Collaboration diagram for Utility programs:
|
Modules | |
| Utility programs for list mode data | |
| ECAT6 and ECAT7 utilities | |
| Utility programs for motion and motion correction | |
Files | |
| file | get_singles_info.cxx |
| Utility program that lists the singles per bucket in a frame to a text file. | |
| file | non_rigid_transform.cxx |
| Non-rigid transformation with b-splines. | |
| file | add_ecat7_header_to_sgl.cxx |
| Prepend contents of ECAT7 header to a new sgl file (from list mode acquisition) | |
| file | add_side_shields.cxx |
| A preliminary utility to add side shields to an attenuation image. | |
| file | add_time_frame_info.cxx |
| Add the Time Frame Information to Dynamic Images. | |
| file | apply_plane_rescale_factors.cxx |
| This program rescales planes of an image according to a file with scale factors. | |
| file | Bland_Altman_plot.cxx |
| Writes the Bland-Altman values for two images in a text file. | |
| file | change_mhead_file_type.cxx |
| A small utility that changes the file type in an ECAT7 main header. | |
| file | CoG.cxx |
| This program computes the centre of gravity in each plane and writes its coordinates to file, together with a weight for each plane. | |
| file | compute_gradient.cxx |
| file | compute_plane_rescale_factors.cxx |
| This programme finds plane rescaling factors. | |
| file | create_normfactors.cxx |
| Create sample normalisation factors for the ML approach to normalisation. | |
| file | create_normfactors3D.cxx |
| Create sample normalisation factors for the ML approach to normalisation. | |
| file | fillwith1.cxx |
| A utility that just fills the projection data with 1. | |
| file | fillwithotherprojdata.cxx |
| A utility that just fills the projection data with input from somewhere else. Only useful when the first file is an a different file format (i.e. ECAT 7) | |
| file | find_sinogram_rescaling_factors.cxx |
| Find sinogram rescaling factors. | |
| file | fit_cylinder.cxx |
| file | image_flip_x.cxx |
| A preliminary utility to flip the x-axis of an image. | |
| file | interpolate_blocks.cxx |
| A utility to set data corresponding to a certain detector block by interpolating from neighbouring data. | |
| file | interpolate_projdata.cxx |
| Interpolate projdata using BSplines. | |
| file | inverse_proj_data.cxx |
| Find the inverse of ProjData. | |
| file | inverse_SSRB.cxx |
| Create 4D projdata from 3D using stir::inverse_SSRB. | |
| file | line_profiles_through_projdata.cxx |
| Extracting profiles from projection data. | |
| file | list_TAC_ROI_values.cxx |
| Utility program for getting TAC for ROI values. | |
| file | make_grid_image.cxx |
| This program creates a simple grid image. | |
| file | normalizedbckproj.cxx |
| This programm was based on bck_project originnal code with the difference that here we normalize the final value of a single pixel with a sum of all values in the corresponding LOR. | |
| file | prepare_projdata.cxx |
| A utility preparing some projection data for further processing with iterative reconstructions. See stir::PrepareProjData. | |
| file | remove_sinograms.cxx |
| A utility to remove (or add) some sinograms at the end of each segment. | |
| file | set_blocks_to_value.cxx |
| A utility to set data corresponding to a certain detector block to a desired value. | |
| file | shift_projdata_along_axis.cxx |
| A utility to shift projection data along the axial direction. | |
| file | show_ecat7_header.cxx |
| Show contents of ECAT7 header. | |
| file | threshold_norm_data.cxx |
| Threshold normalisation data. | |
| file | zero_projdata_from_norm.cxx |
| Zero projection data when corresponding normalisation factors are too high. | |
| file | add_ecat7_header_to_sgl.cxx |
| Prepend contents of ECAT7 header to a new sgl file (from list mode acquisition) | |
| file | conv_NiftyPET_stir.cxx |
| Convert between NiftyPET and STIR imagees and projdata. | |
| file | print_sgl_values.cxx |
| Utility program that prints out values from an sgl file. | |
| file | rebin_sgl_file.cxx |
| Utility program scans the singles file looking for anomalous values. | |
| file | scan_sgl_file.cxx |
| Utility program scans the singles file looking for anomalous values. | |
| file | apply_patlak_to_images.cxx |
