Field Detail

• PREF_SAVE_ALL_ON_SAVE

  public static final java.lang.String PREF_SAVE_ALL_ON_SAVE

  Constant that indicates use of saving images, vois, and transfer functions.

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• PREF_SAVE_XML_THUMBNAIL

  public static final java.lang.String PREF_SAVE_XML_THUMBNAIL

  Constant that indicates the saving of the xml thumbnail during a save.

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• PREF_FLIP_NIFTI_READ

  public static final java.lang.String PREF_FLIP_NIFTI_READ

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• PREF_FILE_TEMP_DIR

  public static final java.lang.String PREF_FILE_TEMP_DIR

  Constant that indicates the file temp directory.

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• PREF_LAX_CHECK

  public static final java.lang.String PREF_LAX_CHECK

  Constant that indicates if lax file should be checked on mipav start.

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• PREF_CLOSE_FRAME_CHECK

  public static final java.lang.String PREF_CLOSE_FRAME_CHECK

  Constant that indicates if user should be prompted on closing a frame.

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• PREF_OVERWRITE_VOI_STATS

  public static final java.lang.String PREF_OVERWRITE_VOI_STATS

  Constant indicating if VOI statistics file should be overwritten.

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• PREF_DATA_PROVENANCE

  public static final java.lang.String PREF_DATA_PROVENANCE

  Constant that indicates if data provenance is turned on.

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• PREF_IMAGE_LEVEL_DATA_PROVENANCE

  public static final java.lang.String PREF_IMAGE_LEVEL_DATA_PROVENANCE

  Constant that indicates if data provenance is turned on for individual images (and saved on image-save).

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• PREF_DATA_PROVENANCE_FILENAME

  public static final java.lang.String PREF_DATA_PROVENANCE_FILENAME

  Constant that indicates the path where the system data provenance should be stored

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• PREF_DEBUG

  public static final java.lang.String PREF_DEBUG

  Constant for debug string.

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• PREF_LOGGING_ENABLED

  public static final java.lang.String PREF_LOGGING_ENABLED

  Constant for whether logging is enabled

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• PREF_QUICK_MASK_NEW

  public static final java.lang.String PREF_QUICK_MASK_NEW

  Constant that indicates if the Quick Mask operation should output to a new image

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• PREF_PAINT_TO_MASK_NEW

  public static final java.lang.String PREF_PAINT_TO_MASK_NEW

  Constant that indicates if the Paint-to-Mask operation should output to a new image

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• PREF_ZOOM_LINEAR

  public static final java.lang.String PREF_ZOOM_LINEAR

  Constant that indicates if the zoom should be linear (otherwise geometric)

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• PREF_INTENSITY_LABEL_COLOR

  public static final java.lang.String PREF_INTENSITY_LABEL_COLOR

  Constant that indicates the intensity label color.

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• PREF_INTENSITY_LABEL_BACKGROUND_COLOR

  public static final java.lang.String PREF_INTENSITY_LABEL_BACKGROUND_COLOR

  Constant that indicates the intensity label background color.

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• PREF_DEFAULT_FRAME_RATE

  public static final java.lang.String PREF_DEFAULT_FRAME_RATE

  Constant that indicates the default frame rate

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• PREF_SAVE_DEFAULTS

  public static final java.lang.String PREF_SAVE_DEFAULTS

  Constant that indicates if the last used parameters for algorithm dialogs should be used when they are opened.

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• PREF_SAVE_PROMPT_OVERWRITE

  public static final java.lang.String PREF_SAVE_PROMPT_OVERWRITE

  Constant that indicates if a prompt should be shown before an image file is overwritten.

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• PREF_SHOW_DICOM_OVERLAYS

  public static final java.lang.String PREF_SHOW_DICOM_OVERLAYS

  Constant that indicates if the DICOM overlay should be shown.

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• PREF_SHOW_IMAGE_OVERLAYS

  public static final java.lang.String PREF_SHOW_IMAGE_OVERLAYS

  Constant that indicates if the image overlay should be shown.

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• PREF_SHOW_PAINT_BORDER

  public static final java.lang.String PREF_SHOW_PAINT_BORDER

  Constant that indicates if the paint border shown.

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• PREF_SHOW_PRIVATE_TAGS

  public static final java.lang.String PREF_SHOW_PRIVATE_TAGS

  Constant that indicates if the private DICOM tags are to be shown

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• PREF_SHOW_SPLASH

  public static final java.lang.String PREF_SHOW_SPLASH

  Constant that indicates if the splash graphic should be shown when mipav starts.

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• PREF_SHOW_UI_LF

  public static final java.lang.String PREF_SHOW_UI_LF

  Class name for selected look and feel type, can also be "None" (default selection)

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• PREF_LOG_FILENAME

  public static final java.lang.String PREF_LOG_FILENAME

  Constant that indicates the pathname of the log file.

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• PREF_IMAGE_TOOLBAR_ON

  public static final java.lang.String PREF_IMAGE_TOOLBAR_ON

  Constant identifying if the miscellaneous toolbar is on by default.

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• PREF_PAINT_TOOLBAR_ON

  public static final java.lang.String PREF_PAINT_TOOLBAR_ON

  Constant indicating if the Paint Toolbar is on by default.

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• PREF_SCRIPTING_TOOLBAR_ON

  public static final java.lang.String PREF_SCRIPTING_TOOLBAR_ON

  Constant that indicates if the Scripting toolbar should be shown by default.

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• PREF_VOI_TOOLBAR_ON

  public static final java.lang.String PREF_VOI_TOOLBAR_ON

  Constant indicating if the VOI Toolbar is on by default.

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• PREF_SHORTCUTS

  public static final java.lang.String PREF_SHORTCUTS

  Constant indicating the application shortcuts (user defined).

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• PREF_DICOM_BROWSER_CONFIG

  public static final java.lang.String PREF_DICOM_BROWSER_CONFIG

  Constant indicating the DICOM browser configuration.

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• PREF_FAST_TRIPLANAR_REPAINT

  public static final java.lang.String PREF_FAST_TRIPLANAR_REPAINT

  Constant that indicates whether the triplanar frame should wait for a mouse released event before repainting all 9 tri-planar images. Inserted here because repainting 9 images in real time gets to be tedious.

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• PREF_TRIPLANAR_SNAP90

  public static final java.lang.String PREF_TRIPLANAR_SNAP90

  Constant that indicates if triplanar protractor should snap to nearest multiple of 90 degrees.

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• PREF_TRIPLANAR_SCROLL_ORIGINAL

  public static final java.lang.String PREF_TRIPLANAR_SCROLL_ORIGINAL

  Constant that indicates if the triplanar should scroll the original image

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• PREF_SHOW_LINE_ANGLE

  public static final java.lang.String PREF_SHOW_LINE_ANGLE

  Constant that indicates whether the angle of line VOIs should be shown on screen.

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• PREF_CONTINUOUS_VOI_CONTOUR

  public static final java.lang.String PREF_CONTINUOUS_VOI_CONTOUR

  Constant that indicates whether [SHIFT] must be held down to draw continuous contours (false = hold-shift).

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• PREF_VOI_POINT_DRAW_TYPE

  public static final java.lang.String PREF_VOI_POINT_DRAW_TYPE

  Constant indicating the look of VOI Points drawn on an image.

