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* initial sphinx docEdoardo Pasca2019-03-197-0/+489
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* Merge pull request #226 from vais-ral/CVX_test_tryexceptEdoardo Pasca2019-03-191-109/+117
|\ | | | | add try/catch in test with CVX
| * add try/catchEdoardo Pasca2019-03-191-109/+117
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* fixed table with conda badgesEdoardo Pasca2019-03-191-1/+1
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* added conda badgesEdoardo Pasca2019-03-191-3/+3
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* update Norm2sq for SIRF compatibility (#222)Edoardo Pasca2019-03-151-2/+7
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* Dataprocessor opt (#216)Edoardo Pasca2019-03-054-16/+446
| | | | | | | | | | | | | | * initial implementation of Algorithm and Gradient Descent * added example on gradient descent * refined definition of Algorithm and Gradient Descent * allow memory efficient code in dataprocessor * revert to master version * added test for DataProcessor
* use bullet pointEdoardo Pasca2019-03-041-3/+3
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* added info on Algorithm classEdoardo Pasca2019-03-041-4/+22
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* added dot product between DataContainer s (#215)Edoardo Pasca2019-03-042-0/+48
| | | | | | | | | | | | * added dot product between datacontainers closes #208 implements dot product by flattening the data in a vector and calculating the inner product on the vectors added unittest * use more efficient ravel than flatten
* Geometry allocation (#211)Edoardo Pasca2019-03-014-122/+176
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * initial revision * Removed class members of Algorithm class added update_objective * initial version. Fix inline __idiv__ * First implementation of CompositeOperator/DataContainer * removed __getitem__ added get_item added shape * added CGLS * working unit test, initial tomography test * added reverse multiplication of operator with number * added operators directory * fixed typo * added unittest for CompositeDataContainer * fix TomoIdentity with scalar * check numerical types from numpy * add default stop criterion and run method * add run method * first working implementation of CGLS with CompositeOperator/DataContainer notice problem with _rmul_ and _mul_ methods precedence with numpy. * removed line endings * removed dos line ending * Added allocate to ImageGeometry and AcquisitionGeometry * remove composite operator * Delete Algorithms.py * remove setup.py from PR * readded setup.py * added newline at the end of the file * added newline at EOF in setup.py
* removed gitattributesEdoardo Pasca2019-03-011-1/+0
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* Proposal of Algorithm class (#179)Edoardo Pasca2019-02-2818-1131/+1903
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * initial revision * Removed class members of Algorithm class added update_objective * initial version. Fix inline __idiv__ * First implementation of CompositeOperator/DataContainer * removed __getitem__ added get_item added shape * added CGLS * working unit test, initial tomography test * added reverse multiplication of operator with number * added operators directory * fixed typo * added unittest for CompositeDataContainer * fix TomoIdentity with scalar * check numerical types from numpy * add default stop criterion and run method * add run method * first working implementation of CGLS with CompositeOperator/DataContainer notice problem with _rmul_ and _mul_ methods precedence with numpy. * new Algorithm class and algorithms in separate files Added new Algorithm class and derivatives in different files for GradientDescent, CGLS, FBPD, FISTA * added algorithms and restored CIL_VERSION env variable * removed Algorithms.py * modified run and renamed a few members/methods * uses squared_norm * renamed get_current_objective to get_last_objective update_objective can be issued every N iteration, default 1. fixed run method to run N iterations within the stop criterion. * load class as module files * force py line endings to LF * updates * call super __init__ as first thing * unit tests are now to be found in test directory unit tests are now split in several files in the directory test * install algorithms module * Implementation with Algorithm * skip Reader tests * unittest for linux * commented not needed import Iterable * removed explicit return from __init__ * remove composite operator file
* added squared_norm (#204)Edoardo Pasca2019-02-275-16/+38
| | | | | | | | | | | | | | * added squared_norm closes #203 * added norm and squared_norm closes #203 * Power method uses norm, bugfixes * fix power method
* add norm to DataContainer (#195)Edoardo Pasca2019-02-151-0/+4
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* Merge pull request #186 from vais-ral/colourbay_initial_demojakobsj2019-02-142-7/+7
|\ | | | | Colourbay initial demo
| * Merge branch 'master' into colourbay_initial_demojakobsj2019-02-1420-282/+2951
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* | Update README.mdvais-ral2019-01-291-1/+5
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* | Merge pull request #177 from TomasKulhanek/mastervais-ral2019-01-294-44/+7
|\ \ | | | | | | Universal build script
| * \ Merge branch 'master' into masterTomas Kulhanek2019-01-282-7/+11
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* | | UPDATE: CIL VERSION needs to be set (#173)Tomas Kulhanek2019-01-115-5/+59
| | | | | | | | | | | | | | | | | | | | | | | | * UPDATE: CIL VERSION needs to be set * UPDATE: jenkins build and variants * UPDATE: channels conda-forge and ccpi
* | | Norm2sq does not fail if cannot calculate Lipschitz constantEdoardo Pasca2019-01-081-5/+9
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* | | added L member to FunctionEdoardo Pasca2019-01-081-1/+1
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| * | UPDATEKulhanek2019-01-282-1/+4
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| | * | Update README.mdTomas Kulhanek2019-01-181-1/+1
