Field Detail

• VERSION

  public static final String VERSION

Method Detail

• getReadableVersion

  public static String getReadableVersion()

• addViewer

  public static void addViewer(Viewer3D viewer)

• removeViewer

  public static void removeViewer(Viewer3D viewer)

• getViewers

  protected static HashMap<Integer,Viewer3D> getViewers()

• error

  public static void error(String string)

• setPlugin

  protected static void setPlugin(SNT plugin)

• getPluginInstance

  public static SNT getPluginInstance()

• nonDebugError

  protected static void nonDebugError(String string)

• error

  public static void error(String string,
                           Throwable t)

• log

  public static void log(String string)

• warn

  protected static void warn(String string)

• convertTo32bit

  protected static void convertTo32bit(ij.ImagePlus imp)
                                throws IllegalArgumentException

  Throws:

  IllegalArgumentException

• convertTo8bit

  public static void convertTo8bit(ij.ImagePlus imp)

• getMIP

  public static ij.ImagePlus getMIP(ij.ImagePlus imp)

• csvQuoteAndPrint

  public static void csvQuoteAndPrint(PrintWriter pw,
                                      Object o)

• getColorString

  protected static String getColorString(Color color)

• getColor

  protected static Color getColor(String colorName)

• stripExtension

  public static String stripExtension(String filename)

• getUniquelySuffixedTifFile

  public static File getUniquelySuffixedTifFile(File referenceFile)

• getUniquelySuffixedFile

  public static File getUniquelySuffixedFile(File referenceFile)

• saveTable

  public static void saveTable(Table<?,?> table,
                               char columnSep,
                               boolean saveColHeaders,
                               boolean saveRowHeaders,
                               File outputFile)
                        throws IOException

  Throws:

  IOException

• fileAvailable

  protected static boolean fileAvailable(File file)

• isValidURL

  protected static boolean isValidURL(String url)

• formatDouble

  public static String formatDouble(double value,
                                    int digits)

• getDecimalFormat

  public static DecimalFormat getDecimalFormat(double value,
                                               int digits)

• isDebugMode

  public static boolean isDebugMode()

  Assesses if SNT is running in debug mode

  Returns:

  the debug flag

• setDebugMode

  public static void setDebugMode(boolean b)

  Enables/disables debug mode

  Parameters:

  b - verbose flag

• findClosestPair

  public static File findClosestPair(File file,
                                     String[] pairExts)

• findClosestPair

  public static File findClosestPair(File file,
                                     String pairExt)

• similarCalibrations

  public static boolean similarCalibrations(ij.measure.Calibration a,
                                            ij.measure.Calibration b)

• getSanitizedUnit

  public static String getSanitizedUnit(String unit)

• randomPaths

  public static List<Path> randomPaths()

  Generates a list of random paths. Only useful for debugging purposes

  Returns:

  the list of random Paths

• getLut

  public static ij.process.LUT getLut(ColorTable cTable)

• getElapsedTime

  public static String getElapsedTime(long fromStart)

• buildDate

  public static String buildDate()

  Retrieves Sholl Analysis implementation date

  Returns:

  the implementation date or an empty strong if date could not be retrieved.

• getReconstructionFiles

  public static File[] getReconstructionFiles(File dir,
                                              String pattern)

  Retrieves a list of reconstruction files stored in a common directory matching the specified criteria.

  Parameters:

  dir - the directory containing the reconstruction files (.(e)swc, .traces, .json extension)

  pattern - the filename substring (case sensitive) to be matched. Only filenames containing pattern will be imported from the directory. null allowed.

  Returns:

  the list of files. An empty list is retrieved if dir is not a valid, readable directory.

• setIsLoading

  public static void setIsLoading(boolean isLoading)

• getContext

  public static Context getContext()

  Convenience method to access the context of the running Fiji instance (mainly for IJ1 plugins.

  Returns:

  the context of the running Fiji instance

• setContext

  public static void setContext(Context context)