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value | path stringlengths 12 229 | size int64 23 843k | source_encoding stringclasses 9
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github | ismrmrd/ismrmrd-paper-master | mri_field_map_reg.m | .m | ismrmrd-paper-master/code/extern/irt/mri/mri_field_map_reg.m | 7,131 | utf_8 | 060936a8e947d274b686441899604db5 | function [wmap, wconv] = mri_field_map_reg(yik, etime, varargin)
%|function [wmap, wconv] = mri_field_map_reg(yik, etime, varargin)
%|
%| MRI field map estimation using regularization and optimization transfer,
%| based on a multiple image model:
%| y_ik = mag_i * phase_ik * decay_ik + noise_ik
%| phase_ik = exp(1i *... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_coil_combine.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_coil_combine.m | 5,187 | utf_8 | ed3604f5c4cbd9cd73d25ec2772a7b9a | function [xhat smap ref] = ir_mri_coil_combine(ykj, varargin)
%function [xhat smap ref] = ir_mri_coil_combine(ykj, varargin)
%|
%| Given multiple MRI surface coil images, estimate their sensitivity maps,
%| relative to the sqrt-sum-of-squares (SSOS) map, and then perform the
%| "best" linear combination using the sens... |
github | ismrmrd/ismrmrd-paper-master | mri_r2_fit_normalize.m | .m | ismrmrd-paper-master/code/extern/irt/mri/mri_r2_fit_normalize.m | 1,369 | utf_8 | e2909081f333009675769c7e4868d6eb | function [images kappa_typical] = mri_r2_fit_normalize(images, te, varargin)
%|function [images kappa_typical] = mri_r2_fit_normalize(images, te, varargin)
%|
%| Normalize images for R2=1/T2 mapping so that typical "kappa" is unity.
%|
%| in
%| images [(nd) nt] images with nt different echo times
%| te [nt] echo tim... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_partial_fourier_3d.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_partial_fourier_3d.m | 9,054 | utf_8 | cf785a9fa8a71c5ee362a3dee8d4a8b2 | function [img_est, full_kspace] = ...
ir_mri_partial_fourier_3d(partial_kspace, full_dims, varargin)
%function [img, full_kspace] = ...
%| ir_mri_partial_fourier_3d(partial_kspace, full_dims, varargin)
%|
%| 2D and 3D versions of Xu and Haacke's 2001 "Partial Fourier imaging in
%| multi-dimensions: A means to save a ... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_density_comp.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_density_comp.m | 8,539 | utf_8 | 440c2e8bcca8a937b2fafb31edaea75c | function wi = ir_mri_density_comp(kspace, dtype, varargin)
%function wi = ir_mri_density_comp(kspace, dtype, varargin)
%|
%| todo: THIS NEEDS A LOT OF WORK!
%|
%| Compute density compensation factors for the conjugate phase
%| method for image reconstruction from Fourier samples.
%|
%| in
%| kspace [M 1] kspace sample... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_sensemap_sim.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_sensemap_sim.m | 10,925 | utf_8 | 2d0a384573712df692c79e095c7ce125 | function [smap x y z] = ir_mri_sensemap_sim(varargin)
%function [smap x y z] = ir_mri_sensemap_sim(varargin)
%|
%| Simulate 2D or 3D sensitivity maps for sensitivity-encoded MRI
%| based grivich:00:tmf doi:10.1119/1.19461
%|
%| option
%| nx, ny, nz image size (default: [64 64 1])
%| dx, dy, dz pixel/voxel dimensions... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_dce_aif1.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_dce_aif1.m | 4,041 | utf_8 | f08a600e1485dd210e25c0b4f5b2f9b2 | function [Ct, Cp, Ca, ht] = ir_mri_dce_aif1(ti, Ktrans, kep, varargin)
%function [Ct, Cp, Ca, ht] = ir_mri_dce_aif1(ti, Ktrans, kep, varargin)
%|
%| Generate tissue contrast concentration curves according to Yang et al.
%| "Multiple reference tissue..." MRM Dec. 07 (yang:07:mrt)
%|
%| in
%| ti [Nt] [min] time sample... |
github | ismrmrd/ismrmrd-paper-master | image_geom_mri.m | .m | ismrmrd-paper-master/code/extern/irt/mri/image_geom_mri.m | 555 | utf_8 | a0e8b960eb317d570a067c05572901ee | function st = image_geom_mri(varargin)
%function st = image_geom_mri(varargin)
%|
%| Same as image_geom() but default offsets are 0.5 so that
%| image pixel indices go from -N/2 to N/2-1.
%|
%| Copyright 2007-2-22, Jeff Fessler, University of Michigan
if nargin < 1, help(mfilename), error(mfilename), end
if nargin ==... |
github | ismrmrd/ismrmrd-paper-master | mri_trajectory.m | .m | ismrmrd-paper-master/code/extern/irt/mri/mri_trajectory.m | 9,908 | utf_8 | 45ad29e505a0ed9b9ccc29b2afd993e7 | function [kspace, omega, wi] = mri_trajectory(ktype, arg_traj, N, fov, arg_wi)
%function [kspace, omega, wi] = mri_trajectory(ktype, arg_traj, N, fov, arg_wi)
%|
%| generate kspace trajectory samples and density compensation functions.
%|
%| in
%| ktype string k-space trajectory type. see choices below.
%| arg_traj ... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_dce_r1d.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_dce_r1d.m | 1,628 | utf_8 | 65609d9de11f9546bd06ac2aaf7fbed5 | function r1d = ir_mri_dce_r1d(r10, Ct, varargin)
%function r1d = ir_mri_dce_r1d(r10, Ct, varargin)
%|
%| Make time series of R1=1/T1 values given baseline value(s) R10
%| and contrast agent time-concentration curves Ct.
%|
%| in
%| r10 [1] | [Nc] [1/s] baseline R1 values
%| for Nc tissue classes
%| Ct [Nc Nt] [mMm... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_sensemap_admm.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_sensemap_admm.m | 9,248 | utf_8 | 60d78c56732788b001e123a3e51ef95f | function [smap, sinit] = ir_mri_sensemap_admm(ykj, varargin)
%function [smap, sinit] = ir_mri_sensemap_admm(ykj, [options])
%|
%| Regularized estimation of sensitivity maps for parallel MRI
%| using augmented Lagrangian methods with variable splitting.
%| See M.J. Allison et al., IEEE TMI, 32(3), 556-564, Mar. 2013.
%... |
github | ismrmrd/ismrmrd-paper-master | mri_fun_approx.m | .m | ismrmrd-paper-master/code/extern/irt/mri/mri_fun_approx.m | 9,763 | utf_8 | 826c84a680d86c573030ec4dc356a878 | function [B, C, hk, wk] = mri_fun_approx(ti, uj, vj, f1, f2, varargin)
%|function [B, C, hk, wk] = mri_fun_approx(ti, uj, vj, f1, f2, [options])
%|
%| UNDER DEVELOPMENT
%| For certain iterative MR image reconstruction problems, we have
%| signals of the form f1(uj ti) f2(vj ti), for some functions f1() and f2(),
%| a... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_sensemap_init.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_sensemap_init.m | 3,647 | utf_8 | d03a9a052defc25427ec89aa366c5b08 | function sinit = ir_mri_sensemap_init(init, ykj, bodycoil, sizeI, thresh, maskObj)
nx = sizeI(1);
ny = sizeI(2);
ncoil = sizeI(3);
if ~isempty(maskObj)
warning('using the maskObj instead of thresholding to determine good pixels');
end
if isempty(init) || ischar(init)
sinit = zeros(nx, ny, ncoil);
for ic... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_dce_gre.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_dce_gre.m | 2,269 | utf_8 | 3ffbbafdc2ae6e0e8977d45590c72880 | function sig = ir_mri_dce_gre(r1d, varargin)
%function sig = ir_mri_dce_gre(r1d, varargin)
%|
%| Given dynamic time curves for R1=1/T1, compute corresponding MRI signal
%| for (spoiled) gradient echo (GRE) signal model.
