[SyneRBI/SIRF] PET/MR Simulation (#1007)

Johannes Mayer

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Aug 27, 2021, 5:48:49 AM8/27/21

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PET/MR Simulation Framework for Dynamic Data including Ground Truth information.

You can view, comment on, or merge this pull request online at:

https://github.com/SyneRBI/SIRF/pull/1007

Commit Summary

added constructor to CoilensitivtitesVector
Merge branch 'img-from-rawdata' into petmr-simulation
deleted old encoding files
Deleted use getter for sptr_acquisitions
Renamed folder Testing into tests
Deleted main file
Modified cmake file to new strucutre
Updating contrast generator to current classes
Adapted contrast generator to curretn image classes
Replaced sptr access to acquisitoins
Updated copyright statements
Corrected Typos
deleted comments
deleted using namespace in .h file
Corrected Typos and updated email addresses
Added suggested sourcing of sirf_env to github workflow
Switched re-running of testdata back to on to see if exe will run
Revert "Added suggested sourcing of sirf_env to github workflow"
Renamed fourierencoding and trajectorypreparation
had to switch the running of the exe off again
Renamed noncartesian_encoding files
Merge branch 'rpe-encoding' into petmr-simulation
Updated Changes.md
Merge branch 'rpe-encoding' into petmr-simulation
Resolved problem with resampler output
Renamed resample to resampler
Corrected false calls to members
Updated calls in PETContrastGenerator::resample_to_template_image again
Fixed old calls in noise generator
Deleted some comments
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Merge branch 'img-from-rawdata' into petmr-simulation
Made the branch build
Added test directory to build in cmake
deleted inclusion of input filenames
Giving simulation test access to mr test auxiliary functions
Modified contrast generator tests
added noise generator tests
Deleted tests for memory usage
Fixed tests
Added better structure for test main
deleted simulation test headers
Updated first test with try cathc block
Fixed mock acquisitions vector test
Corrected modified shared folder path
Changed testfiles input
Added counter in std coutput of tests
Deleted function to read acquisitions that is in the vector calss already
Changed output folder
Added auxiliary input tests -> pass
Added tissue parameter tests to succeess
started tests for contrastgenerator
changed parameters of tissue label mapper tests
cont gen test improvement
changed header setter of mr contgen
Merge branch 'img-from-rawdata' into petmr-simulation
Corrected segfault for mr cont gen
corrected call to csm constr
changed tests to stop printing the test number
tests contgen now print the tset name
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Corrected include path of mr auxiliary function header for tests
Added interface for MRrawdata to cont gen
deleted some spaces lines
Updated tests for tissue parameters
Updated test input filenames
formatted tests
Updated contrast generator tests to run with new rawdata interface
Changed cf image vector writer to be able to use a path in prefix
Calling sorting after reading in kspace data
Deleted unnecessary code
Updated contgen tests to write to shared folder
Changed output testpath
Fixed pet writer in cont gen tests
corrected tests for wrong gyromagn. moment in ref data computation
Added tests for phantom input
deleted old pahntom reader except for nifti interface
included forgotten header
Updated tests
changed temporary folder name
Fixed dyanmics test
changed output of contgen tests
fixed noise generator tests
Running tests except deformer and simulation
Updated tests for dynsim deformer
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Updated dynsimdeformer class and tests
Merge branch 'update-img-constructor' into petmr-simulation
Added reorienting to MR data deformer
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Deleted size output
Deactivated all tests except reorienting
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Added test in python for iamge geometry
Modified tests to write the nii files correctly
Merge branch 'master' of https://github.com/SyneRBI/SIRF into fix-mr-geometry
Added test for reorientation of mr images
Calculates MR geometry less wrong for stacks of 2D slices
Changed GeometricalInfo::operator==() to allow flaot comparison
Merge branch 'fix-mr-geometry' into petmr-simulation
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Changed reorient and set_up_geom_info
Added 3D reorientation test with bad test data path
Revert "Added 3D reorientation test with bad test data path"
Merge branch 'fix-mr-geometry' into petmr-simulation
Reorienting PET images prior to deformation with mvfs
Running all simulation tests
Switched off reorientation of PET images
Made PET images move by copying resampler output
Renamed test
deleted test of memory management
Renamed methods
commented in dynamic simulation methods
formatted tests
Formatted tests
moved add_dynamics and write_groundtruth to abstract claass
Deleted old simulation
Deleted filename interface for simulation
Using all tests now
Corrected interface
Restructured tests
Switched to coilsensitvitiesvector in mock gaussian csm aux fun
Corrected fallout from changing CSM mock type
Changed interface of noise generator
