PET/MR Simulation#1007

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johannesmayer wants to merge 1327 commits intoSyneRBI:masterfrom

johannesmayer:petmr-simulation

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Commits on Jul 27, 2021

Merge branch 'master' of https://github.com/SyneRBI/SIRF into fix-mr-geometry
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Merge branch 'fix-mr-geometry' into petmr-simulation
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Implemented python tests for simulation in CMake
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Added Python test to recon simulation test output
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Updated simulation function to work without motion dynamics
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Changed interface of adding dynamics
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Changed location of preprocess c++ function to gadgetron_x
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Ensured ability to run multiple tests from the same file in python tests
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Added statics and dynamic test for simulation
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Mock signals now start at t=0
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Added second test to recon dynamic simualtion test data
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Commits on Jul 28, 2021

Renamed simulate_dynamics to simulate_data
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Renamed simulate_dynamics to simulate_data
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Added test to run simulation with
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Added Python file for simulation and SWIG in CMAKE
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CHanged # of motion states in 5d motion test
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Commits on Jul 29, 2021

added pysimulation package to aliasing
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Added time sorting to mock sawtooth signal
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Fixed 5D motion bug
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Added recon of 5D test output
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Changed name of interface funtion for dyn sim construcotr
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Got working Python constructor for simulation
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Wrapped setter for template acquisitions
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Updated test for recon of simulation data
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Wrapped everything necessary for a static simulation
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Modified test to simulate static random tissues
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Commits on Jul 30, 2021

Added single dvf addition to motion dynamics
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Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
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Included stddef header to allow size_t defines
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Switched location of the header for size_t declaration
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Added test for MR simulations in python
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Deleted test for individual mr simulations
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Continued wrapping of dynamics
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Renamed aMRDynamic to MRDynamic
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Changed interface of bin_mr_acquisisionts
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Wrappend binning of acuisitions
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Fixed bug
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Updated test to pass sources for dvf correctly
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Got running test for dyn mo sim but output is empyt
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Commits on Aug 17, 2021

Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
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Added constness of passed surrogate signal to setter
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fixed type for setting up surrogate signal
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fixed typoe error after merge
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extended mr simulation test
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Commits on Aug 18, 2021

Added test for c-interface from C++
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changed bin number to type unsinged
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Added getter for num ber of signal points in python
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Added test for setter for dynamic signal
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Commits on Aug 19, 2021

Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
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Took care of merge fallout
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Commits on Aug 20, 2021

Renamed aPETDynamic to PETDynamic
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Added signal and bin processors
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Deleted uncesseray method
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Switched tests to test processors
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Shifted whole functionality of dynamic into new class
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Updated method name
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Updated method name
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Updated dynamics classes
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Renamed the motoin dynamics to processors
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COntinued change of interface
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Commits on Aug 23, 2021

Changed namespaces for dynamcis test
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did nothing practically
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New dynamic interface
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Brougth new interface to compile
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Updated python to new inheritance scheme
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fixed segfault by making methods virtual
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Updated tests to write niftis
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Renamed for recon to run after smuilation
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Deleted redundant function
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deleted comment blocks
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Added storing of GT to python tests
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Added C test to convert input data from h5 into nii
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Commits on Aug 24, 2021

Added example for patientdata simulation
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Extended example to recon data on the fly
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Renamed variable in python test
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Finalised 3D cartesian example
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Commits on Aug 25, 2021

Switched to time unit of secodns
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udpated tests
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Renamed variabels with time unit suffix
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Switched to settingg dynamics rawdata inside the simulation
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Updated test
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Added some comments to clarify function outcome
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added dynsim deformer memeber to simulation
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Enabled setting template image in deformer
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Deleted access to setter of rawdata for dynamics
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Commits on Aug 26, 2021

Differentiation between acquisition and contrast rawdata
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Corrected segfault for wrong calls in dynsim deformer
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Updated test for new interface
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Added setter for images in contrastgenerator
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Added test for geometry and transfnormations for siulation data
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Updated simualtion example to work with diff sets of acquisition data
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Added shift in z-direction to transformations during rawdata acquiistion
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Compute CSM based on acquisition template rawdata
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Swtiched to affine transform to compute offset in dynsim deformer
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Commits on Aug 27, 2021