%| It is known this model is inaccurate for imperfect spoiling
%| but it is useful for simulations ... |
github | ismrmrd/ismrmrd-paper-master | mri_r2_fit_costgrad_r2.m | .m | ismrmrd-paper-master/code/extern/irt/mri/mri_r2_fit_costgrad_r2.m | 1,634 | utf_8 | eaf558521318bb8e70d438bda9d1965b | function [cost grad] = mri_r2_fit_costgrad_r2(r2, data)
%|function [cost grad] = mri_r2_fit_costgrad_r2(r2, data)
%| for R2=1/T2 estimation from images
if nargin == 1 && streq(r2, 'test'), mri_r2_fit_costgrad_r2_test, return, end
if nargin < 2, help(mfilename), error(mfilename), end
yi = data.yi; % [(nd) nt] images... |
github | ismrmrd/ismrmrd-paper-master | mri_sensemap_denoise.m | .m | ismrmrd-paper-master/code/extern/irt/mri/mri_sensemap_denoise.m | 6,146 | utf_8 | e0d5bd6969aa536c47b1e7b67e4cb0e0 | function [smap, sinit, cost] = mri_sensemap_denoise(ykj, varargin)
%function [smap, sinit, cost] = mri_sensemap_denoise(ykj, [options])
%|
%| Regularized estimation of (smooth) sensitivity maps for parallel MRI.
%| Signal model: y_kj = s_kj f_j + noise_kj
%| s_kj sensitivity map (relative to "bodycoil" reference image... |
github | ismrmrd/ismrmrd-paper-master | mri_phase_denoise.m | .m | ismrmrd-paper-master/code/extern/irt/mri/mri_phase_denoise.m | 5,882 | utf_8 | fb7738e5d0c08a0d6d264d51b51d97d2 | function [x, mask0] = mri_phase_denoise(yi, varargin)
%function [x, mask0] = mri_phase_denoise(yi, [options]) <- recommended usage
%|function [x] = mri_phase_denoise(yi, l2b, niter, chat, wthresh) <- old way
%|
%| in
%| yi [(N)] noisy complex image: y = mag .* exp(1i * x)
%| can be any size: 1D, 2D, 3D, ...
%|
%| op... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_kspace_ga_radial.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_kspace_ga_radial.m | 2,002 | utf_8 | a16181069045a7c814ca4be44c848e5d | function kspace = ir_mri_kspace_ga_radial(Nspoke, Nro, varargin)
%function kspace = ir_mri_kspace_ga_radial(Nspoke, Nro, varargin)
%|
%| Generate k-space sampling pattern for "golden angle" radial sampling.
%|
%| in
%| Nspoke number of spokes
%| Nro number of samples in each readout/spoke
%|
%| option
%| start firs... |
github | ismrmrd/ismrmrd-paper-master | mri_r2_fit_costgrad_pd.m | .m | ismrmrd-paper-master/code/extern/irt/mri/mri_r2_fit_costgrad_pd.m | 1,647 | utf_8 | 427edfe6e78954f98a05ea7c2c925be4 | function [cost grad] = mri_r2_fit_costgrad_pd(pd, data)
%|function [cost grad] = mri_r2_fit_costgrad_pd(pd, data)
%| gradient wrt "proton density" (pd) image
%| for R2=1/T2 estimation from images
if nargin == 1 && streq(pd, 'test'), mri_r2_fit_costgrad_pd_test, return, end
if nargin < 2, help(mfilename), error(mfile... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_dce_kspace1.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_dce_kspace1.m | 3,136 | utf_8 | 3c2061ddc8d1cd1881f26bd9e0fcda7f | function kspace = ir_mri_dce_kspace1(dyn_obj, samp, varargin)
%function kspace = ir_mri_dce_kspace1(dyn_obj, samp, varargin)
%|
%| Generate dynamic kspace data for DCE MRI simulations.
%|
%| in
%| dyn_obj [(N) Nt] complex dynamic object
%| samp [(N) Nt] sampling pattern
%| (reshaped from [(N) Nt/Nframe Nframe])
%|
... |
github | ismrmrd/ismrmrd-paper-master | ir_mri_dce_obj1.m | .m | ismrmrd-paper-master/code/extern/irt/mri/ir_mri_dce_obj1.m | 5,356 | utf_8 | 4888c96e2e7afd44a96b51b67c6f40a1 | function [dyn_obj dce] = ir_mri_dce_obj1(varargin)
%function [dyn_obj dce] = ir_mri_dce_obj1(varargin)
%|
%| Generate dynamic object for DCE MRI simulations of GRE sequence.
%|
%| option
%| 'TR' [s] repetition time (default: 5e-3)
%| 'TE' [s] echo time (default: 0)
%| 'flip' [rad] flip angle (default: pi/6)
%| '... |
github | ismrmrd/ismrmrd-paper-master | mri_field_map_sim.m | .m | ismrmrd-paper-master/code/extern/irt/mri/mri_field_map_sim.m | 4,105 | utf_8 | afc4e6fcb85f9fd047984b0782010bce | function [f0, Bz] = mri_field_map_sim(x, z, varargin)
%|function [f0, Bz] = mri_field_map_sim(x, z, varargin)
%|
%| Analytically simulate the magnetic field variation caused simple
%| geometric shapes of various susceptibilties in a uniform magnetic field.
%|
%| Currently there are two geometries impemented:
%| 1) a ... |
github | ismrmrd/ismrmrd-paper-master | ir_gen_spiral_vd.m | .m | ismrmrd-paper-master/code/extern/irt/mri/contrib/ir_gen_spiral_vd.m | 9,464 | utf_8 | 1768cabd88463fdc5124049aec1d2255 | function [Gx, Gy, kxvec, kyvec, sx, sy] = ir_gen_spiral_vd(D, N, nl, gamp, gslew, dsamp)
%function [Gx, Gy, kxvec, kyvec, sx, sy] = ir_gens_piral_vd(D, N, nl, gamp, gslew, dsamp)
%| Subroutine for generating slew-rate-limited spirals.
%| Returns length of resulting gradients, after adding downramp.
%| Craig Meyer, Cop... |
github | ismrmrd/ismrmrd-paper-master | mri_objects_2d.m | .m | ismrmrd-paper-master/code/extern/irt/mri/arch/mri_objects_2d.m | 3,299 | utf_8 | f60fd76c1a10dd35402375348e3ba155 | function [xf, yf] = mri_objects_2d(varargin)
%function [xf, yf] = mri_objects_2d('type1', params1, 'type', params2, ...)
% Generate inline functions for describing image-domain objects
% and Fourier domain spectra of simple structures such as rectangles.
