B: The Tool DLLs

 

 

SliceO_Tool\2&3D Automation.dll

 

Auto: page (main|file|script|start)

Change the current page displayed.

 

Auto: stop (never|group|db|count|file)

Change the stop condition of the loop.

 

Auto: max value

Change the maximum number of loop in the "Count" mode.

 

Auto: delay value

Change the wait delay between each llop.

 

Auto: file dir dir_name

Set the directory where the files are taken in mode "file"

 

Auto: file sort (name|date|num|pos)

Set the order the files are visited in mode "file"

 

Auto: file delete (on|off)

if "on", the files are deleted after being visited in mode "file".

 

Auto: reset

Reset the loop counter in mode "count".

 

Auto: script file_name

Set the script file used in mode "script"

 

SliceO_Tool\2&3D Memory.dll

 

Memory: Clear (*|images|undo|geom)

Clear the memory buffers for one (or all) of the categories.

 

SliceO_Tool\2&3D Point.dll

 

System Variables defined in this library:

 

 

$POINT_NB

(U32)

Total number of points.

 

$POINT_ON

(U8)

Bit field to select which class of points are visible.

 

$POINT_LABEL

(U8)

The labels are visible (=1) or not (=0). (Default = 1)

 

 

$POINT_CUR

(P)

Pointer to the current point

 

$POINT_PT

(P)

Array of pointers to the points.

 

Commands recognized in this library:

 

Point: Label (on|off|toggle)

Make the point's label visible or not.

 

Point: t_point Color R G B

Change the color of the points matching the template t_point.

 

Point: t_point  Delete

Delete the points matching the template t_point.

 

Point: t_point  Position x y z

Change the position (3D) of the points matching the template t_point.

 

Point: t_point  Size value

Change the size of the points matching the template t_point.

 

Point: t_point  Save file_name

Save the points matching the template t_point to a script file.

 

Templates:

 

t_point is a template for the point names

 

SliceO_Tool\2D Scout Lines.dll

 

Scout: Mode bit_field

Toggle the the current scout line mode:

0x01 = "Lines for visible frames"

0x02 = "Lines for all the frames"

0x04 = "Track cursor"

0x08 = "Track frames"

 

Scout: Select

Activating this command while over a scout will change the current frame of a group to the frame at the corresponding position on the scout.  If the cursor is over a geometry in a 3D window, the program compute the position on the polygons under the cursor, and change the current frames to the frames that contain that position in their image plane.

 

Note:

 

The "Scout: Select" command use the current mouse position.  So the command is only valid while the cursor is over a frame or a 3D geometry.

 

SliceO_Tool\2&3D Snapshot.dll

 

System Variables defined in this library:

 

 

$SNAPSHOT_FORMAT_NB

(U8,R)

Number of formats supported (=5).

 

$SNAPSHOT_FORMAT_CUR

(U8)

Format of the snapshot files (0=TIFF, 1=PNG, 2=JPEG, 3=GIF, 4=BMP, 5=TARGA)

 

$SNAPSHOT_QUALITY

(U8)

Compression quality (1=poor, 100=best)

 

Commands recognized in this library:

 

Snapshot: Format (TIFF,PNG,JPEG,GIF,BMP|TARGA)

assign a value to the $SNAPSHOT_FORMAT variable that control the format used when creating the snapshot files.  Supported formats are:

•TIFF ($SNAPSHOT_FORMAT=0)

•PNG ($SNAPSHOT_FORMAT=1)

•JPEG ($SNAPSHOT_FORMAT=2)

•GIF ($SNAPSHOT_FORMAT=3)

•BMP ($SNAPSHOT_FORMAT=4)

•TARGA ($SNAPSHOT_FORMAT=5)

 

Snapshot: [t_window] Click [file_name]

Create a "Snapshot" of a specific window (specified by the t_window template) or the complete interface (if no template is specified) and save it to the file "file_name".  If "file_name" is not specified, the file will be save to the scratch directory using the name "sliceO_xx.yyy". Where xx is an increasing number from 00 to 99 and yy is the extension for the selected file format (".tif", ".png", ".jpg", ".gif", ".bmp" or ".tga").

