de.mpg.biochem.mars.table

Class MarsTable

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList<E>

java.util.ArrayList<E>

org.scijava.util.SizableArrayList<C>

org.scijava.table.AbstractTable<org.scijava.table.Column<?>,java.lang.Object>

de.mpg.biochem.mars.table.MarsTable

All Implemented Interfaces:

JsonConvertibleRecord, java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<org.scijava.table.Column<?>>, java.util.Collection<org.scijava.table.Column<?>>, java.util.List<org.scijava.table.Column<?>>, java.util.RandomAccess, org.scijava.table.GenericTable, org.scijava.table.Table<org.scijava.table.Column<?>,java.lang.Object>, org.scijava.util.Sizable

public class MarsTable
extends org.scijava.table.AbstractTable<org.scijava.table.Column<?>,java.lang.Object>
implements org.scijava.table.GenericTable, JsonConvertibleRecord

Mars implementation of a scijava results table. All numbers are stored as doubles (as DoubleColumn). Convenience methods and constructors are provided for common operations (min, max, mean, std, variance, linearRegression, sorting, filtering, etc), for saving and opening tables in csv or json format, and retrieval of values in many formats. Throughout (org.apache.commons.math3) is used for common operations where possible.

GenericColumns containing Strings can also be added to MarsTables. Their primary intended use is for generating output tables that need to combine numbers and strings or static data storage of tables composed entirely of strings (for example, with frame metadata information for time points as rows).

More complex row filtering operations can be accomplished using the rowStream method and java 8 stream framework. The optimal implementation would return an ArrayList<Integer> with a set of rows to remove or keep. This list can then be used with the deleteRows or keepRows methods.

All sorting and filtering operations are performed in place. This allows for processing of larger tables in memory without requiring enough memory for a copy. If a copy is desired. For example, if several filtering and sorting steps are performed from the same primary table, prior to each operation a copy can be made using the clone() method.

See Also:

Serialized Form

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor and Description
MarsTable() Creates an empty results table.
MarsTable(java.io.File file) Opens a results table from the file provided.
MarsTable(java.io.File file, org.scijava.app.StatusService statusService) Opens a results table from the file provided.
MarsTable(int columnCount, int rowCount) Creates a results table with the given row and column dimensions.
MarsTable(java.lang.String name) Creates an empty results table with the name given.
MarsTable(java.lang.String name, int columnCount, int rowCount) Creates a results table with the given name and column and row dimensions.
MarsTable(java.lang.String name, java.lang.String... headers) Creates a results table with the name given and column headers.
MarsTable(org.scijava.table.Table<org.scijava.table.Column<?>,java.lang.Object> table) Creates a results table with the given a scijava Table.

