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Python implementations of GRAPPA-like algorithms.

Home Page: https://pygrappa.readthedocs.io/en/latest/

License: MIT License

Python 88.56% Shell 0.25% C++ 3.49% Cython 5.13% Meson 2.58%

mri grappa parallel-imaging python image-reconstruction sms grog sense

pygrappa's Introduction

About

Online documentation here

GRAPPA is a popular parallel imaging reconstruction algorithm. Unfortunately there aren't a lot of easy to use Python implementations of it or its many variants available, so I decided to release this simple package.

There are also a couple reference SENSE-like implementations that have made their way into the package. This is to be expected -- a lot of later parallel imaging algorithms have hints of both GRAPPA-and SENSE-like inspirations.

Installation should be quick:

pip install pygrappa

pygrappa's People

Contributors

Stargazers

Watchers

Forkers

photonsarefree poonono shahdloo zongjg xpjiang lihua199710 nadrx zimuhuo mylyu hdocmsu schmidt-jo abhishekpandey127 jiantaiz

pygrappa's Issues

Windows installation

Windows 10, python 3.7.3, pygrappa v0.4.0.

In clean virtual environment
command: pip install pygrappa

Output:

...
building 'pygrappa.cgrappa' extension
error: Microsoft Visual C++ 14.0 is required. Get it with "Microsoft Visual C++ Build Tools": https://visualstudio.microsoft.com/downloads/

BUG: radialgrappaop should use lamda0, not lamda

pygrappa/pygrappa/radialgrappaop.py

Line 131 in 025ed54

res = np.linalg.solve(RtR + lamda*np.eye(RtR.shape[0]), RtG)

TypeError: iteration over a 0-d array

validP array sometimes turns out to be a 0-d array and can't be iterated over. I don't know why this happens.

Automagically find the ACS

Given the assumption that the ACS region is a hyper-rectangle with origin at the center, we would like to be able to able to detect it inside of kspace instead of passing it separately in calib.

Useful for Siemens data which comes as kspace + calib when twixread is used
Without restriction that hyper-rectangle is at origin, this is a very hard problem with increasing dimensionality, so it would be reasonable to restrict to ndim<=3
Some work already done for 2D case in utils

Use numpy.distutils for build

Mimic numpy/scipy style for building C/C++ sources

Will make cross-platform build more robust

Unit tests

Basic unit tests to make sure things don't break too bad during development/maintenance

iGRAPPA RuntimeWarning

pygrappa/pygrappa/igrappa.py:128: RuntimeWarning: invalid value encountered in double_scalars
  p = Tp/(k*Fp)

Defination of kernel sizes not agree with most papers

First, thanks for such a great project. I really love using this toolbox.

I noticed this problem when using kernel size (5,5) at high acceleration factor (R), because the results were too poor. After increasing the kernel size to about R times, the results became normal. Then I checked the code, and found the kernel size is used as a region? Then the actual number of data points used to interpolate may be far less than the "kernel size". I believe that in most published papers, the kernel size means exactly how many points are used to interpolate the missing point.

Am I right?

VC-GRAPPA for nonsquare matrices

Tried doing a clever thing to quickly compute conjugate coils, but it will break for non-square matrices or square matrix with even size dimension

radial grappa op dies when traj not consistent

There's a consistency check meant to ensure that (kx, ky) is shaped correctly, but this dies on real traj data (usually single precision). Maybe add an option to skip check? Lower tolerance?

ENH: multidimensional data support for cgsense

cgsense can only handle 2d images currently, would be easy and useful to extent to n-dimensional reconstruction.