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• PREF_VOI_LPS_SAVE

  public static final java.lang.String PREF_VOI_LPS_SAVE

  Constant indicating if VOIs should be saved as LPS or file coordinates

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• PREF_TRIPLANAR_2X2_LAYOUT

  public static final java.lang.String PREF_TRIPLANAR_2X2_LAYOUT

  Constant that indicates whether the triplanar frame should use the old 2x2 layout or the newer 3x1 layout.

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• PREF_CROSSHAIR_PIXEL_GAP

  public static final java.lang.String PREF_CROSSHAIR_PIXEL_GAP

  Constant that indicates the pixel gap away from the center of the crosshair (in one direction) actual gap is 2x.

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• PREF_MENU_FONT

  public static final java.lang.String PREF_MENU_FONT

  Constant that indicates the menu font.

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• PREF_MENU_FONT_SIZE

  public static final java.lang.String PREF_MENU_FONT_SIZE

  Constant that indicates the menu font size.

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• PREF_MENU_FONT_COLOR

  public static final java.lang.String PREF_MENU_FONT_COLOR

  Constant that indicates the menu font color.

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• PREF_SHOW_VOI_NAME

  public static final java.lang.String PREF_SHOW_VOI_NAME

  Constant that indicates whether to show the VOI name.

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• PREF_SHOW_OUTPUT

  public static final java.lang.String PREF_SHOW_OUTPUT

  Constant that indicates whether to show output.

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• PREF_LAST_STACK_FLAG

  public static final java.lang.String PREF_LAST_STACK_FLAG

  Constant that indicates the last stack flag.

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• PREF_DEFAULT_IMAGE_BROWSER_DIR

  public static final java.lang.String PREF_DEFAULT_IMAGE_BROWSER_DIR

  Constant that indicates the initial directory in which to open the file chooser of the image browser.

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• PREF_MULTI_THREADING_ENABLED

  public static final java.lang.String PREF_MULTI_THREADING_ENABLED

  Constant that indicated if the multi-theading is enabled

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• PREF_GPU_COMP_ENABLED

  public static final java.lang.String PREF_GPU_COMP_ENABLED

  Constant that indicates if computing on the GPU is enabled

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• PREF_NUMBER_OF_THREADS

  public static final java.lang.String PREF_NUMBER_OF_THREADS

  Constant that specifies how many system threads user would like MIPAV to use

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• PREF_SHOW_INTENSITY_ON_LEFT_CLICK

  public static final java.lang.String PREF_SHOW_INTENSITY_ON_LEFT_CLICK

  Constant that indicates if left mouse click inside image should cause intensity value to display

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• PREF_SHOW_WINLEV_ON_RIGHT_CLICK

  public static final java.lang.String PREF_SHOW_WINLEV_ON_RIGHT_CLICK

  Constant that indicates if right mouse click inside image should cause window/level changes

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• PREF_RELATIVE_WINDOW_LEVEL

  public static final java.lang.String PREF_RELATIVE_WINDOW_LEVEL

  Constant that indicates if window/level changes should be relative to the current transfer function values

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• PREF_OPEN_IMAGES_IN_TILED_FORMAT

  public static final java.lang.String PREF_OPEN_IMAGES_IN_TILED_FORMAT

  Constant that indicates if images are to be open im tiled format

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• PREF_LAST_PAINT_BRUSH

  public static final java.lang.String PREF_LAST_PAINT_BRUSH

  Constant that indicates the last used paint brush so that it will be set as the default when new images are opened or mipav is restarted.

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• PREF_USER_FILETYPE_ASSOC

  public static final java.lang.String PREF_USER_FILETYPE_ASSOC

  Constant that indicates the user defined file type associations.

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• PREF_USER_FILETYPES

  public static final java.lang.String PREF_USER_FILETYPES

  Constant that indicates the user defined file types.

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• PREF_USER_FILETYPES_TEXTFIELDS

  public static final java.lang.String PREF_USER_FILETYPES_TEXTFIELDS

  ?

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• PREF_FILENAME_FILTER

  public static final java.lang.String PREF_FILENAME_FILTER

  Constant that indicates the filename filter.

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• PREF_IMAGE_DIR

  public static final java.lang.String PREF_IMAGE_DIR

  Constant that indicates the current image directory.

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• PREF_PLUGIN_INSTALL_DIR

  public static final java.lang.String PREF_PLUGIN_INSTALL_DIR

  Constant that indicates the current directory where plugins can be installed from.

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• PREF_VOI_TEXT_COLOR

  public static final java.lang.String PREF_VOI_TEXT_COLOR

  Constant that indicates the last used VOI text color.

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• PREF_VOI_TEXT_BACKGROUND_COLOR

  public static final java.lang.String PREF_VOI_TEXT_BACKGROUND_COLOR

  Constant that indicates the last used VOI text background color.

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• PREF_DICOM_STORAGE_DIR

  public static final java.lang.String PREF_DICOM_STORAGE_DIR

  Constant that indicates the default dicom storage directory.

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• PREF_AUTOSTART_DICOM_RECEIVER

  public static final java.lang.String PREF_AUTOSTART_DICOM_RECEIVER

  Constant that indicates whether to enable the dicom receiver on startup.

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• PREF_ASK_DICOM_RECEIVER

  public static final java.lang.String PREF_ASK_DICOM_RECEIVER

  Constant that indicates whether to ask about starting dicom receiver on startup.

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• PREF_ACTIVE_IMAGE_COLOR

  public static final java.lang.String PREF_ACTIVE_IMAGE_COLOR

  Constant that indicates the active image color.

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• PREF_ACTIVE_IMAGE_COLOR_BORDERSIZE

  public static final java.lang.String PREF_ACTIVE_IMAGE_COLOR_BORDERSIZE

  Constant that indicates the active image color border size

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• PREF_QUICKLIST_NUMBER

  public static final java.lang.String PREF_QUICKLIST_NUMBER

  number of recently used images to store in quicklist.

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• PREF_LAST_X_IMAGES

  public static final java.lang.String PREF_LAST_X_IMAGES

  constant for the names of the last X number of images used to be shown in quicklist.

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• PREF_WARN_AUDIO_AVI

  public static final java.lang.String PREF_WARN_AUDIO_AVI

  constant for warning the user when audio will be discarded from opened AVIs.

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• PREF_OVERWRITE_STATISTICS

  public static final java.lang.String PREF_OVERWRITE_STATISTICS

  constant on whether to overwrite the voi statistics file automatically

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• PREF_CROSSHAIR_CURSOR

  public static final java.lang.String PREF_CROSSHAIR_CURSOR

  Constant that indicates the crosshair cursor to be used.

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• PREF_DEFAULT_DISPLAY

  public static final java.lang.String PREF_DEFAULT_DISPLAY

  Constant to indicate default brightness and color display to screen

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• PREF_COMPLEX_DISPLAY

  public static final java.lang.String PREF_COMPLEX_DISPLAY

  Constant that indicates method used to display complex data values on MIPAV toolbar (MIPAV visually always shows magnitude or log magnitude).

