KEYWORD Selecting_Windows File Movie Object_Pulldown Markers_Pulldown Rotation-Position Scalebar Animation Clipping Display_Options Lighting Automatic_Modeling Wire_Frame/Solid Measurements Color Stereo Picking Current_Object_Info Global_Model WT_Display_Options DESCRIPTION : 3DModel 3DModel lets you create models of the structures in your image data. Objects can be rotated around interactively, and object attributes such as color, radius, display, solid/wire, etc can be changed at any time. Five dimensions are actually handled in that you can create a 3DModel model for each wave and time set. If you have live data, you can model each time set and then watch the model move through time. The model program interacts with multiple image windows allowing the user to build the model and view it on the image from different angles and on rotation projections. Models are stored in real space coordinates and are written out to an ascii file. The models created here are the input for the Straight program which creates a straitened 3D data volume of the tubular data. Straight can connect directly to the model if 3DModel is running and is attached to the input window or run alone using the saved model file. Several different types of objects can be created in 3DModel and several more are created using other programs and then are displayed in 3DModel. Types of models that may be created within 3DModel are a connected string of points, possibly branched This type of object can have sphere or cube markers at any or all points on the model. This type of model can be given a radius so that it appears as a cylinder or branched cylinder. When creating this type of object, points can be added, deleted and inserted as needed. a set of points This type of object is displayed as pixel-sized dots without connections between the points. Another type of object supported in the program is made by creating a set of 2D polygons with EditPolygon or 2DObjFinder and putting them together into a 3D object in Volume Builder. The model can then be viewed in wire frame or as a solid object here. Selecting_Windows When you first start 3DModel, it will automatically attach to all the image windows that are currently displayed. Any window that was iconified when 3DModel was started or was opened after 3DModel was started can be attached to the model at any time by selecting the "select windows" entry from 3DModel's "options" menu. This causes a dialog to be displayed with toggles for each window number (up to window 19). When a toggle is on that window will be considered by 3D Model. Otherwise it will not be used. You can use any of the attached windows to create your model by clicking on the image at the point where you want to add a point. All of the image windows will update to the section that contains the current focus point of the model, and the model will be clipped to show the part of the model that falls in the currently displayed section. The reason for using multiple windows is that by rotating your image data into several orientations you can see where the model falls in each orientation making it much easier to tell that you've modeled your structure correctly in 3 dimensions. In addition, 3DModel will work with the output of Volume Viewer's interactive or movie options. File The functions available from the File menu are: save Presents a file selection dialog to choose where to save the current model as a file. load Presents a file selection dialog to select a model file. new model Clears all objects. autosave By default, the current model is periodically saved so that if the program crashes most of your work can be retrieved. Selecting autosave causes a dialog to be displayed in which you can choose whether or not the periodic saves should be performed and how often they should be performed. In the case of a crash, the model from the last periodic save will be in the directory /var/tmp under the name _SAVE.MOD movie Animates the model display and saves each frame shown. For more information see the Movie topic. Movie To animate the model and save the result as a movie or sequence of image files, use the "movie" option in 3DModel's "file" menu. That option will open a dialog with the following controls: File format Use this menu to select the format used to store the captured images. To view and edit the parameters specific to the currently selected format, press the "options..." button. Supported file formats include: 1) JPEG compressed images stored as JFIF files (see JFIF_Save.hlp) 2) PGM and PPM image files (see PGM_PPM_Save.hlp) 3) QuickTime movies: available on Mac OS X via the native libraries (see AppleQT.hlp), on Linux via libquicktime (see LQT.hlp), and on IRIX via the dmconvert utility (see DMCONVERT.hlp) 4) SGI movie format: only available on SGIs via the dmconvert utility (see DMCONVERT.hlp) Images from 3D Model are not well suited to JPEG compression so the JFIF format and JPEG compression schemes for QuickTime and SGI movies are not particularly useful. Spin axis Use this menu to control which axis is used as the axis of rotation. Time order If the animation follows the model through time points in the data, this menu controls what happens when the animation reaches the last time point. With the "Loop" option the animation will start over again at the first time point. With the "Back and forth" option, the animation will proceed to go through the time points in reverse order. Angle increment Use the this slider or the field immediately to its left to set the amount of rotation about the spin axis between frames. The value shown in the field has units of degrees. Time increment Use this slider or the field immediately adjacent to it to set the amount by which the time point coordinate changes between frames. Frame count Enter the number of frames to generate in this field. File prefix Use this field to enter the name (including directories if desired) that you want to use for the output file or files. If the file format you selected stores each frame in a separate file, 3D Model will generate the actual file names by append the frame number and default file format extension to what you have entered in the "File prefix" field. If the file format you selected stores the frames in a single files, 3D Model will generate the output file name by appending the default file format extension to what you have entered in the "File prefix" field. Create Press this button to start generating the movie. Interrupt Press this button to stop recording a movie that is still in progress. Close Closes the movie dialog. If 3D Model is currently recording a movie, closing the dialog will stop the recording. The images saved are read back from