Density Map Editor

Access: CP::Editor::MAP

The main function of the MAP-Editor is for 3D density map display, rendering and editing.  Designed to be simple and light, this editor loads and processes one map at a time.

Example of the CP and DP display for the Density Map Editor.

Display a Density Map

The data input/output functions are organized in the File group (at the upper-left region of the page).  Once a density map is loaded into the editor, the 3D volume will be displayed in DP::MainDisplay under a default lighting scheme.  The filename, map dimensions and voxel size (modifiable, assumed to be isotropic) will be displayed in the designated value-boxes.  A set of functional buttons on top of the filename box control the data I/O:

• : open a file browser to select and load a map into the editor.
• : prompt for a filename to save the density map in the editor.
• : display the image statistics (in CP::MessageBoard) of the density map.
•  C : close the map in the editor and clear the display.  Will prompt to save if the map has been modified.

Graphics Rendering

A 3D density map can be visualized in either Surface or Mash style and the color is customizable at DP::Map-Toolbox.  To slice through the 3D volume along the viewing direction, adjust the X-Plane and Depth sliders to reach a proper location and slab-thickness.  When the Contour Set button is on, the map will be displayed in multiple level-sets, with customizable intensity Minimum, Maximum and multiplicity Levels.  Each contour surface will be colored according to a pre-defined scheme.  The Reset button will bring the density map display back to the original orientation and scale.

The positioning of the map display is controlled intuitively by the computer mouse in the DP::MainDisplay window:

• Rotation: LeftClick & Drag.
• Translation: MidClick & Drag.
• Zoom: RightClick & Drag.

Euler Angles

The orientation of a density map in the 3D-space is uniquely defined by an Euler-angle triplet (α, β, γ).  These angles are associated with the respective sliders in the Euler tab.  In addition, this tab contains functional buttons for

• Model Projection : when activated, an inset will appear in the lower-right region of the DP::MainDisplay window, displaying the 2D projection of the density map at the present orientation.

• Angular Coverage : an evaluation tool that monitors the particle distribution in a model reconstruction.  When activated, an Euler sphere will appear in the upper-right region of the DP::MainDisplay window, showing the angular distribution of the particle images in the model reconstruction.  Each dot represents one particle image.  The statistics takes into account the Symmetry property of the density map (defined at the pull-down menu above the tabs).

Cinema / Animation

In the Cinema tab, the movement and viewing of a density map can be animated by

• : slice through the volume (the slab-thickness is defined by the Depth slider in the Graphics Rendering group);
• : rotate the map counter-clockwise;
• : rotate the map clockwise;
• : rock back-and-forth (the rotational range is defined by the Rock Range slider);

In the animation, the frame-rate can be adjusted via the Animation Speed slider.  Toggling an activated button will stop the animation.

Model Projection

In the Projection tab, systematic projections of the 3D map in the editor can be generated at user-defined angular range and interval.  When the Symmetry property is specified (at the pull-down menu above the tabs), 2D projections will be produced within an asymmetric unit only.  The projected images will be displayed in the CP::PTK stack editor, which can then be exported to a file.

Image Processing Functions

A set of the 3D filtering and voxel-based arithmetic functions can be accessed from the pull-down menu and activated by the Apply button.  After processing, the density map display will be automatically updated in DP::MainDisplay to reflect the result.

• Normalization : voxel value is normalized to N(0, 1).
• Gaussian Filter : filter the map by a Gaussian kernel.  Sigma is a ratio to the Nyquist frequency.
• Laplacian Filter : filter the map by a Laplacian kernel.
• Band-pass Filter : filter the map by the specified High-pass & Low-pass resolution thresholds (in Å).
• Sharpening Filter : sharpen the map using an inversed Gaussian kernel.
• Map Centering : center the map in the volume by the "center-of-mass" approximation.
• Map Binning : isotropically bin the map voxels by the Bin Size factor.  Integer arithmetic (e.g., 9/2=4) is used to calculate the new dimensions.
• Density Scaling : each voxel value p is modified to (k*p+b).  For example, (k=-1, b=0) inverts the density contrast.
• Cropping / Padding : crop or pad the map (from the center) to the specified new dimensions.  In padding, the average intensity of the volume is used to fill the empty space.
• Volume Resampling : resample the map to the specified new dimensions via tri-linear interpolation.
• Rotate Density Map : rotate the map by the user-defined angles along each axis in the order of X, Y and Z.
• Mirror Density Map : generate a mirrored version of the density map.
• Add Two Maps : prompt to load a new map and calculate the voxel-wise sum.  The two maps should share the same X/Y/Z-dimension.
• UDF Plug-in : call the User Defined Function.

The 3D image processing functions will change the value of voxels and update the display afterwards.  However, the resulting density map is not automatically saved back to the original file.  It is at the user's discretion to export the result to a map file.  As a safe-guard, PARTICLE will prompt to save a modified map upon its closing.