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• PREF_LOGMAG_DISPLAY

  public static final java.lang.String PREF_LOGMAG_DISPLAY

  Constant that indicates whether the log of the magnitude of an image is used for image display

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• PREF_AFNI_ORDER_LOAD

  public static final java.lang.String PREF_AFNI_ORDER_LOAD

  Constant that indicates whether DICOM ordering should be used by default for loading AFNI images

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• PREF_FILE_LUT_DISPLAY

  public static final java.lang.String PREF_FILE_LUT_DISPLAY

  Constant that indicates whether image will display using a stored LUT (from image file or generic to image type)

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• PREF_INTERPOLATE_MODE

  public static final java.lang.String PREF_INTERPOLATE_MODE

  Constant that indicates the mode of image interpolation used for display

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• PREF_HISTOGRAM_DISPLAY

  public static final java.lang.String PREF_HISTOGRAM_DISPLAY

  Constant that indicates whether image is updated in real-time on histogram changes

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• PREF_TRIM_VOI

  public static final java.lang.String PREF_TRIM_VOI

  Constant that indicates the VOI Trim level variable.

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• PREF_TRIM_MASK

  public static final java.lang.String PREF_TRIM_MASK

  Constant that indicates the mask trim level variable.

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• PREF_TRIM_FLAG

  public static final java.lang.String PREF_TRIM_FLAG

  Constant that indicates the VOI Trim flag for trimming adjacent points.

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• PREF_VOI_THICKNESS

  public static final java.lang.String PREF_VOI_THICKNESS

  Constant indicating the VOI Thickness.

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• PREF_VOI_DRAW_COLOR

  public static final java.lang.String PREF_VOI_DRAW_COLOR

  the voi draw color constant.

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• PREF_VOI_START_COLOR

  public static final java.lang.String PREF_VOI_START_COLOR

  the starting color for VOIs (first drawn).

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• PREF_DATA_PROVENANCE_MODE

  public static final java.lang.String PREF_DATA_PROVENANCE_MODE

  constant for logging.

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• PREF_RGB_PAINT_COMPONENTS

  public static final java.lang.String PREF_RGB_PAINT_COMPONENTS

  Constant indicating which channels should be used for applying paint to a RGB image

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• PREF_ALWAYS_SAVE_IMG_AS_ANALYZE

  public static final java.lang.String PREF_ALWAYS_SAVE_IMG_AS_ANALYZE

  Constant that indicates whether .hdr/.img files should always be written in analyze format (as opposed to asking whether to save as interfile or nifti).

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• PREF_ALWAYS_SAVE_IMG_AS_INTERFILE

  public static final java.lang.String PREF_ALWAYS_SAVE_IMG_AS_INTERFILE

  Constant that indicates whether .hdr/.img files should always be written in interfile format (as opposed to asking whether to save as analyze or nifti).

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• PREF_ALWAYS_SAVE_IMG_AS_NIFTI

  public static final java.lang.String PREF_ALWAYS_SAVE_IMG_AS_NIFTI

  Constant that indicates whether .hdr/.img files should always be written in nifti format (as opposed to asking whether to save as analyze or interfile).

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• PREF_ALWAYS_SAVE_MNC_AS_MINC1

  public static final java.lang.String PREF_ALWAYS_SAVE_MNC_AS_MINC1

  Constant that indicates whether .mnc files should always be written in minc1 CDF format (as opposed to asking whether to save as minc1 or minc2).

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• PREF_ALWAYS_SAVE_MNC_AS_MINC2

  public static final java.lang.String PREF_ALWAYS_SAVE_MNC_AS_MINC2

  Constant that indicates whether .mnc files should always be written in minc2 HDF5 format (as opposed to asking whether to save as minc1 or minc2).

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• PREF_SCRIPT_DIR

  public static final java.lang.String PREF_SCRIPT_DIR

  Constant that indicates the script directory.

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• PREF_LAST_SCRIPT

  public static final java.lang.String PREF_LAST_SCRIPT

  Constant that indicates the last script that was run.

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• PREF_DICOM_SAVE_DICTIONARY

  public static final java.lang.String PREF_DICOM_SAVE_DICTIONARY

  constant that indicates the dicom save dictionary.

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• PREF_STARTING_HEAP_SIZE

  public static final java.lang.String PREF_STARTING_HEAP_SIZE

  The starting heap size.

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• PREF_MAX_HEAP_SIZE

  public static final java.lang.String PREF_MAX_HEAP_SIZE

  The maximum heap size.

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• PREF_RAW_EXTENTS

  public static final java.lang.String PREF_RAW_EXTENTS

  Constant that indicates the default raw image extents.

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• PREF_RAW_BIG_ENDIAN

  public static final java.lang.String PREF_RAW_BIG_ENDIAN

  Constant that indicates the default raw image big endian.

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• PREF_RAW_RESOLUTIONS

  public static final java.lang.String PREF_RAW_RESOLUTIONS

  Constant that indicates the default raw image resolutions.

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• PREF_RAW_UNITS

  public static final java.lang.String PREF_RAW_UNITS

  Constant that indicates the default raw image units.

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• PREF_RAW_TYPE

  public static final java.lang.String PREF_RAW_TYPE

  Constant that indicates the default raw image type.

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• PREF_RAW_DATA_OFFSET

  public static final java.lang.String PREF_RAW_DATA_OFFSET

  Constant that indicates the default raw image data offset.

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• PREF_LB_ROW_DEPENDENT

  public static final java.lang.String PREF_LB_ROW_DEPENDENT

  Constant that indicates the LightBox row dependant variable.

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• PREF_LB_GRID_ROW

  public static final java.lang.String PREF_LB_GRID_ROW

  Constant that indicates the LightBox grid row variable.

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• PREF_LB_GRID_COL

  public static final java.lang.String PREF_LB_GRID_COL

  Constant that indicates the LightBox grid column variable.

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• PREF_LB_GRID_SIZE

  public static final java.lang.String PREF_LB_GRID_SIZE

  Constant that indicates the LightBox grid size variable.

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• PREF_LB_INCREMENT

  public static final java.lang.String PREF_LB_INCREMENT

  Constant that indicates the increment between displayed lightbox slices

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• PREF_LB_GRID_COLOR

  public static final java.lang.String PREF_LB_GRID_COLOR

  Constant that indicates the LightBox grid color variable.

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• PREF_LB_BORDER_SIZE

  public static final java.lang.String PREF_LB_BORDER_SIZE

  Constant that indicates the LightBox border size variable.

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• PREF_LB_BORDER_COLOR

  public static final java.lang.String PREF_LB_BORDER_COLOR

  Constant that indicates the LightBox border color variable.

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• PREF_LB_SELECTED_BORDER_SIZE

  public static final java.lang.String PREF_LB_SELECTED_BORDER_SIZE

  Constant that indicates the LightBox selected border size variable.

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• PREF_LB_SELECTED_BORDER_COLOR

  public static final java.lang.String PREF_LB_SELECTED_BORDER_COLOR

  Constant that indicates the LightBox selected border color variable.

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• PREF_LB_MAG

  public static final java.lang.String PREF_LB_MAG

  Constant that indicates the LightBox magnification variable.

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• PREF_LB_LOCATION

  public static final java.lang.String PREF_LB_LOCATION

  Constant that indicates the LightBox location variable.

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• PREF_LB_TSLICE

  public static final java.lang.String PREF_LB_TSLICE

  Constant that indicates the LightBox individual t-slice variable.

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• PREF_LB_CUPDATE

  public static final java.lang.String PREF_LB_CUPDATE

  Constant that indicates continuous update of LightBox

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• PREF_APP_TITLE

  public static final java.lang.String PREF_APP_TITLE

  Constant that indicates the application title.

