Utility programs

Collaboration diagram for Utility programs:

Topics
	Utility programs for list mode data
	ClearPET listmode support (unfinished)
	ECAT6 and ECAT7 utilities
	Utility programs for motion and motion correction

Files
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/listmode_utilities/get_singles_info.cxx
	Utility program that lists the singles per bucket in a frame to a text file.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/motion_utilities/non_rigid_transform.cxx
	Non-rigid transformation with b-splines.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/add_ecat7_header_to_sgl.cxx
	Prepend contents of ECAT7 header to a new sgl file (from list mode acquisition).
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/add_side_shields.cxx
	A preliminary utility to add side shields to an attenuation image.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/add_time_frame_info.cxx
	Add the Time Frame Information to Dynamic Images.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/apply_plane_rescale_factors.cxx
	This program rescales planes of an image according to a file with scale factors.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/Bland_Altman_plot.cxx
	Writes the Bland-Altman values for two images in a text file.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/change_mhead_file_type.cxx
	A small utility that changes the file type in an ECAT7 main header.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/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	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/compute_gradient.cxx
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/compute_plane_rescale_factors.cxx
	This programme finds plane rescaling factors.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/create_normfactors.cxx
	Create sample normalisation factors for the ML approach to normalisation.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/create_normfactors3D.cxx
	Create sample normalisation factors for the ML approach to normalisation.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/fillwith1.cxx
	A utility that just fills the projection data with 1.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/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	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/find_sinogram_rescaling_factors.cxx
	Find sinogram rescaling factors.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/fit_cylinder.cxx
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/image_flip_x.cxx
	A preliminary utility to flip the x-axis of an image.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/interpolate_blocks.cxx
	A utility to set data corresponding to a certain detector block by interpolating from neighbouring data.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/interpolate_projdata.cxx
	Interpolate projdata using BSplines.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/inverse_proj_data.cxx
	Find the inverse of ProjData.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/inverse_SSRB.cxx
	Create 4D projdata from 3D using stir::inverse_SSRB.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/line_profiles_through_projdata.cxx
	Extracting profiles from projection data.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/list_TAC_ROI_values.cxx
	Utility program for getting TAC for ROI values.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/make_grid_image.cxx
	This program creates a simple grid image.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/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	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/prepare_projdata.cxx
	A utility preparing some projection data for further processing with iterative reconstructions. See stir::PrepareProjData.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/remove_sinograms.cxx
	A utility to remove (or add) some sinograms at the end of each segment.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/set_blocks_to_value.cxx
	A utility to set data corresponding to a certain detector block to a desired value.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/shift_projdata_along_axis.cxx
	A utility to shift projection data along the axial direction.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/show_ecat7_header.cxx
	Show contents of ECAT7 header.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/threshold_norm_data.cxx
	Threshold normalisation data.
file	/home/kris/devel/STIRdistrib/STIR/src/experimental/utilities/zero_projdata_from_norm.cxx
	Zero projection data when corresponding normalisation factors are too high.
file	/home/kris/devel/STIRdistrib/STIR/src/listmode_utilities/add_ecat7_header_to_sgl.cxx
	Prepend contents of ECAT7 header to a new sgl file (from list mode acquisition).
file	/home/kris/devel/STIRdistrib/STIR/src/listmode_utilities/conv_NiftyPET_stir.cxx
	Convert between NiftyPET and STIR imagees and projdata.
file	/home/kris/devel/STIRdistrib/STIR/src/listmode_utilities/print_sgl_values.cxx
	Utility program that prints out values from an sgl file.
file	/home/kris/devel/STIRdistrib/STIR/src/listmode_utilities/rebin_sgl_file.cxx
	Utility program scans the singles file looking for anomalous values.
file	/home/kris/devel/STIRdistrib/STIR/src/listmode_utilities/scan_sgl_file.cxx
	Utility program scans the singles file looking for anomalous values.
file	/home/kris/devel/STIRdistrib/STIR/src/modelling_utilities/apply_patlak_to_images.cxx
	Apply the Patlak linear fit using Dynamic Images.
file	/home/kris/devel/STIRdistrib/STIR/src/modelling_utilities/extract_single_images_from_parametric_image.cxx
	Split parametric image into individual images.
file	/home/kris/devel/STIRdistrib/STIR/src/modelling_utilities/get_dynamic_images_from_parametric_images.cxx
	Multiplies Parametric Images with the Model Matrix creating Dynamic Images.
file	/home/kris/devel/STIRdistrib/STIR/src/modelling_utilities/make_parametric_image_from_components.cxx
	Create parametric image from individual components.
file	/home/kris/devel/STIRdistrib/STIR/src/modelling_utilities/mult_image_parameters.cxx
	It multiplies the two parametric images and produces one-parameter image.
file	/home/kris/devel/STIRdistrib/STIR/src/modelling_utilities/mult_model_with_dyn_images.cxx
	Multiplies Dynamic Images with the Model Matrix creating image in the Parametric Space.
file	/home/kris/devel/STIRdistrib/STIR/src/modelling_utilities/write_patlak_matrix.cxx
	Write the Model Matrix for the Patlak plot (e.g., for debugging).
file	/home/kris/devel/STIRdistrib/STIR/src/recon_test/recontest.cxx
	Demo for Realtime reconstruction initialization.
file	/home/kris/devel/STIRdistrib/STIR/src/scatter_utilities/create_tail_mask_from_ACFs.cxx
	Compute a mask for the "tails" in the sinogram.
file	/home/kris/devel/STIRdistrib/STIR/src/scatter_utilities/estimate_scatter.cxx
	Estimates a coarse scatter sinogram.
file	/home/kris/devel/STIRdistrib/STIR/src/scatter_utilities/simulate_scatter.cxx
	Simulates a coarse scatter sinogram.
file	/home/kris/devel/STIRdistrib/STIR/src/scatter_utilities/upsample_and_fit_single_scatter.cxx
	upsample a coarse scatter estimate and fit it to emission data using a weight/mask projection data
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/abs_image.cxx
	It produces the absolute value image of an image.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/apply_normfactors.cxx
	Apply normalisation factors using an ML approach.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/apply_normfactors3D.cxx
	Apply normalisation factors estimated using the ML code to projection data.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/attenuation_coefficients_to_projections.cxx
	Takes the logarithm of attenuation coefficients to 'convert' them to line integrals.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/back_project.cxx