Online docs

Probably a static readthedocs Sphinx documentation

Use numpy style docstrings

Images with odd dimension seems to break GRAPPA

Cropping shepp_logan to an odd number in one dimension (i.e., 128x127) in examples seems to break GRAPPA recon.

even kernel sizes break

When an even kernel dimension is used, e.g., kernel_size=(4, 4), grappa function breaks. lustig_grappa can deal with this, however.

bad result in vcgrappa when R=3

I am quite confused...
the code in basic_vcgrappa.py is modified as

    kspace[1::3, ...] = 0
    kspace[2::3, ...] = 0

While the results are quite good when R equals to 2 or 4

API references missing cgrappa

Readthedocs missing pygrappa.cgrappa

Precision on the kernel size

Hi,

I wanted to have some clarifications on the kernel_size argument of the grappa methods.
Let's say that I undersample in the y direction, with a rate of 5, meaning that one line out of 5 in the y direction is sampled.

How should I set ky if I want to consider only the 2 neighbouring sampled lines to fill in a non-sampled line? I thought it should be 5, but with this number I am having weird results where not all the kspace undersampled lines are filled.

In the figure, the first image is the kspace grappa reconstruction, the second is the (retrospectively) undersampled kspace, and the third is the original ground truth kspace.

I used cgrappa with a kernel size of (5, 5).

If you want I can try to give you a reproducible example with the data I am using (fastMRI).

pip installation fails in Mac

env: macOS 1015.4
acOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.3 (clang-1103.0.32.59)
Target: x86_64-apple-darwin19.4.0

(base) abu:~ abu$ pip install pygrappa
Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Collecting pygrappa
Using cached https://pypi.tuna.tsinghua.edu.cn/packages/5c/c2/fd4532079321ae7cc88f8cf5fc96a96b00f918b162d803011d8f83e017c4/pygrappa-0.21.1.tar.gz
ERROR: Complete output from command python setup.py egg_info:
ERROR: Traceback (most recent call last):
File "", line 1, in
File "/private/var/folders/my/s_lbvtcn6nb3mylc5cvtp0240000gn/T/pip-install-xg7ghxo8/pygrappa/setup.py", line 8, in
from setup_helpers import get_build_ext_override
ModuleNotFoundError: No module named 'setup_helpers'
----------------------------------------
ERROR: Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/my/s_lbvtcn6nb3mylc5cvtp0240000gn/T/pip-install-xg7ghxo8/pygrappa/

API simplification

It would probably be best to group GRAPPA-like functions under one banner and SENSE-like things under another one instead of having a menagerie of functions scattered about the pygrappa namespace

Proposed:

res = pygrappa.grappa(kspace, calib=None, method='grappa', coil_axis=-1, options=None)

method specifies which flavor of GRAPPA to use for reconstruction:

grappa: vanilla GRAPPA with mdgrappa backend
tgrappa: TGRAPPA
etc.

options is a dictionary containing options specific to the chosen method, e.g.,:

lamda
time_axis
'fov'
etc.

Similarly, SENSE-like methods go under the umbrella:

res = pygrappa.sense(kspace, sens, coil_axis=-1, options=None)

PyGrappa Setup Barfs on CentOS 7

PyGrappa Setup Barfs on CentOS 7, python36.