| Apply the Patlak linear fit using Dynamic Images. | |
| file | extract_single_images_from_parametric_image.cxx |
| Split parametric image into individual images. | |
| file | get_dynamic_images_from_parametric_images.cxx |
| Multiplies Parametric Images with the Model Matrix creating Dynamic Images. | |
| file | make_parametric_image_from_components.cxx |
| Create parametric image from individual components. | |
| file | mult_image_parameters.cxx |
| It multiplies the two parametric images and produces one-parameter image. | |
| file | mult_model_with_dyn_images.cxx |
| Multiplies Dynamic Images with the Model Matrix creating image in the Parametric Space. | |
| file | write_patlak_matrix.cxx |
| Write the Model Matrix for the Patlak plot (e.g., for debugging) | |
| file | recontest.cxx |
| Demo for Realtime reconstruction initialization. | |
| file | create_tail_mask_from_ACFs.cxx |
| Compute a mask for the "tails" in the sinogram. | |
| file | estimate_scatter.cxx |
| Estimates a coarse scatter sinogram. | |
| file | simulate_scatter.cxx |
| Simulates a coarse scatter sinogram. | |
| file | upsample_and_fit_single_scatter.cxx |
| upsample a coarse scatter estimate and fit it to emission data using a weight/mask projection data | |
| file | abs_image.cxx |
| It produces the absolute value image of an image. | |
| file | apply_normfactors.cxx |
| Apply normalisation factors using an ML approach. | |
| file | apply_normfactors3D.cxx |
| Apply normalisation factors estimated using the ML code to projection data. | |
| file | attenuation_coefficients_to_projections.cxx |
| Takes the logarithm of attenuation coefficients to 'convert' them to line integrals. | |
| file | back_project.cxx |
| Back project an image. | |
| file | calculate_attenuation_coefficients.cxx |
Calculates attenuation coefficients (as an alternative to correct_projdata). | |
| file | compare_image.cxx |
| compare images to see if they are identical, allowing for small differences | |
| file | compare_projdata.cxx |
| compare 2 files with sinogram data | |
| file | compute_sqrt_Hessian_row_sum.cxx |
| Computes the Square Root of the Hessian Row Sum of the objective function. | |
| file | construct_randoms_from_GEsingles.cxx |
| Construct randoms as a product of singles estimates. | |
| file | construct_randoms_from_singles.cxx |
| Construct randoms as a product of singles estimates. | |
| file | conv_GATE_raw_ECAT_projdata_to_interfile.cxx |
| This program converts GATE ECAT output (.ima) into STIR interfile format. | |
| file | conv_gipl_to_interfile.cxx |
| This program converts Images from GIPL (Guy's Imaging Processing Lab) format to Interfile Format. | |
| file | conv_interfile_to_gipl.cxx |
| This program converts Images from Interfile Format to GIPL (Guy's Imaging Processing Lab) format. | |
| file | convert_to_binary_image.cxx |
| This program outputs a binary image (voxel values 0 or 1) where all values strictly below a threshold are set to 0, and others to 1. | |
| file | correct_projdata.cxx |
| A utility applying/undoing some corrections on projection data. | |
| file | create_multi_header.cxx |
| create a "Multi" header for a set of data | |
| file | create_projdata_template.cxx |
| A utility that creates a template projection data. | |
| file | ctac_to_mu_values.cxx |
| Produces an image of mu-values from a CT/CTAC. | |
| file | display_projdata.cxx |
| This program displays projection data by segment. | |
| file | do_linear_regression.cxx |
| A simple programme to perform weighted least squares. | |
| file | copy_ecat7_header.cxx |
| Copy contents of an ECAT7 header from 1 file to another. | |
| file | ecat_swap_corners.cxx |
| A (slightly dangerous) utility to perform so-called corner-swapping for ECAT6 projection data. | |
| file | is_ecat7_file.cxx |
| A simple utility that allows to check if a file is in the ECAT7 format. | |
| file | estimate_triple_energy_window_scatter_sinogram.cxx |
| Calculate Triple energy window scatter. | |
| file | extract_segments.cxx |
| This program extracts projection data by segment into 3d image files. | |
| file | extract_single_images_from_dynamic_image.cxx |
| Split dynamic image into individual images. | |
| file | find_fwhm_in_image.cxx |
