Package adams.data.io.input

Class DeepLabCutCSVReader

java.lang.Object

adams.core.logging.LoggingObject

adams.core.logging.CustomLoggingLevelObject

adams.core.option.AbstractOptionHandler

adams.data.io.input.AbstractReportReader<Report>

adams.data.io.input.DeepLabCutCSVReader

All Implemented Interfaces:

CleanUpHandler, Destroyable, GlobalInfoSupporter, FileFormatHandler, LoggingLevelHandler, LoggingSupporter, OptionHandler, ShallowCopySupporter<AbstractReportReader>, SizeOfHandler, Stoppable, StoppableWithFeedback, ReportReader<Report>, Serializable, Comparable

public class DeepLabCutCSVReader
extends AbstractReportReader<Report>

Reads point annotations into multiple reports from DeepLabCut's CSV format.

-logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
 

-input <adams.core.io.PlaceholderFile> (property: input)
    The file to read and turn into a report.
    default: ${CWD}
 

-prefix <java.lang.String> (property: prefix)
    The report field prefix used in the report.
    default: Point.
 

-file-regexp <adams.core.base.BaseRegExp> (property: fileRegExp)
    The regular expression that the file names must match in order to be turned
    into reports.
    default: .*
    more: https://docs.oracle.com/javase/tutorial/essential/regex/
    https://docs.oracle.com/javase/8/docs/api/java/util/regex/Pattern.html
 

Author:

FracPete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static String	KEY_FILENAME
static String	KEY_INDIVIDUALS
static String	KEY_LABELS
protected BaseRegExp	m_FileRegExp	the regexp the files must match.
protected String	m_Prefix	the prefix of the points in the report.

Fields inherited from class adams.data.io.input.AbstractReportReader

m_Input, m_Stopped

Fields inherited from class adams.core.option.AbstractOptionHandler

m_OptionManager

Fields inherited from class adams.core.logging.LoggingObject

m_Logger, m_LoggingIsEnabled, m_LoggingLevel

Constructor Summary

Constructors

Constructor	Description
DeepLabCutCSVReader()

Method Summary

Modifier and Type	Method	Description
void	defineOptions()	Adds options to the internal list of options.
protected int	determineParentID(Report report)	Tries to determine the parent ID for the current report.
String	fileRegExpTipText()	Returns the tip text for this property.
BaseRegExp	getFileRegExp()	Returns the regexp the file names must match.
String	getFormatDescription()	Returns a string describing the format (used in the file chooser).
String[]	getFormatExtensions()	Returns the extension(s) of the format.
String	getPrefix()	Returns the field prefix used in the report.
String	globalInfo()	Returns a string describing the object.
Report	newInstance()	Returns a new instance of the report class in use.
String	prefixTipText()	Returns the tip text for this property.
protected List<Report>	readData()	Performs the actual reading.
void	setFileRegExp(BaseRegExp value)	Sets the regexp the file names must match.
void	setPrefix(String value)	Sets the field prefix used in the report.

Methods inherited from class adams.data.io.input.AbstractReportReader

checkData, cleanUp, compareTo, destroy, equals, forCommandLine, forName, getDefaultFormatExtension, getInput, getReaders, inputTipText, isStopped, postRead, read, reset, setInput, shallowCopy, shallowCopy, stopExecution

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, initialize, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

Methods inherited from class adams.core.logging.LoggingObject

configureLogger, getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled, sizeOf

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface adams.core.logging.LoggingLevelHandler

getLoggingLevel

Field Detail

KEY_FILENAME

public static final String KEY_FILENAME

See Also:

Constant Field Values

KEY_INDIVIDUALS

public static final String KEY_INDIVIDUALS

See Also:

Constant Field Values

KEY_LABELS

public static final String KEY_LABELS

See Also:

Constant Field Values

m_Prefix

protected String m_Prefix

the prefix of the points in the report.

m_FileRegExp

protected BaseRegExp m_FileRegExp

the regexp the files must match.

Constructor Detail

DeepLabCutCSVReader

public DeepLabCutCSVReader()

Method Detail

globalInfo

public String globalInfo()

Returns a string describing the object.

Specified by:

globalInfo in interface GlobalInfoSupporter

Specified by:

globalInfo in class AbstractOptionHandler

Returns:

a description suitable for displaying in the gui

defineOptions

public void defineOptions()

Adds options to the internal list of options.

Specified by:

defineOptions in interface OptionHandler

Overrides:

defineOptions in class AbstractReportReader<Report>

setPrefix

public void setPrefix(String value)

Sets the field prefix used in the report.

Parameters:

value - the field prefix

getPrefix

public String getPrefix()

Returns the field prefix used in the report.

Returns:

the field prefix

prefixTipText

public String prefixTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

setFileRegExp

public void setFileRegExp(BaseRegExp value)

Sets the regexp the file names must match.

Parameters:

value - the expression

getFileRegExp

public BaseRegExp getFileRegExp()

Returns the regexp the file names must match.

Returns:

the expression

fileRegExpTipText

public String fileRegExpTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

getFormatDescription

public String getFormatDescription()

Returns a string describing the format (used in the file chooser).

Specified by:

getFormatDescription in interface FileFormatHandler

Specified by:

getFormatDescription in class AbstractReportReader<Report>

Returns:

a description suitable for displaying in the file chooser

getFormatExtensions

public String[] getFormatExtensions()

Returns the extension(s) of the format.

Specified by:

getFormatExtensions in interface FileFormatHandler

Specified by:

getFormatExtensions in class AbstractReportReader<Report>

Returns:

the extension(s) (without the dot!)

determineParentID

protected int determineParentID(Report report)

Tries to determine the parent ID for the current report.

Specified by:

determineParentID in class AbstractReportReader<Report>

Parameters:

report - the report to determine the ID for

Returns:

the parent database ID, -1 if it cannot be determined

newInstance

public Report newInstance()

Returns a new instance of the report class in use.

Specified by:

newInstance in class AbstractReportReader<Report>

Returns:

the new (empty) report

readData

protected List<Report> readData()

Performs the actual reading.

Specified by:

readData in class AbstractReportReader<Report>

Returns:

the reports that were read