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* Cache computed lipschitz constant, seed random number generator to ensure ↵fast_tnvSuren A. Chilingaryan2020-03-271-4/+27
| | | | that different runs give exactly the same result
* Operator composition (#493)Edoardo Pasca2020-02-2114-186/+932
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * CompositionOperator and some refactoring * Added SumOperator and CompositionOperator added domain_geometry and optional range_geometry as parameter of Operator. These are saved in _domain_geometry and _range_geometry. Updated all operator and tests to take notice of this change. * fighting with Composition * fix direct and adjoint for CompositeOperator * fix composition Operator * remove target OUTPUT to trigger build * added unit tests * add test for ZeroOperator * fixes * add numba * removed hard coded path * removed comments * fix direct/adjoint with out parameter * removed __rmul__ * use calculate_norm inherited from LinearOperator * removed hard coded version tag * removed cached string version * use add_custom_target instead add_custom_command
* explicitly point to build directory (#496)Edoardo Pasca2020-02-121-1/+1
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* fix limits of docstring (#495)Edoardo Pasca2020-02-062-2/+14
| | | | | | * fix limits of docstring * add test for IndicatorBox
* axpby as concrete method in DataContainer and BlockDataContainer (#489)Edoardo Pasca2020-01-2415-130/+300
| | | | | | | | | | | | | | | | | | * axpby as concrete method in DataContainer and BlockDataContainer * fixed axpby and added unittest * PDHG to use axpby * pass num_threads to axpby * void commit * add seed to random in test * NUM_THREADS can be imported from ccpi.utilities * added test to axpby with num_threads
* Allows user to set number of threads used by openMP in C library grad… (#476)Gemma Fardell2020-01-234-214/+111
| | | | | | | | | | | | | | | | * Allows user to set number of threads used by openMP in C library gradient operator. Changed to release build flags * closes #477 * added test function for c lib thread deployment * improved thread scaling for neumann algoritims * removed unnecessary thread sync * reverts omp number of threads at the end of the c function call Co-authored-by: Edoardo Pasca <edo.paskino@gmail.com>
* working osx build (#491)Edoardo Pasca2020-01-234-16/+39
| | | | | | | | | * working osx build * correct omp lib name * add cache parameter closes #470
* add force recalculation of norm (#487)Edoardo Pasca2020-01-163-8/+74
| | | | | | | | | * add force recalculation of norm closes #394 better handling and documentation of Operator norm method. * added docstring and test for dot_test
* add reduction min and max (#486)Edoardo Pasca2020-01-162-2/+27
| | | | | | | | * add reduction min and max closes #441 * add spacing
* added developer guide (#485)Edoardo Pasca2020-01-152-0/+5
| | | closes #460
* Function m (#482)Edoardo Pasca2020-01-1551-995/+2072
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fix func style * update pnorm not quite right * add test for SumFunction * passed test for SumFunction * passed test for SumFunction * passed test for SumFunction * rename Norm2Sq to LeastSquares * rename Norm2Sq to LeastSquares * delete files and move to Function.py * fix accuracy convex conjugate * comment proximal conjugate, have generic expression * remove some imports * remove imports and comment gradient, proximal conjugate , rmul * remove imports and comment prox conj * fix init * fix out gradient * fix init * SumFunction full test * rename Norm2Sq * rename Norm2Sq * change kwargs in KL, not ready yet * change def of KL cases * change kwargs in KL, not ready yet * LinearOperatorMatrix FISTA cvx is not working * change name in KL * minor fix * BlockDataContainer should give a geometry when shape is the same * change convex conj when we have BDC * remove space * fix out for prox * rename x to b * add SumFunctionScalar test * fix convex conj of constant * fix convex conj of constant * minor fix * fix con conj * add new tests * KL not ready yet * add docs, not ready yet * fix documentation * fix docs * fix doc scaled function * fix doc translate function * fix modules path for documentation * minor doc fix * fix doc prox conj for KL * fix vector geometry in vectordata * fix direct/adjpint LinearOperator * add test LinearOperatorMatrix * fix doc and