Switched to having a sptr-instance of acquisition data to store simulation data into
Changed sett interface to shared ptr
Changed interface of dynamics intersect data
Switched to all sptrs in dyn sim
Merge branch 'master' of https://github.com/SyneRBI/SIRF into fix-mr-geometry
Forgot to save before commit merge
Edited some comments
Added random parameters for reorientation test
Changed input files for python reorientation test
Updated comment
Reordered setup steps for 2D mr image
Modified output data path
Merge branch 'fix-mr-geometry' into petmr-simulation
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Merge branch 'master' of https://github.com/SyneRBI/SIRF into fix-mr-geometry
Updated test to store data incorrect location
Added files to reconstruct simulation output
Fixed position computation of 2D MR images
Cleaned mr cpp tests [ci skip]
Modified MR dicom python test
Scales output image before writing dicom in test
Merge branch 'master' of https://github.com/SyneRBI/SIRF into fix-mr-geometry
Merge branch 'fix-mr-geometry' into petmr-simulation
Implemented python tests for simulation in CMake
Added Python test to recon simulation test output
Updated simulation function to work without motion dynamics
Changed interface of adding dynamics
Changed location of preprocess c++ function to gadgetron_x
Ensured ability to run multiple tests from the same file in python tests
Added statics and dynamic test for simulation
Mock signals now start at t=0
Added second test to recon dynamic simualtion test data
Renamed simulate_dynamics to simulate_data
Renamed simulate_dynamics to simulate_data
Added test to run simulation with
Added Python file for simulation and SWIG in CMAKE
CHanged # of motion states in 5d motion test
added pysimulation package to aliasing
Added time sorting to mock sawtooth signal
Fixed 5D motion bug
Added recon of 5D test output
Changed name of interface funtion for dyn sim construcotr
Got working Python constructor for simulation
Wrapped setter for template acquisitions
Updated test for recon of simulation data
Wrapped everything necessary for a static simulation
Modified test to simulate static random tissues
Added single dvf addition to motion dynamics
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Included stddef header to allow size_t defines
Switched location of the header for size_t declaration
Added test for MR simulations in python
Deleted test for individual mr simulations
Continued wrapping of dynamics
Renamed aMRDynamic to MRDynamic
Changed interface of bin_mr_acquisisionts
Wrappend binning of acuisitions
Fixed bug
Updated test to pass sources for dvf correctly
Got running test for dyn mo sim but output is empyt
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Added constness of passed surrogate signal to setter
fixed type for setting up surrogate signal
fixed typoe error after merge
extended mr simulation test
Added test for c-interface from C++
changed bin number to type unsinged
Added getter for num ber of signal points in python
Added test for setter for dynamic signal
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Took care of merge fallout
Renamed aPETDynamic to PETDynamic
Added signal and bin processors
Deleted uncesseray method
Switched tests to test processors
Shifted whole functionality of dynamic into new class
Updated method name
Updated method name
Updated dynamics classes
Renamed the motoin dynamics to processors
COntinued change of interface
Changed namespaces for dynamcis test
did nothing practically
New dynamic interface
Brougth new interface to compile
Updated python to new inheritance scheme
fixed segfault by making methods virtual
Updated tests to write niftis
Renamed for recon to run after smuilation
Deleted redundant function
deleted comment blocks
Added storing of GT to python tests
Added C test to convert input data from h5 into nii
Added example for patientdata simulation
Extended example to recon data on the fly
Renamed variable in python test
Finalised 3D cartesian example
Switched to time unit of secodns
udpated tests
Renamed variabels with time unit suffix
Switched to settingg dynamics rawdata inside the simulation
Updated test
Added some comments to clarify function outcome
added dynsim deformer memeber to simulation
Enabled setting template image in deformer
Deleted access to setter of rawdata for dynamics
Differentiation between acquisition and contrast rawdata
Corrected segfault for wrong calls in dynsim deformer
Updated test for new interface
Added setter for images in contrastgenerator
Added test for geometry and transfnormations for siulation data
Updated simualtion example to work with diff sets of acquisition data
Added shift in z-direction to transformations during rawdata acquiistion
Compute CSM based on acquisition template rawdata
Swtiched to affine transform to compute offset in dynsim deformer
Added interface to pass external affine trafo to simultion
Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
Changed arguments to be passed correctly
Merge branch 'fix-afftrafo-constructor' into petmr-simulation
Added formatter to make sure numpy arrays get passed correctly
Merge branch 'fix-afftrafo-constructor' into petmr-simulation
Fixed interface for passing offset trafo to simulation
Added euler parameters to python example
Deleted commented line