	Back project an image.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/calculate_attenuation_coefficients.cxx
	Calculates attenuation coefficients (as an alternative to correct_projdata).
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/compare_image.cxx
	compare images to see if they are identical, allowing for small differences
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/compare_projdata.cxx
	compare 2 files with sinogram data
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/compute_sqrt_Hessian_row_sum.cxx
	Computes the Square Root of the Hessian Row Sum of the objective function.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/construct_randoms_from_GEsingles.cxx
	Construct randoms as a product of singles estimates.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/construct_randoms_from_singles.cxx
	Construct randoms as a product of singles estimates.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/conv_GATE_raw_ECAT_projdata_to_interfile.cxx
	This program converts GATE ECAT output (.ima) into STIR interfile format.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/conv_gipl_to_interfile.cxx
	This program converts Images from GIPL (Guy's Imaging Processing Lab) format to Interfile Format.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/conv_interfile_to_gipl.cxx
	This program converts Images from Interfile Format to GIPL (Guy's Imaging Processing Lab) format.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/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	/home/kris/devel/STIRdistrib/STIR/src/utilities/correct_projdata.cxx
	A utility applying/undoing some corrections on projection data.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/create_multi_header.cxx
	create a "Multi" header for a set of data
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/create_projdata_template.cxx
	A utility that creates a template projection data.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/ctac_to_mu_values.cxx
	Produces an image of mu-values from a CT/CTAC.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/display_projdata.cxx
	This program displays projection data by segment.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/do_linear_regression.cxx
	A simple programme to perform weighted least squares.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/ecat/copy_ecat7_header.cxx
	Copy contents of an ECAT7 header from 1 file to another.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/ecat/ecat_swap_corners.cxx
	A (slightly dangerous) utility to perform so-called corner-swapping for ECAT6 projection data.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/ecat/is_ecat7_file.cxx
	A simple utility that allows to check if a file is in the ECAT7 format.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/estimate_triple_energy_window_scatter_sinogram.cxx
	Calculate Triple energy window scatter.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/extract_segments.cxx
	This program extracts projection data by segment into 3d image files.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/extract_single_images_from_dynamic_image.cxx
	Split dynamic image into individual images.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/find_fwhm_in_image.cxx
	List of FWHM and location of maximum in the image.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/find_maxima_in_image.cxx
	List coordinates of maxima in the image to stdout.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/find_ML_normfactors.cxx
	Find normalisation factors using an ML approach.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/find_ML_normfactors3D.cxx
	Find normalisation factors using an ML approach.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/find_ML_singles_from_delayed.cxx
	Find singles (and hence randoms) from delayed events using an ML approach.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/find_normfactors_from_cylinder_data.cxx
	Find normalisation factors given projection data of a cylinder (direct method).
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/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	/home/kris/devel/STIRdistrib/STIR/src/utilities/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	/home/kris/devel/STIRdistrib/STIR/src/utilities/forward_project.cxx
	Forward project an image.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/generate_image.cxx
	A utility to generate images consisting of uniform objects added/subtracted together.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/get_time_frame_info.cxx
	Prints start time and duration of a frame to stdout.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/invert_axis.cxx
	This program inverts x y or z axis.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/list_detector_and_bin_info.cxx
	A utility that lists bin and detector info for a given (cylindrical) scanner on stdout.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/list_image_info.cxx
	This program lists basic image info. It works for dynamic images.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/list_image_values.cxx
	Utility to extract image values along profiles (or another box-shape).
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/list_projdata_info.cxx
	A utility that lists size info on the projection data on stdout.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/list_ROI_values.cxx
	Utility program for getting ROI values.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/manip_image.cxx
	This program performs operations on image data.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/manip_projdata.cxx
	process sinogram data
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/poisson_noise.cxx
	Generates a noise realisation according to Poisson statistics for some projection data.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/postfilter.cxx
	This program performs filtering on image data.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/rebin_projdata.cxx
	A utility to rebin projection data.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/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	/home/kris/devel/STIRdistrib/STIR/src/utilities/shift_image.cxx
	This program shifts the origin of an image.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/shift_image_origin.cxx
	This program shifts the origin of an image.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/SPECT_dicom_to_interfile.cxx
	Convert SPECT DICOM projection data to Interfile.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/SSRB.cxx
	Main program for stir::SSRB.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/stir_config.cxx
	Prints configuration directory and STIR version.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/stir_list_registries.cxx
	Prints all registered names for many registries.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/stir_math.cxx
	add or multiply data, with some other basic math manipulations
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/stir_timings.cxx
	Perform timings.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/stir_write_pgm.cxx
	This program writes a PGM bitmap for an image (preliminary).
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/UPENN/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	/home/kris/devel/STIRdistrib/STIR/src/utilities/warp_and_accumulate_gated_images.cxx
	This program corrects the motion from an image.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/warp_image.cxx
	This program warps an image.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/write_proj_matrix_by_bin.cxx
	Program that writes a projection matrix by bin to file.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/zeropad_planes.cxx
	This program zero pads the start & end planes of an image.
file	/home/kris/devel/STIRdistrib/STIR/src/utilities/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...

Detailed Description