check methods for functionOperaCom * add new test for FunctionOperCom with LinearOperMatr * get vector geometry in vector data * minor changes and docs * fix docs * check Lips cons * rename Norm2Sq to LeastSquares for docs * fix KL, docs, background term, conve conj * add KL test * fix KL * minor fix doc * add back prox conj work with smoothTV * smooth TV not ready yet * add prox conj back * minor change * no change * fixing docs, not ready yet * uncomment prox_conj for ScaledFunction * fix doc for BlockFunction * add smoothTV not ready yet * no change * fix doc and uncomment prox conj * remove unicode literals * sphnix is a nightmare * fixing ADMM * remove conv conj, prox, prox conj from smooth TV * merge edo's docs * fix docs for L2Norm after edo's PR * fix docs * remove ADMM * add docs for Function module * remove unicode_literals from future imports https://stackoverflow.com/questions/7602171/unicode-error-unicodeescape-codec-cant-decode-bytes-string-with-u * remove ADMM * removed unicode literals from future imports * fix init for functions * remove main * add explcit KL prox conj, does not work with generic prox conj of function * add elif pass for vector geometry * fixes from comments on the PR * minor changes * fix mul in Function and Identity in TranslateFunction * remove from call * remove BlockGeometr from BDC * remove min, max * cleaned Function * add test for constant function * remove smooth mixed L21 Norm * fixed fill method and test of SumFunction * Functions dev (#479) * v19.10 docs (#467) updated docstrings and documentation * add Gemma in the authors * update docs * Installs with make install (#478) * closes #477 * install from build dir Co-authored-by: Vaggelis Papoutsellis <22398586+epapoutsellis@users.noreply.github.com>
* Installs with make install (#478)Edoardo Pasca2020-01-102-11/+16
| | | | | | * closes #477 * install from build dir
* add Gemma in the authorsEdoardo Pasca2020-01-071-0/+1
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* v19.10 docs (#467)Edoardo Pasca2020-01-0637-187/+1022
| | | updated docstrings and documentation
* C lib (#458)Edoardo Pasca2019-12-0623-38/+1695
| | | | C library implemented with optimised axpy fucntions and gradient operator in c
* added default input to CentreOfRotationFinder set_slice. Added check on ↵Gemma Fardell2019-11-202-13/+16
| | | | value input. (#419)
* added armijo rule (#390)Edoardo Pasca2019-11-196-31/+254
| | | | | | | | | | | | | | | | | | | | | | | | * added armijo rule * added info and kwarg for alpha * updated Armijo rule * modified stop criterion to GD * added kmax to limit the while True loop * fix raise comment * change default stopping criterion * updated test * added Rosenbrock function and test Gradient descent on that * removed test code * added missing import
* moved plotting utilities from demos (#424)Edoardo Pasca2019-11-136-1/+516
| | | | | | | | | | | | * moved plotting utilities from demos * added plt.show() * add utilities package * removed print statement * added numpy import
* fix MixedL21Norm (#417)Vaggelis Papoutsellis2019-10-301-75/+87
| | | | | | | | * fix MixedL21Norm * merged master * re added future imports
* Indicator box to use as_array, for SIRF (#418)Edoardo Pasca2019-10-291-2/+2
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* Bug fix: Input data change updates mtime (#416)Gemma Fardell2019-10-291-0/+3
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* Block geometry (#415)Vaggelis Papoutsellis2019-10-291-4/+3
| | | | `BlockGeometry` passes `max_value` to `ImageGeometry` or `AcquisitionGeometry`
* CenterOfRotationFinder() fixes #406 fixes #400 (#414)Gemma Fardell2019-10-294-49/+153
| | | | | * closes #406 closes #400 * Processors check modification and run time before running process
* defines shape for a subset slice (#410)Edoardo Pasca2019-10-283-14/+234
| | | | | | | | | | | | | | | | | | | | | | | | | | * defines shape for a subset slice closes #408 * fix subset for AcquisitionData * add future imports (#411) * override the dimension parameter, set angles to None by default (#412) * defines shape for a subset slice * fix subset for AcquisitionData * added initial unittest for subset * added .gitignore * adds unittest for subset, fix subset for AcquisitionData * reverted change of behaviour of as_array * removed empty line
* override the dimension parameter, set angles to None by default (#412)Edoardo Pasca2019-10-281-2/+11