 

Snapshot: [t_frame] Click [file_name]

Create a "Snapshot" of a the frames matching "t_frame".   If "file_name" is not specified, the file will be save to the scratch directory using the name "sliceO_xx.yyy". Where xx is an increasing number from 00 to 99 and yy is the extension for the selected file format (".tif", ".png", ".jpg", ".gif", ".bmp" or ".tga").

 

Templates:

 

t_window is a template for the window. It match either the widow ID ("1" to "4") or "cur" for the currently selected window.

t_frame is a template for the frame names.

 

 

SliceO_Tool\2&3D Window.dll

 

System Variables defined in this library:

 

 

$WINDOW_MAX

(U32,R)

Maximum number of windows (=10)

 

$WINDOW_NB

(U32)

Current number of windows (1 <= $WINDOW_NB <= $WINDOW_MAX)

 

$WINDOW_LIST

(U32)

List of all windows (1, 2, ..., n)

 

 

$POINT_CUR

(P)

 Pointer to the current window

 

$POINT_OVR

(P)

 Pointer to the window under the cursor

 

$POINT_PT

(P)

 Array of pointers to the windows.

 

Commands recognized in this library:

 

Window: Config (split|floating|free)

Specify the window's modes (at this time only "split" is supported):

•Split: the Display Area is split in 4 windows

•Floating: you can have up to $WINDOW_MAX windows.  They are floating but limited to the Display Area.

•Free:  you can have up to $WINDOW_MAX windows.  They are floating and are not limited to the Display Area.

 

Window: Split horizontal vertical

Specify the vertical and horizontal divider in the Display Area.  This will reformat the 4 windows.

 

Window: t_window Mode (one|all|toggle)

Specify the current mode of the windows matching the template "t_window"

 

Window: t_window Color R G B

Specify the color of the borders of windows matching the template "t_window"

 

Window: t_window State (one|off)

Specify the current state of the windows matching the template "t_window"

 

Window: t_window Position left top width height

Specify the position of the windows matching the template "t_window"

 

Window: t_window Sliders horizontal vertical

Specify the value of the horizontal and vertical sliders of the windows matching the template "t_window"

 

Templates:

 

t_window is a template for the window. It match either the widow ID ("1" to "4") or "cur" for the currently selected window.

 

 

 

 

SliceO_Tool\2D Color_Map.dll

 

System Variables defined in this library:

 

 

$COLORMAP_GLI_INVALID

(C)

Displayed color for invalid GLI pixel

 

$COLORMAP_GLI_FILL

(C)

Displayed color for GLI pixel outside the FOV

 

$COLORMAP_GLI_CUR

(U16)

Currently used colormap (Default=0)

 

$COLORMAP_GLI_NB

(U16)

Number of defined colormaps (Default=5)

 

$COLORMAP_GLI_SIZE

(U16)

Size of each colormap (Default=4096)

 

 

$COLORMAP_GLI_PT

(P)

 Array of pointers to the GLI colormaps.

 

 

SliceO_Tool\2D Color_Scheme.dll

 

System Variables defined in this library:

 

 

$COLOR_SCHEME

(U8)

Curently selected color scheme (0=Grey, 1=Mixed, 2=Tint, 3=Over, 4=Tag)

 

$COLOR_VAL_MIN

(F32)

"Black" slider;s value

 

$COLOR_VAL_MAX

(F32)

"White" slider's value

 

$COLOR_CLASIC

(U8)

0=new style, 1=old style of "Mix" mode

 

Commands recognized in this library:

 

Color: Grey

Assign the value 0 (=Grey) to the $COLOR_SCHEME variable.

 

Color: Mix [value]

Assign the value 1 (=Mixed) to the $COLOR_SCHEME variable. If "value" is present, assign its value to the variable $TAG_MIX that control the mix of GLI and TAG colors The accepted range

for "value" is from 0.1 to 0.9.

 

Color: Over

Assign the value 2 (=Over)  to the $COLOR_SCHEME variable.

 

Color: Tag

Assign the value 2 (=TAG) to the $COLOR_SCHEME variable.

 

Color: Black value

Assign the value "value" to the $COLOR_VAL_MIN variable that control the color of the GLI images. (see Color Scheme in The 2D Tools)

 

Color: White value

Assign the value "value" to the $COLOR_VAL_MAX variable that control the color of the GLI images. (see Color Scheme in The 2D Tools)

 

 

SliceO_Tool\2D Debug.dll

 

Commands recognized in this library:

 

Debug: Database

List the content of the database classes (this is equivalent to the "Database: List" command)

 

Debug: Filter (on|off|toggle)

Change the displayed GLI image from the normal image to the "Filtered" image.  The filtered image is used in some modes such as Morpho and Snakes.  It is the first step in the computation of the image's gradients.  Before the gradient are computed a 3x3 smoothing filter is applied on the images.