% These functions are useful for simple "idealized" MRI simulati... |
github | ismrmrd/ismrmrd-paper-master | mri_brainweb_params.m | .m | ismrmrd-paper-master/code/extern/irt/mri/arch/mri_brainweb_params.m | 1,917 | utf_8 | 8fd494fc77b41ee55ec346d2aa0a6292 | function f = mri_brainweb_params(label, varargin)
%function f = mri_brainweb_params(label, varargin)
%|
%| tissue parameters for brainweb brain images, based on
%| http://mouldy.bic.mni.mcgill.ca/brainweb/tissue_mr_parameters.txt
%| units of t* are msec
%|
%| in
%| label {0,1,...,10} or 'fat', etc.
%| option
%| b0 1... |
github | ismrmrd/ismrmrd-paper-master | mri_field_map_reg_2d.m | .m | ismrmrd-paper-master/code/extern/irt/mri/arch/mri_field_map_reg_2d.m | 5,894 | utf_8 | e5c6b8fcf085788521e0e6bc63423f9e | function [wmap, wconv] = mri_field_map_reg_2d(yi, etime, varargin)
%function [wmap, wconv] = mri_field_map_reg_2d(yik, etime, varargin)
%
% MRI field map estimation using regularization and optimization transfer,
% based on a multiple image model:
% y_ik = mag_i * phase_ik * decay_ik + noise_ik
% phase_ik = exp(1i * w... |
github | ismrmrd/ismrmrd-paper-master | mri_objects_3d.m | .m | ismrmrd-paper-master/code/extern/irt/mri/arch/mri_objects_3d.m | 5,821 | utf_8 | 532585a014bec2ea7294dc27494d0a4f | function [xf, yf] = mri_objects_3d(varargin)
%function [xf, yf] = mri_objects_3d('type1', params1, 'type', params2, ...)
% Generate inline functions for describing image-domain objects
% and Fourier domain spectra of simple structures such as rectangles.
% These functions are useful for simple "idealized" MRI simulati... |
github | ismrmrd/ismrmrd-paper-master | Gnufft.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gnufft.m | 3,376 | utf_8 | ca66eb91eebfe695a29fdb11b2f91d65 | function ob = Gnufft(varargin)
%function ob = Gnufft([mask,] args)
%|
%| Construct Gnufft object that computes nonunform samples of the FT
%| of signals with dimensions [(Nd)] approximately via the NUFFT.
%| For exact (but slow) computation, use Gdsft instead.
%|
%| The arguments (args) are simply a cell array of the ... |
github | ismrmrd/ismrmrd-paper-master | Gnufft_gram.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gnufft_gram.m | 12,248 | utf_8 | cbaad624222c98466a7b4e8d065e098e | function [T, reuse] = Gnufft_gram(ob, W, reuse)
%|function [T, reuse] = Gnufft_gram(A, W, reuse)
%|
%| construct Toeplitz gram matrix object T = A'WA for a Gnufft object
%| in
%| A [M np] Gnufft object (Fatrix or fatrix2)
%| W [M M] W = diag_sp(wi) (often simply "1" or [])
%| W = Gdiag() for fatrix2
%| reuse str... |
github | ismrmrd/ismrmrd-paper-master | Gtranslate.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gtranslate.m | 9,637 | utf_8 | 40d6410494b3e57d0ab5106dd397bcf0 | function ob = Gtranslate(mask, varargin)
%function ob = Gtranslate(mask, options)
%|
%| Construct Gtranslate object for image registration.
%| (Internally stores image-sized arrays so not very memory efficient.)
%|
%| See Gtranslate_test() below for example usage.
%|
%| in
%| mask size(image) logical array of object s... |
github | ismrmrd/ismrmrd-paper-master | Gtomosyn.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gtomosyn.m | 2,549 | utf_8 | 4d7bce4e1cc9573916bc143f0ce0fc00 | function ob = Gtomosyn(cg, ig, varargin)
%function ob = Gtomosyn(cg, ig, [options])
%|
%| Construct object for forward and back-projection with
%| a 3D tomosynthesis geometry having a flat detector and source moving in arc.
%| Currently is simply a "stack" of 1-view Gcone objects (see Gcone.m)
%| by default each of wh... |
github | ismrmrd/ismrmrd-paper-master | block_fatrix.m | .m | ismrmrd-paper-master/code/extern/irt/systems/block_fatrix.m | 10,602 | utf_8 | d35bfc1800ef6309f697bdf2b196964d | function ob = block_fatrix(blocks, varargin)
%|function ob = block_fatrix(blocks, options)
%|
%| Construct block_fatrix object, a meta-Fatrix composed of Fatrix blocks,
%| such as block_diag(A_1, A_2, ..., A_M)
%| See block_fatrix_test.m for example usage.
%|
%| in
%| blocks {cell} cell array of the blocks
%|
%| opti... |
github | ismrmrd/ismrmrd-paper-master | Gmatrix.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gmatrix.m | 4,371 | utf_8 | af3ae3f610595ed1374bc2e461fa0dd5 | function ob = Gmatrix(matrix, varargin)
%|function ob = Gmatrix(matrix, [options])
%|
%| Construct fatrix2 object from an object (such as a matrix) that can do
%| multiplication and transpose. The point of this would be to endow
%| the matrix with the masking features provided by fatrix2.
%|
%| in
%| matrix [M N] c... |
github | ismrmrd/ismrmrd-paper-master | wtf_write.m | .m | ismrmrd-paper-master/code/extern/irt/systems/wtf_write.m | 1,507 | utf_8 | 0b4d5047bf518e6a92fbb5f812c9e824 | function wtf_write(file, mat, nx, ny, nb, na, varargin)
%|function wtf_write(file, mat, nx, ny, nb, na, [options])
%| write (usually sparse) matrix mat to file (usually file.wtf)
%| mat can be Gsparse Fatrix or Gmatrix fatrix2 also.
%| option
%| 'row_grouped' 1|0 1 to write in row grouping (default: 0 col)
%| 'chat'
... |
github | ismrmrd/ismrmrd-paper-master | aspire_buff2mat.m | .m | ismrmrd-paper-master/code/extern/irt/systems/aspire_buff2mat.m | 1,861 | utf_8 | 4fe1e5b6f97f270438abdb10996180ab | function [mat sp] = aspire_buff2mat(buff)
%|function [mat sp] = aspire_buff2mat(buff)
%|
%| convert 'buffer' read from .wtf to matlab sparse matrix
%| primarily for testing
%|
%| in
%| buff byte read using wtfmex()
%|
%| out
%| mat sparse matlab sparse matrix, full sized
%| sp struct header information etc.
%|
%| Cop... |
github | ismrmrd/ismrmrd-paper-master | Gsparse.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gsparse.m | 9,512 | utf_8 | e9905ce5cbba041d9959641e85672f40 | function ob = Gsparse(arg1, varargin)
%function ob = Gsparse(file.wtf | sparse | cell, options)
%|
%| Construct Gsparse object, either from a sparse matrix itself,
%| or from the arguments that would be passed to matlab's sparse() command,
%| or from an Aspire binary .wtf file.
%|
%| The Gsparse object overcomes some ... |
github | ismrmrd/ismrmrd-paper-master | Glinear.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Glinear.m | 3,306 | utf_8 | c7b49170dff92c494b2079bd9fba6748 | function A = Glinear(varargin)
%|function A = Glinear(options)
%|
%| Generate a geometric system matrix for tomographic projection
%| based on simple linear interpolation.
%| Contains exactly two a_ij values per pixel per projection angle.