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• PREF_APP_ICON

  public static final java.lang.String PREF_APP_ICON

  Constant that indicates the application icon.

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• PREF_SHOW_OVERLAYS

  public static final java.lang.String PREF_SHOW_OVERLAYS

  Constant that indicates whether to show image overlays.

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• PREF_PLUGIN_ALGORITHM

  public static final java.lang.String PREF_PLUGIN_ALGORITHM

  plugin of algorithm type.

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• PREF_PLUGIN_FILE

  public static final java.lang.String PREF_PLUGIN_FILE

  plugin of file type.

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• PREF_PLUGIN_VIEW

  public static final java.lang.String PREF_PLUGIN_VIEW

  plugin of view type.

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• PREF_NINDS_ANON_PLUGIN_INPUTDIR

  public static final java.lang.String PREF_NINDS_ANON_PLUGIN_INPUTDIR

  ?

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• PREF_NINDS_ANON_PLUGIN_OUTPUTDIR

  public static final java.lang.String PREF_NINDS_ANON_PLUGIN_OUTPUTDIR

  ?

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• PREF_NINDS_ANON_PLUGIN_CSVDIR

  public static final java.lang.String PREF_NINDS_ANON_PLUGIN_CSVDIR

  ?

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  Constant Field Values

• ITEM_SEPARATOR

  public static final java.lang.String ITEM_SEPARATOR

  The character that separates items (such as in the user file type definitions).

  See Also:

  Constant Field Values

• PREF_LEVEL

  public static final java.lang.String PREF_LEVEL

  See Also:

  Constant Field Values

• PREF_WINDOW

  public static final java.lang.String PREF_WINDOW

  See Also:

  Constant Field Values

• PREF_MIN

  public static final java.lang.String PREF_MIN

  See Also:

  Constant Field Values

• PREF_MAX

  public static final java.lang.String PREF_MAX

  See Also:

  Constant Field Values

• PREF_NDAR_PLUGIN_SERVER

  public static final java.lang.String PREF_NDAR_PLUGIN_SERVER

  See Also:

  Constant Field Values

• PREF_NDAR_PLUGIN_DATASTRUCT_NAME

  public static final java.lang.String PREF_NDAR_PLUGIN_DATASTRUCT_NAME

  See Also:

  Constant Field Values

• PREF_NDAR_PLUGIN_OUTPUT_DIR

  public static final java.lang.String PREF_NDAR_PLUGIN_OUTPUT_DIR

  See Also:

  Constant Field Values

• PREF_NDAR_PLUGIN_CSV_DIR

  public static final java.lang.String PREF_NDAR_PLUGIN_CSV_DIR

  See Also:

  Constant Field Values

• PREF_BRICS_PLUGIN_OUTPUT_DIR

  public static final java.lang.String PREF_BRICS_PLUGIN_OUTPUT_DIR

  See Also:

  Constant Field Values

• PREF_BRICS_PLUGIN_CSV_DIR

  public static final java.lang.String PREF_BRICS_PLUGIN_CSV_DIR

  See Also:

  Constant Field Values

• PREF_BRICS_PLUGIN_BIDS_DIR

  public static final java.lang.String PREF_BRICS_PLUGIN_BIDS_DIR

  See Also:

  Constant Field Values

• PREF_BRICS_CONFLICT_RESOLUTION

  public static final java.lang.String PREF_BRICS_CONFLICT_RESOLUTION

  See Also:

  Constant Field Values

• PREF_PAINT_OPACITY

  public static final java.lang.String PREF_PAINT_OPACITY

  See Also:

  Constant Field Values

• PREF_BUG_REPORT_NAME

  public static final java.lang.String PREF_BUG_REPORT_NAME

  See Also:

  Constant Field Values

• PREF_BUG_REPORT_EMAIL

  public static final java.lang.String PREF_BUG_REPORT_EMAIL

  See Also:

  Constant Field Values

• PREF_BUG_REPORT_URGENCY

  public static final java.lang.String PREF_BUG_REPORT_URGENCY

  See Also:

  Constant Field Values

• PREF_USE_INCORRECT_ACPC_XDIM

  public static final java.lang.String PREF_USE_INCORRECT_ACPC_XDIM

  See Also:

  Constant Field Values

• PREF_FORCE_HISTO_UBYTE

  public static final java.lang.String PREF_FORCE_HISTO_UBYTE

  See Also:

  Constant Field Values

• PREF_MAX_DEBUG_LINES

  public static final java.lang.String PREF_MAX_DEBUG_LINES

  See Also:

  Constant Field Values

• PREF_DEBUG_MINOR

  public static final java.lang.String PREF_DEBUG_MINOR

  See Also:

  Constant Field Values

• PREF_DEBUG_ALGORITHM

  public static final java.lang.String PREF_DEBUG_ALGORITHM

  See Also:

  Constant Field Values

• PREF_DEBUG_FILEIO

  public static final java.lang.String PREF_DEBUG_FILEIO

  See Also:

  Constant Field Values

• PREF_DEBUG_COMMS

  public static final java.lang.String PREF_DEBUG_COMMS

  See Also:

  Constant Field Values

• PREF_DEBUG_SCRIPTING

  public static final java.lang.String PREF_DEBUG_SCRIPTING

  See Also:

  Constant Field Values

• DEFINITION_SEPARATOR

  public static final java.lang.String DEFINITION_SEPARATOR

  The character that separates an item from its value in a definition or mapping (such as in the user file type definitions).

  See Also:

  Constant Field Values

• DEBUG_MINOR

  public static final int DEBUG_MINOR

  Constant used to identify debugging category for general output.

  See Also:

  Constant Field Values

• DEBUG_ALGORITHM

  public static final int DEBUG_ALGORITHM

  Constant used to identify debugging category for general output by algorithms.

  See Also:

  Constant Field Values

• DEBUG_FILEIO

  public static final int DEBUG_FILEIO

  Constant used to identify debugging category for general output by FileIO.

  See Also:

  Constant Field Values

• DEBUG_COMMS

  public static final int DEBUG_COMMS

  Constant used to identify debugging category for general output by communications.

  See Also:

  Constant Field Values

• DEBUG_SCRIPTING

  public static final int DEBUG_SCRIPTING

  Constant used to identify debugging category for output of scripting system messages.

  See Also:

  Constant Field Values

• CACHED_MAX_DEBUG_LINES

  public static int CACHED_MAX_DEBUG_LINES

  Constant used to identify the maximum number of lines in the debugging panel. This is initialized from the properties file and updated whenever changed via the options panel (this value is used every time a debug line is output so access to this value needs to be as fast as possible)

• DATA_PROVENANCE_SCHEMA

  public static final java.lang.String DATA_PROVENANCE_SCHEMA

  The schema for the data provenance xml files

  See Also:

  Constant Field Values

• SAVE_DICOM_TAGS

  public static final java.lang.String SAVE_DICOM_TAGS

  Dicom tags to be saved

  See Also:

  Constant Field Values

• mipavProps

  private static java.util.Properties mipavProps

  A list of MIPAV properties.

• defaultProps

  private static java.util.Properties defaultProps

  A default list of properties used if the mipav.preferences file cannot be found.

• messageFrame

  private static ViewJFrameMessage messageFrame

  Reference to the message frame where debug information can be displayed.

• preferencesFileName

  private static java.lang.String preferencesFileName

  The MIPAV preferences file name (without path).