Method Summary

Modifier and Type	Method and Description
MarsTable	addRow(MarsTableRow row) Add MarsTableRow to the end of the table.
MarsTable	clone() Create a copy of the MarsTable.
protected org.scijava.table.DoubleColumn	createColumn(java.lang.String header)
MarsTable	deleteRows(int[] rows) Remove rows at the positions specified in the ordered list given.
MarsTable	deleteRows(java.util.List<java.lang.Integer> rows) Remove rows at the positions specified in the ordered list given.
java.lang.String	dumpJSON() Get the record in Json string format.
void	fromJSON(com.fasterxml.jackson.core.JsonParser jParser) JSON deserialization of table values.
double[]	getColumnAsDoubles(java.lang.String column) Returns an array of double values for the column given.
double[]	getColumnAsDoublesNoNaNs(java.lang.String column) Returns an array of double values for the column given.
double[]	getColumnAsDoublesNoNaNs(java.lang.String column, java.lang.String rowSelectionColumn, double lowerBound, double upperBound) Returns an array of double values for the column within the range given for a rowSelectionColumn (inclusive of bounds).
java.util.List<java.lang.String>	getColumnHeadingList() Returns the column headings as an ArrayList of strings.
java.lang.String[]	getColumnHeadings() Returns the column headings as an array of strings.
java.io.File	getFile()
java.util.function.Predicate<com.fasterxml.jackson.core.JsonGenerator>	getJsonGenerator(java.lang.String field) Get the JsonGenerator for a field.
java.util.function.Predicate<com.fasterxml.jackson.core.JsonParser>	getJsonParser(java.lang.String field) Get the JsonParser for a field.
java.lang.String	getName() Retrieves the name of the table.
java.util.List<java.lang.Object>	getRowAsList(int row) Returns the row specified as a List of Objects.
java.lang.String	getRowAsString(int row) Returns a comma delimited string of the values in the row specified.
java.lang.String	getStringValue(int col, int row) Returns the string value at the column and row indices specified.
java.lang.String	getStringValue(java.lang.String column, int row) Returns the string value for the column header and row index specified.
double	getValue(int col, int row) Returns the double value at the column and row indices specified.
double	getValue(java.lang.String column, int row) Returns the double value at the column header and row index specified.
MarsTableWindow	getWindow() Returns a reference to the window containing the table if there is one.
boolean	hasColumn(java.lang.String colName) Returns true if the table contains a column with the name specified.
MarsTable	keepRows(int[] rows) Remove rows at the positions specified in the ordered list given.
MarsTable	keepRows(java.util.List<java.lang.Integer> rows) Keep rows at the positions specified in the ordered list given.
double[]	linearRegression(java.lang.String xColumn, java.lang.String yColumn) Calculates the linear fit given an xColumn and yColumn pair.
double[]	linearRegression(java.lang.String xColumn, java.lang.String yColumn, double lowerBound, double upperBound) Calculates the linear fit given an xColumn and yColumn pair.
double	mad(java.lang.String column) Calculates the median absolute deviation.
double	mad(java.lang.String madColumn, java.lang.String rowSelectionColumn, double lowerBound, double upperBound) Calculates the median absolute deviation of the values for the madColumn within the range given for a rowSelectionColumn (inclusive of bounds).
double	max(java.lang.String column) Finds the maximum of the column values.
double	max(java.lang.String maxColumn, java.lang.String rowSelectionColumn, double lowerBound, double upperBound) Finds the max of the values for the maxColumn within the range given for a rowSelectionColumn (inclusive of bounds).
double	mean(java.lang.String column) Calculates the mean of the values for the column given.
double	mean(java.lang.String meanColumn, java.lang.String rowSelectionColumn, double lowerBound, double upperBound) Calculates the mean of the values for the meanColumn within the range given for a rowSelectionColumn (inclusive of bounds).
double	median(java.lang.String column) Calculates the median of the column values.
double	median(java.lang.String medianColumn, java.lang.String rowSelectionColumn, double lowerBound, double upperBound) Finds the median of the values for the medianColumn within the range given for a rowSelectionColumn (inclusive of bounds).
double	min(java.lang.String column) Finds the minimum of the column values.
double	min(java.lang.String minColumn, java.lang.String rowSelectionColumn, double lowerBound, double upperBound) Finds the min of the values for the maxColumn within the range given for a rowSelectionColumn (inclusive of bounds).
java.util.stream.Stream<MarsTableRow>	rows() Returns a stream of MarsTableRow.
boolean	saveAs(java.io.File file) Saves the table to the file path in smile encoded json format.
void	saveAsCSV(java.lang.String path) Saves the table to the string file path specified in csv format.
void	saveAsJSON(java.lang.String path) Saves the table to the file path specified in json format.
void	saveAsYAMT(java.lang.String path) Saves the table to the file path specified in yamt format.
double	sem(java.lang.String column) Calculates the standard error of the mean for the column given.
double	sem(java.lang.String meanColumn, java.lang.String rowSelectionColumn, double lowerBound, double upperBound) Calculates the standard error of the mean for the meanColumn within the range given for a rowSelectionColumn (inclusive of bounds).
void	setFile(java.io.File file)
void	setJsonField(java.lang.String field, MarsUtil.ThrowingConsumer<com.fasterxml.jackson.core.JsonGenerator,java.io.IOException> output, MarsUtil.ThrowingConsumer<com.fasterxml.jackson.core.JsonParser,java.io.IOException> input)
void	setName(java.lang.String name) Sets the name of the table.
MarsTable	setPrecision(int decimalPlacePrecision)
void	setShowWarnings(boolean showWarnings)
void	setValue(int col, int row, double value) Set the double value for a pair of column and row indices.
void	setValue(int col, int row, java.lang.String value) Set the String value for a pair of column and row indices.
void	setValue(java.lang.String column, int row, double value) Set the double value for the column heading and row index specified.
void	setValue(java.lang.String column, int row, java.lang.String value) Set the String value for the column heading and row index specified.
MarsTableWindow	setWindow(MarsTableWindow win) Sets a reference to the window holding the table.
MarsTable	sort(boolean ascending, java.lang.String... columns) Sort the table on one or more columns either in ascending or descending order.
MarsTable	sort(java.lang.String... columns) Sort the table in ascending order on one or more columns.
double	std(java.lang.String column) Calculates the standard deviation of the column.
double	std(java.lang.String stdColumn, java.lang.String rowSelectionColumn, double lowerBound, double upperBound) Calculates the standard deviation of the values for the stdColumn within the range given for a rowSelectionColumn (inclusive of bounds).
double	sum(java.lang.String column) Calculates the sum of the values for the column given.
double	sum(java.lang.String sumColumn, java.lang.String rowSelectionColumn, double lowerBound, double upperBound) Calculates the sum of the values for the sumColumn within the range given for a rowSelectionColumn (inclusive of bounds).
void	toJSON(com.fasterxml.jackson.core.JsonGenerator jGenerator) JSON serialization of table values.
java.lang.String	toString()
double	variance(java.lang.String varianceColumn) Calculates the variance for the column given.
double	variance(java.lang.String varianceColumn, java.lang.String rowSelectionColumn, double lowerBound, double upperBound) Calculates the variance for the varianceColumn within the range given for a rowSelectionColumn (inclusive of bounds).
static MarsTable	wrap(org.scijava.table.Table<org.scijava.table.Column<?>,java.lang.Object> table) Wraps a scijava table or anything implementing the scijava Table interface inside a MarsTable without copying.