 

Debug: Gradient (amp|x|y|z) (on|off|toggle)

Change the displayed GLI image from the normal image to the "Gradient" image.  The gradient image is used in some modes such as Morpho and Snakes. You can display either the intensity of the gradient, or the amplitude of one of the direction component of the direction of the gradient.

 

Debug: WS (on|off|toggle)

Change the displayed TAG image from the normal image to the Watreshed "WS" image.  The watershed is compute in the Morpho mode.

 

Debug: Merge (1|2|3|4) (on|off|toggle)

Change the displayed TAG image from the normal image to the one of the Morpho merge images.

 

 

SliceO_Tool\2D Frame.dll

 

System Variables defined in this library:

 

 

$FRAME_SCALING

(F32)

Scaling factor to apply when increasing or decreasing images (Default = 1.5)

 

Commands recognized in this library:

 

Frame: Scale (value|inc|dec)

Change the scaling factor for all the selected frames

 

Frame: Current (value|inc|dec)

Change the current frame by selecting one of the children of the current parent of the current frame.

 

Frame: Offset Pos x y z

Offset the position of the current frame.

 

Frame: Offset d value

Offset the position of the current frame by adding an offset value in the "z" direction.

 

Frame: Offset t value

Change the time value of the current frame.

 

Frame: Parent (value|inc|dec)

Frame the current frame by making one of the parent class the current class.

 

Frame: Frame value

Change the current frame by selecting one of the frames of all the available frames.  This command enable to go through all the frames in the DB.

example:

 

for $cur in ( $FRAME_LIST ) {

          echo: Frame -> $cur

          frame: frame $cur

}

 

 

SliceO_Tool\2D Gamma.dll

 

System Variables defined in this library:

 

 

$GAMMA_CUR

(F32)

Curent Gamma value (Default = 1.0)

 

$GAMMA_NB

(U16,R)

Number on entries in the Gamma table (= 256)

 

$GAMMA_ALPHA

(A,F32)

Array of $GAMMA_NB Gamma map values used to remap the "Aplha" color values (glPixelMapfv( GL_PIXEL_MAP_A_TO_A, nb, alpha))

 

$GAMMA_PT

(A,F32)

Array of $GAMMA_NB Gamma map values used to remap the R G and B color values (glPixelMapfv( GL_PIXEL_MAP_R_TO_R, nb, pt))

 

Commands recognized in this library:

 

Gamma: Set value

Assign the value to the $GAMMA_CUR variable that set the current Gamma correction value (0.3 <= Gamma <= 3.0)

 

 

SliceO_Tool\2D Overlay.dll

 

System Variables defined in this library:

 

 

$OVERLAY_2D

(U32)

Bit field that control the 2D overlay display:

•x01: file overlay on/off

•x02: name overlay on/off

•x04: patient overlay on/off

•x08: technical overlay on/off

 

Commands recognized in this library:

 

Overlay: 2D bit_field

Overlay: (file|name|patient|technical) (on|off|toggle)

Assign a value to the $OVERLAY_2D variable.

 

 

SliceO_Tool\2D Pixel Grid.dll

 

System Variables defined in this library:

 

 

$GRID_ON

(U8)

Display (=1) or not (=0) a grid on top of the image's pixels. (Default=0)

 

$GRID_MIN

(U8)

Minimum scale value for the grid to be displayed (Default=5)

 

$GRID_COLOR

(C)

Color of the grid

 

Commands recognized in this library:

 

Grid: On (on|off|toggle)

Assign a value to the variable $GRID_ON.

 

Grid: Min value

Assign a value to the variable $GRID_MIN.

 

Grid: Color R G B

Assign a value to the variable $GRID_COLOR.

 

 

SliceO_Tool\2D Results.dll

 

Commands recognized in this library:

 

Result: 2D Flag (backup | append | path | file) (0 | 1 [|2])

Set the one of the configuration flags:

backup:          (0=do not, or 1=always) automatically create a backup file when appending or overwriting an exiting file.

append:          0=when writing to an existing file, ask the user if he wants to overwrite or append at the end of the file.

