From 8b427d82acfaeb4671484bc459343c5e2e412736 Mon Sep 17 00:00:00 2001 From: Edoardo Pasca Date: Thu, 19 Oct 2017 17:01:55 +0100 Subject: Initial revision of build environment made with CMake Initial revision of build environment made with CMake First commit of CMakeLists.txt attempt to use CMake to create the build environment First commit of CMakeLists.txt attempting to locate conda python environment Added a few files for CMake Many changes for the CMake compilation. Tested CMake build Bugfixes --- src/Python/conda-recipe/bld.bat | 14 ++++++++++++++ src/Python/conda-recipe/build.sh | 14 ++++++++++++++ src/Python/conda-recipe/meta.yaml | 30 ++++++++++++++++++++++++++++++ 3 files changed, 58 insertions(+) create mode 100644 src/Python/conda-recipe/bld.bat create mode 100644 src/Python/conda-recipe/build.sh create mode 100644 src/Python/conda-recipe/meta.yaml (limited to 'src/Python/conda-recipe') diff --git a/src/Python/conda-recipe/bld.bat b/src/Python/conda-recipe/bld.bat new file mode 100644 index 0000000..69491de --- /dev/null +++ b/src/Python/conda-recipe/bld.bat @@ -0,0 +1,14 @@ +IF NOT DEFINED CIL_VERSION ( +ECHO CIL_VERSION Not Defined. +exit 1 +) + +mkdir "%SRC_DIR%\ccpi" +xcopy /e "%RECIPE_DIR%\..\.." "%SRC_DIR%\ccpi" + +cd %SRC_DIR%\ccpi\Python + +%PYTHON% setup.py build_ext +if errorlevel 1 exit 1 +%PYTHON% setup.py install +if errorlevel 1 exit 1 diff --git a/src/Python/conda-recipe/build.sh b/src/Python/conda-recipe/build.sh new file mode 100644 index 0000000..855047f --- /dev/null +++ b/src/Python/conda-recipe/build.sh @@ -0,0 +1,14 @@ + +if [ -z "$CIL_VERSION" ]; then + echo "Need to set CIL_VERSION" + exit 1 +fi +mkdir "$SRC_DIR/ccpi" +cp -r "$RECIPE_DIR/../.." "$SRC_DIR/ccpi" + +cd $SRC_DIR/ccpi/Python + +$PYTHON setup.py build_ext +$PYTHON setup.py install + + diff --git a/src/Python/conda-recipe/meta.yaml b/src/Python/conda-recipe/meta.yaml new file mode 100644 index 0000000..c5b7a89 --- /dev/null +++ b/src/Python/conda-recipe/meta.yaml @@ -0,0 +1,30 @@ +package: + name: ccpi-fista + version: {{ environ['CIL_VERSION'] }} + + +build: + preserve_egg_dir: False + script_env: + - CIL_VERSION +# number: 0 + +requirements: + build: + - python + - numpy + - setuptools + - boost ==1.64 + - boost-cpp ==1.64 + - cython + + run: + - python + - numpy + - boost ==1.64 + + +about: + home: http://www.ccpi.ac.uk + license: BSD license + summary: 'CCPi Core Imaging Library Quantification Toolbox' -- cgit v1.2.3 From 4fd4f187a70c0e4f56d5194b09ab4a528d20ee51 Mon Sep 17 00:00:00 2001 From: Edoardo Pasca Date: Tue, 24 Oct 2017 10:38:37 +0100 Subject: Builds 2 packages fista and regularizers --- src/Python/CMakeLists.txt | 63 ++++--- src/Python/compile-fista.bat.in | 7 + src/Python/compile-fista.sh.in | 9 + src/Python/conda-recipe/meta.yaml | 2 +- src/Python/fista-recipe/meta.yaml | 3 +- src/Python/test/test_reconstructor.py | 301 ++++++++++++++++++++++++++++++++++ 6 files changed, 359 insertions(+), 26 deletions(-) create mode 100644 src/Python/compile-fista.bat.in create mode 100644 src/Python/compile-fista.sh.in create mode 100644 src/Python/test/test_reconstructor.py (limited to 'src/Python/conda-recipe') diff --git a/src/Python/CMakeLists.txt b/src/Python/CMakeLists.txt index 33ebc08..c5e14ea 100644 --- a/src/Python/CMakeLists.txt +++ b/src/Python/CMakeLists.txt @@ -20,6 +20,7 @@ set (NUMPY_VERSION 1.12) ## Tries to parse the output of conda env list to determine the current ## active conda environment +message ("Trying to determine your active conda environment...") execute_process(COMMAND "conda" "env" "list" OUTPUT_VARIABLE _CONDA_ENVS RESULT_VARIABLE _CONDA_RESULT @@ -43,12 +44,12 @@ execute_process(COMMAND "conda" "env" "list" endif() endforeach() else() - message(FATAL_ERROR "conda error " ${_CONDA_ERR}) + message(FATAL_ERROR "ERROR with conda command " ${_CONDA_ERR}) endif() message("**********************************************************") -message("Using current conda environmnet " ${CONDA_ENVIRONMENT}) -message("Using current conda environmnet path" ${CONDA_ENVIRONMENT_PATH}) +message("Active conda