Rebins a SimSET block-detector weight file, binned by crystal pair, into STIR projection data. More...

#include "stir/ProjData.h"
#include "stir/ProjDataInMemory.h"
#include "stir/ProjDataInfoPETScannerWithDiscreteDetectors.h"
#include "stir/DetectionPositionPair.h"
#include "stir/Bin.h"
#include "stir/Scanner.h"
#include "stir/format.h"
#include "stir/info.h"
#include "stir/warning.h"
#include "stir/error.h"
#include <algorithm>
#include <cstdint>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <string>
#include <vector>

Functions
int	main (int argc, char **argv)

Detailed Description

Rebins a SimSET block-detector weight file, binned by crystal pair, into STIR projection data.

SimSET run with a block detector and bin_by_crystal = true writes its weights indexed by crystal pair, not by sinogram bin. This utility maps each bin of a STIR template onto its detection position pairs, and sums the corresponding crystal-pair weights.

Usage: conv_SimSET_crystal_pairs_to_STIR output_prefix template_projdata weight_file mode

Parameters

output_prefix	outputs are written as output_prefix_<label>.hs
template_projdata	projection data describing the scanner and the output sinogram
weight_file	SimSET's weight_image_path from the `bin.rec` file
mode	`multiples` or `singles_scat`, see below

The block layout is taken from the template's scanner, which has to agree with the simulated SimSET detector:

number of rings / crystals per block in axial direction: number of block rings in det.rec that contain active crystals (rings with only shielding do not count)
number of detectors per ring / crystals per block in transaxial direction: ring_num_blocks_in_ring in the ring parameter file
crystals per block in axial direction: number of active crystals per block along z
crystals per block in transaxial direction: number of active crystals per block along y

When every element of the block is an active crystal, the last two are block_layer_num_z_changes + 1 and block_layer_num_y_changes + 1.

File format and modes

A weight file is a SimSET header of 32768 bytes, followed by one or more grids of num_crystals x num_crystals native-endian floats. How many grids there are was decided at simulation time by the bin.rec file.

multiples expects 1 grid (e.g. scatter_param = 5, min_s = max_s = 2), written as label multiples.
singles_scat expects 2 grids, [unscattered][single Scatter estimation building blocks] (e.g. scatter_param = 4, min_s = 0, max_s = 1), written as labels unscattered and singles_scat. The number of grids in the file has to match the mode.

Crystal numbering: The template's scanner has to describe the simulated detector, including its block subdivision. The crystal index of a detection position is
block_index * (crystals_per_block_axial * crystals_per_block_transaxial)

+ axial_index_in_block * crystals_per_block_transaxial + transaxial_index_in_block

with block_index = axial_block * num_transaxial_blocks + transaxial_block. A template with the right total number of crystals but a different block subdivision would give a permuted, wrong, sinogram without any error. Only the upper triangle of each grid (crystal1 < crystal2) is used.

The views of the output are stored in reverse order (view -> num_views - 1 - view). SimSET's y axis points up (voxel row 0 is at yMax) and STIR's points down, so an image written row by row for SimSET is the same picture in both, with y_SimSET = -y_STIR. Both number their crystals counter-clockwise in their own frame, so seen from the object the two rings are numbered in opposite directions: SimSET crystal k is the mirror image of STIR detector k. Reversing the views undoes this mirror. The exact alignment depends on the template's view offset.

Warning: The whole grid is read into memory (4 num_crystals^2 bytes, 5.8 GB for 38016 crystals).; Only Cylindrical and BlocksOnCylindrical non-arc-corrected, non-TOF, templates are supported.

Author: Antonia Reeves

Functions

Detailed Description