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SPDHG algorithm from CIL #238

Merged
merged 47 commits into from
Oct 23, 2019
Merged

SPDHG algorithm from CIL #238

merged 47 commits into from
Oct 23, 2019

Commits on Jul 27, 2018

  1. Added methods to MRI data container 

    added: copy, conjugate
closes Hackathon-SIRF/#7
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  2. Added clone to PET DataContainer

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  3. Added direct and adjoint 

    notice that it's not taking into consideration
SyneRBI/Hackathon-SIRF#2 (comment)
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  4. removed conjugate 

    for MR images dot operator calculates the inner product with conjugate
by itself.
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  5. added get_linear_acquisition_model and direct

    @paskino
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  6. add spdhg example

    @mehrhardt
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  7. added direct method 

    changed AcquisitionModel to inherit from object.
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  8. added test for new methods

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  9. added adjoint

    @paskino
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  10. add spdhg example

    @mehrhardt
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  11. added test of adjoint

    @paskino
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  12. add spdhg + Kullback Leibler + example without subsets

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  13. merge two versions of spdhg example

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Commits on Jul 30, 2018

  1. added conjugate 

    closes #7
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Commits on Sep 20, 2018

  1. self.x is a ImageData not numpy array 

    fixes an assertion error
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Commits on Sep 21, 2018

  1. Merge master branch from main SIRF repo

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  2. Merge branch 'convert_spdhg_to_cil' of https://github.com/CCPPETMR/Ha… 

    …ckathon-SIRF into convert_spdhg_to_cil
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  3. update spdhg with updated SIRF

    @paskino
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  4. added ccpi regularisers

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Commits on Sep 28, 2018

  1. use Function and ZeroFun from ccpi

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Commits on Oct 15, 2018

  1. Merge remote-tracking branch 'origin/add_to_sirf_classes' into conver… 

    …t_spdhg_to_cil
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Commits on Oct 17, 2018

  1. use copy instead of clone to be compatible with numpy

    @mehrhardt
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  2. fix bug in extrapolation and add references

    @mehrhardt
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  3. make more arguments optional and enhance doc

    @mehrhardt
    mehrhardt committed Oct 17, 2018
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  4. enhance the default value allocation

    @mehrhardt
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  5. allow KL to work on numpy arrays

    @mehrhardt
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  6. add subset support for spdhg

    @mehrhardt
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Commits on Nov 14, 2018

  1. polish clone vs copy

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  2. Merge branch 'master' into add_to_sirf_classes

    @paskino
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  3. use SPDHG from CIL repo

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  4. initial work using spdhg from cil

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Commits on Nov 15, 2018

  1. polish

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  2. SPDHG algorithm from CCPi optimisation working

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  3. Merge branch 'master' into spdhg_from_cil

    @paskino
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  4. removed trailing blanks

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  5. Merge branch 'add_to_sirf_classes' into spdhg_from_cil

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Commits on Nov 16, 2018

  1. removed pCIL

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Commits on Nov 20, 2018

  1. conjugate returns a different object

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Commits on Dec 18, 2018

  1. adds methods for CIL compatibility 

    STIR.py:
  adds:
    * get_background_term
    * saves background term in self.bt member of AcquisitionModel
    * get_linear_acquisition_model
    * direct
    * adjoint
    * is_linear
    * is_affine
addresses #237 (comment)
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  2. Merge remote-tracking branch 'origin/master' into add_to_sirf_classes

    @paskino
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  3. added conjugate and comments

    @paskino
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  4. fixed is_affine to return True 

    added get_constant_term
added get_additive_term

           PET acquisition model that relates an image x to the
           acquisition data y as
           (F)    y = [1/n] (G x + [a]) + [b]
           where:
           G is the geometric (ray tracing) projector from the image voxels
           to the scanner's pairs of detectors (bins);
           a and b are otional additive and background terms representing
           the effects of noise and scattering;

           Returns [a] + [b]
    @paskino
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  5. added methods for background and additive term

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  6. fixed get_constant_term and is_linear

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Commits on Dec 19, 2018

  1. Merge branch 'add_to_sirf_classes' into spdhg_from_cil

    @paskino
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  2. added copy method 

    added copy method to SIRF.DatContainer class
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  3. Merge branch 'add_to_sirf_classes' into spdhg_from_cil

    @paskino
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