the computer's video system; for best results the 3D Model display window should be fully on the screen and not obscured by any other window. Object_Pulldown The functions in this menu apply only to the current object or to all the objects. There are different types of objects so some functions may only apply to certain types. Unless specific types are stated below you can assume it applies to all types of objects. Please see the WT_Display_Options topic for detailed information on the different object types. create new Starts a new object. Every time you want to start a separate object you will need to use this menu entry. delete obj Deletes the current object. del pt list Deletes the list of points from the object but does not delete the object itself. Only applies to objects of types 1 and 2. delete dots Deletes the list of dots from the object but does not delete the object itself. A dot list is a special extra list of points that can be added onto any object type. undisplay all Turns off the drawing of all objects. Once this is done, any of the objects can be independently turned back on for drawing. If there are a large number of objects, drawing all the objects could be slow, so when picking new objects, turning all other objects off could increase speed. redisplay all Turns on the drawing of all objects. undisplay cur Turns off the drawing of the current object. redisplay cur Turns on the drawing of the current object. connect two Opens a dialog to allow you to select two objects to paste together. You will need to enter the object numbers and have the current point of each object set to the points that you want to connect. cut in two Cuts the current object into two objects. The cut will be made at the current point. Only applies to objects of types 1 and 2. reverse pts Reverses the order of the points in the object so that the last point becomes the first point and vice versa. Only applies to objects of types 1 and 2. radius Display a dialog in which you select the radius of tubular objects. You can choose to set the radius of the current object or all objects; the radius may be entered directly or adjusted using the slider. Only applies to objects of types 1 and 2. wire-solid If the current object is displayed as a wire frame causes it to be displayed with sold surfaces; if it is displayed with solid surfaces, causes it to be displayed as a wire frame. This applies to model types 1 and 2 if they have a nonzero radius (i.e. they are shown as tubes) or have spherical or cubic markers for the points. It also applies to objects of types 3 and 4 imported from Volume Builder. name object Displays a dialog to allow you to enter a name for the current object. This name will be shown next to the first point on the object in the 3DModel display if "object labels" are turned on from the options->display options menu. Also, the "WT display options" dialog will display the name of each object. Markers_Pulldown All of these functions affect the current point or all the points in the current object. label point Displays a dialog to allow you to enter a label for the current point. Press ok to cause the new label to be displayed next to the point. remove label Removes the label, if any, for the current point. sphere curr. pt. Causes a spherically-shaped marker to be used for the position of the current point. sphere curr. obj. Causes spherically-shaped markers to be used for the positions of all points in the current object. sphere marker all Causes spherically-shaped markers to be used for the positions of all points in all the objects. cube curr. pt. Causes a cube-shaped marker to be used for the position of the current point. cube curr. obj. Causes a cube-shaped marker to be used for the positions of all points in the current object. cube marker all Causes cube-shaped markers to be used for the positions of all points in all the objects. remove marker Removes the marker, if any, used for the current point. rm mkrs curr. obj. Removes all markers in the current object. rm mkrs all obj. Removes all markers from all objects. resize markers Opens a dialog to allow you to choose the size of the marker for the current point, the size of all markers in the current object, or the size of all markers. The radius is shown in the "current radius" field and may be entered directly or adjusted with the slider. Rotation-Position The positioning of the model in the "3DModel: display" window can be adjusted with the mouse. Exactly how the mouse buttons are used is set from the "mouse control" entry in the "options" menu. The default is: pressing the left mouse button picks a point from one of the models, pressing the middle mouse button and dragging the mouse rotates the model display, and pressing the right mouse button and dragging the mouse zooms in and out. The available functions that a mouse button could perform are: pick Causes the nearest object to the point selected to become the current object. The last point in that object is the new current point. rotate Dragging the mouse while the button is down rotates the model display. zoom Dragging the mouse upward while the button is pressed zooms in on the model; dragging it downward zooms out. translate Dragging the mouse while the button is pressed translates the model relative to the axes. time Dragging the mouse vertically while the button is pressed moves the model through time. The rotation applied to the model display can be adjusted directly by selected "specify rotation" from the "options" menu and entering the angles in the dialog that appears. To restore the model to its default orientation and zoom, select "reset 3D-model" from the "options" menu. The point used as the center of rotation when rotating and the size of the bounding box shown can be selected using the dialog opened by the "rotation center" entry in the "options" menu. The available options are: From window Use the size of the data volume in the window to set the size of the bounding box. The geometric center of that box is used as the center of rotation. From model file Use the center information stored in the model file. From all points Use the mean position of all points in the model as the center of rotation. The bounding box is chosen to be the smallest such box that contains all the points. Pick center Select a position in an image window with the mouse to set the center of rotation. The size of the data volume in that window sets the dimensions of the bounding box. Scalebar To display a scale bar with the model or to alter the positioning of the currently displayed scale bar, select "scale bar" from the "options" menu. In the dialog that appears, there is a menu at the top that controls whether no