Methods inherited from class org.scijava.table.AbstractTable

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

Methods inherited from class org.scijava.util.SizableArrayList

ensureCapacity, setSize

Methods inherited from class java.util.ArrayList

clear, contains, forEach, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, removeAll, removeIf, removeRange, replaceAll, retainAll, size, sort, spliterator, subList, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode

Methods inherited from class java.util.AbstractCollection

containsAll

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.scijava.table.Table

add, add, addAll, addAll, appendColumn, appendColumn, appendColumns, appendColumns, appendRow, appendRow, appendRows, appendRows, clear, 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, removeColumn, removeColumns, removeColumns, removeRow, removeRow, removeRows, removeRows, retainAll, set, set, set, setColumnCount, setColumnHeader, setDimensions, setRowCount, setRowHeader, size, subList, toArray, toArray

Methods inherited from interface java.util.List

equals, hashCode, replaceAll, sort, spliterator

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Methods inherited from interface org.scijava.util.Sizable

size

Constructor Detail

MarsTable

public MarsTable()

Creates an empty results table.

MarsTable

public MarsTable(java.lang.String name)

Creates an empty results table with the name given.

Parameters:

name - Table name.

MarsTable

public MarsTable(java.lang.String name,
                 java.lang.String... headers)

Creates a results table with the name given and column headers.

Parameters:

name - Table name.

headers - Names of column headers to initialize.

MarsTable

public MarsTable(java.io.File file)
          throws com.fasterxml.jackson.core.JsonParseException,
                 java.io.IOException

Opens a results table from the file provided. The values are loaded in based on the extension of the file provided, which can be json or csv. If no file extension is found it is assumed the file has csv format.

Parameters:

file - File to load table from.

Throws:

com.fasterxml.jackson.core.JsonParseException - Thrown if unable to parse Json.

java.io.IOException - Thrown if unable to read file.

MarsTable

public MarsTable(java.io.File file,
                 org.scijava.app.StatusService statusService)
          throws com.fasterxml.jackson.core.JsonParseException,
                 java.io.IOException

Opens a results table from the file provided. The values are loaded in based on the extension of the file provided, which can be json or csv. If no file extension is found it is assumed the file has csv format. If the StatusService is provided, then a progress bar is shown during loading of csv files.

Parameters:

file - File to load the table from.

statusService - StatusService from the current Context to provide the user with progress updates.

Throws:

java.io.IOException - If unable to load the file.

com.fasterxml.jackson.core.JsonParseException - If a problem is encountered when parsing Json.

MarsTable

public MarsTable(int columnCount,
                 int rowCount)

Creates a results table with the given row and column dimensions.

