List of Menu commands
File Menu
| Load Proj File: | Loads the sinogram from a local file. Data is stored in text files. |
| Save Current Projs.: | Save the currently loaded sinogram. |
| Import Proj Data: | Import sinogram data from an image, perhaps created from another application such as Matlab. User can select whether data is in rows or columns and the program will attempt to fill the 2D projection data array with the pixel values of the image. Results may be noisy data. Can work for 8 or 16 bit input images. |
| Open Image: | Open an image, uses ImageJ FileOpener to create an ImagePlus object, which is then used to create a bufferedImage. Images of many times to be opened, such as tif, png, jpg, gif and dicom |
| Save Image: | Saves the current image as a png |
Phantom Menu
| Select: | |
| SheppLogan | Well known shepp logan phantom |
| Test Object1 | Low contrast phantom |
| Test Object2 | Low contrast phantom with disks of varying contrast levels located radial lines around the center |
| Test Object3 | Another low contrast phantom, with three sets of disks at various sizes. |
| Test Object4 |
| Proj Phantom: | Create projection data for selected phantom, data is then automatically backprojected and displayed |
| Phantom Image: | Create images raster of current phantom data. can be used as a reference image. |
| Set count rate: | For noise addition |
Settings Menu
| Method: | |
| FBP | Use Filtered Back Projection. Default Value. |
| Iterative | An iterative reconstruction algorithm, still a test version and poor quality |
| Set No. Iterations | Sets number of iterations |
| Reprojection: | |
| Fast | Uses nearest neighbour interpolation |
| Accurate | Uses a type of linear interpolation. Default Value. |
| Filter: | |
| Filtering | Toggles filtering on and off. Default is on. The filtering is FFT-based and filters are implemented as 1D arrays for use in the frequency domain, by multiplying them with the FFT of each projection array. |
| Set Filter Cutoff | Sets the normalised cut-off frequency for the chosen filter. Default value is 1, which corresponds to the band-limit of the data. |
| Graph Filters | Displays a window that graphs the filters in the frequency domain, allowing the user to visualize the shape of each filter at the current cut-off frequency. |
| -------------------------------- | |
| Simple Ramp | Uses the simplest form of ramp filter. Has the form |n*pi|, where n is the current array index and corresponds to the sampling frequency. This is the default. |
| Shepp-Logan | This filter has the form n*pi * sin(n*pi/width/2)/(n*pi/width/2), where width is the maximum sampling frequency and is determined also by the filter cut-off |
| Hamming | This filter has the form n*pi * α+(1-α)*cos(2.n*pi/width) for -width/2 <n<+width/2 and 0 elsewhere. α=0.54 |
| Hann | Same as Hamming, but α=0.5 |
| Cosine | Has the form n*pi * cos(n*pi/width) for -width/2 <n<+width/2 and 0 elsewhere |
| Interpolation: | The type of interpolation used for back projection |
| Nearest | Uses nearest neighbour interpolation |
| Linear | Uses linear interpolation. Default Value. |
| Noise: | |
| No noise | Adds no noise. Default value. |
| Add noise to data | Adds additive noise with a poisson distribution to the projection data, before back projection is done. |
| Reconstruct with noise | Puts noise on the data prior to the back projection, but leaves the original data intact. So that recreating the data is not necessary. |
| Set Count Rate | Sets the number of 'counts' to be used when creating the poisson distribution of noise values. |
| ROI: | Region-of-interest menu. |
| Truncate | Sets the data to be truncated. |
| Crop to ROI | Crops the reconstructed image to the current ROI size, which corresponds to the truncation width. |
| Add ROI Outline | Adds the outline of the ROI to the reconstructed image. |
| Set ROI Radius | Allows user to enter a truncation radius, range is from non-zero positive to 0.5. Default is 0.165 |
| Method: | Selection sub-menu of method to correct truncation. |
| None | Performs no correction |
| Simple | Default cos-squared extrapolation used in the project. |
| Adaptive | Sets extrapolation width depending on width if data in corresponding view of untruncated data. Experimental. |
| VanGompel | Gaussian window method proposed by Van Gompel et al. Poor results. |
Tools Menu:
| Selection: | |
| Copy | Copy the current image selection |
| Paste as Image | Paste the selection as a new Image |
| Measure | Gives pixel statistics, mean max, min, standard dev. on current selection |
| Show Ray Data | Gives data on the last back projection, number of rays projected etc. |
| Graph Data | Opens a simple graphing utility |