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Motion Phantom #183

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Motion Phantom #183

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pvillacorta
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@pvillacorta pvillacorta commented Oct 5, 2023 •
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This branch is meant to implement Koma's HDF5 Phantom file format (.phantom) in a way that supports different motion models (Related with #73). For this we need to implement:

  • SimpleMotion<:MotionModel struct that will replace the currently used ux, uy, and ux fields to have more extensible motion models.
  • ArbitraryMotion<:MotionModel struct designed to generate arbitrary non-rigid motions. This will enable different structures (spin groups) to have separated motions, in contrast to SimpleMotion that applies the same displacement field to all the spins.
  • HDF5 Phantom file format (.phantom), read .phantom specification file.
  • read_phantom that will read a .phantom file and generate an indexed or explicit Phantom struct.
  • write_phantom that will write a .phantom file from a Phantom struct.

@pvillacorta
Added function read_phantom_file
c6f6447
@pvillacorta
Created new simulation method: BlochMov
f26d9bf
@pvillacorta
Redefined Phantom struct: ux, uy, uz are now vectors
46b4179
@pvillacorta
Extended read_phantom_file function (movement)
cbf84f0
@pvillacorta
Included BlochMov method in Core
2b6d71b
@pvillacorta
Export read_phantom_file
c6561f6
@pvillacorta
export fftc, ifftc
d84c0e2
@pvillacorta
Added motion run_spin_precession and excitation
b7b0df9
@pvillacorta
Initialize Phantom correctly
6344f9c
@pvillacorta
Bloch method as the basis for BlochMov
d7f1a30
@pvillacorta
Beta parameters parsing to Float32
2d5bd73
@pvillacorta
Function read_nifti_file
f81a2dc
@pvillacorta
export time_partitioner
5e325f0
@pvillacorta
Replaced u functions by the new motion parameters
cc3a427
@pvillacorta
Added 3 functions to calculate spin displacements
d6655fe
@pvillacorta
plot_phantom_map adapted to new Phantom format
b259577
@pvillacorta
Added some new .phantom files and their corresponding creation scripts
170cf6e
@pvillacorta
Corrected errors in default Phantom values
8e81357
@pvillacorta
Exported get_displacements, get_pieces_limits
8e818d4
@pvillacorta
Corrected string format error
6585c4a
@pvillacorta
Moved time_partitioner and get_pieces_limits
6532e08
@pvillacorta
added NIfTI example maps
a612c25
@pvillacorta
Function read_nifti_file improved
9ac350b
@pvillacorta
Added NIfTI, removed PlotlyJS from main module
73a0bef
@pvillacorta
Optimizing interpolation functions is pending
4f79f7f
@pvillacorta
Improved motion simulation (issue: only with small phantoms)
aad1a57
@pvillacorta
Deleted FuncWrapper struct
0a8eb25
@pvillacorta
Changed read_phantom_NIfTI function to a new IO file
90346c3
@pvillacorta
Improvement in simulation with no motion in any of the axes
a1f42db
@pvillacorta
Created get_itp_functions function and commented unused functions
a1ac911
@pvillacorta
Corrected plot_phantom_map function
9c57df1
@pvillacorta
Fixed: wrong function call
149e988
@pvillacorta
rotation_matrix function into Grad.jl file
2dce21a
@pvillacorta
GRE sequence function
6cdc965
@pvillacorta
rotation_matrix function
17eab80
@pvillacorta
Fixed get_itp_functions for more than one segment
14f9826
@pvillacorta
TODO: Consider trapezoid and not only FlatTop area
5c3b215
@pvillacorta
Using LinearAlgebra
9f316ba
@pvillacorta
Trapezoid pulses considered
e7370e5
@pvillacorta
RF_sinc bug
d211860
@pvillacorta
Fixed bug in rotation_matrix function
a610031
@pvillacorta
Deleted BlochMov, added SimpleMotion and ArbitraryMotion
421f2b0
@pvillacorta
Minor changes in initialize_motion
c286f9d
@pvillacorta
Modified heart_phantom and deleted some comments
1ddab00
@pvillacorta
Modified heart_phantom and deleted some comments
fc94066
@pvillacorta
Export initialize_motion
34509c9
@pvillacorta
Addapted plot_phantom_map to new motion functions
62722d8
@pvillacorta
Deleted some comments
591f175
@pvillacorta
New definitions for getindex and view
bfe8b8c
@pvillacorta
New SE function
788f25a
@pvillacorta pvillacorta closed this Oct 9, 2023
@pvillacorta pvillacorta deleted the new_phantom_parallel branch October 9, 2023 20:41
@pvillacorta pvillacorta restored the new_phantom_parallel branch October 9, 2023 20:43
@pvillacorta pvillacorta deleted the new_phantom_parallel branch October 9, 2023 20:46
@cncastillo cncastillo mentioned this pull request Oct 21, 2023
Closed
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@pvillacorta pvillacorta restored the new_phantom_parallel branch January 5, 2024 09:52
@pvillacorta pvillacorta deleted the new_phantom_parallel branch January 5, 2024 09:56
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@cncastillo cncastillo Awaiting requested review from cncastillo cncastillo will be requested when the pull request is marked ready for review cncastillo is a code owner

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