Parameters:

columnCount - Number of columns.

rowCount - Number of rows.

MarsTable

public MarsTable(org.scijava.table.Table<org.scijava.table.Column<?>,java.lang.Object> table)

Creates a results table with the given a scijava Table. Creates DoubleColumns if those exist. Otherwise, generic columns are created.

Parameters:

table - Something implementing the Table interface.

MarsTable

public MarsTable(java.lang.String name,
                 int columnCount,
                 int rowCount)

Creates a results table with the given name and column and row dimensions.

Parameters:

name - Table name.

columnCount - Number of columns.

rowCount - Number of rows.

Method Detail

wrap

public static MarsTable wrap(org.scijava.table.Table<org.scijava.table.Column<?>,java.lang.Object> table)

Wraps a scijava table or anything implementing the scijava Table interface inside a MarsTable without copying. Provides fast access to MarsTable functions without the need to copy all values.

Parameters:

table - Something implementing the Table interface.

Returns:

The wrapped MarsTable.

setName

public void setName(java.lang.String name)

Sets the name of the table.

Parameters:

name - Name of the table.

getName

public java.lang.String getName()

Retrieves the name of the table.

Returns:

The name of the table.

setPrecision

public MarsTable setPrecision(int decimalPlacePrecision)

getColumnHeadings

public java.lang.String[] getColumnHeadings()

Returns the column headings as an array of strings.

Returns:

String array contain the column headers.

getColumnHeadingList

public java.util.List<java.lang.String> getColumnHeadingList()

Returns the column headings as an ArrayList of strings.

Returns:

ArrayList containing the column headers.

getWindow

public MarsTableWindow getWindow()

Returns a reference to the window containing the table if there is one. This could be a swing or javafx window.

Returns:

The window containing the table if working with a gui.

setWindow

public MarsTableWindow setWindow(MarsTableWindow win)

Sets a reference to the window holding the table. This could be a swing or javafx window.

Parameters:

win - The window containing the table if working with a gui.

Returns:

A reference to the MarsTableWindow provided.

getColumnAsDoubles

public double[] getColumnAsDoubles(java.lang.String column)

Returns an array of double values for the column given. All rows will have an entry in the array even if they have NaN values.

Parameters:

column - Header of the column to retrieve.

Returns:

Array of double values for the column. With NaN values included.

getColumnAsDoublesNoNaNs

public double[] getColumnAsDoublesNoNaNs(java.lang.String column)

Returns an array of double values for the column given. NaN values are ignored.

Parameters:

column - Header of the column to retrieve.

Returns:

Array of double values for the column with NaN values removed.

getColumnAsDoublesNoNaNs

public double[] getColumnAsDoublesNoNaNs(java.lang.String column,
                                         java.lang.String rowSelectionColumn,
                                         double lowerBound,
                                         double upperBound)

Returns an array of double values for the column within the range given for a rowSelectionColumn (inclusive of bounds). NaN values are not included in the list.

Parameters:

column - Header of the column to retrieve.

rowSelectionColumn - name of the column used for filtering a range of values.

lowerBound - smallest value included in the row selection range.

upperBound - largest value included in the row selection range.

Returns:

Array of double values for the column within the range given. NaN values removed.

getRowAsString

public java.lang.String getRowAsString(int row)

Returns a comma delimited string of the values in the row specified.

Parameters:

row - The row index to retrieve as a string.

Returns:

Comma delimited string containing the row items.

getRowAsList

public java.util.List<java.lang.Object> getRowAsList(int row)

Returns the row specified as a List of Objects. These could be Doubles or Strings.

Parameters:

row - The row index to retrieve as a string.

Returns:

Object list of items in each column for the row index provided.

saveAs

public boolean saveAs(java.io.File file)

Saves the table to the file path in smile encoded json format.

Parameters:

file - File where the table is written.

Returns:

Return true if no IO error is encountered.

saveAsCSV

public void saveAsCSV(java.lang.String path)
               throws java.io.IOException

Saves the table to the string file path specified in csv format.

Parameters:

path - The string path for saving.

Throws:

java.io.IOException - Thrown if unable to write the file.

toJSON

public void toJSON(com.fasterxml.jackson.core.JsonGenerator jGenerator)
            throws java.io.IOException

JSON serialization of table values. Includes schema with column type definitions of either string or number. values specified in records format, with each row an object containing column:value pairs.