File Changes

Patch Links:

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Kris Thielemans

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Aug 30, 2021, 4:25:52 AM8/30/21

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@KrisThielemans requested changes on this pull request.

some housekeeping comments to set you going :-)

Also, rename include/sirf/cDynamicSimulation to include/sirf/DynamicSimulation as for all the others

In .gitattributes:

> +src/xDynamicSimulation/cDynamicSimulation/Testing/tests_dynamicsimulation.h merge=ours
+src/xDynamicSimulation/cDynamicSimulation/Testing/tests_dynamicsimulation.cpp merge=ours
+src/xGadgetron/cGadgetron/gadgetron_data_containers.h merge=ours
+src/xGadgetron/cGadgetron/gadgetron_data_containers.cpp merge=ours

do we really need this? seems weird to keep it on master.

In .gitignore:

> @@ -1,6 +1,11 @@
 ## Ignore Visual Studio temporary files, build results, and
 ## files generated by popular Visual Studio add-ons.
 
+# CMake
+*.cmake

definitely not ignore those! We have them our own

In .gitignore:

> @@ -20,6 +25,14 @@ bld/
 [Bb]in/
 [Oo]bj/
 
+# CMake
+CMakeCache.txt
+CMakeFiles*

aargh. ignore CMakeFiles.txt ?

I think you're trying to ignore files because you did an "in-source" build, which isn't recommended in any case.

In .gitignore:

> @@ -20,6 +25,14 @@ bld/
 [Bb]in/
 [Oo]bj/
 
+# CMake
+CMakeCache.txt
+CMakeFiles*
+
+# Makefiles
+**/Makefile*

who knows, maybe we have some valid ones at some point

In README.md:

> @@ -1,3 +1,4 @@
+<<<<<<< HEAD

conflict marker

In README.md:

> @@ -34,6 +35,13 @@ what was found/built:
 
 [coveralls-badge]: https://coveralls.io/repos/github/CCPPETMR/SIRF/badge.svg?branch=master
 [coveralls]: https://coveralls.io/github/CCPPETMR/SIRF?branch=master
+<<<<<<< HEAD

here as well (and below)

In cmake/setup.py.cmake:

>        install(CODE "execute_process(COMMAND\n\
+<<<<<<< HEAD

conflict marker

In examples/Python/Simulation/cartesian_3D_simulation.py:

> @@ -0,0 +1,193 @@
+'''
+bla bla

maybe not

In examples/Python/Simulation/cartesian_3D_simulation.py:

> @@ -0,0 +1,193 @@
+'''
+bla bla
+
+Usage:
+cartesian_3D_simulation.py [--help | options]
+
+Options:
+--non-interactive           do not show plots
+'''
+
+## SyneRBI Synergistic Image Reconstruction Framework (SIRF).
+## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC.
+## Copyright 2015 - 2017 University College London.
+## Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt.

surely not

In examples/Python/Simulation/cartesian_3D_simulation.py:

> +	mvfs = read_motionfields(fpath_prefix)
+
+	for m in mvfs:
+		modyn.add_displacement_field(m)
+
+
+def get_normed_surrogate_signal(t0_s, tmax_s, Nt, f_Hz):
+
+	t_s = np.linspace(t0_s, tmax_s, Nt)
+	sig = 0.5 * (1 + np.sin( 2*np.pi*f_Hz*t_s))
+	return t_s, sig
+
+
+def main():
+
+	fpath_testdata_prefix = '/media/sf_CCPPETMR/TestData/'

will have to change

In examples/Python/Simulation/simulation_2D_subsampling.py:

> @@ -0,0 +1,156 @@
+'''
+bla bla

I guess everywhere

In src/CMakeLists.txt:

> @@ -151,4 +151,14 @@ else()
   endif()
 endif()
 
+##########################################################################
+#                              Simulation                                #
+##########################################################################
+option(DISABLE_Simulation "Disable building the SIRF simulation package" OFF)
+if (DISABLE_Simulation)
+  message(STATUS "Gadgetron support disabled.")

wrong message

In src/iUtilities/pyiutilities.py:

