Package qupath.ext.biop.utils

Class Channels

  • public class Channels
extends java.lang.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

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.util.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 java.util.List<qupath.ext.biop.utils.Channels.Channel> readChannelSettings​(java.io.File settingsFile)
      Read the settings from a simple text file, generally made using writeChannelSettings(List, File) but could also be made manually
      static java.util.List<qupath.ext.biop.utils.Channels.Channel> readChannelSettings​(java.lang.String settingsString)
      Read the parameters of a simple string with each line formatted as: position, name, color, minDisplay, maxDisplay eg.
      static void setChannelSettings​(java.io.File settingsFile)
      Set the channels directly from a text file
      static void setChannelSettings​(java.util.List<qupath.ext.biop.utils.Channels.Channel> channels)
      This method actually sets the channel displays based on the channels list.
      static void writeChannelSettings​(java.util.List<qupath.ext.biop.utils.Channels.Channel> channelSettings, java.io.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 Detail

      • Channels

        public Channels()

    • Method Detail

      • setChannelSettings

        public static void setChannelSettings​(java.io.File settingsFile)
        Set the channels directly from a text file
        Parameters:
        settingsFile - the file containing the channel settings, generally produced using writeChannelSettings(List, File)

      • getCurrentChannelSettings

        public static java.util.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 or {@link Channels#setChannelSettings(List)}

      • readChannelSettings

        public static java.util.List<qupath.ext.biop.utils.Channels.Channel> readChannelSettings​(java.lang.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 or {@link Channels#setChannelSettings(List)}

      • readChannelSettings

        public static java.util.List<qupath.ext.biop.utils.Channels.Channel> readChannelSettings​(java.io.File settingsFile)
                                                                                  throws java.io.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 or {@link Channels#setChannelSettings(List)}
        Throws:
        java.io.FileNotFoundException - in case the file does not exist

      • writeChannelSettings

        public static void writeChannelSettings​(java.util.List<qupath.ext.biop.utils.Channels.Channel> channelSettings,
                                        java.io.File settingsFile)
                                 throws java.io.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:
        java.io.IOException - in case the file cannot be written