• preferencesDir

  private static java.lang.String preferencesDir

  The place where user-individual mipav files should be put.

• preferencesFile

  private static java.lang.String preferencesFile

  The MIPAV preferences file path and name.

• userShortcutTable

  private static java.util.Hashtable<java.lang.String,​javax.swing.KeyStroke> userShortcutTable

  Hashtable that holds all user-defined shortcuts

• defaultShortcutTable

  private static java.util.Hashtable<java.lang.String,​javax.swing.KeyStroke> defaultShortcutTable

  Hashtable that holds the default shortcuts

• currentShortcut

  private static javax.swing.KeyStroke currentShortcut

  The current shortcut

• logConfig

  private static Preferences.LogConfig logConfig

  The current logging configuration

• DEFAULT_LOG_LEVEL

  private static Preferences.LogLevel DEFAULT_LOG_LEVEL

  The default log level

Constructor Detail

• Preferences

  public Preferences()

Method Detail

• addShortcut

  public static boolean addShortcut​(java.lang.String command)

  Adds a new shortcut to the hashtable. if there is already a command predefined for the keystroke set from setShortcut(), it will be removed then replaced with the new command.

  Parameters:

  command - the command to map

  Returns:

  DOCUMENT ME!

• addShortcut

  public static boolean addShortcut​(java.lang.String command,
                                    javax.swing.KeyStroke shortcut)

  Adds a new shortcut to the hashtable with a given keystroke. if there is already a command predefined for the keystroke set from setShortcut(), it will be removed then replaced with the new command.

  Parameters:

  command - the command to map

  Returns:

  DOCUMENT ME!

• buildShortcutTable

  public static final void buildShortcutTable()

  Builds a hashtable of actioncommands (keys) with associated keystrokes from the Preferences file.

• getDebug

  public static final java.lang.String getDebug()

  Gets all the text printed to the debug panel.

  Returns:

  String representation of debug panel (new lines are removed)

• data

  public static final void data​(java.lang.String string)

  Prints to data tab

  Parameters:

  string - String string to be output

• getData

  public static final java.lang.String getData()

  Gets all the text printed to the data panel.

  Returns:

  String representation of data panel (new lines are removed)

• debug

  public static final void debug​(java.lang.String string)

  If at least one debug level is turned on, output the string.

  Parameters:

  string - String string to be output

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2)

  If at least one debug level is turned on, output the string. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String string to be output

  string2 - String string to be output

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2,
                                 java.lang.String string3)

  If at least one debug level is turned on, output the string. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String string to be output

  string2 - String string to be output

  string3 - String string to be output

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2,
                                 java.lang.String string3,
                                 java.lang.String string4)

  If at least one debug level is turned on, output the string. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String string to be output

  string2 - String string to be output

  string3 - String string to be output

  string4 - String string to be output

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2,
                                 java.lang.String string3,
                                 java.lang.String string4,
                                 java.lang.String string5)

  If at least one debug level is turned on, output the string. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String string to be output

  string2 - String string to be output

  string3 - String string to be output

  string4 - String string to be output

  string5 - String string to be output

• debug

  public static final void debug​(java.lang.String string,
                                 int category)

  If the debug is turned on for the given level, output to the messageFrame.

  Parameters:

  string - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2,
                                 int category)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2,
                                 java.lang.String string3,
                                 int category)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 char string2,
                                 java.lang.String string3,
                                 int category)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 boolean string2,
                                 java.lang.String string3,
                                 int category)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 double string2,
                                 java.lang.String string3,
                                 int category)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.Object string2,
                                 java.lang.String string3,
                                 int category)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2,
                                 java.lang.String string3,
                                 java.lang.String string4,
                                 int category)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  string4 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2,
                                 java.lang.String string3,
                                 java.lang.String string4,
                                 java.lang.String string5,
                                 int category)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  string4 - String to be output

  string5 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string,
                                 int category,
                                 Preferences.LogLevel level)

  If the debug is turned on for the given level, output to the messageFrame.

  Parameters:

  string - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2,
                                 int category,
                                 Preferences.LogLevel level)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2,
                                 java.lang.String string3,
                                 int category,
                                 Preferences.LogLevel level)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 char string2,
                                 java.lang.String string3,
                                 int category,
                                 Preferences.LogLevel level)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 boolean string2,
                                 java.lang.String string3,
                                 int category,
                                 Preferences.LogLevel level)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 double string2,
                                 java.lang.String string3,
                                 int category,
                                 Preferences.LogLevel level)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.Object string2,
                                 java.lang.String string3,
                                 int category,
                                 Preferences.LogLevel level)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2,
                                 java.lang.String string3,
                                 java.lang.String string4,
                                 int category,
                                 Preferences.LogLevel level)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  string4 - String to be output

  level - int level of debug to check

• debug

  public static final void debug​(java.lang.String string1,
                                 java.lang.String string2,
                                 java.lang.String string3,
                                 java.lang.String string4,
                                 java.lang.String string5,
                                 int category,
                                 Preferences.LogLevel level)

  If the debug is turned on for the given level, output to the messageFrame. This is a overriden method variant that takes multiple string parameters.

  Parameters:

  string1 - String to be output

  string2 - String to be output

  string3 - String to be output

  string4 - String to be output

  string5 - String to be output

  level - int level of debug to check

• debugLevel

  public static final boolean debugLevel​(int category)

  Indicates whether debug is turned on for the given level.

  Parameters:

  level - debugging level to check for

  Returns:

  true if the given debugging level is activated

• getDefaultDisplay

  public static Preferences.DefaultDisplay getDefaultDisplay()

  Returns how pixel values of images are displayed in terms or brightness values and possible colors.

  Returns:

  The default display enumeration.

• getComplexDisplay

  public static Preferences.ComplexDisplay getComplexDisplay()

  Returns how pixel values are displayed on the MIPAV toolbar for complex images. Although MIPAV always displays the magnitude or log magnitude when viewing an image, the toolbar can display both real and complex components.

  Returns:

  The complex display enumeration, includes number of parts that the complex display requires

• getInterpolateDisplay

  public static Preferences.InterpolateDisplay getInterpolateDisplay()

  Returns how pixel values are interpolated for displayed slices. Default is nearest neighbor.

• initDebugPreferences

  public static final void initDebugPreferences()

  this method must be invoked very early on in the startup sequence (typically in the startup main method or ViewUserInterface. This sets up the logging which other initialization code relies on - for example, if there is another error later in the initialization process, that error might call a debug method which means the debug variables must already have been initialized.

• getDebugPreferences

  public static final Preferences.LogConfig getDebugPreferences()

  Gets the LogConfiguration for logging categories (minor, algorithm, fileIO, comms, scripting).

  Returns:

  LogConfig the logging configuration

• getDefaultFrameRate

  public static float getDefaultFrameRate()

  Gets the default frame rate used in saving AVI movies. Default value is 10.0.

  Returns:

  the default frame rate as a floating point number.

• getDefaultHostKey

  public static java.lang.String getDefaultHostKey()

  Accessor to get the default chat/file server host key.

  Returns:

  default host key

• getDefaultServerKey

  public static java.lang.String getDefaultServerKey()

  Accessor to get default DICOM image server key.

  Returns:

  default server key

• getDefaultShortcutTable

  public static java.util.Hashtable<java.lang.String,​javax.swing.KeyStroke> getDefaultShortcutTable()

  Gets the Default Hashtable used to store the shortcut keystrokes and commands.