Installing collected packages: pygrappa
  Running setup.py install for pygrappa ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python36 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-sm_cp7o2/pygrappa/setup.py'"'"'; __file__='"'"'/tmp/pip-install-sm_cp7o2/pygrappa/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-vyb4bb48/install-record.txt --single-version-externally-managed --compile --user --prefix=
         cwd: /tmp/pip-install-sm_cp7o2/pygrappa/
    Complete output (47 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.6
    creating build/lib.linux-x86_64-3.6/tests
    copying tests/test_basic_recon.py -> build/lib.linux-x86_64-3.6/tests
    copying tests/benchmark.py -> build/lib.linux-x86_64-3.6/tests
    copying tests/__init__.py -> build/lib.linux-x86_64-3.6/tests
    copying tests/test_validP_issue.py -> build/lib.linux-x86_64-3.6/tests
    creating build/lib.linux-x86_64-3.6/utils
    copying utils/disjoint_csm.py -> build/lib.linux-x86_64-3.6/utils
    copying utils/__init__.py -> build/lib.linux-x86_64-3.6/utils
    copying utils/gaussian_csm.py -> build/lib.linux-x86_64-3.6/utils
    creating build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/tgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/grappaop.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/slicegrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/vcgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/igrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/splitslicegrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/grappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/seggrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/hpgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/__init__.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/lustig_grappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    running build_ext
    building 'pygrappa.cgrappa' extension
    creating build/temp.linux-x86_64-3.6
    creating build/temp.linux-x86_64-3.6/src
    gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Isrc/ -I/usr/include/python3.6m -I/xxx/xxx/.local/lib/python3.6/site-packages/numpy/core/include -c src/cgrappa.cpp -o build/temp.linux-x86_64-3.6/src/cgrappa.o
    In file included from /xxx/xxx/.local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0,
                     from /xxx/xxx/.local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                     from /xxx/xxx/.local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from src/cgrappa.cpp:636:
    /xxx/xxx/.local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it with " \
      ^
    gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Isrc/ -I/usr/include/python3.6m -I/xxx/xxx/.local/lib/python3.6/site-packages/numpy/core/include -c src/get_sampling_patterns.cpp -o build/temp.linux-x86_64-3.6/src/get_sampling_patterns.o
    src/get_sampling_patterns.cpp: In function ‘std::map<long long unsigned int, std::vector<unsigned int> > get_sampling_patterns(int*, unsigned int, unsigned int, unsigned int, unsigned int)’:
    src/get_sampling_patterns.cpp:45:17: error: ‘stderr’ was not declared in this scope
             fprintf(stderr, "Something wild is happening with kernel size, choosing (ksx, ksy) = (5, 5).\n");
                     ^
    src/get_sampling_patterns.cpp:45:104: error: ‘fprintf’ was not declared in this scope
             fprintf(stderr, "Something wild is happening with kernel size, choosing (ksx, ksy) = (5, 5).\n");
                                                                                                            ^
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python36 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-sm_cp7o2/pygrappa/setup.py'"'"'; __file__='"'"'/tmp/pip-install-sm_cp7o2/pygrappa/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-vyb4bb48/install-record.txt --single-version-externally-managed --compile --user --prefix= Check the logs for full command output.

NL-GRAPPA can't import utils

utils module not included in pip install, breaks imports in init.py

grappa,py or cgrappa.py not working on anisotropic matrices

First, I am very impressed with your implementations.
However, when applying the grappa for my data which has image size of 300x192
And I found out that neither grappa.py or cgrappa.py (except for lustig_grappa) works on these images.
Thank you.

CI build tests

Continuous integration tests to make sure builds and unit tests pass before release

GROG primefac-fork

use_primefac option uses library which is not pip installable and which includes libraries not generally present on linux systems. Find another way to get prime factorizations?

igrappa doesn't return coil dimension

igrappa moves coil axis to back but never returns it to original position

Add link to readthedocs

Add link to readme pointing to the readthedocs page

Local utils package cannot be imported properly

Hi,

I just found that after pip installing this package, all my projects' local submodules located in ./utils cannot be imported properly. After uninstalling pygrappa they worked again. So I think this might because the utils package in grappa get the highest priority.

So I'm wondering is there any way to fix this instead of staying away from subfolder named 'utils' in all of my local projects? Thanks!

macOS installation via pip

Command: pip3 install pygrappa --user

Problems:

If cython and numpy are not installed, then the installation fails
On macOS, cython trying to use clang instead of gcc, compilation fails because cpp files

Regularly undersampled GRAPPA

@zaccharieramzi, some of the issues you've been noticing with runtime might be due to the extra work pygrappa does to make sure it works for any arbitrarily sampling pattern. A lot of work is spent finding out what the unique sampling patterns (geometries) are and where the targets need to be interpolated -- this could be done away with if regular under-sampling was assumed.