| | | | | | | | | | | | ADD: build status from jenkins embeddable build status plugin
| | * | Update README.mdTomas Kulhanek2019-01-181-1/+2
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| | * | Update README.mdTomas Kulhanek2019-01-181-0/+1
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| | * | Update conda_build_config.yamlTomas Kulhanek2019-01-181-2/+3
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| | * | Update conda_build_config.yamlTomas Kulhanek2019-01-181-1/+1
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| | * | Update jenkins-build.shTomas Kulhanek2019-01-181-3/+3
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| | * | Update jenkins-build.shTomas Kulhanek2019-01-181-4/+4
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| * | | UPDATE: using universal buildKulhanek2019-01-281-42/+2
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| * | updateKulhanek2019-01-141-1/+0
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| * | update pin-compatibleKulhanek2019-01-141-0/+1
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| * | UPDATE: channels conda-roge and ccpKulhanek2019-01-111-4/+2
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| * | UPDATE: jenkins build and variantsKulhanek2019-01-113-0/+49
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| * | UPDATE: CIL VERSION needs to be setTomas Kulhanek2019-01-033-5/+12
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* | changed titleEdoardo Pasca2018-11-271-1/+1
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* | fix import errorEdoardo Pasca2018-11-161-3/+3
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* | Spdhg (#166)Edoardo Pasca2018-11-153-8/+350
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * replaces in with explicit test closes #139 * add read of single slice or subset * get_image_keys * reader reads single slice * adds get_acquisition_data_slice and get_acquisition_data_subset it is possible to read in only a subset of the dataset. * added multifile_nexus.py * cleaned example * fix normaliser and reader * wip * wip for reader * added support for non standard?? nexus files updated example with normalisation. * fix camelcase * Added initial unittest for reader bugfix for python 2.7 * fixes for python 2.7 * remove duplicate test requirement * minimal unittest for get_acquisition_data_subset * added SPDHG * work in progress
* | Nexus read slice (#144)Edoardo Pasca2018-11-107-71/+762
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * replaces in with explicit test closes #139 * add read of single slice or subset * get_image_keys * reader reads single slice * adds get_acquisition_data_slice and get_acquisition_data_subset it is possible to read in only a subset of the dataset. * added multifile_nexus.py * cleaned example * fix normaliser and reader * wip * wip for reader * added support for non standard?? nexus files updated example with normalisation. * fix camelcase * Added initial unittest for reader bugfix for python 2.7 * fixes for python 2.7 * remove duplicate test requirement * minimal unittest for get_acquisition_data_subset
* | increased version number (#163)Edoardo Pasca2018-11-072-2/+2
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* | Test norm (#162)Edoardo Pasca2018-11-076-538/+673
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * enable win build with unittest. skip cvx * unittest on funcs * fixed Norm1 and function * test chaining * a few fixes for unittest * investigating Norm2 * restored Norm2 TODO: rewrite it and test * removed comment
* | added build variants (#160)Edoardo Pasca2018-11-022-2/+9
| | | | | | fixed unit test for python2.7
* | Build fix (#159)Edoardo Pasca2018-11-028-47/+173
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | closes #148 closes #156 closes #157 closes #158 * split run_test for algorithms * fix FBPD adds operator as input argument changes naming of variables to explicit * implement proximal for ZeroFun and Norm1 proximal method must be correctly implemented. lead to error #158 * fix unit test and cvx demo
* | Added working demo of colourbay data load and recon. (#132)jakobsj2018-10-223-0/+426
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Added working demo of colourbay data load and recon. * Added IMAT white-beam demo loading summed fits files * corrections to normalization and log with zeroes in flats * IMAT data multichannel script started * script to reconstruct multi-channel imat data updated * some updates to demo
* | removed default behaviour of Function as Identity (#155)Edoardo Pasca2018-10-181-6/+6
| | | | | | addresses this loophole https://github.com/CCPPETMR/Hackathon-SIRF/issues/12#issuecomment-430944064
* | closes #151 (#152)Edoardo Pasca2018-10-171-8/+8
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* | Memhandle (#136)Edoardo Pasca2018-09-298-133/+1200
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * added inplace algebra correctly * readded object to AcquisitionGeometry and ImageGeometry * Add more memory management * added unary and binary operations to DataContainer * Added unary and binary operations added also unittest * added unittest * added unit tests for binary operators * bugfixes and remove prints * dafault initialisation behaviour not to deep_copy * FISTA to use the efficient memory handling additions * add calls with input out=None Starts to address #134 * add methods with arg out=None * add test for memhandle * major bugfix after removal of create_image_data * fixed FISTA memhandle * some bugfix in FISTA and funcs ops * debug in progress * Fixed several bugs in memory optimised code Added methods allocate_adjoint and allocate_direct to Operator. * test with cvx and adjustments * fixed unittest, need to fix inline algebra * fixed inline algebra definition * initial cvxpy unittest * adds cvx demo as unit test closes #150 check equality of cvx calculated with respect to FISTA and FBDP
* | Add SIRT and Box constraints (#125)jakobsj2018-09-184-0/+270
| | | | | | | | | | | | * Quick prototype of SIRT with nonnegativity added * Add indicator function for boxconstrint in SIRT and FISTA with demo
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