Specified by:

toJSON in interface JsonConvertibleRecord

Parameters:

jGenerator - JsonGenerator stream the table should be serialized to.

Throws:

java.io.IOException - Thrown if unable to write to the JsonGenerator stream.

fromJSON

public void fromJSON(com.fasterxml.jackson.core.JsonParser jParser)
              throws java.io.IOException

JSON deserialization of table values. Schema is used to determine column type of either DoubleColumn or GenericColumn. Record objects are added as the stream is parsed. The Double value types of NaN, Infinity, -Infinity are serialized and deserialized.

Specified by:

fromJSON in interface JsonConvertibleRecord

Parameters:

jParser - JsonParser stream to read objects and fields from.

Throws:

java.io.IOException - Thrown if unable to read from the JsonParser stream.

saveAsJSON

public void saveAsJSON(java.lang.String path)
                throws java.io.IOException

Saves the table to the file path specified in json format.

Parameters:

path - String path for writing.

Throws:

java.io.IOException - Thrown if unable to write to the path given.

saveAsYAMT

public void saveAsYAMT(java.lang.String path)
                throws java.io.IOException

Saves the table to the file path specified in yamt format. This is a smile encoded json file.

Parameters:

path - String path for writing.

Throws:

java.io.IOException - Thrown if unable to save to path given.

toString

public java.lang.String toString()

Overrides:

toString in class java.util.AbstractCollection<org.scijava.table.Column<?>>

setValue

public void setValue(int col,
                     int row,
                     double value)

Set the double value for a pair of column and row indices. Sets a double value for a DoubleColumn and a String value for a GenericColumn.

Parameters:

col - Index of the column that contains the value to set.

row - Index of the row that contains the value to set.

value - The new value to set at the position given.

setValue

public void setValue(int col,
                     int row,
                     java.lang.String value)

Set the String value for a pair of column and row indices. Sets a String value for a GenericColumn and tries to convert to a double value for a DoubleColumn. If conversion is not possible an NaN value is set.

Parameters:

col - Index of the column that contains the value to set.

row - Index of the row that contains the value to set.

value - The new String value to set at the position given.

setValue

public void setValue(java.lang.String column,
                     int row,
                     double value)

Set the double value for the column heading and row index specified. Sets a double value for a DoubleColumn and a String value for a GenericColumn.

Parameters:

column - Heading of the column that contains the value to set.

row - Index of the row that contains the value to set.

value - The new double value to set at the position given.

setValue

public void setValue(java.lang.String column,
                     int row,
                     java.lang.String value)

Set the String value for the column heading and row index specified. Sets a String value for a GenericColumn and attempts to convert to a double value for DoubleColumns. If conversion is not possible an NaN value is set.

Parameters:

column - Heading of the column that contains the value to set.

row - Index of the row that contains the value to set.

value - The new double value to set at the position given.

getValue

public double getValue(int col,
                       int row)

Returns the double value at the column and row indices specified. NaN is returned if the position given does not exist.

Parameters:

col - Index of the column that contains the value.

row - Index of the row that contains the value.

Returns:

The value at the specified col and row indices.

getValue

public double getValue(java.lang.String column,
                       int row)

Returns the double value at the column header and row index specified. NaN is returned if the position given does not exist. If the column is of type GenericColumn conversion to double is attempted. If conversion is not possible NaN is returned;

Parameters:

column - Header of the column that contains the value.

row - Index of the row that contains the value.

Returns:

The double value at the column header and row index specified.

getStringValue

public java.lang.String getStringValue(java.lang.String column,
                                       int row)

Returns the string value for the column header and row index specified. If the column type is DoubleColumn the double value is converted to a string.

Parameters:

column - Header of the column that contains the value.

row - Index of the row that contains the value.

Returns:

The String value at the column header and row index specified.

getStringValue

public java.lang.String getStringValue(int col,
                                       int row)

Returns the string value at the column and row indices specified. If the column type is DoubleColumn the double value is converted to a string.

Parameters:

col - Index of the column that contains the value.

row - Index of the row that contains the value.

Returns:

The double value at the column and row indices specified.

hasColumn

public boolean hasColumn(java.lang.String colName)

Returns true if the table contains a column with the name specified.