I do like that pygrappa can "just work": if you hand it a set of under-sampled data it will do a reasonable thing (with the newest addition of an ACS region finder, the user doesn't even need to supply a calibration region if it is embedded in the data). But for users that need more efficiency/speed, it would be nice to provide a GRAPPA implementation more in line with regular under-sampling, e.g. similar to the GRAPPA Recon Tools found here.

cgrappa breaks on 7T real data

7T knee data R=3 breaks cgrappa

Depreciation warning

It appears that everything calling cgrappa is getting the following the error:

DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead

Windows type errors

Compiling using new distutils branch on Windows 10 and running python -m pygrappa.examples.basic_radialgrappaop gives the following error:

ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long'

ndarray is not C-contiguous error, when using grog and switching the coil axis

Hi Nicholas,
thank you for this amazing python implementation!
I tried to use the grog and got an error, when changing the location of the coil axis.
This is because using np.moveaxis to move the coils to the back makes the ndarray not C-contiguous.
A fix would be to apply np.ascontiguousarray() after the np.moveaxis()-operation.

Best regards,
Olli

GROG doesn't support complex float

GROG should be be written as a templated function to deal with multiple datatypes, currently coded only for double types.

ValueError when using complex64 with cgrappa

Hi, thanks very much for this implementation.

I tried to use cgrappa with np.complex64 data and got the following error:

ValueError                                Traceback (most recent call last)
<ipython-input-4-2802ffa5c73b> in <module>
     12 # coil_axis=-1 is default, so if coil dimension is last we don't
     13 # need to explicity provide it
---> 14 res = cgrappa(kspace, calib, kernel_size=(5, 5))
     15 sx, sy, ncoils = res.shape[:]

src/cgrappa.pyx in cgrappa.cgrappa()

ValueError: Buffer dtype mismatch, expected 'double complex' but got 'complex float'

The code to reproduce the error is the following:

from pygrappa import cgrappa 
import numpy as np 

kspace = np.random.normal(size=[640, 372, 15]) 
kspace = kspace.astype(np.complex64) 


sx, sy, ncoils = kspace.shape[:] # center 20 lines are ACS 
ctr, pd = int(sy/2), 10 
calib = kspace[:, ctr-pd:ctr+pd, :].copy() # call copy()! 

# coil_axis=-1 is default, so if coil dimension is last we don't 
# need to explicity provide it 
res = cgrappa(kspace, calib, kernel_size=(5, 5)) 
sx, sy, ncoils = res.shape[:]

CI error for python 3.5

pygrappa/igrappa.py:151: in igrappa
    W = {key:(1 - p)*Wn0 + p*W0 for (key, Wn0), (_, W0) in zip(Wn.items(), W.items())}
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

.0 = <zip object at 0x7fd4b073ce88>

>   W = {key:(1 - p)*Wn0 + p*W0 for (key, Wn0), (_, W0) in zip(Wn.items(), W.items())}
E   ValueError: operands could not be broadcast together with shapes (24,4) (40,4)

pygrappa/igrappa.py:151: ValueError
_ TestiGRAPPA.test_recon_shepp_logan2d_M30_N32_nc4_calib2d_cM10_cN10_undersample_y2_complex64 _

Keeping calibration weights for reuse?

Thanks so much for sharing this code - it's just what I've been looking for as I'm trying to migrate my projects away from being tied to MATLAB.

For my particular application I have a whole series of 3D volumes that need 2D GRAPPA reconstruction using the same calibration pre-scan. Do you already have a way of handling this, so the weights don't need to be recalculated for each volume? - I couldn't spot this by scanning through the code.

skimage.util.pad not available

Recent install fails due to the latest scikit-image release: https://github.com/scikit-image/scikit-image/releases which dropped skimage.util.pad.
Should be possible to fix this by replacing it with np.pad.

Memory Allocation

Hello,

I tried to use your code to reconstruct 3D anatomical brain MRI data of 1mm iso resolution with the mdgrappa function, it works well even if it is time-consuming, however when going to 0.7mm data with a large matrix (252, 52, 350, 256), and 52 the number of coils. ACS built-in (252, 52, 33, 256), the program crashes as it tries to allocate 471 GB of Ram. Do you please have an optimized version of your code to manage better the compute server resources?