Added interface to pass external affine trafo to simultion
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Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
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Merge branch 'fix-afftrafo-constructor' into petmr-simulation
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Merge branch 'fix-afftrafo-constructor' into petmr-simulation
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Fixed interface for passing offset trafo to simulation
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Added euler parameters to python example
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Deleted commented line
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Commits on Aug 31, 2021

Merge branch 'radial-2D-encoding' into petmr-simulation
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Commits on Sep 1, 2021

Added reorientation of MR volumes into segmentation after contrast generation
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Added resampling into template acquisition image without motionfields
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Making subset with the appropriate acuqisitions info
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added some try_callings to catch exceptions
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Added special case to deformer when nothing moves
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Added radial option to simulation
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Commits on Sep 6, 2021

Merge branch 'radial-2D-encoding' into petmr-simulation
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Commits on Sep 23, 2021

Merge branch 'master' of https://github.com/SyneRBI/SIRF into fix-mr-geometry
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Deleted obsolete test
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Updated comment
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Added check for float tolerance instead of == comparison
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Commits on Oct 20, 2021

Merge branch 'master' of https://github.com/SyneRBI/SIRF into fix-mr-geometry
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Updated comment
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Commits on Oct 21, 2021

Merge branch 'radial-2D-encoding' into petmr-simulation
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Merge branch 'fix-mr-geometry' into petmr-simulation
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Added external contrast member to contrast generator
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Made getter function const in tissue label mapper
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Wrote mock external signal generator
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Wrote test for external signal contrast mapping
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Provided interface to map signal based on external input in mr contrast
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Commits on Oct 26, 2021

Refactored motion-contrast simualtion loop
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Added external contrast dynamics class
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did some whitespace/tabs cleanup
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Commits on Oct 27, 2021

Added function to motiondynamics to get mvf at timepoint
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Added test to run external contrast simulation on C++
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Added compiling version of simulating external contrast signals
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fixed bug for missing return
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Added missing binning of external acquisitions
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Commits on Oct 28, 2021

Fixed problem of not finding binned acuqisitions
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Merge branch 'master' of https://github.com/SyneRBI/SIRF into add-ext-contrast
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Corrected accessing error on acquisition vector
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Commits on Nov 3, 2021

Added function to push back single signal timepoint
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Started implementing the external dynamic class in python
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started adding c glue code for external contrast variations
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Commits on Nov 4, 2021

Added test for external contrast dynamics
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added helper class for python external signals
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Wrapped external signal into c
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Updated test to use external contrast signal
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Added recon of simulation data as addition to test
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Commits on Nov 5, 2021

Renamed method
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Renamed method
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Added parallel code in contrast mapping
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Updated test to use XCAT
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Commits on Nov 15, 2021

Improved usability of example for 2d from 3d simulation
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Commits on Jan 3, 2022

Merge branch 'add-ext-contrast' into petmr-simulation
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Started wrapping contrast dynamics into simulation
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running version of contrast dynamics with bug in binning
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Changed to non-static contrast dynamic members
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Cleaned up debuggin
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Commits on Jan 5, 2022

Added method to discard data in acquisition object
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Added method to discard data in acquisition object
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Added reconstruction to python test
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Reforamtting
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switched of pragma parallels
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Enabled setting of spin density for tissue parameters
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Commits on Jan 7, 2022

Corrected contrast simulation for wrong time scaling (sec instead of ms)
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Renamed temporary variables in loop
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Commits on Jan 20, 2022

Added simulation demo for non-cubic phantom
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Commits on Jan 31, 2022

Commits on Feb 1, 2022

Commits on Feb 2, 2022

Commits on Feb 11, 2022

added example script for 3D RPE
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Commits on Feb 15, 2022

[ci skip] Continued work on geometry of simulation erxample
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Commits on Feb 21, 2022

Merge branch 'master' of https://github.com/SyneRBI/SIRF into petmr-simulation
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Commits on Feb 24, 2022

Commits on Mar 2, 2022

[ci-skip] Replaced wrong command for vector clearance
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Commits on Mar 3, 2022

Fixed bug for signal == 1 in cyclic dynamics
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Commits on Mar 14, 2022

[ci skip] Added set template function that sets both types simultaneously
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Commits on Mar 16, 2022

Commits on Mar 23, 2022

Changed time unit for external contrast
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Commits on Mar 24, 2022

Commits on Mar 29, 2022

Commits on Mar 30, 2022

Added non-nearestneightbor reasmpler for labels
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Commits on Jun 14, 2022

Commits on Jun 27, 2022