Package sc.fiji.snt.analysis.sholl.gui

Class ShollTable

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
sc.fiji.snt.analysis.sholl.gui.ShollTable
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
public class ShollTable extends SNTTable
Implementation of SNTTable for Sholl metrics and Profile lists.
Author:
Tiago Ferreira
See Also:

  • Constructor Details

    • ShollTable

      public ShollTable()
      Instantiates a new empty table.

    • ShollTable

      public ShollTable(Profile profile)
      Instantiates a new table from a Profile
      Parameters:
      profile - the profile to be listed and/or summarized by this table

    • ShollTable

      public ShollTable(ShollStats... stats)
      Instantiates a new table capable of detailing metrics from a LinearProfileStats, a NormalizedProfileStats instance or both.
      Parameters:
      stats - the ShollStats instances from which metrics should be retrieved. It is assumed that all instances analyze the same Profile

  • Method Details

    • listProfileEntries

      public void listProfileEntries()
      Lists (details) the Profile entries. If this table is aware of ShollStats that successfully fitted a model to the profile, XY coordinates of the fitted curve are also be listed.

    • setDetailedSummary

      public void setDetailedSummary(boolean detailed)
      Sets whether extensive metrics should be listed when outputting summaries.
      Parameters:
      detailed - if true summaries will list verbose details, otherwise summaries will fall back to the 'default' repertoire of metrics

    • summarize

      public void summarize(ShollTable table, String header)
      Runs summarize(String) and appends (copies) the summary row to the specified table
      Parameters:
      table - the table to which the summary row should be copied
      header - the header for the summary row. If empty or null, the profile identifier is used
      See Also:

    • summarize

      public void summarize(String header)
      Summarizes Profile and ShollStats metrics to a new row. Note that some of the reported metrics rely on the options set in ShollAnalysisPrefsCmd. To ensure that those are read, you should run setContext(Context), so that a PrefService is set.
      Parameters:
      header - the header for the summary row. If empty or null, the profile identifier is used
      See Also:

    • setContext

      public void setContext(org.scijava.Context context) throws IllegalStateException, IllegalArgumentException
      Sets the services required by this ShollTable, namely PrefService, used to read advanced options set by ShollAnalysisPrefsCmd.
      Overrides:
      setContext in class SNTTable
      Parameters:
      context - the SciJava application context
      Throws:
      IllegalStateException - If this ShollTable already has a context
      IllegalArgumentException - If context cannot provide the services required by this ShollTable

    • hasContext

      public boolean hasContext()

    • saveSilently

      public boolean saveSilently(File file)

    • setTitle

      public void setTitle(String title)
      Description copied from class: SNTTable
      Sets the title of the table.
      Overrides:
      setTitle in class SNTTable
      Parameters:
      title - the table's title

    • getTitle

      public String getTitle()
      Description copied from class: SNTTable
      Gets the title of the table.

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

      Overrides:
      getTitle in class SNTTable
      Returns:
      the table title