The configuration I have:

128 CPU cores.
512 GB RAM, with 35x GB on SWP
32 GB GPU in VRAM.

Thank you,
Zakaria

ERROR when installing pygrappa in a singularity image

I am trying to have pygrappa installed in a singularity image, and I have the following error when installing:

Building wheels for collected packages: pygrappa
  Building wheel for pygrappa (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-c7s46can/pygrappa/setup.py'"'"'; __file__='"'"'/tmp/pip-install-c7s46can/pygrappa/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-vq3t3qkm
       cwd: /tmp/pip-install-c7s46can/pygrappa/
  Complete output (109 lines):
  running bdist_wheel
  running build
  running config_cc
  unifing config_cc, config, build_clib, build_ext, build commands --compiler options
  running config_fc
  unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
  running build_src
  build_src
  building extension "pygrappa.cgrappa" sources
  building extension "pygrappa.grog_powers" sources
  building extension "pygrappa.grog_gridding" sources
  build_src: building npy-pkg config files
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.6
  creating build/lib.linux-x86_64-3.6/benchmarks
  copying benchmarks/__init__.py -> build/lib.linux-x86_64-3.6/benchmarks
  copying benchmarks/benchmark.py -> build/lib.linux-x86_64-3.6/benchmarks
  creating build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/cgsense.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/grappa_kdtree.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/igrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/lustig_grappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/simple_pruno.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/ttgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/__init__.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/gfactor.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/radialgrappaop.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/seggrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/pruno.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/mdgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/kernels.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/nlgrappa_matlab.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/nlgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/hpgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/slicegrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/sense1d.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/splitslicegrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/ncgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/tgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/pars.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/kspa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/grappaop.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/grog.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/vcgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  copying pygrappa/grappa.py -> build/lib.linux-x86_64-3.6/pygrappa
  creating build/lib.linux-x86_64-3.6/utils
  copying utils/__init__.py -> build/lib.linux-x86_64-3.6/utils
  copying utils/radial_sms_sim.py -> build/lib.linux-x86_64-3.6/utils
  copying utils/gridder.py -> build/lib.linux-x86_64-3.6/utils
  copying utils/find_acs.py -> build/lib.linux-x86_64-3.6/utils
  copying utils/disjoint_csm.py -> build/lib.linux-x86_64-3.6/utils
  copying utils/findRectangle2d.py -> build/lib.linux-x86_64-3.6/utils
  copying utils/gaussian_csm.py -> build/lib.linux-x86_64-3.6/utils
  creating build/lib.linux-x86_64-3.6/pygrappa/tests
  copying pygrappa/tests/test_mdgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
  copying pygrappa/tests/__init__.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
  copying pygrappa/tests/test_igrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
  copying pygrappa/tests/test_vcgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
  copying pygrappa/tests/test_hpgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
  copying pygrappa/tests/test_cgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
  copying pygrappa/tests/helpers.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
  copying pygrappa/tests/test_grappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
  creating build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_splitslicegrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_gfactor.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_nlgrappa_matlab.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_gridding.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/mdgrappa_autofind_calib.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/inverse_grog.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_tgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_cgsense.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_grappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/__init__.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_mdgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_pars.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/primefac_grog_cardiac.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/primefac_grog.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_hpgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/use_memmap.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_grappaop.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_radialgrappaop.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/bart_pars.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/7t_knee_data.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_vcgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_nlgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/tikhonov_regularization.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_ttgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/bart_kspa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_ncgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_seggrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_sense1d.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_cgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_igrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  copying pygrappa/examples/basic_slicegrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
  running build_ext
  customize UnixCCompiler
  customize UnixCCompiler using build_ext
  customize UnixCCompiler
  customize UnixCCompiler using build_ext
  building 'pygrappa.cgrappa' extension
  compiling C++ sources
  C compiler: x86_64-linux-gnu-g++ -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
  