%| This system model is very inadequate for reconstructing
%| real tomographic... |
github | ismrmrd/ismrmrd-paper-master | Gcone.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gcone.m | 16,284 | utf_8 | b1570c3ee4154079634cdd36237e1ddb | function ob = Gcone(cg, ig, varargin)
%function ob = Gcone(cg, ig, [options])
%|
%| Construct Gcone object, for 3D axial cone-beam or helical cone-beam
%| forward and back-projection. Works with flat detectors or 3rd-gen CT arcs.
%| Also supports 3D parallel-beam geometry, but no polar angle.
%|
%| in
%| cg ct_geom o... |
github | ismrmrd/ismrmrd-paper-master | Gtomo2_dscmex.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gtomo2_dscmex.m | 4,362 | utf_8 | dbdb05d948b70e0410f5578afb6344ca | function ob = Gtomo2_dscmex(arg1, varargin)
%|function ob = Gtomo2_dscmex(sg, ig, options)
%|function ob = Gtomo2_dscmex(file, options)
%|function ob = Gtomo2_dscmex(arg_pairs, options)
%|
%| Tomographic system model based on aspire's wtfmex() routine, using its
%| dsc,proj and dsc,back commands for on-the-fly forwar... |
github | ismrmrd/ismrmrd-paper-master | Gtomo3.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gtomo3.m | 7,334 | utf_8 | fdae28528bba97c7edd82b06873ac235 | function ob = Gtomo3(sys_type, mask, nx, ny, nz, varargin)
%function ob = Gtomo3(sys_type, mask, nx, ny, nz, options)
%|
%| alternate usage for CT (however, Gcone() is recommended instead):
%|function ob = Gtomo3(cg, ig, options)
%|
%| Construct Gtomo3 object, for 3D tomographic image reconstruction.
%| This object do... |
github | ismrmrd/ismrmrd-paper-master | Gmri_gram.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gmri_gram.m | 3,607 | utf_8 | b805e893a769c46a533974b9878f35b1 | function [T, reuse] = Gmri_gram(ob, W, reuse)
%|function [T, reuse] = Gmri_gram(ob, W, reuse)
%|
%| build Toeplitz-like gram-matrix object for G'WG gram matrix
%| to be called by build_gram() indirectly rather than directly by user!
%|
%| Jeff Fessler
if nargin < 1, help(mfilename), error(mfilename), end
if streq(ob... |
github | ismrmrd/ismrmrd-paper-master | Gmri.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gmri.m | 14,799 | utf_8 | 0066224e31ce2022b38d169919899ea6 | function ob = Gmri(kspace, mask, varargin)
%|function ob = Gmri(kspace, mask, 'option name', option, ...)
%|
%| Construct Gmri object for MR image reconstruction, or for other problems
%| that require reconstruction of a function from nonuniform Fourier samples.
%| This object can also model relaxation and/or off-res... |
github | ismrmrd/ismrmrd-paper-master | wtf_read.m | .m | ismrmrd-paper-master/code/extern/irt/systems/wtf_read.m | 4,339 | utf_8 | bae1b39d50bf04642b4fa9521898545a | function [mat nx ny nb na] = wtf_read(file, varargin)
%|function [mat nx ny nb na] = wtf_read(file, [options])
%| read aspire sparse matrix file (usually file.wtf)
%| and return matlab sparse matrix
%| option
%| 'parse' 0|1 if 1, do it by old matlab parsing way (old wtfread.m)
%| Copyright 2008-9-26, Jeff Fessler, Un... |
github | ismrmrd/ismrmrd-paper-master | square_strip_int.m | .m | ismrmrd-paper-master/code/extern/irt/systems/square_strip_int.m | 2,602 | utf_8 | 6d1ebe594ba42267e4ebdbb082549231 | function proj = square_strip_int(rr, angles, varargin)
%|function proj = square_strip_int(rr, angles, varargin)
%|
%| strip-integrals of a square pixel basis object model,
%| normalized such that the units are length, not area.
%| In other words, the detector response is h(r) = (1/w) rect(r/w).
%| in
%| rr [] radial ... |
github | ismrmrd/ismrmrd-paper-master | Gdsft_gram.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gdsft_gram.m | 8,894 | utf_8 | ed0be07fc9be7bfcab9820882d81bad8 | function [T, reuse] = Gdsft_gram(ob, W, reuse)
%|function [T, reuse] = Gdsft_gram(A, W, reuse)
%|
%| Construct Toeplitz gram matrix object T = A'WA for a Gdsft object.
%| This object performs T*x rapidly using an over-sampled FFT.
%|
%| in
%| A [M np] Gdsft object (fatrix2)
%| W [M M] W = Gdiag() for fatrix2 (often... |
github | ismrmrd/ismrmrd-paper-master | Gtomo2_wtmex.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gtomo2_wtmex.m | 6,192 | utf_8 | 4aeebc4a5ecdd5ec095329bc443c83dc | function ob = Gtomo2_wtmex(arg1, varargin)
%|function ob = Gtomo2_wtmex(sg, ig, options)
%|function ob = Gtomo2_wtmex(file, options)
%|function ob = Gtomo2_wtmex(arg_pairs, options)
%|
%| Generate a 2D tomographic system model based on aspire's wtfmex() routine.
%|
%| in
%| sg strum sino_geom()
%| ig strum image_ge... |
github | ismrmrd/ismrmrd-paper-master | Gtomo_nufft.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gtomo_nufft.m | 20,262 | utf_8 | be955d76d2b2cf2317f771179a219050 | function ob = Gtomo_nufft(mask, dim_data, varargin)
%|function ob = Gtomo_nufft(mask, dim_data, options)
%|
%| Construct Gtomo_nufft object, for Fourier-based forward and backprojection.
%| Currently handles 2D parallel and fan-beam cases.
%|
%| See Gtomo_nufft_test.m for example usage.
%|
%| Basically, you create an... |
github | ismrmrd/ismrmrd-paper-master | aspire_pair.m | .m | ismrmrd-paper-master/code/extern/irt/systems/aspire_pair.m | 7,283 | utf_8 | e0a649896bfbc193a7f019a2020d861f | function args = aspire_pair(sg, ig, varargin)
%|function args = aspire_pair(sg, ig, [options])
%| see ASPIRE users guide under tech. reports on web page for details
%|
%| options
%| 'scale' default: 0 - transmission scaling
%| 'strip_width' default: from sg.strip_width
%| or, if empty, then 0 (line integrals)
%| '... |
github | ismrmrd/ismrmrd-paper-master | fatrix_one.m | .m | ismrmrd-paper-master/code/extern/irt/systems/fatrix_one.m | 2,754 | utf_8 | 69c58cd2afcbeb3257176b36bca2ae45 | function ob = fatrix_one(dim, fun, arg, varargin)
%|function ob = fatrix_one(dim, fun, arg, varargin)
%|
%| Construct Fatrix object where one column of it is computed at a time by 'fun'
%|
%| in
%| dim [1 2] Fatrix dimension
%| fun @ fun(arg, n) must return nth column of matrix
%| arg struct argument for fun
%|
%| op... |
github | ismrmrd/ismrmrd-paper-master | Gpermute.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gpermute.m | 1,706 | utf_8 | e867d969965a31f2dc221bd4d815e40c | function ob = Gpermute(Nd, varargin)
%function ob = Gpermute(Nd, varargin)
%|
%| Construct Gpermute object, which permutes input image dimensions.
%| This is useful perhaps for converting xyz to zyx order, for example.
%| See Gpermute_test() for example usage.