environmnet: " ${CONDA_ENVIRONMENT}) +message("Active conda environmnet path: " ${CONDA_ENVIRONMENT_PATH}) message("CIL VERSION " ${CIL_VERSION}) @@ -63,19 +64,6 @@ message("Python found Minor " ${PYTHON_VERSION_MINOR}) findPythonPackagesPath() message("PYTHON_PACKAGES_FOUND " ${PYTHON_PACKAGES_PATH}) -######### CONFIGURE REGULARIZER ############# - -# copy the Pyhon files of the package regularizer -file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging/) -file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi) -# regularizers -file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/imaging/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging) -file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/imaging/Regularizer.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging) - -# fista reconstructor -file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/reconstruction/FISTAReconstructor.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/reconstruction) -#file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/reconstruction/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/reconstruction) - if (WIN32) #set (CONDA_ENVIRONMENT_PATH "C:\\Apps\\Miniconda2\\envs\\${CONDA_ENVIRONMENT}" CACHE PATH "Main environment directory") set (CONDA_ENVIRONMENT_PREFIX "${CONDA_ENVIRONMENT_PATH}\\Library" CACHE PATH "env dir") @@ -86,26 +74,53 @@ elseif (UNIX) set (CONDA_ENVIRONMENT_LIBRARY_INC "${CONDA_ENVIRONMENT_PREFIX}/include" CACHE PATH "env dir") endif() +######### CONFIGURE REGULARIZER PACKAGE ############# + +# copy the Pyhon files of the package regularizer +file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging/) +file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi) +# regularizers +file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/imaging/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging) +file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/imaging/Regularizer.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging) + # Copy and configure the relative conda build and recipes configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup.py.in ${CMAKE_CURRENT_BINARY_DIR}/setup.py) file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe) file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/conda-recipe/meta.yaml DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe) +if (WIN32) + + file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/conda-recipe/bld.bat DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe/) + configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile.bat.in ${CMAKE_CURRENT_BINARY_DIR}/compile.bat) + +elseif(UNIX) + + message ("We are on UNIX") + file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/conda-recipe/build.sh DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe/) + # assumes we will use bash + configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile.sh.in ${CMAKE_CURRENT_BINARY_DIR}/compile.sh) + +endif() + +########## CONFIGURE FISTA RECONSTRUCTOR PACKAGE +# fista reconstructor +file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/reconstruction/FISTAReconstructor.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/reconstruction) +file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/reconstruction/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/reconstruction) + configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup-fista.py.in ${CMAKE_CURRENT_BINARY_DIR}/setup-fista.py) file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/fista-recipe) file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/fista-recipe/meta.yaml DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/fista-recipe) if (WIN32) - file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/conda-recipe/bld.bat DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe/) - configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile.bat.in ${CMAKE_CURRENT_BINARY_DIR}/compile.bat) - file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/fista-recipe/bld.bat DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/fista-recipe/) - configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile.bat.in ${CMAKE_CURRENT_BINARY_DIR}/compile.bat) + file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/fista-recipe/bld.bat DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/fista-recipe/) + configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile-fista.bat.in ${CMAKE_CURRENT_BINARY_DIR}/compile-fista.bat) + elseif(UNIX) - message ("We are on UNIX") - file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/conda-recipe/build.sh DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe/) - # assumes we will use bash - configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile.sh.in ${CMAKE_CURRENT_BINARY_DIR}/compile.sh) + message ("We are on UNIX") + file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/fista-recipe/build.sh DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/fista-recipe/) + # assumes we will use bash + configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile-fista.sh.in ${CMAKE_CURRENT_BINARY_DIR}/compile-fista.sh) endif() diff --git a/src/Python/compile-fista.bat.in b/src/Python/compile-fista.bat.in new file mode 100644 index 0000000..b1db686 --- /dev/null +++ b/src/Python/compile-fista.bat.in @@ -0,0 +1,7 @@ +set CIL_VERSION=@CIL_VERSION@ + +set PREFIX=@CONDA_ENVIRONMENT_PREFIX@ +set LIBRARY_INC=@CONDA_ENVIRONMENT_LIBRARY_INC@ + +REM activate @CONDA_ENVIRONMENT@ +conda build fista-recipe --python=@PYTHON_VERSION_MAJOR@.@PYTHON_VERSION_MINOR@ --numpy=@NUMPY_VERSION@ -c ccpi -c conda-forge diff --git a/src/Python/compile-fista.sh.in b/src/Python/compile-fista.sh.in new file mode 100644 index 0000000..267f014 --- /dev/null +++ b/src/Python/compile-fista.sh.in @@ -0,0 +1,9 @@ +#!/bin/sh +# compile within the right conda environment +#module load python/anaconda +#source activate @CONDA_ENVIRONMENT@ + +export CIL_VERSION=@CIL_VERSION@ +export LIBRARY_INC=@CONDA_ENVIRONMENT_LIBRARY_INC@ + +conda build fista-recipe --python=@PYTHON_VERSION_MAJOR@.@PYTHON_VERSION_MINOR@ --numpy=@NUMPY_VERSION@ -c ccpi diff --git a/src/Python/conda-recipe/meta.yaml b/src/Python/conda-recipe/meta.yaml index c5b7a89..7068e9d 100644 --- a/src/Python/conda-recipe/meta.yaml +++ b/src/Python/conda-recipe/meta.yaml @@ -1,5 +1,5 @@ package: - name: ccpi-fista + name: ccpi-regularizers version: {{ environ['CIL_VERSION'] }} diff --git a/src/Python/fista-recipe/meta.yaml b/src/Python/fista-recipe/meta.yaml index 64c9b5d..89bf597 100644 --- a/src/Python/fista-recipe/meta.yaml +++ b/src/Python/fista-recipe/meta.yaml @@ -18,7 +18,8 @@ requirements: run: - python - numpy - - astra + - astra-toolbox + - ccpi-regularizers diff --git a/src/Python/test/test_reconstructor.py b/src/Python/test/test_reconstructor.py new file mode 100644 index 0000000..07668ba --- /dev/null +++ b/src/Python/test/test_reconstructor.py @@ -0,0 +1,301 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Aug 23 16:34:49 2017 + +@author: ofn77899 +Based on DemoRD2.m +""" + +import h5py +import numpy + +from ccpi.fista.FISTAReconstructor import FISTAReconstructor +import astra +import matplotlib.pyplot as plt + +def RMSE(signal1, signal2): + '''RMSE Root Mean Squared Error''' + if numpy.shape(signal1) == numpy.shape(signal2): + err = (signal1 - signal2) + err = numpy.sum( err * err )/numpy.size(signal1); # MSE + err = sqrt(err); # RMSE + return err + else: + raise Exception('Input signals must have the same shape') + +filename = r'/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/demos/DendrData.h5' +nx = h5py.File(filename, "r") +#getEntry(nx, '/') +# I have exported the entries as children of / +entries = [entry for entry in nx['/'].keys()] +print (entries) + +Sino3D = numpy.asarray(nx.get('/Sino3D'), dtype="float32") +Weights3D = numpy.asarray(nx.get('/Weights3D'), dtype="float32") +angSize = numpy.asarray(nx.get('/angSize'), dtype=int)[0] +angles_rad = numpy.asarray(nx.get('/angles_rad'), dtype="float32") +recon_size = numpy.asarray(nx.get('/recon_size'), dtype=int)[0] +size_det = numpy.asarray(nx.get('/size_det'), dtype=int)[0] +slices_tot = numpy.asarray(nx.get('/slices_tot'), dtype=int)[0] + +Z_slices = 20 +det_row_count = Z_slices +# next definition is just for consistency of naming +det_col_count = size_det + +detectorSpacingX = 1.0 +detectorSpacingY = detectorSpacingX + + +proj_geom = astra.creators.create_proj_geom('parallel3d', + detectorSpacingX, + detectorSpacingY, + det_row_count, + det_col_count, + angles_rad) + +#vol_geom = astra_create_vol_geom(recon_size,recon_size,Z_slices); +image_size_x = recon_size +image_size_y = recon_size +image_size_z = Z_slices +vol_geom = astra.creators.create_vol_geom( image_size_x, + image_size_y, + image_size_z) + +## First pass the arguments to the FISTAReconstructor and test the +## Lipschitz constant + +fistaRecon = FISTAReconstructor(proj_geom, + vol_geom, + Sino3D , + weights=Weights3D) + +print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant'])) +fistaRecon.setParameter(number_of_iterations = 12) +fistaRecon.setParameter(Lipschitz_constant = 767893952.0) +fistaRecon.setParameter(ring_alpha = 21) +fistaRecon.setParameter(ring_lambda_R_L1 = 0.002) + +## Ordered subset +if False: + subsets = 16 + angles = fistaRecon.getParameter('projector_geometry')['ProjectionAngles'] + #binEdges = numpy.linspace(angles.min(), + # angles.max(), + # subsets + 1) + binsDiscr, binEdges = numpy.histogram(angles, bins=subsets) + # get rearranged subset indices + IndicesReorg = numpy.zeros((numpy.shape(angles))) + counterM = 0 + for ii in range(binsDiscr.max()): + counter = 0 + for jj in range(subsets): + curr_index = ii + jj + counter + #print ("{0} {1} {2}".format(binsDiscr[jj] , ii, counterM)) + if binsDiscr[jj] > ii: + if (counterM < numpy.size(IndicesReorg)): + IndicesReorg[counterM] = curr_index + counterM = counterM + 1 + + counter = counter + binsDiscr[jj] - 1 + + +if False: + print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant'])) + print ("prepare for iteration") + fistaRecon.prepareForIteration() + + + + print("initializing ...") + if False: + # if X doesn't exist + #N = params.vol_geom.GridColCount + N = vol_geom['GridColCount'] + print ("N " + str(N)) + X = numpy.zeros((N,N,SlicesZ), dtype=numpy.float) + else: + #X = fistaRecon.initialize() + X = numpy.load("X.npy") + + print (numpy.shape(X)) + X_t = X.copy() + print ("initialized") + proj_geom , vol_geom, sino , \ + SlicesZ = fistaRecon.getParameter(['projector_geometry' , + 'output_geometry', + 'input_sinogram', + 'SlicesZ']) + + #fistaRecon.setParameter(number_of_iterations = 3) + iterFISTA = fistaRecon.getParameter('number_of_iterations') + # errors vector (if the ground truth is given) + Resid_error = numpy.zeros((iterFISTA)); + # objective function values vector + objective = numpy.zeros((iterFISTA)); + + + t = 1 + + + print ("starting iterations") +## % Outer FISTA iterations loop + for i in range(fistaRecon.getParameter('number_of_iterations')): + X_old = X.copy() + t_old = t + r_old = fistaRecon.r.copy() + if fistaRecon.getParameter('projector_geometry')['type'] == 'parallel' or \ + fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat' or \ + fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat_vec' : + # if the geometry is parallel use slice-by-slice + # projection-backprojection routine + #sino_updt = zeros(size(sino),'single'); + proj_geomT = proj_geom.copy() + proj_geomT['DetectorRowCount'] = 1 + vol_geomT = vol_geom.copy() + vol_geomT['GridSliceCount'] = 1; + sino_updt = numpy.zeros(numpy.shape(sino), dtype=numpy.float) + for kkk in range(SlicesZ): + sino_id, sino_updt[kkk] = \ + astra.creators.create_sino3d_gpu( + X_t[kkk:kkk+1], proj_geom, vol_geom) + astra.matlab.data3d('delete', sino_id) + else: + # for divergent 3D geometry (watch the GPU memory overflow in + # ASTRA versions < 1.8) + #[sino_id, sino_updt] = astra_create_sino3d_cuda(X_t, proj_geom, vol_geom); + sino_id, sino_updt = astra.creators.create_sino3d_gpu( + X_t, proj_geom, vol_geom) + + ## RING REMOVAL + residual = fistaRecon.residual + lambdaR_L1 , alpha_ring , weights , L_const= \ + fistaRecon.getParameter(['ring_lambda_R_L1', + 