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T162 heterogenous sos #176

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T162 heterogenous sos #176

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cbender98
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Main Changes:

  • heterogenous delay calculation in reconstruction_utils (only 2dim so far due to memory problems for 3d)
  • outsourced homogenous delay calculation in reconstruction_utils
  • considered off-by-one error in FOV creation (to be checked!)
  • bilinear interpolation function in calculation_utils (probably needed for 3dim version)
  • 2 manual tests
  • 1 automatic test
  • ...
    Note:
    Branch was really old (48 commits behind) --> a lot of merge conflicts

@cbender98
Fixed syntax in type hints of the function arguments
1968b05
@cbender98
added Tag which defines whether to consider heterogenous sos
195e62d
@cbender98
1st version of heterogenous sos delay calculation
022bb36
@cbender98
corrected type hints in arguments, add arguments
b63b0fe
@cbender98
improved accuray to ~10^(-13) (compared with homogenous calculation a…
e357d97 
…nd homogen.sos-map) by not adding unneccassary device base position and by fixing dtype error of delays container
@cbender98
fixed interpolation by transposing sos-map
d6eb409
@cbender98
new test for heterogenous reconsruction based on MinimalKWaveTest.py
fa8b083
@cbender98
moved and renamed; added gaussian noise and 2 regions sos-maps
4c9123c
@cbender98
renamed manual test for testing hDAS recon using toy sos-maps
e3c323a
@cbender98
write new test for hDAS using tissue based sos and simulated p0
f9b5ef0
@cbender98
update type hints, comments; differentiate between float/array handli…
9ccfda7 
…ng of speed_of_sound
@cbender98
removed unnecessary comments/prints, replaced prints by logger prints
480ff61
@cbender98
last version using grid_sample function (integral offset by 1 with re…
464149b 
…spect to analytical solution for horizontal gradient)
@cbender98
added bilinear interpolation function of imgs/maps
44f9969
@cbender98
debugged for pixels outside the to interpolated map to take the neare…
d3ef49c 
…st neighbour values and not to linearly interpolate
@cbender98
manual test for testing hDAS using 3 point like vessels
58a2e81
@cbender98
memory optimized version for 2d interpolation, but can be made nicer
13fb5a5
@cbender98
renamed the file again and fixed some typos
090b54c
@cbender98
added new function with own interpolation, changed errors due to offs…
a04779d 
…et bugs in the interpolation, temporary added memory debug prints in order to change function with own interpolation to reduce memory needed (so far the hDASToySoS test does not run with the new function due to out of memory error)
@cbender98
optimized 2d interpolation in terms of gpu memory usage, added print_…
f3304f0 
…memory_stats function for printing used memory
@cbender98
automated test for testing 2d interpolation function
a8ceb2a
@cbender98
fixed typo (one blank space too much)
4b0b95e
@cbender98
debugged 3d interpolation and wrote test for 2d and 3d interpolation
9c4796d
@cbender98
tried some memory reducing methods
39b0c4f
@cbender98
optimized memory usage in interpolation
a13b63f
@cbender98
for 400x400 fov fixed memory issue
6582173
@cbender98
delete comment with old memory expensive 2d interpolation
d508626
@cbender98
renamed file and added one vessel
42b562d
@cbender98
restructured a few lines
3425b22
@cbender98
converted jupyter-notebook into python file
697c69f
@cbender98
convert notebook to automatic test: compares numerically integrated d…
f909b2c 
…elays with analytically integrated delays
@cbender98
added some boolean as input parameters for debugging and verboseness,
8ce85e6 
IMPORTANT: noticed that sensor_positions were globally overwritten --> now copy
@cbender98
decrease computation time down to 70%
4e349fc
@cbender98
outsourced toms homogen delay calculation,
4af3232 
improved comments
@cbender98
applied memory reducing steps also to 3dim case and tested it against…
94d69cb 
… scipy interpolation
@cbender98
added verbosity handling and also changed input parameters to be in t…
daed4bd 
…he PAI-realistic units
@cbender98
renamed class name
448557b 
made input of scalarfield-type more user friendly
@cbender98
delete optionality parameters:
309f52b 
grid_points_middle
verbose
get_interpols
uneven_steps
global_ds_calc
@cbender98
deleted all optional parameters (also mixed_coordinate_system)
f134b63 
also deleted unnecessary speed_of_sound_in_m_per_s input in compute image dimensions
@cbender98
added comments and type hints
3aae172
@cbender98
also works for cpu now
88b5080
@cbender98
deleted function w/ own interpolation due to computation time
ae58450 
float64 in source positions due to detected inaccuracies
@cbender98
added parameter for random sensor
d078547 
fixed bug in sensor positions initializtation (z-components to 0)

vectorized analytical solution
@cbender98
commented and added new plot
d0391f6
@cbender98
save path changes
95b5b04
@cbender98
delete unneccessary import
749f5ee
leoyala and others added 4 commits December 14, 2022 11:52
@leoyala
Merge branch 'develop' into T162_HeterogenousSOS
fcebc8a 
# Conflicts:
#	simpa/core/simulation_modules/reconstruction_module/reconstruction_utils.py
@leoyala
added logger as parameter to calculate_delays_for_homogen_sos
74896f1
@cbender98
debugged assert error (correct position boundaries of sensor sampling)
dccdbb3 
improved plotting and added critical sensor computation
@cbender98
corrected heterogeneous spelling
0c0fb8b 
removed print_memory_stats

corrected hDAS tissue (heterogenous DAS is now calculated using the mean sos value not a fixed one)
@cbender98
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Code is ready for review

@jgroehl
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jgroehl commented Aug 13, 2024

Were there any additional changes that need to be updated?

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@kdreher kdreher Awaiting requested review from kdreher

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3 participants
@cbender98 @jgroehl @leoyala