  Returns:

  Hashtable the shortcut hashtable

• getDefaultStorageKey

  public static java.lang.String getDefaultStorageKey()

  Accessor to get default DICOM image storage location.

  Returns:

  default storage information

• getDICOMBrowserTableConfiguration

  public static java.util.Vector<java.lang.String> getDICOMBrowserTableConfiguration()

  Gets the user-configured columns that indicate the DICOM tags that are displayed in the DICOM browser table.

  Returns:

  Vector List of strings that identify the columns.

• getDICOMSaveDictionary

  public static final java.lang.String getDICOMSaveDictionary()

  Accessor to get the default DICOM Save Dictionary (which tags to save into XML header.

  Returns:

  String The full path of the dictionary in which a subset of the DICOM tags are stored.

• getFileFilter

  public static int getFileFilter()

  Returns the index of the latest used file filter.

  Returns:

  the index of the latest used file filter.

• getFileTempDir

  public static java.lang.String getFileTempDir()

  Returns the temporary directory which is used to store files to be deleted.

  Returns:

  the temporary directory which is used to store files to be deleted.

• getHostIP

  public static java.lang.String getHostIP​(java.lang.String AETitle)

  Accessor to get host (chat/file) server Internet Protocol for selected Name.

  Parameters:

  AETitle - application entity title

  Returns:

  IP address of asssociated Name

• getIconName

  public static final java.lang.String getIconName()

  Returns the name of the application icon.

  Returns:

  string containing the name of the system icon

• getImageDirectory

  public static java.lang.String getImageDirectory()

  Returns the image directory used last time.

  Returns:

  the image directory used last time.

• getIP

  public static java.lang.String getIP​(java.lang.String AETitle)

  Accessor to get DICOM image server Internet Protocol for selected AETitle.

  Parameters:

  AETitle - application entity title

  Returns:

  IP address of asssociated AETitle

• getLastImageAt

  public static final java.lang.String getLastImageAt​(int index)

  Returns the image name of "last X images" at the given index. Index should be between 0 and 3.

  Parameters:

  index - Index of image.

  Returns:

  Name of image at index.

• getLastOpenSequenceChannels

  public static final java.lang.String getLastOpenSequenceChannels()

  Used by ViewOpenImageSequence to get the saved number of channels used when opening an image sequence.

  Returns:

  String - the value that was saved to the preferences file, represented by a String, of the number of channels that were used in the corresponding text box of this frame the last time the value was saved

• getLastOpenSequenceOrdering

  public static final java.lang.String getLastOpenSequenceOrdering()

  Used by ViewOpenImageSequence to get the Z-C-T ordering of data used when opening an image sequence.

  Returns:

  String - the value that was saved to the preferences file, represented by a String, of the Z-C-T ordering of data that was used in the corresponding text box of this frame the last time the value was saved

• getLastOpenSequencePath

  public static final java.lang.String getLastOpenSequencePath()

  Used by ViewOpenImageSequence to get the last path used when opening an image sequence.

  Returns:

  String

• getLastOpenSequenceSlices

  public static final java.lang.String getLastOpenSequenceSlices()

  Used by ViewOpenImageSequence to get the saved number of slices used when opening an image sequence.

  Returns:

  String - the value that was saved to the preferences file, represented by a String, of the number of slices that were used in the corresponding text box of this frame the last time the value was saved

• getLastOpenSequenceTimePoints

  public static final java.lang.String getLastOpenSequenceTimePoints()

  Used by ViewOpenImageSequence to get the saved number of time points used when opening an image sequence.

  Returns:

  String - the value that was saved to the preferences file, represented by a String, of the number of time points that were used in the corresponding text box of this frame the last time the value was saved

• getLastXImages

  public static final java.lang.String[] getLastXImages()

  Gets the names of the last X number of images that were loaded from the Preferences file. Shortens the names so the menu isn't too wide.

  Returns:

  Array of strings representing the last images that were loaded

• getMaxDebugLines

  public static int getMaxDebugLines()

  Returns:

  the max number of debug lines that are output

• getMipavProps

  public static java.util.Properties getMipavProps()

  Returns:

  the mipavProps

• getNextHostKey

  public static java.lang.String getNextHostKey()

  Returns the next host key.

  Returns:

  The next host key.

• getNextServerKey

  public static java.lang.String getNextServerKey()

  Returns the next server key.

  Returns:

  The next server key.

• getNextStorageKey

  public static java.lang.String getNextStorageKey()

  Returns the next storage key.

  Returns:

  The next storage key.

• getNumberOfThreads

  public static int getNumberOfThreads()

  The number of threads available for MIPAV for processing. MIPAV typically uses this number for highly-parallel algorithm computations.

  Returns:

  the number of threads available for mipav

• getOverlayNames

  public static final java.lang.String[] getOverlayNames​(boolean isDicom)

  Retrieves the list of overlay names (user can type whatever).

  Parameters:

  isDicom - boolean is this a dicom image

  Returns:

  String[] array of strings for overlay labeling

• getOverlays

  public static final java.lang.String[] getOverlays​(boolean isDicom)

  Gets the image overlay codes (they identify what to display in the corners of the image), from the preference file.

  Parameters:

  isDicom - if true loads the overlay IDs for a DICOM image

  Returns:

  the overlay codes that identifies what should be displayed.

• getPluginUserDir

  public static final java.lang.String getPluginUserDir()

  Returns String indicating the directory where plugin class files are stored. If this property has not been set, then the image Directory is returned.

  Returns:

  directory name for the property PluginUserDir or the directory name for the property ImageDirectory if PluginUserDir is not set.

• getPluginInstallDirectory

  public static java.lang.String getPluginInstallDirectory()

  Returns the directory last used for installing plugins.

  Returns:

  the directory last used for installing plugins.

• getPort

  public static int getPort​(java.lang.String AETitle)

  Accessor to get DICOM image server's port for selected AETitle.

  Parameters:

  AETitle - application entity title

  Returns:

  port address of asssociated AETitle

• getPreferencesDir

  public static final java.lang.String getPreferencesDir()

  Return the directory where mipav-generated, user-specific files should be placed.

  Returns:

  the place to put user-specific files

• getProperty

  public static final java.lang.String getProperty​(java.lang.String key)

  Accessor to return a specfic properties given a key.

  Parameters:

  key - the property key.

  Returns:

  the mipav property. The method returns null if the property is not found.

• getScriptFile

  public static final java.lang.String getScriptFile()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• getScriptsDirectory

  public static final java.lang.String getScriptsDirectory()

  Returns the default script directory. if null, returns the user's current working directory + "scripts"

  Returns:

  script dir

• getShortcut

  public static javax.swing.KeyStroke getShortcut​(java.lang.String command)

  Returns a keystroke shortcut for the given command.

  Parameters:

  command - String the command to check

  Returns:

  KeyStroke the shortcut's keystroke

• getShortcutCommand

  public static java.lang.String getShortcutCommand​(javax.swing.KeyStroke ks)

  Gets the command associated with the shortcut (if there is one).

  Parameters:

  ks - KeyStroke the keystroke to check

  Returns:

  String the command associated (or null if none)

• getSubsampleDimensions

  public static final java.awt.Dimension getSubsampleDimensions()

  Used by ViewOpenImageSequence to get the subsample dimensions that were saved in the preferences file.