%|
%| in
%| Nd [1 D] input signal dimensions
%|
%| option... |
github | ismrmrd/ismrmrd-paper-master | embed_mult.m | .m | ismrmrd-paper-master/code/extern/irt/systems/embed_mult.m | 4,396 | utf_8 | fbfa02d6a7b0c8c7085319a70a960040 | function y = embed_mult(fun, arg, is_transpose, x, istart, nblock, ...
mask, np, odim, is_array, varargin)
%|function y = embed_mult(fun, arg, is_transpose, x, istart, nblock, ...
%| mask, np, odim, is_array, varargin)
%|
%| The matrix-vector versions of the linear forward models used herein
%| expect an input x of ... |
github | ismrmrd/ismrmrd-paper-master | Gtomo_blob.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gtomo_blob.m | 12,216 | utf_8 | e2a583d692d0c5bf740db9c956ec9ee8 | function ob = Gtomo_blob(mask, dim_data, varargin)
%function ob = Gtomo_blob(mask, dim_data, options)
%|
%| Construct Gtomo_blob object, for fast forward and backprojection.
%| INCOMPLETE, WORK-IN-PROGRESS!
%|
%| Currently handles 2D parallel and fan-beam cases.
%|
%| See Gtomo_blob_test.m for example usage.
%|
%| in
... |
github | ismrmrd/ismrmrd-paper-master | embed_out.m | .m | ismrmrd-paper-master/code/extern/irt/systems/embed_out.m | 2,523 | utf_8 | d08a24d35ed104726653ce3218d22371 | function [y, eo_fun] = embed_out(y, Mdim)
%|function [y, eo_fun] = embed_out(y, Mdim)
%|
%| Dual or adjoint of embed_in(). See embed_in() for details.
%| To be used around _back() routines that expect [(M) *L]
%| input and produce [(N) *L] output that then must be reshaped
%| to be either [(N) (L)] or [np *L]
%|
%| ... |
github | ismrmrd/ismrmrd-paper-master | Gblur.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gblur.m | 7,642 | utf_8 | fd462e658b2ae7f54412d460d58c45fa | function ob = Gblur(mask, varargin)
%function ob = Gblur(mask, options)
%|
%| Construct Gblur object for image restoration.
%|
%| See Gblur_test.m for example usage.
%|
%| in
%| mask size(image) logical array of object support.
%|
%| options
%| 'chat' verbose printing of debug messages
%| 'psf' point spread function... |
github | ismrmrd/ismrmrd-paper-master | Gdelaysum1.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gdelaysum1.m | 3,338 | utf_8 | a52eefba53fa63aaf77cdee6dc2c996b | function ob = Gdelaysum(varargin)
%|function ob = Gdelaysum([options])
%|
%| Construct Gdelaysum object, which performs weighted sums of a delayed signal.
%| This is useful for model-based reconstruction of THz images.
%| See Gdelaysum_test() at end for example usage.
%|
%| y[n;m] = sum_{k=0}^{Nx-1} x[k] h[n - d[k;m]... |
github | ismrmrd/ismrmrd-paper-master | aspire_buff_parse.m | .m | ismrmrd-paper-master/code/extern/irt/systems/aspire_buff_parse.m | 2,192 | utf_8 | b0054843b54f772d94e7e1be66d0ebf8 | function sp = aspire_buff_parse(buff)
%|function sp = aspire_buff_parse(buff)
%|
%| parse 'buffer' read from aspire .wtf
%| primarily for testing
%|
%| in
%| buff byte read using wtfmex()
%|
%| out
%| sp struct header information etc.
%|
%| Copyright 2011-3-4, Jeff Fessler, University of Michigan
if nargin < 1, help... |
github | ismrmrd/ismrmrd-paper-master | Gdft.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gdft.m | 6,277 | utf_8 | d397e81839e58b955b5182632ae215b6 | function ob = Gdft(varargin)
%|function ob = Gdft([args])
%| Construct Gdft object that computes samples of the DFT of a signal
%| with dimensions [(N)]. This is useful for "under-sampled" MRI.
%|
%| options (at least one of first two must be provided):
%| 'mask' logical [(N)] image-domain mask, usually: true(nx,ny)... |
github | ismrmrd/ismrmrd-paper-master | embed_in.m | .m | ismrmrd-paper-master/code/extern/irt/systems/embed_in.m | 3,271 | utf_8 | 860d4dd7df99c91d0529a57f7c0bd5d2 | function [x, ei_fun] = embed_in(x, mask, np)
%|function [x, ei_fun] = embed_in(x, mask, np)
%|
%| The matrix-vector versions of the linear forward models used herein
%| expect an input x of size [np *L] and produce an output y of size [nd *L],
%| where np = sum(mask(:)) is the number of estimated pixel values,
%| and... |
github | ismrmrd/ismrmrd-paper-master | Gdown.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gdown.m | 2,668 | utf_8 | 8eb9c0ab6830aee7f0e0746371a13e81 | function ob = Gdown(Nd, varargin)
%|function ob = Gdown(Nd, varargin)
%| Construct Gdown object, which performs downsampling.
%| This is useful perhaps for iterative zooming methods.
%| See Gdown_test.m for example usage.
%|
%| in
%| Nd [1 D] input signal dimensions
%|
%| options
%| mask logical default: true(Nd)
... |
github | ismrmrd/ismrmrd-paper-master | Ginterp1.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Ginterp1.m | 1,923 | utf_8 | 863d529667def95b436fd99165cb25e1 | function ob = Ginterp1(mask, varargin)
%|function ob = Ginterp1(mask, options)
%|
%| Construct Ginterp1 object for 1D image registration.
%| This method does not have an adjoint.
%|
%| See Ginterp1_test() below for example usage.
%|
%| in
%| mask size(image) logical array of object support.
%|
%| options
%| 'interp1_... |
github | ismrmrd/ismrmrd-paper-master | Gdiag.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gdiag.m | 3,695 | utf_8 | fdb9872c3b1e322bc7b8d11bd9df3bff | function ob = Gdiag(diag, varargin)
%function ob = Gdiag(diag, [options])
%|
%| Construct diagonal "sparse" object, that does D * x = diag(d) * x via d .* x.
%|
%| in
%| diag [] numeric array
%|
%| option
%| 'mask' logical with sum(mask(:)) = numel(diag)
%| 'class' 'fatrix2' (default) or 'Fatrix' (obsolete)
%|
%| out... |
github | ismrmrd/ismrmrd-paper-master | diag_sp.m | .m | ismrmrd-paper-master/code/extern/irt/systems/diag_sp.m | 2,250 | utf_8 | 386ccbd0a7ec273d2b47c731d673414c | function ob = diag_sp(diag, varargin)
%|function ob = diag_sp(diag)
%| Construct diagonal "sparse" object, that does D * x = diag(d) * x via d .* x.
%|
%| Copyright 2005-4-6, Jeff Fessler, University of Michigan
if nargin == 1 && streq(diag, 'test'), diag_sp_test, return, end
if nargin < 1, help(mfilename), error(mf... |
github | ismrmrd/ismrmrd-paper-master | Gtomo2_strip.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gtomo2_strip.m | 8,459 | utf_8 | 4b5772e696962bd5b8329b707bd13fb6 | function A = Gtomo2_strip(sg, ig, varargin)
%|function A = Gtomo2_strip(sg, ig, options)
%|
%| Generate a 2D system matrix for tomographic image reconstruction,
%| based on a square pixel basis and strip-integral detector model,
%| i.e., a rectangular detector response.