Parameters:

colName - String column header to check for.

Returns:

Returns true if the table contains the column.

max

public double max(java.lang.String column)

Finds the maximum of the column values. NaN values are ignored.

Parameters:

column - name of the column.

Returns:

maximum value in the column values. NaN is returned if all values are NaN or the column does not exist.

max

public double max(java.lang.String maxColumn,
                  java.lang.String rowSelectionColumn,
                  double lowerBound,
                  double upperBound)

Finds the max of the values for the maxColumn within the range given for a rowSelectionColumn (inclusive of bounds). NaN values are ignored. If no values exist for the bounds provided NaN is returned.

Parameters:

maxColumn - name of the column used for finding the max.

rowSelectionColumn - name of the column used for filtering a range of values.

lowerBound - smallest value included in the row selection range.

upperBound - largest value included in the row selection range.

Returns:

max of the column values. NaN is returned if all values are NaN or one of the columns does not exist.

min

public double min(java.lang.String column)

Finds the minimum of the column values. NaN values are ignored.

Parameters:

column - name of the column.

Returns:

minimum value in the column values. NaN is returned if all values are NaN or the column does not exist.

min

public double min(java.lang.String minColumn,
                  java.lang.String rowSelectionColumn,
                  double lowerBound,
                  double upperBound)

Finds the min of the values for the maxColumn within the range given for a rowSelectionColumn (inclusive of bounds). NaN values are ignored. If no values exist for the bounds provided NaN is returned.

Parameters:

minColumn - name of the column used for finding the min.

rowSelectionColumn - name of the column used for filtering a range of values.

lowerBound - smallest value included in the row selection range.

upperBound - largest value included in the row selection range.

Returns:

min of the column values. NaN is returned if all values are NaN or one of the columns does not exist.

mean

public double mean(java.lang.String column)

Calculates the mean of the values for the column given. NaN values are ignored.

Parameters:

column - name of the column.

Returns:

mean value of the column values. NaN is returned if all values are NaN or the column does not exist.

mean

public double mean(java.lang.String meanColumn,
                   java.lang.String rowSelectionColumn,
                   double lowerBound,
                   double upperBound)

Calculates the mean of the values for the meanColumn within the range given for a rowSelectionColumn (inclusive of bounds). NaN values are ignored. If no values exist for the bounds provided NaN is returned.

Parameters:

meanColumn - name of the column used for calculating the mean.

rowSelectionColumn - name of the column used for filtering a range of values.

lowerBound - smallest value included in the row selection range.

upperBound - largest value included in the row selection range.

Returns:

mean value of the column values. NaN is returned if all values are NaN or one of the columns does not exist.

sum

public double sum(java.lang.String column)

Calculates the sum of the values for the column given. NaN values are ignored.

Parameters:

column - name of the column.

Returns:

sum value of the column values. NaN is returned if all values are NaN or the column does not exist.

sum

public double sum(java.lang.String sumColumn,
                  java.lang.String rowSelectionColumn,
                  double lowerBound,
                  double upperBound)

Calculates the sum of the values for the sumColumn within the range given for a rowSelectionColumn (inclusive of bounds). NaN values are ignored. If no values exist for the bounds provided NaN is returned.

Parameters:

sumColumn - name of the column used for calculating the mean.

rowSelectionColumn - name of the column used for filtering a range of values.

lowerBound - smallest value included in the row selection range.

upperBound - largest value included in the row selection range.

Returns:

sum value of the column values. NaN is returned if all values are NaN or one of the columns does not exist.

median

public double median(java.lang.String column)

Calculates the median of the column values. NaN values are ignored.

Parameters:

column - name of the column.

Returns:

median value of the column values. NaN is returned if all values are NaN or the column does not exist.

median

public double median(java.lang.String medianColumn,
                     java.lang.String rowSelectionColumn,
                     double lowerBound,
                     double upperBound)

Finds the median of the values for the medianColumn within the range given for a rowSelectionColumn (inclusive of bounds). NaN values are ignored. If no values exist for the bounds provided NaN is returned.

Parameters:

medianColumn - name of the column used for finding the median.

rowSelectionColumn - name of the column used for filtering a range of values.

lowerBound - smallest value included in the row selection range.

upperBound - largest value included in the row selection range.