                    1=always append at the end of the file.

path:          0=use a fixed path.

                    1=use the same path as the last opened file.

file:          0=use a fixed file name.

                    1=use a fix file name and append a counter number at its end.

                    2=open a file selection menu.

 

Result: 2D Path path_name

Path name used for the fixed path option

 

Result: 2D File file_name

file name used either as fixed name or as starting option.

 

Result: 2D Clear 

Clear the list of selected cells.

 

Result: 2D Add level_1 [level_2 [level_3] ]

Add a cell to the list of selected cells.

 

 

 

 

SliceO_Tool\3D Background.dll

 

System Variables defined in this library:

 

 

$BACKGROUND_CORNER

(A,C)

Array of 4 colors. One for each corner of the windows.

 

Commands recognized in this library:

 

Background: (top|bottom) (left|right) R G B

Assign a value to the elements of the $BACKGROUND_CORNER variable.

 

 

SliceO_Tool\3D Light.dll

 

System Variables defined in this library:

 

 

$LIGHT_MAX

(U16,R)

Maximum number of light sources. (= 8)

 

$LIGHT_NB

(U16)

Current number of defined lights (Default=5)

 

$LIGHT_LIST

(A,U16)

List of all the lights (1,..., n)

 

$LIGHT_STATE

(A,U8)

Array of light states (0=Off, 1=On, 3=Ambient)

 

$LIGHT_COLOR

(A,C)

Array of light colors

 

$LIGHT_DIR

(A,P)

Array of pointer to the light's directions

 

Commands recognized in this library:

 

Light: t_light State (on|off)

Assign values to the elements of $LIGHT_STATE specifying the state of the light sources. (0=Off, 1=On). 

 

Light: t_light Dir x y z

Assign values to the elements of $LIGHT_DIR specifying the direction of the light sources.

 

Light: t_light Color R G B

Assign values to the elements of $LIGHT_COLOR specifying the color of the light sources.

 

Templates:

 

t_light is a template for the light names ("amb", "1" to "4")

 

 

SliceO_Tool\3D Measures.dll

 

Commands recognized in this library:

 

Measure: t_geom 3D file_name

Write to file "file_name" the measures for all the geometries matching "t_geom".

 

Note:

 

If optional headers have been requested (see File in The Configuration Menu), they will be written to the file.

 

Templates:

 

t_geom is a template for the 3D geometries

 

 

SliceO_Tool\3D Overlay.dll

 

System Variables defined in this library:

 

 

$OVERLAY_3D

(U32)

Bit field that control the 2D overlay display:

•x01: global overlay on/off

•x02: local overlay on/off

•x04: box overlay on/off

•x08: slice overlay on/off

 

Commands recognized in this library:

 

Overlay: 3D bit_field

Overlay: (global|local|box|slices) (on|off|toggle)

Assign a value to the $OVERLAY_3D variable.

 

 

SliceO_Tool\3D Shading.dll

 

Shading:

 

 

 

SliceO_Tool\3D Slices.dll

 

Slice: Transparency value

Set the transparency level for the 3D slices. if value=0, the slices will have no transparency. (0 <= value <= 1.0)

 

 

SliceO_Tool\3D Smooth.dll

 

System Variables defined in this library:

 

 

$SMOOTH_NB

(U16,R)

Number of "Smoothing" levels. (= 5)

 

$SMOOTH_LIST

(A,U16)

List of the parameters (1, ..., n)

 

$SMOOTH_PARAM

(A,U16)

Array of number of recursion used in each smoothing levels.

 

 

SliceO_Tool\3D Transfo.dll

 

System Variables defined in this library:

 

 

$TRANSFORM_INTERFACE

(U16)

Type of 3D mouse interface. (0=Track, 1=Classic, 2=Patient)

 

Commands recognized in this library:

 

Transform: Mode (track|classic|patient)

Assign a value to the $TRANSFORM_INTERFACE variable. (See Transform in The 3D Tools)

 

Transform: t_window Camera x y z

Place the observer at the position x, y, z for all the windows matching the template "t_window".

 

Transform: t_window Center x y z

Center all the windows matching the template "t_window" around the point x, y, z.