scale bar is show, a scale bar is shown but without a label indicating its length, or if the scale bar is shown with a label. The remaining controls are: x y pos The entries in this field are the position of the bottom left of the scale bar relative to the bottom left corner of the display window. (0, 0) is the lower left corner, (100, 0) is the lower right corner, (0, 100) is the upper left corner, and (100, 100) is the upper right. size Specifies the length of the scale bar in the units used for the pixel spacing (typically microns for data from optical microscopes and Angstroms from electron microscopes). thickness Specifies the thickness of the scale bar in pixels. vertical If this toggle is off, the scale bar is horizontal; if it is on the scale bar is shown vertical. Animation To create an animation of the model display select "animation" from the "options" menu. During the animation, the model display will automatically spin about the x, y, or z axis and / or follow the model through the time points in the data. While the animation is in progress, you can still use the mouse to reposition your model so you can have it spinning in any orientation. The controls in the animation dialog are: Spin axis Use this menu to control which axis is used as the axis of rotation. Time order If the animation follows the model through time points in the data, this menu controls what happens when the animation reaches the last time point. With the "Loop" option the animation will start over again at the first time point. With the "Back and forth" option, the animation will proceed to go through the time points in reverse order. Angle increment Use the top slider or the field immediately to its left to set the amount of rotation about the spin axis between frames. The value shown in the field has units of degrees. Time increment Use the middle slider or the field immediately adjacent to its left to set the amount by which the time point coordinate changes between frames. Redraw delay Use the bottom slider or the field immediately adjacent to its left to set the amount of time the animation waits before drawing the next frame. The value shown in the field has units of milliseconds. Pause While this toggle is off and the animation menu is open, the movie will proceed; when this toggle is on the animation will not run. Close Closes the animation dialog and stops the animation. Clipping Select "clipping" from the options menu to display a dialog that lets you cut off a portion of the image. Moving a slider farther to the left cuts out more of the image from one of the sides. You can cut off from the top, bottom, left, right, far, and most useful, near. Each slider ranges from showing the whole volume to cutting to the middle of the model. Display_Options There are various attributes that apply to the whole model in the model display window. These attributes can be modified by selecting "display options" from the "options" menu. Doing so opens a dialog. At the top are toggles for the 5 possible waves that a data set can have. Use these toggles to turn on and off display of the objects made in the individual waves. The other controls are: obj labels If this toggle is on, the name of the object (or just its number if it has no name) is shown next to its first point. cur pt mkr If this toggle is on, a red dot is shown where the current point is. display all If this toggle is on, all objects are displayed regardless of whether or not they are individually marked to not be displayed. mirror Since the data may be collected in two different directions, there is a question of whether to place the zero point in z at the front or back of the volume. If this toggle is off (the default), the zero point is in front; if it is on, the zero point is in back. show box If this toggle is on, the bounding box is shown in the model display. show ticks If this toggle is on, the tick marks on the sides of the bounding box are shown when the bounding box is shown. antialiasing If this toggle is on, an effect is applied to reduce pixelation artifacts ("jaggies") in lines. Doing so generally increases the time needed to redraw the model. flat shading When lighting is on and this toggle is off, smooth shading is used (this is the default). When lighting is on and this toggle is on, flat shading is used. Lighting Lighting enhances the three-dimensional feel of the model when the objects are wire or solid cylinders or objects from Volume Builder. To set the lighting parameters, select the "lighting" entry from the "options" menu. This opens a dialog that has a toggle to turn lighting on and off, sliders to vary the components of the light, and sliders to adjust the position of the light. In the "display options" dialog there is a control to set what type of shading is done when lighting is on. Automatic_Modeling A semiautomatic searching tool to trace the axis of a tubular structure is available. To use it, select the "automodel" entry from the "options" menu. That will open a dialog to control the search. For more information about the search parameters consult Tracer.hlp. Wire_Frame/Solid Some types of objects can either be viewed as wire frames (only the lines defining the edges of surfaces are drawn) or with the surfaces filled in. In the "options" menu, you can select "all obj wire" to change all objects to be displayed as wire frames or "all obj solid" to change all objects to be displayed with the surfaces filled in. To modify whether a wire frame or solid shading is used for an individual object use the "wire-solid" entry in the "object" menu or change the object type in the "WT display options" dialog. Measurements 3DModel can make some simple measurements from the objects in the model. The measurements that can be performed are all available from the "measurements" menu in the main dialog and are: 2D angle at cur pt If a point has both a point previous to it (one step along the axis of the object towards the first point in an object) and one after it (one step towards the end of the branch containing the current point), reports the angle (possible range is 0 to 180 degrees) between the vector from the current point to the previous point and the vector from the current point to the next point. The calculation ignores the z coordinates for the three points. 3D angle at cur pt Is the same as "2D angle at cur pt", but the z coordinates of the points involved are included. printout lengths Displays a dialog to select an output file. The total lengths for each object will be computed and saved to this file in a text format. The objects from the same wavelength and time point are grouped together; each such grouping begins with a line of the form wave time