Returns:

median value of the column values. NaN is returned if all values are NaN or one of the columns does not exist.

std

public double std(java.lang.String column)

Calculates the standard deviation of the column. NaN values are ignored.

Parameters:

column - name of the column.

Returns:

standard deviation of the column values. NaN is returned if all values are NaN or the column does not exist.

std

public double std(java.lang.String stdColumn,
                  java.lang.String rowSelectionColumn,
                  double lowerBound,
                  double upperBound)

Calculates the standard deviation of the values for the stdColumn within the range given for a rowSelectionColumn (inclusive of bounds). NaN values are ignored. If no values exist for the bounds provided NaN is returned.

Parameters:

stdColumn - name of the column to use for the standard deviation calculation.

rowSelectionColumn - name of the column used for filtering a range of values.

lowerBound - smallest value included in the row selection range.

upperBound - largest value included in the row selection range.

Returns:

standard deviation of the stdColumn for the rowSelection. NaN is returned if all values are NaN or one of the columns does not exist.

mad

public double mad(java.lang.String column)

Calculates the median absolute deviation. NaN values are ignored.

Parameters:

column - name of the column.

Returns:

median absolute deviation of the column values. NaN is returned if all values are NaN or the column does not exist.

mad

public double mad(java.lang.String madColumn,
                  java.lang.String rowSelectionColumn,
                  double lowerBound,
                  double upperBound)

Calculates the median absolute deviation of the values for the madColumn within the range given for a rowSelectionColumn (inclusive of bounds). NaN values are ignored. If no values exist for the bounds provided NaN is returned.

Parameters:

madColumn - Name of the column used to calculate the median absolute deviation.

rowSelectionColumn - name of the column used for filtering a range of values.

lowerBound - smallest value included in the row selection range.

upperBound - largest value included in the row selection range.

Returns:

standard deviation of the stdColumn for the rowSelection. NaN is returned if all values are NaN or one of the columns does not exist.

sem

public double sem(java.lang.String column)

Calculates the standard error of the mean for the column given. NaN values are ignored.

Parameters:

column - Name of the column used to calculate the median absolute deviation.

Returns:

The standard error of the mean for the column given. NaN is returned if all values are NaN or one the column does not exist.

sem

public double sem(java.lang.String meanColumn,
                  java.lang.String rowSelectionColumn,
                  double lowerBound,
                  double upperBound)

Calculates the standard error of the mean for the meanColumn within the range given for a rowSelectionColumn (inclusive of bounds). NaN values are ignored. If no values exist for the bounds provided NaN is returned.

Parameters:

meanColumn - Name of the column used to calculate the standard error of the mean.

rowSelectionColumn - name of the column used for filtering a range of values.

lowerBound - smallest value included in the row selection range.

upperBound - largest value included in the row selection range.

Returns:

Standard error of the mean. NaN is returned if all values are NaN or one of the columns does not exist.

variance

public double variance(java.lang.String varianceColumn)

Calculates the variance for the column given. NaN values are ignored.

Parameters:

varianceColumn - Name of the column used to calculate the variance.

Returns:

The variance for the column given. NaN is returned if all values are NaN or the column does not exist.

variance

public double variance(java.lang.String varianceColumn,
                       java.lang.String rowSelectionColumn,
                       double lowerBound,
                       double upperBound)

Calculates the variance for the varianceColumn within the range given for a rowSelectionColumn (inclusive of bounds). NaN values are ignored. If no values exist for the bounds provided NaN is returned.

Parameters:

varianceColumn - Name of the column used to calculate the variance.

rowSelectionColumn - name of the column used for filtering a range of values.

lowerBound - smallest value included in the row selection range.

upperBound - largest value included in the row selection range.

Returns:

Variance. NaN is returned if all values are NaN or one of the columns does not exist.

linearRegression

public double[] linearRegression(java.lang.String xColumn,
                                 java.lang.String yColumn)

Calculates the linear fit given an xColumn and yColumn pair. NaN values are ignored. y = A + Bx A = output[0] +/- output[1] B = output[2] +/- output[3] Standard error is reported.

Parameters:

xColumn - Name of the column containing the x values.

yColumn - Name of the column containing the y values.

