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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
* replaces in with explicit test (#141)Edoardo Pasca2018-08-151-2/+3
| | | closes #139
* add scipy as dependency (#138)Edoardo Pasca2018-08-151-0/+1
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* added alias to prox and grad (#130)Edoardo Pasca2018-07-311-3/+5
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* Added copy as alias of clone, use copy in algs (#131)Edoardo Pasca2018-07-312-4/+7
| | | closes #126
* move padder to plugins (#121)Edoardo Pasca2018-05-152-106/+0
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* Cvx (#118)jakobsj2018-05-083-3/+253
| | | | | | | | * add CVX test script * Add L1 and TV CVX and denoising. TV FBPD bug. * Fix TV2D bug and update cvx demo
* Remove already moved files (#116)jakobsj2018-05-084-666/+0
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* Merge pull request #115 from vais-ral/remove_camelcasejakobsj2018-04-271-8/+8
|\ | | | | removes camelcase
| * fix camel case inputsJakob Jorgensen2018-04-271-4/+4
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| * removes camelcaseEdoardo Pasca2018-04-241-4/+4
| | | | | | | | addresses #107
* | Ip removal (#109)jakobsj2018-04-244-168/+0
|/ | | | | | * Removing IP data and files. Still in IP_parking branch. #102 * Also remove IP pyc file
* move demo to plugins (#112)Edoardo Pasca2018-04-241-181/+0
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* Merge pull request #108 from vais-ral/fix_tv_fbpdjakobsj2018-04-231-6/+4
|\ | | | | Fix ordering #106
| * Fix ordering #106Jakob Jorgensen2018-04-231-6/+4
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* Simple comma bugfixJakob Jorgensen2018-04-231-1/+1
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* Merge pull request #105 from vais-ral/demo_cleanupjakobsj2018-04-192-2/+33
|\ | | | | Demo cleanup
| * added angle_unit to AcquisitionGeometryEdoardo Pasca2018-04-171-0/+1
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| * few fixes cleaning the simple_demo_ccpiEdoardo Pasca2018-04-172-2/+32
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* | Merge pull request #104 from vais-ral/add_processorsjakobsj2018-04-171-0/+495
|\| | | | | added processors.py
| * added processors.pyEdoardo Pasca2018-04-171-0/+495
|/ | | | closes #100
* Merge pull request #101 from vais-ral/opti_initjakobsj2018-04-121-0/+18
|\ | | | | Added init file in optimisation to make package
| * Added init file in optimisation to make packageJakob Jorgensen2018-04-121-0/+18
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* update aboutEdoardo Pasca2018-04-111-2/+2
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* renamed DataSetProcessor to DataProcessor (#99)Edoardo Pasca2018-04-111-18/+18
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* Merge pull request #90 from vais-ral/doc_optijakobsj2018-04-113-21/+65
|\ | | | | First opti doc
| * Replaced BaseFunction by FunctionJakob Jorgensen2018-04-112-11/+11
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| * Updated READMEJakob Jorgensen2018-04-101-4/+6
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| * Replaces .fun in funcs by .__call__Jakob Jorgensen2018-04-102-7/+7
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| * First opti docJakob Jorgensen2018-04-091-3/+45
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* initial work on docsEdoardo Pasca2018-04-051-0/+48
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* removed unused recipe (#89)Edoardo Pasca2018-04-043-46/+0
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* updated licenseEdoardo Pasca2018-04-041-13/+3
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* Rename (#88)Edoardo Pasca2018-04-048-946/+21
| | | | | | | | | | | | | | | | | | | | * create optimisation package * renamed to framework * added FiniteDiff2D operator * fixed dependencies * fix import packages * added ccpiops.py and move processors.py * updated imports * renamed but not split * Removed reconstruction as moved to optimisation
* Move astra (#85)Edoardo Pasca2018-03-287-608/+20
| | | | | | | | | | | | * removed astra stuff * removed astra and added dependency on ccpi-reconstruction * removed astra test * renamed to ccpi-framework * little changes to demo
* Simple demo ip (#79)jakobsj2018-03-225-540/+107
| | | | | | | | | | * Removed regularizers * DemoIP running. MC Lipschitz incorrect * Fixed MC Lipschitz * Removed old import
* Merge pull request #82 from vais-ral/demo_diamondjakobsj2018-03-223-12/+203
|\ | | | | Demo diamond
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