> +# This file was automatically generated by SWIG (http://www.swig.org).
+# Version 3.0.8

SWIG generated files should not be checked in

In src/xDynamicSimulation/CMakeLists.txt:

> +if (CMAKE_VERSION VERSION_LESS "3.1")
+   set (CMAKE_CXX_FLAGS "--std=c++11 ${CMAKE_CXX_FLAGS}")
+else ()
+   set (CMAKE_CXX_STANDARD 11)
+endif ()

can't see we need that in this file

In src/xDynamicSimulation/cDynamicSimulation/CMakeLists.txt:

> +if (SIRF_INSTALL_DEPENDENCIES AND WIN32)
+    set(Boost_DLL_DIR ${Boost_LIBRARY_DIR_RELEASE})
+    message(STATUS "Install boost shared libraries from ${Boost_DLL_DIR} ")
+	foreach (__boost_lib system filesystem thread date_time chrono)
+	   file(GLOB Boost_DLL "${Boost_DLL_DIR}/boost_${__boost_lib}*.dll")
+       install( FILES ${Boost_DLL} DESTINATION bin )
+	endforeach()
+  endif()

probably shouldn't be here

In src/xDynamicSimulation/cDynamicSimulation/CMakeLists.txt:

> @@ -0,0 +1,66 @@
+#========================================================================
+# Author: Johannes Mayer
+# Date: 15.03.2018
+#=========================================================================
+
+add_definitions(-DBOOST_ALL_NO_LIB)

probably shouldn't be here

In src/xDynamicSimulation/cDynamicSimulation/CMakeLists.txt:

> +include_directories(${PROJECT_SOURCE_DIR}/src/common/include)
+include_directories(${PROJECT_SOURCE_DIR}/src/xGadgetron/cGadgetron)
+include_directories(${PROJECT_SOURCE_DIR}/src/xSTIR/cSTIR)
+include_directories(${PROJECT_SOURCE_DIR}/src/Registration/Reg)
+include_directories(${PROJECT_SOURCE_DIR}/src/iUtilities)
+include_directories("${GADGETRON_INCLUDE_DIR}/../")

probably shouldn't be here as should be taken care of by target_link_libraries

In src/xDynamicSimulation/cDynamicSimulation/CMakeLists.txt:

> +# Note: cannot use ISMRMRD_LIBRARIES on Windows as it generally contains 
+# a list of filenames with spaces. There doesn't seem to be a way to pass this through (strange).
+# Luckily, we know what libraries it uses

delete

In src/xDynamicSimulation/cDynamicSimulation/auxiliary_input_output.cpp:

> @@ -0,0 +1,113 @@
+/* ================================================
+
+Author: Johannes Mayer
+Date: 2018.04.05
+Institution: Physikalisch-Technische Bundesanstalt Berlin

will need standard SIRF header with AL2 license etc

In src/xDynamicSimulation/cDynamicSimulation/cdynamicsimulation.cpp:

> @@ -0,0 +1,363 @@
+/*
+SyneRBI Synergistic Image Reconstruction Framework (SIRF)
+
+Copyright 2021 Physikalisch-Technische Bundesanstalt (PTB)

add yourself as author

In src/xDynamicSimulation/cDynamicSimulation/cdynamicsimulation.cpp:

> +// extern "C"
+// void*
+// cGT_ISMRMRDAcquisitionsFromFile(const char* file)
+// {
+// 	if (!file_exists(file))
+// 		return fileNotFound(file, __FILE__, __LINE__);
+// 	try {
+// 		shared_ptr<MRAcquisitionData>
+// 			acquisitions(new AcquisitionsVector);
+// 		acquisitions->read(file);
+// 		return newObjectHandle<MRAcquisitionData>(acquisitions);
+// 	}
+// 	CATCH;
+// }
+

delete

Johannes Mayer

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Sep 1, 2021, 11:43:07 AM9/1/21

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@johannesmayer pushed 27 commits.