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* add future imports (#411)Edoardo Pasca2019-10-281-1/+3
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* Pdhg last objective (#407)Edoardo Pasca2019-10-223-21/+33
| | | | | | | | | * save previous iteration at start of iteration * adds very_verbose to run method * modified test closes #396
* update Lipschitz constant (#404)Edoardo Pasca2019-10-181-1/+1
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* closes #370 (#395)Edoardo Pasca2019-10-181-1/+1
| | | closes #370
* copy list compatible with python <3.3 (#399)Edoardo Pasca2019-10-181-2/+2
| | | closes #398
* Fix sym grad (#393)Vaggelis Papoutsellis2019-10-156-112/+160
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fix func style * fix symGrad * recover from master * fix L1 * fix L1 * Update KullbackLeibler.py * correct adjoint FD * fix symgrad * no change in adjoint FD * add comment on FD * added unittest * changed syntax for assert_almost_equal * split test of sym gradient * fixed test
* Run to run all iterations (#391)Edoardo Pasca2019-10-143-345/+352
| | | | | | | | | | * run to run all iterations possible * add test without specifying number of iterations to run * removed print closes #383
* Finite diff allocate (#389)Edoardo Pasca2019-10-142-77/+82
| | | | | | * allocate output from geometry * removed non-default location of TestData
* Add log exp (#381)Edoardo Pasca2019-10-112-0/+19
| | | | | | | | | | | | * add test for algorithm * fix conflict * suppress warning * pass kwargs to Algorithm class creator * added unary operation exp and log
* Pass kwargs to algorithm (#380)Edoardo Pasca2019-10-117-53/+145
| | | | | | | | | | * add test for algorithm * fix conflict * suppress warning * pass kwargs to Algorithm class creator
* fix subset doesn't return ImageGeometry (#376)evelinaametova2019-10-118-93/+351
| | | | | closes #235 closes #312 closes #375
* remove angle from ImageGeometry (#378)Edoardo Pasca2019-10-101-1/+0
| | | closes #371
* Finite diff for sirf (#367)Edoardo Pasca2019-10-0931-125/+417
| | | | | | | | | | | | | * python2 compatibility import future * add staticmethod dot to test LinearOperators * a little more efficient code * skips all tests if module wget is not present * removed sirf import and simplified code
* Subset for ndim 1 (#373)Edoardo Pasca2019-10-074-257/+68
| | | | | | | | | | | | * subset to return VectorData if dim=1 * move Vector to framework this removes circular dependency * repeat test * skip test
* use dimension_labels in clone of Acquisition/ImageGeometry (#366)Edoardo Pasca2019-09-201-2/+4
| | | closes #365
* added min info on Block FrameworkEdoardo Pasca2019-07-081-0/+13
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* added changelogEdoardo Pasca2019-07-081-0/+15
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* Merge pull request #352 from vais-ral/Remove_demosgfardell2019-07-0523-4526/+0
|\ | | | | Removed demos
| * Removed demosGemma Fardell2019-07-0523-4526/+0
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* Norm2Sq and FISTA to give hints of why they fail (#351)Edoardo Pasca2019-07-054-10/+239
| | | | | | | | | | | | * Norm2Sq and FISTA to give hints of why they fail * added denoising tests from demos * L1Norm store instance of ShrinkageOperator * relax limit for python2 * added source of tests
* Fix documentation (#343)Vaggelis Papoutsellis2019-07-0530-552/+837
| | | | | | | | | | | | * fix documentation algs * fix docum functions dir * fix docum operator dir * docstring title * updated math in docstring
* Merge gf branch (#350)Edoardo Pasca2019-07-047-207/+95
| | | | | | | | * Algorithms updated to initalise all member variables in set_up() * Added missing data files * Removed memopts=False path
* Revert "Gf algorithm bug fix (#348)" (#349)Edoardo Pasca2019-07-047-95/+207
| | | This reverts commit 6876bda04cde114642ebce3d6bd577da40fa34e9.
* Gf algorithm bug fix (#348)gfardell2019-07-047-207/+95
| | | | | | | | * Algorithms updated to initalise all member variables in set_up() * Added missing data files * Removed memopts=False path
* Headers comment (#342)Edoardo Pasca2019-07-0268-384/+787
| | | | | | | | | | | | | | | | * added to autoclass doc * added header * file permission * remove x permission * spdhg x mode * removed file * reset permission to 644
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