Package qupath.ext.biop.utils

Class Channels

java.lang.Object

qupath.ext.biop.utils.Channels

public class Channels
extends Object

Channels class to handle loading and saving channel settings It can modify channels based on either a simple text file or a string of the type position, name, color, minDisplay, maxDisplay eg.

1, First, #0300ff, 0, 100
 3, Third, #ff3300, 10, 1200

Also includes the possibility to save the settings to a textfile in the above format.

Constructor Summary

Constructors

Constructor	Description
Channels()

Method Summary

Modifier and Type	Method	Description
static List<qupath.ext.biop.utils.Channels.Channel>	getCurrentChannelSettings()	Return the current channel names, colors and minMax displays to a list NOTE: Channels that are not currently selected will not be sent
static List<qupath.ext.biop.utils.Channels.Channel>	readChannelSettings(File settingsFile)	Read the settings from a simple text file, generally made using writeChannelSettings(List, File) but could also be made manually
static List<qupath.ext.biop.utils.Channels.Channel>	readChannelSettings(String settingsString)	Read the parameters of a simple string with each line formatted as: position, name, color, minDisplay, maxDisplay eg.
static void	setChannelSettings(File settingsFile)	Set the channels directly from a text file
static void	setChannelSettings(List<qupath.ext.biop.utils.Channels.Channel> channels)	This method actually sets the channel displays based on the channels list.
static void	writeChannelSettings(List<qupath.ext.biop.utils.Channels.Channel> channelSettings, File settingsFile)	Write the provided Channels to a file

Methods inherited from class java.lang.Object

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

Constructor Details

Channels

public Channels()

Method Details

setChannelSettings

public static void setChannelSettings(File settingsFile)

Set the channels directly from a text file

Parameters:

settingsFile - the file containing the channel settings, generally produced using writeChannelSettings(List, File)

setChannelSettings

public static void setChannelSettings(List<qupath.ext.biop.utils.Channels.Channel> channels)

This method actually sets the channel displays based on the channels list.

Parameters:

channels - the list of channels, created with readChannelSettings(File), getCurrentChannelSettings() or readChannelSettings(String)

getCurrentChannelSettings

public static List<qupath.ext.biop.utils.Channels.Channel> getCurrentChannelSettings()

Return the current channel names, colors and minMax displays to a list NOTE: Channels that are not currently selected will not be sent

Returns:

a list that can be used with writeChannelSettings(List, File) or setChannelSettings(List)

readChannelSettings

public static List<qupath.ext.biop.utils.Channels.Channel> readChannelSettings(String settingsString)

Read the parameters of a simple string with each line formatted as: position, name, color, minDisplay, maxDisplay eg.

1, One channel, #0300ff, 0, 100
 3, Another channel, #ff3300, 10, 1200

Parameters:

settingsString - a manually created String

Returns:

a list that can be used with writeChannelSettings(List, File) or setChannelSettings(List)

readChannelSettings

public static List<qupath.ext.biop.utils.Channels.Channel> readChannelSettings(File settingsFile)
                                                                        throws FileNotFoundException

Read the settings from a simple text file, generally made using writeChannelSettings(List, File) but could also be made manually

Parameters:

settingsFile - the file with the settings.

Returns:

a list that can be used with writeChannelSettings(List, File) or setChannelSettings(List)

Throws:

FileNotFoundException - in case the file does not exist

writeChannelSettings

public static void writeChannelSettings(List<qupath.ext.biop.utils.Channels.Channel> channelSettings,
 File settingsFile)
                                 throws IOException

Write the provided Channels to a file

Parameters:

channelSettings - settings, obtained using readChannelSettings(String), readChannelSettings(File) or getCurrentChannelSettings()

settingsFile - a file that will be created or overwritten with the settings converted to text.

Throws:

IOException - in case the file cannot be written