c2638e9 Templatisation of gridder for arbitrary dimensions
de70a6d Templatized the trajectory prep
9d2b7e8 Fixed wrong dimensionality bug for new rpe computation
c3dc16e Added trajectory prep for 2D linear radial acquisition
128588d Wrapped 2D linear radial traj prep
64e75a4 Added example for 2D radial encoding
99e4565 Added backward for 2D radial operator
d50974a Added placeholder for radial dcw
f1fe8a3 Added 2D density compensation
64c8afd Undid prints
dcb80ef Added interface to get a sorted trajectory instead of the order in the acquisition container
1ad2588 Making sure that the getter gives you all trajectory points from python
1c0a10c Implemented 2D stack of stars fwd and bwd
a855d51 Deleted old print
4bf38b3 Added plotting of csm into 2d radial example
5222253 Updated calls to trajectory prep for rpe
634089e Deleted bad assert for 2d radial operation
8859585 Added interface for radial examples to rpe script
6836df0 Fixed bug in noncartesian sense example
45d8a86 Moved radial examples all into noncartesian file
4595857 Merge branch 'radial-2D-encoding' into petmr-simulation
0a6bcdf Added reorientation of MR volumes into segmentation after contrast generation
ec149e3 Added resampling into template acquisition image without motionfields
dee2cef Making subset with the appropriate acuqisitions info
f43716b added some try_callings to catch exceptions
9fb5267 Added special case to deformer when nothing moves
7719651 Added radial option to simulation

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Johannes Mayer

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Sep 6, 2021, 11:46:50 AM9/6/21

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@johannesmayer pushed 14 commits.

491e195 Fixed bug for 2D forward model for undersampled data
1dc1fa1 Reverted unique z trajectory getter
1654e5c wrote nonworking version of backward and forward
19f7f6e Added more plots for noncartesian recon example
9f025da Corrected backward methods for 2d radial
1158824 Continued debugging 2d radial forward
d4a475c Added test for adjointness of radial 2d model
066e23d Rewrote fwd and bwd
7368d6d Copied img data content from getDataPtr instead of memcpy
ce73185 added function to extract slice encode step 2 subset index
74d897b deleted virtual for definition of function
6961887 Modified fordward to satisfy the adjointness test
38cfd7c Commented in the MR tests
64ba984 Merge branch 'radial-2D-encoding' into petmr-simulation

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Johannes Mayer

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Nov 15, 2021, 5:59:42 AM11/15/21

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@johannesmayer pushed 23 commits.

4c15439 Merge branch 'master' of https://github.com/SyneRBI/SIRF into radial-2D-encoding
dd62aad Added 2d golden angle to possible trajectory preparations
aa61aea Wrapped trajectory computation in Python
e563799 Got working version of golden angle reconstruction
24b57de Merge branch 'master' of https://github.com/SyneRBI/SIRF into radial-2D-encoding
cdaec32 Added documentation to trajectory classes
d195c34 Corrected title displayed in example script
b8b76d1 Renamed trajectory preparation implementations
ccbd5b6 Updated comments
d64760a Made the gadgetron nufft mutable
35cd062 Merge branch 'master' of https://github.com/SyneRBI/SIRF into fix-mr-geometry
7df20a3 Deleted obsolete test
f389a9f Updated comment
2c49585 Added check for float tolerance instead of == comparison
aa77667 Merge branch 'master' of https://github.com/SyneRBI/SIRF into fix-mr-geometry
6cd8ca0 Updated comment
6b8533a Merge branch 'master' of https://github.com/SyneRBI/SIRF into radial-2D-encoding
f1a963c Renamed SENSE into ConjugateGradient in example script
2405929 Added std prefix to uint16_t types
60eeec3 Used same container for cartesian and radial test data
83d6011 Merge branch 'radial-2D-encoding' into petmr-simulation
b903c7a Merge branch 'fix-mr-geometry' into petmr-simulation
eb38f34 Improved usability of example for 2d from 3d simulation

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Johannes Mayer

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Jan 3, 2022, 8:16:14 AM1/3/22

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@johannesmayer pushed 30 commits.

1c46c84 Added external contrast member to contrast generator
b83376c Made getter function const in tissue label mapper
2511979 Wrote mock external signal generator
6dc7443 Wrote test for external signal contrast mapping
7f90d31 Provided interface to map signal based on external input in mr contrast
34fbe0e Refactored motion-contrast simualtion loop
ad4e4e0 Added external contrast dynamics class
e282b0d did some whitespace/tabs cleanup
9133b0b Added function to motiondynamics to get mvf at timepoint
7eba8b3 Added test to run external contrast simulation on C++
c1d3593 Added compiling version of simulating external contrast signals
9922df9 fixed bug for missing return
819284f Added missing binning of external acquisitions
984be53 Fixed problem of not finding binned acuqisitions
6d17c46 Merge branch 'master' of https://github.com/SyneRBI/SIRF into add-ext-contrast
ce553ea Corrected accessing error on acquisition vector
18e1d0f Added function to push back single signal timepoint
889b587 Started implementing the external dynamic class in python
008c93b started adding c glue code for external contrast variations
fd43556 Added test for external contrast dynamics
5991c54 added helper class for python external signals
9d331e0 Wrapped external signal into c
04d5772 Updated test to use external contrast signal
e38de5d Added recon of simulation data as addition to test
db59edc Renamed method
5734cbb Renamed method
39d841f Added parallel code in contrast mapping
5fae741 Updated test to use XCAT
9f377ae Merge branch 'add-ext-contrast' into petmr-simulation
69708ce Started wrapping contrast dynamics into simulation