Returns:

Array with fit result.

linearRegression

public double[] linearRegression(java.lang.String xColumn,
                                 java.lang.String yColumn,
                                 double lowerBound,
                                 double upperBound)

Calculates the linear fit given an xColumn and yColumn pair. NaN values are ignored. y = A + Bx A = output[0] +/- output[1] B = output[2] +/- output[3] Standard error is reported.

Parameters:

xColumn - Name of the column containing the x values.

yColumn - Name of the column containing the y values.

lowerBound - LowerBound of fitting region in x values.

upperBound - UpperBound of fitting region in x values.

Returns:

Array with fit result.

sort

public MarsTable sort(java.lang.String... columns)

Sort the table in ascending order on one or more columns.

Parameters:

columns - Comma separated list of columns to sort by.

Returns:

MarsTable for next operation.

sort

public MarsTable sort(boolean ascending,
                      java.lang.String... columns)

Sort the table on one or more columns either in ascending or descending order.

Parameters:

ascending - Determines sort order.

columns - Comma separated list of columns to sort by.

Returns:

MarsTable for next operation.

rows

public java.util.stream.Stream<MarsTableRow> rows()

Returns a stream of MarsTableRow. This is useful for performing operations on all rows using Consumers.

Returns:

A stream of MarsTableRows.

addRow

public MarsTable addRow(MarsTableRow row)

Add MarsTableRow to the end of the table. Assumes the table has all the columns listed in the row.

Parameters:

row - A MarsTableRow that should be added to the end of the table.

Returns:

MarsTable for next operation.

deleteRows

public MarsTable deleteRows(int[] rows)

Remove rows at the positions specified in the ordered list given.

Parameters:

rows - The list of rows to remove.

Returns:

MarsTable for next operation.

deleteRows

public MarsTable deleteRows(java.util.List<java.lang.Integer> rows)

Remove rows at the positions specified in the ordered list given.

Parameters:

rows - An ArrayList containing the rows to remove.

Returns:

MarsTable for next operation.

keepRows

public MarsTable keepRows(int[] rows)

Remove rows at the positions specified in the ordered list given.

Parameters:

rows - The list of rows to remove.

Returns:

MarsTable for next operation.

keepRows

public MarsTable keepRows(java.util.List<java.lang.Integer> rows)

Keep rows at the positions specified in the ordered list given. Remove all other rows.

Parameters:

rows - A List containing the rows to keep.

Returns:

MarsTable for next operation.

createColumn

protected org.scijava.table.DoubleColumn createColumn(java.lang.String header)

Specified by:

createColumn in class org.scijava.table.AbstractTable<org.scijava.table.Column<?>,java.lang.Object>

dumpJSON

public java.lang.String dumpJSON()

Get the record in Json string format.

Specified by:

dumpJSON in interface JsonConvertibleRecord

Returns:

Json string representation of the record.

getFile

public java.io.File getFile()

setFile

public void setFile(java.io.File file)

clone

public MarsTable clone()

Create a copy of the MarsTable.

Overrides:

clone in class java.util.ArrayList<org.scijava.table.Column<?>>

Returns:

A copy of the MarsTable.

setShowWarnings

public void setShowWarnings(boolean showWarnings)

Specified by:

setShowWarnings in interface JsonConvertibleRecord

setJsonField

public void setJsonField(java.lang.String field,
                         MarsUtil.ThrowingConsumer<com.fasterxml.jackson.core.JsonGenerator,java.io.IOException> output,
                         MarsUtil.ThrowingConsumer<com.fasterxml.jackson.core.JsonParser,java.io.IOException> input)

Specified by:

setJsonField in interface JsonConvertibleRecord

getJsonGenerator

public java.util.function.Predicate<com.fasterxml.jackson.core.JsonGenerator> getJsonGenerator(java.lang.String field)

Description copied from interface: JsonConvertibleRecord

Get the JsonGenerator for a field.

Specified by:

getJsonGenerator in interface JsonConvertibleRecord

Parameters:

field - Json field.

Returns:

JsonGenerator predicate for field.

getJsonParser

public java.util.function.Predicate<com.fasterxml.jackson.core.JsonParser> getJsonParser(java.lang.String field)

Description copied from interface: JsonConvertibleRecord

Get the JsonParser for a field.

Specified by:

getJsonParser in interface JsonConvertibleRecord

Parameters:

field - Json field.

Returns:

JsonParser predicate for field.