| List of FWHM and location of maximum in the image. | |
| file | find_maxima_in_image.cxx |
| List coordinates of maxima in the image to stdout. | |
| file | find_ML_normfactors.cxx |
| Find normalisation factors using an ML approach. | |
| file | find_ML_normfactors3D.cxx |
| Find normalisation factors using an ML approach. | |
| file | find_ML_singles_from_delayed.cxx |
| Find singles (and hence randoms) from delayed events using an ML approach. | |
| file | find_normfactors_from_cylinder_data.cxx |
| Find normalisation factors given projection data of a cylinder (direct method) | |
| file | find_recovery_coefficients_in_image_quality_phantom_nema_nu4.cxx |
| Utility program for calculating recovery coeficient values in the image quality phantom described in NEMA NU 4. | |
| file | find_sum_projection_of_viewgram_and_sinogram.cxx |
| This program reads a projection data file and squeezes a given sinogrm or viewgram of it (from a 2D matrix to a 1D vector). | |
| file | forward_project.cxx |
| Forward project an image. | |
| file | generate_image.cxx |
| A utility to generate images consisting of uniform objects added/subtracted together. | |
| file | get_time_frame_info.cxx |
| Prints start time and duration of a frame to stdout. | |
| file | invert_axis.cxx |
| This program inverts x y or z axis. | |
| file | list_detector_and_bin_info.cxx |
| A utility that lists bin and detector info for a given (cylindrical) scanner on stdout. | |
| file | list_image_info.cxx |
| This program lists basic image info. It works for dynamic images. | |
| file | list_image_values.cxx |
| Utility to extract image values along profiles (or another box-shape) | |
| file | list_projdata_info.cxx |
| A utility that lists size info on the projection data on stdout. | |
| file | list_ROI_values.cxx |
| Utility program for getting ROI values. | |
| file | manip_image.cxx |
| This program performs operations on image data. | |
| file | manip_projdata.cxx |
| process sinogram data | |
| file | poisson_noise.cxx |
| Generates a noise realisation according to Poisson statistics for some projection data. | |
| file | postfilter.cxx |
| This program performs filtering on image data. | |
| file | rebin_projdata.cxx |
| A utility to rebin projection data. | |
| file | separate_true_from_random_scatter_for_necr.cxx |
| This program gets a projection data file of a mouse/rat scatter phantom measured according to NEMA NU 4. It seperates number of true events from number of random+scatter events. | |
| file | shift_image.cxx |
| This program shifts the origin of an image. | |
| file | shift_image_origin.cxx |
| This program shifts the origin of an image. | |
| file | SPECT_dicom_to_interfile.cxx |
| Convert SPECT DICOM projection data to Interfile. | |
| file | SSRB.cxx |
| Main program for stir::SSRB. | |
| file | stir_config.cxx |
| Prints configuration directory and STIR version. | |
| file | stir_list_registries.cxx |
| Prints all registered names for many registries. | |
| file | stir_math.cxx |
| add or multiply data, with some other basic math manipulations | |
| file | stir_timings.cxx |
| Perform timings. | |
| file | stir_write_pgm.cxx |
| This program writes a PGM bitmap for an image (preliminary) | |
| file | conv_UPENN_projdata_to_STIR.cxx |
| Convert PennPET Explorer-type of sinogram to STIR-type The PennPET projdata skip over the gaps, the –gaps options adds them back to STIR's projdata. Without the –gaps flag the output will match the input (as closely as possibly). –inv: should be used for the attenuation correction –up_treshold should be used with normalisation (typically 13) | |
| file | warp_and_accumulate_gated_images.cxx |
| This program corrects the motion from an image. | |
| file | warp_image.cxx |
| This program warps an image. | |
| file | write_proj_matrix_by_bin.cxx |
| Program that writes a projection matrix by bin to file. | |
| file | zeropad_planes.cxx |
| This program zero pads the start & end planes of an image. | |
| file | zoom_image.cxx |
| This program serves as a stand-alone zoom/trim utility for image files Run without arguments to get a usage message. | |
Classes | |
| class | stir::CorrectProjDataApplication |
| class to do precorrections More... | |
