Volume Builder

Overview

Volume Builder assembles polygons in different sections to build 3D objects. The required input is an image file or window and corresponding polygon data. Once these are entered, press the Create Objects button to assemble the 3D objects; alternatively, a list of which polygons belong to which objects can be read in by pressing the load object list button. If the source of the images is a window, then the polygons will be displayed there and the object number to which each polygon belongs will appear in the center of each polygon.

Once the objects are assembled, they can be modified directly by entering the object to be modified in the Current wave, time, object field and then pressing the change, rename, or delete buttons. A number of measurements can be made of the object properties and their interrelationships via the options in the measurements and relationship menus. The surface models menu provides options to convert the assembled objects into a model that can be used with 3D Model. The object information topic describes available measurements, relationships, and models in more detail.

For notes on how to approach the Modeling process, consult 3D Modeling Strategies.

Topics

Input image | Polygon data | Z | Time | Wavelengths | Maximum z gap | Create objects | Current object | Highlight | Correct | Rename | Object files | Object information

Related Priism Topics

Edit Polygon | SurfHarmMod | FindPoints | Clouds | 3D Model | 3D modeling strategies | Priism


Input image

Volume Builder requires an image file or window. Press the Image file button to open a file selection dialog to select the image file or directly enter the file name or window number in the adjacent field. If a window is used, the outlines of the polygons and the number of the object to which each polygon is assigned will be displayed there.

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Polygon data

The polygon data can be from Edit Polygon, 2DObjFinder, FPPolygons, or SurfHarmMod. When the image source is a window, Volume Builder will automatically detect if polygons are associated with the window and use those by default. It is also possible to read the polygons from file: press the Polygon data button to open a file selection dialog or enter the file name directly in the adjacent field. If polygons are loaded for an image window that already has polygons associated with it, you will be prompted whether the new polygons should replace the existing ones or whether the new polygons should be added to the existing polygons.

Alternatively, loading an object list in the new object library format will import polygon data and how the polygons are grouped into objects.

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Z

The Z field displays the range of sections that are considered when building objects. The first value is the starting section number, the second value is the maximum section number, and the last value is the section number increment.

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Time

The T field displays the range of time points that are considered when building objects or reporting object information. The first value is the index of the first time point, the second value is the maximum time point index, and the last value is the index increment.

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Wavelengths

The toggles next to the W button indicate which wavelengths are considered when building objects or reporting object information. If a toggle is on, that wavelength is considered; if it is off, that wavelength is not used.

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Maximum z gap

When assembling objects, Volume Builder will search up to m z sections from a polygon already in an object to find another polygon to add to the object. The value of m is displayed in the max z gap field.

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Create objects

When an image file or window and a set of polygons has been loaded, pressing the Create Objects button assembles the polygons into objects. The assembly process is affected by the settings of the Z, T, W, and max z gap controls.

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Current object

The wavelength, time point index, and object number for the object affected by the highlight toggle and change, rename, and delete buttons is displayed in the Current wave, time, obj field. To modify a different object, enter new values in that field.

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Highlight

If this toggle is on and the input images are from a window, the current object will be displayed in light blue instead of the color normally used for polygons in the same wavelength.

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Correct

To manually add or delete a polygon from an object, enter the object's wavelength, time point index, and number in the Current wave, time, obj field and then press the change button. That causes a new dialog to be opened, at the top the number of each polygon in the object and the z section corresponding to that polygon are listed (if the images are from an image window, the polygons are labeled with the object number followed by a slash followed by the polygon number while the correction dialog is open). At the bottom of the dialog, use the Section and Polygon fields to specify a particular polygon: enter the z section containing the polygon in the Section field and the polygon number in the Polygon field. When the Add button is pressed, that polygon will be added to the current object. When the Delete button is pressed, the polygon is deleted from the current object if it is there.

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Rename

To assign a new object number to an object, press the rename button and enter the new object number in the dialog that appears. This can be used to assign the polygons in one object to another object.

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Delete

Remove the current object and all its constituent polygons.