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Johannes Mayer

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Jan 3, 2022, 8:55:22 AM1/3/22

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@johannesmayer pushed 1 commit.

b3304b8 running version of contrast dynamics with bug in binning

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Johannes Mayer

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Jan 3, 2022, 11:26:34 AM1/3/22

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@johannesmayer pushed 2 commits.

bebd168 Changed to non-static contrast dynamic members
bb83a74 Cleaned up debuggin

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Johannes Mayer

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Jan 5, 2022, 8:34:59 AM1/5/22

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@johannesmayer pushed 3 commits.

0f1ddc4 Added method to discard data in acquisition object
bf15e50 Added method to discard data in acquisition object
0a9e952 Added reconstruction to python test

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Johannes Mayer

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Jan 5, 2022, 10:04:46 AM1/5/22

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@johannesmayer pushed 1 commit.

ecb1311 Reforamtting

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Johannes Mayer

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Jan 5, 2022, 11:29:15 AM1/5/22

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@johannesmayer pushed 1 commit.

cc1a7d6 switched of pragma parallels

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Johannes Mayer

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Jan 5, 2022, 12:54:19 PM1/5/22

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@johannesmayer pushed 1 commit.

783625c Enabled setting of spin density for tissue parameters

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Jan 7, 2022, 8:04:41 AM1/7/22

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@johannesmayer pushed 2 commits.

e4f1931 Corrected contrast simulation for wrong time scaling (sec instead of ms)
884bf7c Renamed temporary variables in loop

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Feb 1, 2022, 8:12:41 AM2/1/22

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@johannesmayer pushed 4 commits.

3fca946 Added simulation demo for non-cubic phantom
d369b73 Added example for external contrast
e05a680 Trigger GHA workflow
5a26ea8 Added code to parse tissue XML from Python

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Feb 1, 2022, 9:34:07 AM2/1/22

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@johannesmayer pushed 2 commits.

52712a6 Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
39318ee Leftover from merge

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Feb 2, 2022, 11:39:58 AM2/2/22

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@johannesmayer pushed 7 commits.

410ab00 Added prep script to examples to extract mr parameters from XML
af4ca23 Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
650134c Added script to simulate static mrf
767859c Ensured correct datatype of index passed to c level
a639718 Merge branch 'master' of https://github.com/SyneRBI/SIRF into fix-subset-access
4b993c7 Merge branch 'fix-subset-access' into petmr-simulation
2006c00 Updated example for external contast to have MRF

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Feb 2, 2022, 1:36:06 PM2/2/22

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@johannesmayer pushed 4 commits.

d01aa25 Added test and interface for saving groudn truth parameters maps
310689a Added test for contrast generator mapping tissue parameters
1a961ce updated test for new output class of images
8a47c38 Finished contrast generator parameter map creation

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Feb 3, 2022, 11:23:40 AM2/3/22

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@johannesmayer pushed 5 commits.

3d5ca1c renamed function
acc459e Added writing to dynamic simulation interface without resampling
4ae5d67 Added resampling into template coordinates to parameter maps groudn truths
43b903b deleted useless line
c9ae9e5 Added test to check 2d resampling

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Feb 3, 2022, 12:16:57 PM2/3/22

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@johannesmayer pushed 1 commit.

c9e2a8d Wrapped gr writer in python

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Feb 4, 2022, 12:18:50 PM2/4/22

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@johannesmayer pushed 5 commits.

4881597 Ensuring an empty target header after deserialize
19f224b Deleting temporary files before creating as ISMRMRD appends to files
855024a Merge branch 'fix-tempfile-overflow' into petmr-simulation
a514c68 Merge branch 'fix-deserialize-call' into petmr-simulation
70d7621 Added example for geometry

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Feb 7, 2022, 8:57:09 AM2/7/22

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@johannesmayer pushed 5 commits.