  Returns:

  Dimension - the dimension that was last used to subsample an image while using the ViewOpenImageSequence tool, null if dimension is invalid in the preferences file

• getTrimVoi

  public static final float getTrimVoi()

  Accessor to get the TRIM parameter (trimming VOIcontour of points). Default value is 0.3 which trims some of the points of the contours.

  Returns:

  the trim value.

• getTrimMask

  public static final float getTrimMask()

  Accessor to get the TRIM parameter (trimming VOIcontour of points). Default value is 0.3 which trims no points in the contours.

  Returns:

  the trim value.

• getTrimAdjacient

  public static boolean getTrimAdjacient()

  Accessor to get the trim parameter (trimming contour of adjacent points).

  Returns:

  the trim boolean to indicate if the directly adjacent points should be trimmed.

• getUserShortcutTable

  public static java.util.Hashtable<java.lang.String,​javax.swing.KeyStroke> getUserShortcutTable()

  Gets the User defined Hashtable used to store the shortcut keystrokes and commands.

  Returns:

  Hashtable the shortcut hashtable

• getVOIColorIncrement

  public static int getVOIColorIncrement()

  Gets the VOI color increment value. Ben add here.

  Returns:

  int

• getVOIDrawColor

  public static java.awt.Color getVOIDrawColor()

  Gets the VOI draw color.

  Returns:

  Color color to draw with

• getVOIThickness

  public static int getVOIThickness()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• is

  public static final boolean is​(java.lang.String propertyName)

  Gets the boolean state of the property, where in the preferences file the "yes", "on", "true" all return true, but anything else (or non-existent property) returns false. This method is provided for semantic preference, but is exactly the same as (in fact, calls) isPreference.

  Parameters:

  propertyName - Name of a property in preferences to check.

  Returns:

  boolean true when the named property has the String the "yes", "on", "true". false for any other string, or if the property does not exist.

  See Also:

  isPreference(String)

• isDebug

  public static final boolean isDebug()

  Returns flag indicating if the debug flag is true or false. (and in preferences v2, if debug level is zero, returns false. Returns true if debug level is greater than 0.)

  debug level is the amount of output given for debugging mipav.

  Returns:

  returns true if either debug flag is true or level is greater than zero and false if either debug flag is false or level is zero.

• isDefaultCommand

  public static boolean isDefaultCommand​(java.lang.String command)

  DOCUMENT ME!

  Parameters:

  command - DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• isDefaultKeyStroke

  public static boolean isDefaultKeyStroke​(javax.swing.KeyStroke ks)

  DOCUMENT ME!

  Parameters:

  ks - DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• isGpuCompEnabled

  public static boolean isGpuCompEnabled()

  Indicates whether GPU-computing should be enabled. The renderer and algorithms use this information for processing

  Returns:

  true if gpu compinting is enabled

• isInterpolateDisplay

  public static boolean isInterpolateDisplay()

  Maintained for backwards compatibility. If interpolation mode is equal to nearest neighbor, then returns false, otherwise returns true.

  Returns:

• isMultiThreadingEnabled

  public static boolean isMultiThreadingEnabled()

  Indicates whether multi-threading should be enabled for algorithms. Most algorithms check this before launching highly-parallel processes (such as FFT).

  Returns:

  true if multi-threading is enabled

• isHistogramDisplay

  public static boolean isHistogramDisplay()

  Indicates whether the image display should be updated in real-time as histogram LUTs are changed

  Returns:

  true if real-time operation should occur

• isPreference

  public static final boolean isPreference​(java.lang.String propertyName)

  Gets the boolean state of the property, where in the preferences file the "yes", "on", "true" all return true, but anything else (or non-existent property) returns false. While not as intuitive, perhaps, as some of the specially named property-retrieval methods (eg., isSplashScreen), this method can be used to replace all of those methods when the preferences property is known. It can also be convenient for limited-use properties used in debugging.

  Parameters:

  propertyName - Name of a property in preferences to check.

  Returns:

  boolean true when the named property has the String the "yes", "on", "true". false for any other string, or if the property does not exist.

• isPreferenceSet

  public static final boolean isPreferenceSet​(java.lang.String propertyName)

  Returns whether the user has a preference indicated for a particular property. Note that this just checks for some value, not necessarily a "true" value.

  Parameters:

  propertyName - the name of the property to check for

  Returns:

  true if there is some preference set for the given property name

• print

  public static void print()

  Prints mipav.preferences to System.out.

• read

  public static boolean read()

  Reads the "mipav.preferences" file from the user's 'home' directory.

  Returns:

  true if found else false

• removeProperty

  public static final void removeProperty​(java.lang.String key)

  Removes the property key from the MIPAV property list.

  Parameters:

  key - the property key.

• removeShortcut

  public static void removeShortcut​(java.lang.String commandToRemove)

  Removes a shortcut from the table.

  Parameters:

  commandToRemove - String

• save

  public static boolean save()

  Saves preference file to the user's 'home' directory.

  Returns:

  boolean true if successful, false otherwise

• saveShortcuts

  public static final void saveShortcuts()

  Sets the property for shortcuts by building string from ViewUserInterface's Shortcut Hashtable.

• saveSubsampleDimensions

  public static final void saveSubsampleDimensions​(java.awt.Dimension subsampleDimension)

  Used by ViewOpenImageSequence to save its subsample dimensions for the next time it is opened. The dimension is actually saved as its two parts, width and height

  Parameters:

  subsampleDimension - Dimension - the subsample dimension to save

• setAlwaysSaveImgAsAnalyze

  public static final void setAlwaysSaveImgAsAnalyze​(boolean doSaveAnalyze)

  Sets whether all imgs should be saved in analyze format (i.e., don't ask about whether to save as analyze/interfile/nifti).

  Parameters:

  doSaveAnalyze - whether to always save .hdr/.img files as analyze format files

• setAlwaysSaveImgAsInterfile

  public static final void setAlwaysSaveImgAsInterfile​(boolean doSaveInterfile)

  Sets whether all imgs should be saved in interfile format (i.e., don't ask about whether to save as analyze/interfile/nifti).

  Parameters:

  doSaveInterfile - whether to always save .hdr/.img files as interfile format files

• setAlwaysSaveImgAsNifti

  public static final void setAlwaysSaveImgAsNifti​(boolean doSaveNifti)

  Sets whether all imgs should be saved in nifti format (i.e., don't ask about whether to save as analyze/interfile/nifti).

  Parameters:

  doSaveNifti - whether to always save .hdr/.img files as nifti format files

• setAlwaysSaveMncAsMinc1

  public static final void setAlwaysSaveMncAsMinc1​(boolean doSaveMinc1)

  Sets whether all mncs should be saved in minc1 cdf format (i.e., don't ask about whether to save as minc1/minc2).

  Parameters:

  doSaveMinc1 - whether to always save .mnc files as minc1 cdf format files

• setAlwaysSaveMncAsMinc2

  public static final void setAlwaysSaveMncAsMinc2​(boolean doSaveMinc2)

  Sets whether all mncs should be saved in minc2 hdf5 format (i.e., don't ask about whether to save as minc1/minc2).

  Parameters:

  doSaveMinc2 - whether to always save .mnc files as minc2 hdf5 format files

• setCurrentShortcut

  public static void setCurrentShortcut​(javax.swing.KeyStroke ks)

  Sets the current keystroke shortcut for assignment once a command has been passed in.