'ring_alpha' , 'weights', + 'Lipschitz_constant']) + r_x = fistaRecon.r_x + SlicesZ, anglesNumb, Detectors = \ + numpy.shape(fistaRecon.getParameter('input_sinogram')) + if lambdaR_L1 > 0 : + print ("ring removal") + for kkk in range(anglesNumb): + + residual[:,kkk,:] = (weights[:,kkk,:]).squeeze() * \ + ((sino_updt[:,kkk,:]).squeeze() - \ + (sino[:,kkk,:]).squeeze() -\ + (alpha_ring * r_x) + ) + vec = residual.sum(axis = 1) + #if SlicesZ > 1: + # vec = vec[:,1,:].squeeze() + fistaRecon.r = (r_x - (1./L_const) * vec).copy() + objective[i] = (0.5 * (residual ** 2).sum()) +## % the ring removal part (Group-Huber fidelity) +## for kkk = 1:anglesNumb +## residual(:,kkk,:) = squeeze(weights(:,kkk,:)).* +## (squeeze(sino_updt(:,kkk,:)) - +## (squeeze(sino(:,kkk,:)) - alpha_ring.*r_x)); +## end +## vec = sum(residual,2); +## if (SlicesZ > 1) +## vec = squeeze(vec(:,1,:)); +## end +## r = r_x - (1./L_const).*vec; +## objective(i) = (0.5*sum(residual(:).^2)); % for the objective function output + + + + # Projection/Backprojection Routine + if fistaRecon.getParameter('projector_geometry')['type'] == 'parallel' or \ + fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat' or\ + fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat_vec': + x_temp = numpy.zeros(numpy.shape(X),dtype=numpy.float32) + print ("Projection/Backprojection Routine") + for kkk in range(SlicesZ): + + x_id, x_temp[kkk] = \ + astra.creators.create_backprojection3d_gpu( + residual[kkk:kkk+1], + proj_geomT, vol_geomT) + astra.matlab.data3d('delete', x_id) + else: + x_id, x_temp = \ + astra.creators.create_backprojection3d_gpu( + residual, proj_geom, vol_geom) + + X = X_t - (1/L_const) * x_temp + astra.matlab.data3d('delete', sino_id) + astra.matlab.data3d('delete', x_id) + + + ## REGULARIZATION + ## SKIPPING FOR NOW + ## Should be simpli + # regularizer = fistaRecon.getParameter('regularizer') + # for slices: + # out = regularizer(input=X) + print ("skipping regularizer") + + + ## FINAL + print ("final") + lambdaR_L1 = fistaRecon.getParameter('ring_lambda_R_L1') + if lambdaR_L1 > 0: + fistaRecon.r = numpy.max( + numpy.abs(fistaRecon.r) - lambdaR_L1 , 0) * \ + numpy.sign(fistaRecon.r) + t = (1 + numpy.sqrt(1 + 4 * t**2))/2 + X_t = X + (((t_old -1)/t) * (X - X_old)) + + if lambdaR_L1 > 0: + fistaRecon.r_x = fistaRecon.r + \ + (((t_old-1)/t) * (fistaRecon.r - r_old)) + + if fistaRecon.getParameter('region_of_interest') is None: + string = 'Iteration Number {0} | Objective {1} \n' + print (string.format( i, objective[i])) + else: + ROI , X_ideal = fistaRecon.getParameter('region_of_interest', + 'ideal_image') + + Resid_error[i] = RMSE(X*ROI, X_ideal*ROI) + string = 'Iteration Number {0} | RMS Error {1} | Objective {2} \n' + print (string.format(i,Resid_error[i], objective[i])) + +## if (lambdaR_L1 > 0) +## r = max(abs(r)-lambdaR_L1, 0).*sign(r); % soft-thresholding operator for ring vector +## end +## +## t = (1 + sqrt(1 + 4*t^2))/2; % updating t +## X_t = X + ((t_old-1)/t).*(X - X_old); % updating X +## +## if (lambdaR_L1 > 0) +## r_x = r + ((t_old-1)/t).*(r - r_old); % updating r +## end +## +## if (show == 1) +## figure(10); imshow(X(:,:,slice), [0 maxvalplot]); +## if (lambdaR_L1 > 0) +## figure(11); plot(r); title('Rings offset vector') +## end +## pause(0.01); +## end +## if (strcmp(X_ideal, 'none' ) == 0) +## Resid_error(i) = RMSE(X(ROI), X_ideal(ROI)); +## fprintf('%s %i %s %s %.4f %s %s %f \n', 'Iteration Number:', i, '|', 'Error RMSE:', Resid_error(i), '|', 'Objective:', objective(i)); +## else +## fprintf('%s %i %s %s %f \n', 'Iteration Number:', i, '|', 'Objective:', objective(i)); +## end +else: + fistaRecon = FISTAReconstructor(proj_geom, + vol_geom, + Sino3D , + weights=Weights3D) + + print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant'])) + fistaRecon.setParameter(number_of_iterations = 12) + fistaRecon.setParameter(Lipschitz_constant = 767893952.0) + fistaRecon.setParameter(ring_alpha = 21) + fistaRecon.setParameter(ring_lambda_R_L1 = 0.002) + fistaRecon.prepareForIteration() + X = fistaRecon.iterate(numpy.load("X.npy")) -- cgit v1.2.3