8c3bf96 Deleted unused code from deformer
d669d60 Updated example scripts
4884ee3 ensure that position is also set to zero
1b5a312 Deleted junk code in contrast generator
ef31af4 [ci skip] Updated examples for geometry

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Feb 11, 2022, 12:35:25 PM2/11/22

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@johannesmayer pushed 1 commit.

9756ff7 added example script for 3D RPE

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Feb 15, 2022, 3:49:36 AM2/15/22

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@johannesmayer pushed 1 commit.

469d383 [ci skip] Continued work on geometry of simulation erxample

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Feb 23, 2022, 10:54:24 AM2/23/22

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@johannesmayer pushed 4 commits.

5f7e661 Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
d032157 [ci-skip] return filenames of parametric maps of ground truth
c4a4fcf Calls warning if template acquisition is not set
bffc423 Calls warning if template acquisition is not set

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Feb 24, 2022, 1:55:12 PM2/24/22

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@johannesmayer pushed 4 commits.

cbb9700 Updated norming of acquisition orientation
55cb126 Added test for C++ mr geometry
f043013 rewrote dynsim deformer test to minimal geometry example
0bcea11 Modification of acquisition header with segmentation dimensions:

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Mar 1, 2022, 10:18:35 AM3/1/22

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@johannesmayer pushed 7 commits.

8c21a7a Added the acquisition setter function
c95ba42 Added setter for acquisition parameter in c
d07ee4b Added setter for acquisition index variables in python
8ee8554 Corrected typo
d433293 Merge branch 'master' of https://github.com/SyneRBI/SIRF into add-acquisition-setter
bf0088d Merge branch 'add-acquisition-setter' into petmr-simulation
d016a77 ensured passing of data types for snr is correct

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Mar 1, 2022, 11:31:29 AM3/1/22

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@johannesmayer pushed 5 commits.

ff8ace0 Passing the SNR as a float parameter
1519b2f Added outputs for noise labels
c2e8e53 Changed noise label data tyhpe from size_t to int
0bd675b ending program if contrast template is not set yet in generator
4b8112d [ci skip] Had to ste the acquisition after you add the noise

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Mar 1, 2022, 11:32:42 AM3/1/22

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@johannesmayer pushed 1 commit.

f3adc77 [ci skip] Cleaned up a bit

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Mar 2, 2022, 12:25:48 PM3/2/22

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@johannesmayer pushed 1 commit.

5c50b72 [ci-skip] Replaced wrong command for vector clearance

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Mar 14, 2022, 2:19:40 PM3/14/22

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@johannesmayer pushed 2 commits.

8fb6d26 Fixed bug for signal == 1 in cyclic dynamics
83d25bf [ci skip] Added set template function that sets both types simultaneously

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Mar 15, 2022, 10:10:57 AM3/15/22

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abda270 Added idx_corr to the dynamics class

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Mar 15, 2022, 2:08:32 PM3/15/22

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@johannesmayer pushed 3 commits.

c7599c0 Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
73d1106 [ci skip] Empty the acquisitions prior to motion binning
1a4c2f1 [ci skip]Added interface to get idx_corr. Problem with output, large numbers appear

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Mar 16, 2022, 6:42:53 AM3/16/22

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a380ed4 [ci skip]Implemented return of idx_corr for MR Dynamics objects

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Mar 16, 2022, 6:59:46 AM3/16/22

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e3ac2d4 [ci skip] Updated test and cleared output
4848558 [ci skip] Updated test and cleared output

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Mar 23, 2022, 1:14:57 PM3/23/22

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122bdc4 Changed time unit for external contrast

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Mar 24, 2022, 11:49:36 AM3/24/22

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b6d7159 Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
786be3a enable getting list of names associated with the labels

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Mar 29, 2022, 6:13:42 AM3/29/22

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@johannesmayer pushed 4 commits.

a235eda Added option to return labels
144b4dd Added displacement offset in dynsim deformer
3b9450f Added option to compute average surrogate signal
2be642f Storing labels as parameter ground truth

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Mar 29, 2022, 12:44:43 PM3/29/22

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@johannesmayer pushed 6 commits.