%| Works for parallel-beam, arc-fan, and flat-f... |
github | ismrmrd/ismrmrd-paper-master | block_op.m | .m | ismrmrd-paper-master/code/extern/irt/systems/block_op.m | 2,664 | utf_8 | 2d66161e64eb64a8550b91eea79be709 | function out = block_op(Ab, varargin)
%|function out = block_op(Ab, varargin)
%|
%| Various operations on "block" objects and block data.
%|
%| There are (at least) three types of block objects possible in this toolbox.
%| 1. Cell arrays of matrices (or of some other matrix-like object).
%| 2. A Fatrix object with bl... |
github | ismrmrd/ismrmrd-paper-master | Gtomo2_table.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gtomo2_table.m | 10,315 | utf_8 | e6b227f2a3ced5536ba684b73389d6b3 | function ob = Gtomo2_table(sg, ig, table, varargin)
%|function ob = Gtomo2_table(sg, ig, table, options)
%|
%| Generate a 2D parallel-beam tomographic system model
%| based on finely tabulated footprints.
%|
%| in
%| sg strum sino_geom()
%| ig strum image_geom()
%| table [Ktab Ltab] footprint table, see book: s,geo... |
github | ismrmrd/ismrmrd-paper-master | Gdsft.m | .m | ismrmrd-paper-master/code/extern/irt/systems/Gdsft.m | 3,909 | utf_8 | 45dd574cecc62d825fe1abf6fe49613b | function ob = Gdsft(om, Nd, varargin)
%|function ob = Gdsft(om, Nd, varargin)
%| Construct Gdsft object, which computes (nonuniform) FT samples
%| of signals with dimensions [(Nd)] exactly, e.g., for testing Gnufft
%| For faster computation, use Gnufft instead.
%| See Gdsft_test.m for example usage.
%|
%| in
%| om [M... |
github | ismrmrd/ismrmrd-paper-master | dsft_gram_hermitify.m | .m | ismrmrd-paper-master/code/extern/irt/systems/private/dsft_gram_hermitify.m | 3,087 | utf_8 | 1dcc6708b40a2b33d0d0ebdb56d6c6df | function kern = dsft_gram_hermitify(kern, show)
%|function kern = dsft_gram_hermitify(kern, show)
%|
%| When A is a Gdsft object and W is a Hermitian positive semidefinite matrix,
%| e.g., when W is diagonal with real, nonnegative diagonal elements,
%| the corresponding gram matrix A'WA is positive semidefinite and T... |
github | ismrmrd/ismrmrd-paper-master | Fatrix_test_basic.m | .m | ismrmrd-paper-master/code/extern/irt/systems/tests/Fatrix_test_basic.m | 4,409 | utf_8 | 6f595a7177b650af6f89d8a9a96e9968 | function Fatrix_test_basic(A, mask, varargin)
%|function Fatrix_test_basic(A, mask, [option])
%|
%| perform basic tests of Fatrix objects
%| in
%| A [nd *N] Fatrix object
%| mask [(N)] logical support
%| option
%| 'x' [(N)] optional input test image
%| 'multi' 0|1 if 1, test multiple rhs: A * [x x]. default: 1
%|... |
github | ismrmrd/ismrmrd-paper-master | fatrix2_tests.m | .m | ismrmrd-paper-master/code/extern/irt/systems/tests/fatrix2_tests.m | 9,934 | utf_8 | 463e4fb65ab7fdc4f5b02c4b04fddb79 | function fatrix2_tests(A, varargin)
%|function fatrix2_tests(A, [option])
%|
%| perform basic tests of fatrix2 objects
%| in
%| A [nd np] fatrix2 object
%|
%| option
%| 'x' [idim] optional input test image
%| 'name' char name of input object (optional for display)
%| 'caller' char name of caller (optional for dis... |
github | ismrmrd/ismrmrd-paper-master | tester_tomo2.m | .m | ismrmrd-paper-master/code/extern/irt/systems/tests/tester_tomo2.m | 4,306 | utf_8 | da952893b8645c02f73c2c5213d79081 | function tester_tomo2(A1, mask, varargin)
%|function tester_tomo2(A1, mask, [options])
%| Test suite for a Fatrix-type 2D or 3D system object, including Gblock tests.
%|
%| in
%| A1 Fatrix or fatrix2
%| mask logical [nx ny] or [nx ny nz]
%|
%| option
%| 'A2' Fatrix optional 2nd object for testing and comparisons
%| ... |
github | ismrmrd/ismrmrd-paper-master | test_adjoint.m | .m | ismrmrd-paper-master/code/extern/irt/systems/tests/test_adjoint.m | 3,514 | utf_8 | 183814b9fe030437df198f09572bd716 | function [Af, Aa, dif] = test_adjoint(A, varargin)
%|function [Af, Aa, dif] = test_adjoint(A, varargin)
%|
%| test that the adjoint of a 'matrix object' A really is its transpose
%|
%| in
%| A Fatrix or fatrix2 typically
%|
%| option
%| 'tolre' dbl tolerance (relative) for equality (default: 0)
%| 'big' 0|1 for big ... |
github | ismrmrd/ismrmrd-paper-master | mtimes_block.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@Fatrix/mtimes_block.m | 1,278 | utf_8 | 47f1cd3a254db55d68e9967fa143e37a | function y = mtimes_block(ob, x, istart, nblock)
%function y = mtimes_block(ob, x, istart, nblock)
% y = G(i'th block) * x or y = G'(i'th block) * x
% in either case the projection data will be "small"
% istart is 1,...,nblock
% support 'exists' option for seeing if this routine is available
if nargin == 2 && ischar(... |
github | ismrmrd/ismrmrd-paper-master | mtimes.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@Fatrix/mtimes.m | 1,385 | utf_8 | e22a6887c1aab734b08a743df51390b1 | function y = mtimes(ob, x)
%function y = mtimes(ob, x)
% y = M * x or x = M' * y
if isa(x, 'Fatrix') % {object1 | scalar} * object2, tested in Gcascade
y = Gcascade(ob, x);
return
end
if ~isa(ob, 'Fatrix')
error 'only multiplication on right is done'
end
%
% partial multiplication?
%
if ob.is_subref
error 'subre... |
github | ismrmrd/ismrmrd-paper-master | Gcascade.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@Fatrix/private/Gcascade.m | 2,940 | utf_8 | af8817195f7e46a7897572535ac18f8d | function ob = Gcascade(arg1, arg2, varargin)
%|function ob = Gcascade(A1, A2, options)
%|
%| Construct Gcascade object, which is the cascade of two objects: A = A1 * A2.
%|
%| See Gcascade_test.m for example usage.