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Object files

How polygons are grouped into objects may be saved to a file or loaded from a file. There are two different file formats:

old volume builder
This is a text format that lists the polygons (identified by section and polygon number) in each polygon. Volume Builder and Find Points can read this format.
new object library
This is a binary format that includes both the association information and the polygon vertex data. Volume Builder and Clouds can read this format.

Press the load object list button in the Volume Builder dialog to select an object file to load. When the button is pressed, a dialog will be displayed to select the file name and the file format; press the load button in the dialog to read from the file. Saving an object file is similar: press the save object list button, enter the file name and format in the dialog that appears, and then press the save button.

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Object information

After objects have been assembled or read from file; Volume Builder may be used to calculate the properties of the objects or to convert them into models for use with 3D Model.

Use the options in the measurements and relationship menus to report object properties. In general, any of these options will display the results to the scrolled text field in the Volume Builder and write the results to a text file (a dialog will be displayed to select the file name). The options in the measurements menu are:

2D data
For each polygon in the section range specified by the Z and T fields and the wavelength toggles, compute the number, n, of pixels whose centers are within the polygon, the sum of the intensity of those pixels, the area (simply n times the area of the pixel from the image header), the center of gravity (the average, over all pixels whose centers are within the polygon, of the x and y coordinates for the center of each pixel), and the center of mass (the intensity weighted average, over all pixels whose centers are within the polygon, of the x and y coordinates for the center of each pixel). The center of mass and center of gravity are reported in pixel units.
2D real
Has the same effect as 2D data, but the center of mass and center of gravity are reported in the same units used for the pixel spacing in the image header. The coordinates do not take into account the origin or tilt angles from the header.
3D data
For each object in the given time range and selected wavelengths, compute the number of voxels whose centers are within the object, the sum of the intensity of those voxels, the volume (simply n times the volume of a voxel from the image header), the center of gravity (the average, over all voxels whose centers are within the object, of the x, y, and z coordinates of the center of each pixel), the center of mass (the intensity weighted average, over all voxels whose centers are within the object, of the x, y, and z coordinates of the center of each pixel), and the surface area (the sum of the areas of the triangles in the mesh defining the borders of the object). The center coordinates are reported in voxels and the surface area in units of the pixel spacing squared.
3D real
Has the same effect as 3D data, but the center of mass and gravity are reported in the same units for the pixel spacing in the image header. The center coordinates include the effect of the origin and tilt angles from the image header.

The options in the relationship menu are:

between two objects
A dialog is displayed to select which objects (each specified by a wavelength index, time point index, and object number) are to be compared. No results are written to the scrolled text field, but a summary of the properties of each object (these are the same as reported by the 3D real option from the measurements menu except the surface area is not included and the maximum distance between vertices in polygons in the object is included) and the relationship between the two objects (the distance between their centers and the minimum and maximum distance between the center of a pixel inside the first object to a center of a pixel inside the second object).
wave object overlap
Operates on the first two selected wavelengths. Each object in the first wavelength is compared to each object in the second wavelength and the number of voxels whose centers are in both objects is computed. The number of shared voxels and the number of voxels in the two objects are displayed as volumes (the number of voxels multiplied by the volume per voxel from the image header).

Use the options in the surface models menu to create model files usable by 3D Model. The available models, reflecting different ways of representing the objects, are:

wire frame
Each object is represented by the mesh of triangles that form the object's boundary; only the edges of the triangles are shown when the object is displayed by 3D Model. Within 3D Model, it is possible to switch back and forth between this representation and the solid representation.
solid
Each object is represented by a the mesh of triangles that form the object's boundary; the triangles are filled when the object is displayed by 3D Model. Within 3D Model, it is possible to switch back and forth between this representation and the wire frame representation.
string of pts
Each object is represented by a single line which proceeds, in order first by polygon then by section, through all the vertices of the polygons in the object.
string no cross
Each object is represented by the boundaries of the constituent polygons.
gravity centers
Each object is represented by a point at the object's center of gravity (the average, over all voxels whose centers are within the object, of the x, y, and z coordinates of the center of each pixel).
mass centers
Each object is represented by a point at the object's center of mass (the intensity weighted average, over all voxels whose centers are within the object, of the x, y, and z coordinates of the center of each pixel).

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