4a778d3 Updated tests for avg surrogate and vector ifelds
d4c49d3 Added assertion to make sure we have a signal before interpolationg
08fad2e Added average motion fields to gt offsetl
686595f Removed reorient for dispalcement fields. this is usually applied to segmentation anyway
315c40e Removed reorient for dispalcement fields. this is usually applied to segmentation anyway
633ba7a made avg surrogate isgnal function Virtual

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Mar 30, 2022, 11:48:54 AM3/30/22

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f2ca118 Added non-nearestneightbor reasmpler for labels

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May 23, 2022, 12:02:02 PM5/23/22

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@johannesmayer pushed 3 commits.

fb599e3 [ci skip] deleted unused function
2c207e8 Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
5177e7b Used typedef for datatype

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May 23, 2022, 1:23:46 PM5/23/22

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@johannesmayer pushed 2 commits.

8c0beb8 [ci skip] Added documentation to dynamics
2b46879 [ci skip] Added documentation

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May 24, 2022, 8:05:44 AM5/24/22

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b2df2ce [ci skip] Added documentation
66ddca5 [ci skip] deleted comment

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May 24, 2022, 9:57:50 AM5/24/22

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@johannesmayer pushed 3 commits.

00aaf3b Deleted old includes
c9ed355 [ci skip] put dynsim deformer into namespace sirf
8c86d42 [ci skip] Put dynamics into namespace sirf

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Kris Thielemans

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Jun 9, 2022, 5:04:17 AM6/9/22

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@KrisThielemans commented on this pull request.

In examples/Python/Simulation/preprocess_speedup_testdata.py:

> +    list_files = sorted(fpath_input.glob('mvf_*'))
+
+    for f in list_files:
+        print("loading {}".format(f))
+        
+        mvf = nib.load(str(f))
+        print("The input motoinfield has size {}".format(mvf.shape))
+
+        mvf = mvf.slicer[:,:,slab_start:slab_end,:]
+        print("The output motoinfield has size {}".format(mvf.shape))
+        
+        fname_output = str(prefix_output + folder_pattern + f.name)
+        print("Storing to {}".format(fname_output))
+        nib.save(mvf, fname_output)
+
+root_path = '/media/sf_CCPPETMR/TestData/Input/xDynamicSimulation/pDynamicSimulation/'

hard-coded

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Jun 14, 2022, 10:48:28 AM6/14/22

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@johannesmayer pushed 2 commits.

3ef5377 Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
e6a876f [ci skip] Added Documentation to python interface

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Jun 27, 2022, 4:56:45 AM6/27/22

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@johannesmayer pushed 1 commit.

ac09847 Printing info for only 100th line for external contrast simulations

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Jun 27, 2022, 6:50:41 AM6/27/22

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@johannesmayer pushed 1 commit.

0745b7e [ci skip] Suppressing SIRF Reg cout put

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Edoardo Pasca

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Feb 13, 2025, 5:29:17 AM2/13/25

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@paskino commented on this pull request.

In examples/Python/Simulation/simulate_3D_RPE.py:

> +    fpath_testdata_prefix = '/media/sf_CCPPETMR/TestData/'
+    input_fpath_prefix = fpath_testdata_prefix + 'Input/xDynamicSimulation/pDynamicSimulation/'
+    output_fpath_prefix = fpath_testdata_prefix + 'Output/xDynamicSimulation/pDynamicSimulation/'

hard coded paths are bad

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Edoardo Pasca

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Feb 13, 2025, 5:34:00 AM2/13/25

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@paskino commented on this pull request.

In src/xGadgetron/cGadgetron/cgadgetron.cpp:

> +	// else if  (sirf::iequals(param_name, "position"))
+	// 	acq.position() = dataFromHandle<float*>(val);
+	// else if  (sirf::iequals(param_name, "read_dir"))
+	// 	acq.read_dir() = dataFromHandle<float*>(val);
+	// else if  (sirf::iequals(param_name, "phase_dir"))
+	// 	acq.phase_dir() = dataFromHandle<float*>(val);
+	// else if  (sirf::iequals(param_name, "slice_dir"))
+	// 	acq.slice_dir() = dataFromHandle<float*>(val);
+	// else if  (sirf::iequals(param_name, "patient_table_position"))
+	// 	acq.patient_table_position() = dataFromHandle<float*>(val);

Why are these not read out?

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Edoardo Pasca

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Feb 13, 2025, 5:35:23 AM2/13/25

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@paskino commented on this pull request.

In src/xGadgetron/cGadgetron/gadgetron_data_containers.cpp:

> +    if(combined_img.items() > this->items() )
+        throw LocalisedException("The number of coilmaps is less than the number of images to which they should be applied to.",   __FILE__, __LINE__);