removeColumn

public org.scijava.table.Column<?> removeColumn(String header)

save

public boolean save(String filePath)

setContext

public void setContext(org.scijava.Context context)
                throws IllegalArgumentException

Sets a SciJava context to this table.

Parameters:

context - the SciJava application context

Throws:

IllegalArgumentException

getColumnHeaders

public List<String> getColumnHeaders()

getColumnHeaders

public List<String> getColumnHeaders(String pattern)

isSummarized

public boolean isSummarized()

Checks if the table contains summary statistics.

Returns true if the table has been summarized with statistical measures like mean, standard deviation, etc. This is determined by looking for specific row headers in the expected positions.

Returns:

true if table contains summary statistics, false otherwise

removeSummary

public void removeSummary()

Removes summary statistics from the table.

If the table contains summary statistics, this method removes the summary rows to return the table to its raw data state.

getSummaryRow

public int getSummaryRow()

geRowStats

public org.apache.commons.math3.stat.descriptive.SummaryStatistics geRowStats(String rowHeader,
 int startColumnIndex,
 int endColumnIndex)

geRowStats

public org.apache.commons.math3.stat.descriptive.SummaryStatistics geRowStats(int rowIndex,
 int startColumnIndex,
 int endColumnIndex)

geColumnStats

public org.apache.commons.math3.stat.descriptive.SummaryStatistics geColumnStats(String colHeader,
 int startRowIndex,
 int endRowIndex)

geColumnStats

public org.apache.commons.math3.stat.descriptive.SummaryStatistics geColumnStats(int columnIndex,
 int startRowIndex,
 int endRowIndex)

summarize

public void summarize()

save

public void save(File outputFile)
          throws IOException

Throws:

IOException

show

public void show()

Displays the table in a window.

Creates or updates the table display window. If a display already exists, it is updated with the current table contents.

show

public void show(String windowTitle)

updateDisplay

public void updateDisplay()

Updates the existing table display.

Refreshes the table display with the current table contents without creating a new display window.

createOrUpdateDisplay

public void createOrUpdateDisplay()

Creates a new display or updates an existing one.

If no display exists, creates a new table display window. If a display already exists, updates it with the current table contents.

getTitle

public String getTitle()

Gets the title of the table.

Returns the table's title, or "SNT Measurements" if no title has been set.

Returns:

the table title

setTitle

public void setTitle(String title)

Sets the title of the table.

Parameters:

title - the table's title

fromFile

public static SNTTable fromFile(String filePathOrURL)

Script-friendly method for loading CSV data from a file/URL.

Parameters:

filePathOrURL - the absolute path or URL to the CSV file to be imported

Returns:

the SNTTable or null if file could not be imported

fromFile

public static SNTTable fromFile(String filePathOrURL,
 String delimiter)

Script-friendly method for loading tabular data from a file/URL.

Parameters:

filePathOrURL - the absolute path or URL to the tabular file to be imported

delimiter - the column delimiter (comma, tab, etc.). A single character expected.

Returns:

the SNTTable or null if file could not be imported

toString

public static String toString(org.scijava.table.GenericTable table)

toString

public static String toString(org.scijava.table.GenericTable table,
 int firstRow,
 int lastRow)

save

public static void save(org.scijava.table.Table<?,?> table,
 char columnSep,
 boolean saveColHeaders,
 boolean saveRowHeaders,
 File outputFile)
                 throws IOException

Throws:

IOException

fromGenericTable

public static SNTTable fromGenericTable(org.scijava.table.GenericTable source)