%|
%| in
%| arg1 matrix | Fatrix object that can do "mtimes" and "size"
%| arg2 matrix | Fatrix ''
%|... |
github | ismrmrd/ismrmrd-paper-master | do_cascade.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@Fatrix/private/do_cascade.m | 873 | utf_8 | 0e60b58458bda59a69d48ea9fa7934b4 | function y = do_cascade(cascade, x, is_transpose, istart, nblock, is_before)
%function y = do_cascade(cascade, x, is_transpose, istart, nblock, is_before)
% do cascade * x or cascade' * x
if isempty(cascade)
y = x;
elseif isa(cascade, 'function_handle') || isa(cascade, 'inline')
if nargin(cascade) == 4
y = feval... |
github | ismrmrd/ismrmrd-paper-master | nufft_gram_v2.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/nufft_gram_v2.m | 7,048 | utf_8 | 2f31f3ed929c1a7642ddd22958c3b4c6 | function [T, reuse] = nufft_gram(ob, W, reuse)
%function [T, reuse] = nufft_gram(ob, W, reuse)
% construct Toeplitz matrix object T = G'WG for a Gnufft object
% in
% ob Fatrix a [M,np] Gnufft object
% W [M,M] W = diag_sp(wi) (often simply "1" or [])
% reuse struct stuff from the last call that can be reused
% out
%... |
github | ismrmrd/ismrmrd-paper-master | nufft_gram.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/nufft_gram.m | 6,986 | utf_8 | ed586ae6715c4f071fd923bc7d5ea53b | function [T, reuse] = nufft_gram(ob, W, reuse)
%function [T, reuse] = nufft_gram(ob, W, reuse)
% construct Toeplitz matrix object T = G'WG for a Gnufft object
% in
% ob Fatrix a [M,np] Gnufft object
% W [M,M] W = diag_sp(wi) (often simply "1" or [])
% reuse struct stuff from the last call that can be reused
% out
%... |
github | ismrmrd/ismrmrd-paper-master | Gnufft_gram.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/Gnufft_gram.m | 14,618 | utf_8 | d6c1a27f6d0917fb5aa5d085cd6df8ff | function [T, reuse] = Gnufft_gram(ob, W, reuse)
%|function [T, reuse] = Gnufft_gram(A, W, reuse)
%|
%| construct Toeplitz gram matrix object T = A'WA for a Gnufft object
%| in
%| A [M np] Gnufft object (Fatrix or fatrix2)
%| W [M M] W = diag_sp(wi) (often simply "1" or [])
%| W = Gdiag() for fatrix2
%| reuse str... |
github | ismrmrd/ismrmrd-paper-master | Gtomo_sparse.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/Gtomo_sparse.m | 3,324 | utf_8 | a8bfb72d38b972d3af3f4394b8528a1d | function ob = Gtomo_sparse(arg1, arg2, varargin)
%function ob = Gtomo_sparse(file(or matrix), mask, options)
%
% Construct Gtomo_sparse object, either from a .wtf file,
% or from a Matlab sparse matrix.
% This just uses an ordinary Matlab sparse matrix for the core!
% See Gtomo_sparse_test.m for example usage.
% You c... |
github | ismrmrd/ismrmrd-paper-master | Gsparse.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/Gsparse.m | 8,332 | utf_8 | faa2f08140223c42b74e008cd5b35e36 | function ob = Gsparse(arg1, varargin)
%function ob = Gsparse(file.wtf | sparse | cell, options)
%|
%| Construct Gsparse object, either from a sparse matrix itself,
%| or from the arguments that would be passed to matlab's sparse() command,
%| or from an Aspire binary .wtf file.
%|
%| The Gsparse object overcomes some ... |
github | ismrmrd/ismrmrd-paper-master | Gtomo_nufft_newsample.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/Gtomo_nufft_newsample.m | 15,918 | utf_8 | 57f4640f6732ac09a0d588b073b8803e | function ob = Gtomo_nufft_newsample(mask, dim_data, varargin)
%function ob = Gtomo_nufft_newsample(mask, dim_data, options)
%
% Construct Gtomo_nufft object, for Fourier-based forward and backprojection.
% Currently handles 2D parallel and fan-beam cases.
%
% See Gtomo_nufft_test.m for example usage.
%
% Basically, yo... |
github | ismrmrd/ismrmrd-paper-master | Gtomo2_wtmex.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/Gtomo2_wtmex.m | 5,111 | utf_8 | f80ddcaed70c04f563b2788d54b81a40 | function ob = Gtomo2_wtmex(arg1, varargin)
%function ob = Gtomo2_wtmex(sg, ig, options)
%function ob = Gtomo2_wtmex(file, options)
%function ob = Gtomo2_wtmex(arg_pairs, options)
%
% Generate a tomographic system model based on aspire's wtfmex() routine.
%
% in
% sg strum sino_geom()
% ig strum image_geom()
%
% opti... |
github | ismrmrd/ismrmrd-paper-master | Gtomo_nufft.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/Gtomo_nufft.m | 16,927 | utf_8 | 9aa7b619dceec812ad2c84a8eea53bc4 | function ob = Gtomo_nufft(mask, dim_data, varargin)
%function ob = Gtomo_nufft(mask, dim_data, options)
%
% Construct Gtomo_nufft object, for Fourier-based forward and backprojection.
% Currently handles 2D parallel and fan-beam cases.
%
% See Gtomo_nufft_test.m for example usage.
%
% Basically, you create an object c... |
github | ismrmrd/ismrmrd-paper-master | fatrix_plus.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/fatrix_plus.m | 1,433 | utf_8 | 0ed7e4e5bcb48ae6f019ace7b9ab0e99 | function ob = fatrix_plus(varargin)
%function ob = fatrix_plus(fatrix_objects)
%
% Construct Fatrix object consisting of sum of Fatrix objects, i.e.,
% T1 + T2 + ... + Tn
%
% in
% fatrix_objects one or more fatrix objects
%
% out
% ob T1 + ... + Tn
%
% Copyright 2007-10-16, Jeff Fessler, The University of Michigan
i... |
github | ismrmrd/ismrmrd-paper-master | Gembed.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/Gembed.m | 2,675 | utf_8 | 4728c2561f2c1c4be6cfec19458cfa80 | function ob = Gembed(varargin)
%|function ob = Gembed([args])
%| Construct Gembed object that embes a short vector into a longer vector.
%| with dimensions [(Nd)].
%|
%| option1:
%| 'list' [N] list of array entries
%| 'odim' ndims
%|
%| option2:
%| 'samp' logical [(Nd)] sampling pattern of array entries
%|
%| out
%|... |
github | ismrmrd/ismrmrd-paper-master | Gtomo2_nufft.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/@Gtomo2_nufft/Gtomo2_nufft.m | 14,715 | utf_8 | 9ba2872db713594d3b7b072a30828ae9 | function ob = Gtomo2_nufft(nx, ny, nb, na, varargin)
%function ob = Gtomo2_nufft(nx, ny, nb, na, ...)
%
% Construct Gtomo2_nufft object, which does parallel-beam or fan-beam
% forward projection via the Fourier-slice theorem,
% with the Fourier transform computed via NUFFT.
% See Gtomo2_nufft_test.m for example usage.... |
github | ismrmrd/ismrmrd-paper-master | mtimes.m | .m | ismrmrd-paper-master/code/extern/irt/systems/arch/@Gtomo2_nufft/mtimes.m | 3,487 | utf_8 | 0a0607aaff2b947f2a898c4b4963568f | function y = mtimes(ob, x)
%function y = mtimes(ob, x) for Gtomo2_nufft object
% y = G * x, or x = G' * y
if ob.apower ~= 1, error notdone, end
%
% partial projection or backprojection (for ordered subsets)
%
if ob.is.subref
error 'subref not done'
%
% full "projection"
%
elseif ~ob.is_transpose
if ob.is_masked
... |
github | ismrmrd/ismrmrd-paper-master | eigs.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/eigs.m | 795 | utf_8 | d31c4b50c3e8022449cea1aec13b29ce | function out = eigs(ob, varargin)
% compute largest magnitude eigenvalue of object by calling eigs,
% which in turn probably uses the power method.