 

Transform: t_window FOV angle

Change the camera Field Of View "angle" to all the windows matching the template "t_window". Accepted values for "angle" range from 0.0 to 179.0 degrees. A value of 0 will yield an orthogonal projection. The default Camera has a FOV of 27 degrees.

 

Transform: t_window Matrix a11 a12 a13 a14 a21 ... a44

Directly set the matrix elements. The 16 parameters of this command will be inserted in the 4x4 transformation matrix.of all the windows matching the template "t_window".

 

Transform: t_window Pivot angle x y z

Rotate "angle" degrees around the direction specified by x, y, z all the windows matching the template "t_window".

 

Transform: t_window Restore

Restore the transformation matrix all the windows matching the template "t_window".

 

Transform: t_window Rotate x y z

Rotate all the windows matching the template "t_window".

 

Transform: t_window Scale value

Scale all the windows matching the template "t_window".

 

Transform: t_window Translate x y z

Translate all the windows matching the template "t_window".

 

Templates:

 

t_window is a template for the window. It match either the widow ID ("1" to "4") or "cur" for the currently selected window.

 

 

 

 

SliceO_Tool\Tag Lock.dll

 

System Variables defined in this library:

 

 

$TAG_LOCK

(A,U8)

Array of "lock" values. (0=unlock, 1=lock)

 

Commands recognized in this library:

 

Tag: t_tag Lock

Assign the value "lock" (=1) to all the elements of $TAG_LOCK that match the template "t_tag".

 

Tag: t_tag Unlock

Assign the value "unlock" (=0) to all the elements of $TAG_LOCK that match the template "t_tag".

 

Templates:

 

t_tag is a template for the TAG values.  It match either the TAG ID ("0" to "256") or the TAG label or "cur" for the current TAG value.

 

 

SliceO_Tool\Tag Surface.dll

 

System Variables defined in this library:

 

 

$RESULT_BACKWARD

(U8)

Backward compatibility flag (1=compatible with 4.3)

 

$RESULT_NAME

(A,S)

Array of result computation name

 

$RESULT_UNIT

(A,S)

Array of result computation units

 

$RESULT_ENABLE

(A,C8)

Array of flag for the display/output of the result computations (0x01=in output file, 0x02=displayed)

 

Commands recognized in this library:

 

Results: Backward (on|off|toggle)

Enable or disable the backward compatibility mode.  If enable, the database results will have a "frame number" column, and also a column for each empty tag.

 

Results: Calib (on|off|toggle)

Enable or disable the calibration of the pixel values.

 

Results: Calib File file_name

Read a calibration file. The calibration file is a script file containing commands specific to the pixel calibration. The commands used in the calibration file are explained further down.

 

Results: Display t_measure (on|off|toggle)

Enable or disable the display of the measures matching the template "t_measure" in the tool's window. By default, only the "Surface Units" and "Volume Units" measures are displayed.

 

Results: Enable t_measure (on|off|toggle)

Enable or disable the saving of the measures matching the template "t_measure" in the result files. By default, only the "GLI Variance" measure is disabled.

 

Results: Measure List

list the names of all the measures performed by this tool. These names can then be used in the "results: enable" and "results: display" commands

 

Results: Name string

Specify a default name for the result file.

 

Results: Type (text|db)

Specify a default file type for the result file. The choice is between "db" (spread sheet format) or "text" (simple ASCII text format).

 

Results: Write [text|db] file_name

Write the surface/volumes to the result file "file_name", in either "db" (spread sheet format) or "text" (simple ASCII text format).  If no format is specified, the default value is used.

 

The Calibration File

 

The calibration file is a script file containing commands specific to the pixel calibration.

 

Results: Calib Units string

Specify the name of the new units described by the calibration data

 

If the relationship between the GLI pixel values and the new calibrated values is a simple linear ,transformation, then we can express the calibration with 2 values: offset and scale:

new value = (GLI_Value + offset) * scale

 

Results: Calib Offset value

Specify the offset of the calibration curve (new value = (GLI_Value + offset) * scale).

 

Results: Calib Scale value

Specify the scale of the calibration curve (new value = (GLI_Value + offset) * scale).

 

If the relationship is more complex, we express the calibration with a series of point on calibration curve. All GLI values not specifically defined will be linearly interpolated or extrapolated from the values specified.

 

Results: Calib Point val_GLI val_new

Specify a point on the calibration curve.