  Parameters:

  ks - KeyStroke the shortcut keystroke

• setDebugLevels

  public static final void setDebugLevels​(java.util.Map<java.lang.Integer,​java.lang.String> debugLevels)

  Sets the debug levels

  Parameters:

  levels - a Map of Category (int) -> LogLevel.

• setDefaultDisplay

  public static void setDefaultDisplay​(Preferences.DefaultDisplay display)

  Sets the default display mode for 2D/3D image display.

  Parameters:

  display - the DefaultDisplay type

• setDICOMBrowserTableConfiguration

  public static boolean setDICOMBrowserTableConfiguration​(java.util.Vector<java.lang.String> newConfiguration)

  Sets the user-configured columns that indicate the DICOM tags that are displayed in the DICOM browser table.

  Parameters:

  newConfiguration - Vector List of strings that identify the columns.

  Returns:

  boolean Success or failure of the setting the columns.

• setFileFilter

  public static void setFileFilter​(int fileFilterIndex)

  Sets the current used file filter as the latest used file filter.

  Parameters:

  fileFilterIndex - the index of the current used file filter.

• setFileTempDir

  public static void setFileTempDir​(java.lang.String tempDir)

  Sets the temporary directory which is used for files which will be deleted.

  Parameters:

  tempDir - the temporary directory.

• setImageDirectory

  public static void setImageDirectory​(java.io.File imageDirectory)

  Sets the image directory as the latest used image directory.

  Parameters:

  imageDirectory - the current used image directory.

• setInterpolationMode

  public static void setInterpolationMode​(Preferences.InterpolateDisplay interp)

  Sets the display interpolation mode for 2D image display.

  Parameters:

  interp - the InterpolateDisplay type

• setLastImage

  public static final void setLastImage​(java.lang.String name,
                                        boolean multiFile,
                                        int numDims)

  Sets the last image loaded in the Preferences file. If it is a duplicate, moves it up on the list.

  Parameters:

  name - Full pathname of last image loaded.

  multiFile - true if the last image was a multi-file image, false otherwise

  numDims - DOCUMENT ME!

• setLastOpenSequenceParams

  public static final void setLastOpenSequenceParams​(java.lang.String slices,
                                                     java.lang.String channels,
                                                     java.lang.String timePoints,
                                                     java.lang.String ordering)

  Used by ViewOpenImageSequence to save the user's most recent slices, channels, time points, and ordering that were specified in the component.

  Parameters:

  slices - String - number of slices in the slices text box of the ViewOpenImageSequence frame

  channels - String - number of channels in the channels text box of the ViewOpenImageSequence frame

  timePoints - String - number of time points in the time points text box of the ViewOpenImageSequence frame

  ordering - String - ordering sequence used in the radio button panel of the ViewOpenImageSequence frame

• setLastOpenSequencePath

  public static final void setLastOpenSequencePath​(java.lang.String path)

  Used by ViewOpenImageSequence to save the path used when opening an image sequence.

  Parameters:

  path - DOCUMENT ME!

• setMessageFrame

  public static final void setMessageFrame​(ViewJFrameMessage mFrame)

  Sets the message frame.

  Parameters:

  mFrame - Message frame to set.

• setMaxDebugLines

  public static void setMaxDebugLines​(int lines)

  Sets the maximum number of debug lines that are output

  Parameters:

  int - max number of debug lines

• setOverlayNames

  public static final void setOverlayNames​(boolean isDicom,
                                           java.lang.String[] overlays)

  Sets the labels for each overlay position. The labels can be user input with any text and will be displayed before the overlay values

  Parameters:

  isDicom - boolean is the image DICOM

  overlays - String[] array of strings (16) for each of the overlay positions

• setOverlays

  public static final void setOverlays​(boolean isDicom,
                                       java.lang.String[] overlays)

  Sets the overlay tag identifiers in the preference file.

  Parameters:

  isDicom - if true identifies the tags as a list of DICOMOverlays else identifies the tags as ImageOverlays (i.e., it is not a DICOM image)

  overlays - an array of 16 strings (4 for each corner) that identifies what is to be displayed in the image.

• setPluginInstallDirectory

  public static void setPluginInstallDirectory​(java.io.File pluginInstallDirectory)

  Sets the plugin install directory.

• setPreferencesFileName

  public static final void setPreferencesFileName​(java.lang.String fileName)

  Change the file name of the preferences file we should use (without any path).

  Parameters:

  fileName - the file name (eg mipav.preferences), which should be in $HOME/mipav/

• setPreferencesFileDirectory

  public static final void setPreferencesFileDirectory​(java.lang.String fileDir)

  Change the file directory of the preferences file.

  Parameters:

  fileDir - the file directory, defaults to $HOME/mipav/

• setProperty

  public static final boolean setProperty​(java.lang.String key,
                                          java.lang.Object value)

  Sets the property key in the MIPAV property list and saves it to a file.

  Parameters:

  key - the property key.

  value - the value of the property key.

  Returns:

  true if the property was set and saved successfully, false otherwise

• setScriptFile

  public static final void setScriptFile​(java.lang.String scriptFile)

  DOCUMENT ME!

  Parameters:

  scriptFile - DOCUMENT ME!

• setScriptsDirectory

  public static final void setScriptsDirectory​(java.lang.String scriptsDirectory)

  Sets the scripts directory to the new scripts directory.

  Parameters:

  scriptsDirectory - the new scripts directory

• setShowDICOMOverlays

  public static final void setShowDICOMOverlays​(boolean doShow)

  Sets whether to show the DICOM overlays.

  Parameters:

  doShow - boolean true means show DICOM overlays

• setShowImageOverlays

  public static final void setShowImageOverlays​(boolean doShow)

  Sets whether to show the Image overlays.

  Parameters:

  doShow - boolean true means show image overlays

• buildDefaultShortcuts

  private static java.util.Hashtable<java.lang.String,​javax.swing.KeyStroke> buildDefaultShortcuts()

  Builds the default shortcut hashtable (not user modifiable).

  Returns:

  default shortcut hashtable

• resetToDefaults

  public static void resetToDefaults()

  Resets the current MIPAV properties to the defaults and saves the preferences file. Cannot be undone.

• debugMessageFrameAppend

  public static void debugMessageFrameAppend​(java.lang.String string)

  Appends the specified message to the message frame. Clears the message frame first if the number of lines exceeds the maximum number of lines allowed in the frame.

• isLogMinorEnabled

  public static boolean isLogMinorEnabled()

• isLogAlgorithmEnabled

  public static boolean isLogAlgorithmEnabled()

• isLogFileIOEnabled

  public static boolean isLogFileIOEnabled()

• isLogCommsEnabled

  public boolean isLogCommsEnabled()

• isLogScriptingEnabled

  public boolean isLogScriptingEnabled()

• setLogLevelMinor

  public void setLogLevelMinor​(Preferences.LogLevel level)

• setLogLevelAlgorithm

  public void setLogLevelAlgorithm​(Preferences.LogLevel level)

• setLogLevelFileIO

  public void setLogLevelFileIO​(Preferences.LogLevel level)

• setLogLevelComms

  public void setLogLevelComms​(Preferences.LogLevel level)

• setLogLevelScripting

  public void setLogLevelScripting​(Preferences.LogLevel level)