% this may be slow for big objects because it is iterative.
warn 'todo: i could not get this to work'
% A = Gdft('mask', true(8,6));
% eigs(A, 1)
if numel(varargin) ~= 1... |
github | ismrmrd/ismrmrd-paper-master | fatrix2.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/fatrix2.m | 7,664 | utf_8 | c79ab19c61dccbda730e26260221befa | function ob = fatrix2(varargin)
%|function ob = fatrix2('odim', odim, 'mask', mask, 'arg', arg, [options])
%|
%| Construct fatrix2 object, a matrix generalization for representing
%| any linear operator. The 'f' might stand for 'fake' or 'function-based'
%| or 'fancy' or maybe a last name?
%| The caller can provide ... |
github | ismrmrd/ismrmrd-paper-master | build_gram.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/build_gram.m | 1,839 | utf_8 | d236c359232c2ec12cbb0801f5d81203 | function [T, reuse] = build_gram(ob, W, reuse, varargin)
%|function [T, reuse] = build_gram(ob, W, reuse, varargin)
%| build "gram matrix object" T = A' W A
%| in
%| ob the system matrix A
%| W typically diag(wi), having size [1 1]*size(ob,1)
%| reuse stuff returned by previous call that can be reused
%| the nex... |
github | ismrmrd/ismrmrd-paper-master | subsref.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/subsref.m | 1,490 | utf_8 | 05a3a416c4598a67125f656c218a6a2e | function out = subsref(ob, args)
%function out = subsref(ob, args)
% handle subscript references like ob.ref or ob(ref,:)
% Copyright 2002-2-20, Jeff Fessler, University of Michigan
out = fatrix2_subsref1(ob, args(1)); % handle first subscript
if numel(args) > 1 % handle multiple subscripts, e.g., ob.field()
out = ... |
github | ismrmrd/ismrmrd-paper-master | mtimes.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/mtimes.m | 3,891 | utf_8 | 0b2425b92472e7ff167719f2a7b70c1f | function y = mtimes(ob, x)
%function y = mtimes(ob, x)
% A * x
% A' * y
% y' * A
% x' * A'
% B * A
% etc
if isnumeric(ob)
if isscalar(ob) % scalar * object
y = fatrix2_scalar_times(ob, x);
else % row_vector(s) * object
y = (x' * ob')'; % trick: x <-> ob
end
return
end
if ~isnumeric(x) % object * object
if is... |
github | ismrmrd/ismrmrd-paper-master | block_diag.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/block_diag.m | 3,627 | utf_8 | 67530ea7678d0958a6a8f5af96d0efba | function ob = block_diag(varargin)
%|function ob = block_diag(block1, ..., blockM)
%|
%| Construct fatrix2 object from fatrix2 objects
%| block_diag(A_1, A_2, ..., A_M)
%|
%| in
%| blocks{:} fatrix2 blocks
%|
%| options
%|
%| out
%| ob [nd np] nd = sum_m nrow(A_M), np = sum_m ncol(A_m)
%|
%| Copyright 2012-09-09, Je... |
github | ismrmrd/ismrmrd-paper-master | fatrix2_block_sum.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/private/fatrix2_block_sum.m | 3,445 | utf_8 | 055bfb14bdfb774dc36f96169e295992 | function ob = fatrix2_block_sum(blocks)
%| ob = fatrix2_block_sum(blocks)
%| called for ob1 + ob2 + ...
% find at least one fatrix2 in the collection
ib = [];
for ii=1:numel(blocks)
if isa(blocks{ii}, 'fatrix2')
ib = ii;
break
end
end
if isempty(ib), fail 'no fatrix2? bug', end
bb = blocks{ib}; % reference bloc... |
github | ismrmrd/ismrmrd-paper-master | fatrix2_kroni.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/private/fatrix2_kroni.m | 2,925 | utf_8 | 3741c0da2fb3d2b85c38bd3bae3fac06 | function ob = fatrix2_kroni(Mkron, ob)
%function ob = fatrix2_kroni(Mkron, ob)
%|
%| Construct fatrix2_block object of form kron(eye(Mkron), ob)
%| i.e., a kronecker product of identity matrix with object.
%|
%| in
%| Mkron natural number
%| ob fatrix2
%|
%| out
%| ob fatrix2 equivalent to kron(eye(Mkron), ob)
%|
%... |
github | ismrmrd/ismrmrd-paper-master | fatrix2_vertcat.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/private/fatrix2_vertcat.m | 5,793 | utf_8 | 70fb813489d996d9f1b1533fde8ce2e7 | function ob = fatrix2_vertcat(blocks, varargin)
%function ob = fatrix2_vertcat(blocks, [options])
%| vertcat: B = [A1; A2; ...]
%|
%| in
%| blocks {cell} cell array of the (fatrix2) blocks
%|
%| option
%| 'dim_cat' dimension along which to concatenate odims
%| all other odims must match
%| default is ndim+1 if *al... |
github | ismrmrd/ismrmrd-paper-master | fatrix2_mtimes2.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/private/fatrix2_mtimes2.m | 2,931 | utf_8 | a2b7ec6fa51de76b0329a6de132cdd63 | function ob = fatrix2_mtimes2(ob1, ob2, varargin)
%|function ob = fatrix2_mtimes2(ob1, ob2, options)
%|
%| Construct fatrix2 object that is the product of two objects:
%| ob = ob1 * ob2.
%| Requires size(ob1,2) == size(ob2,1) as in matrix multiplication.
%|
%| in
%| ob1 *atrix any object that can do "mtimes" and "si... |
github | ismrmrd/ismrmrd-paper-master | fatrix2_subsref_colon.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/private/fatrix2_subsref_colon.m | 2,533 | utf_8 | 984e937cde23c07d725fc3435bcc1f42 | function out = fatrix2_subsref_colon(ob, sub2, varargin)
%function out = fatrix2_subsref_colon(ob, sub2, varargin)
%
% handle subscript references like ob(:,sub2)
% This will called from ../subsref with (ob, subs{2})
%
% Copyright 2010-12-02, Jeff Fessler, University of Michigan
if streq(sub2, ':') % ob(:,:)
% do by... |
github | ismrmrd/ismrmrd-paper-master | fatrix2_block.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/private/fatrix2_block.m | 7,290 | utf_8 | 29b7a9381463276f507b6c857d862043 | function ob = fatrix2_block(blocks, varargin)
%|function ob = fatrix2_block(blocks, options)
%|
%| Construct fatrix2_block object, a meta-object composed of fatrix2 blocks,
%| such as block_diag(A_1, A_2, ..., A_M)
%| See fatrix2_block_test.m for example usage.
%|
%| in
%| blocks {cell} cell array of the blocks
%|
%|... |
github | ismrmrd/ismrmrd-paper-master | fatrix2_horzcat.m | .m | ismrmrd-paper-master/code/extern/irt/systems/@fatrix2/private/fatrix2_horzcat.m | 2,654 | utf_8 | a7296a7a662b83420af5e6c0880c5bf1 | function ob = fatrix2_horzcat(blocks, varargin)
%|function ob = fatrix2_horzcat(blocks, [options])
%| horzcat: B = [A1, A2, ...]
%|
%| in
%| blocks {cell} cell array of the (fatrix2) blocks
%|
%| option
%| 'dim_cat' dimension along which to concatenate idims
%| all other idims must match
%| default is ndim+1 if *... |
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