  creating build/temp.linux-x86_64-3.6/src
  compile options: '-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I./src/ -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
  x86_64-linux-gnu-g++: ./src/cgrappa.cpp
  x86_64-linux-gnu-g++: ./src/get_sampling_patterns.cpp
  error: Command "x86_64-linux-gnu-g++ -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I./src/ -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c ./src/cgrappa.cpp -o build/temp.linux-x86_64-3.6/src/cgrappa.o -MMD -MF build/temp.linux-x86_64-3.6/src/cgrappa.o.d" failed with exit status 127
  ----------------------------------------
  ERROR: Failed building wheel for pygrappa
  Running setup.py clean for pygrappa
Failed to build pygrappa
Installing collected packages: scipy, six, cycler, kiwisolver, pyparsing, python-dateutil, matplotlib, tqdm, pillow, imageio, tifffile, PyWavelets, decorator, networkx, scikit-image, ssfp, phantominator, pygrappa
    Running setup.py install for pygrappa ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-c7s46can/pygrappa/setup.py'"'"'; __file__='"'"'/tmp/pip-install-c7s46can/pygrappa/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-7hvszict/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.6/pygrappa
         cwd: /tmp/pip-install-c7s46can/pygrappa/
    Complete output (109 lines):
    running install
    running build
    running config_cc
    unifing config_cc, config, build_clib, build_ext, build commands --compiler options
    running config_fc
    unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
    running build_src
    build_src
    building extension "pygrappa.cgrappa" sources
    building extension "pygrappa.grog_powers" sources
    building extension "pygrappa.grog_gridding" sources
    build_src: building npy-pkg config files
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.6
    creating build/lib.linux-x86_64-3.6/benchmarks
    copying benchmarks/__init__.py -> build/lib.linux-x86_64-3.6/benchmarks
    copying benchmarks/benchmark.py -> build/lib.linux-x86_64-3.6/benchmarks
    creating build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/cgsense.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/grappa_kdtree.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/igrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/lustig_grappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/simple_pruno.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/ttgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/__init__.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/gfactor.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/radialgrappaop.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/seggrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/pruno.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/mdgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/kernels.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/nlgrappa_matlab.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/nlgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/hpgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/slicegrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/sense1d.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/splitslicegrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/ncgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/tgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/pars.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/kspa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/grappaop.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/grog.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/vcgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    copying pygrappa/grappa.py -> build/lib.linux-x86_64-3.6/pygrappa
    creating build/lib.linux-x86_64-3.6/utils
    copying utils/__init__.py -> build/lib.linux-x86_64-3.6/utils
    copying utils/radial_sms_sim.py -> build/lib.linux-x86_64-3.6/utils
    copying utils/gridder.py -> build/lib.linux-x86_64-3.6/utils
    copying utils/find_acs.py -> build/lib.linux-x86_64-3.6/utils
    copying utils/disjoint_csm.py -> build/lib.linux-x86_64-3.6/utils
    copying utils/findRectangle2d.py -> build/lib.linux-x86_64-3.6/utils
    copying utils/gaussian_csm.py -> build/lib.linux-x86_64-3.6/utils
    creating build/lib.linux-x86_64-3.6/pygrappa/tests
    copying pygrappa/tests/test_mdgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
    copying pygrappa/tests/__init__.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
    copying pygrappa/tests/test_igrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
    copying pygrappa/tests/test_vcgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
    copying pygrappa/tests/test_hpgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
    copying pygrappa/tests/test_cgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
    copying pygrappa/tests/helpers.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
    copying pygrappa/tests/test_grappa.py -> build/lib.linux-x86_64-3.6/pygrappa/tests
    creating build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_splitslicegrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_gfactor.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_nlgrappa_matlab.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_gridding.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/mdgrappa_autofind_calib.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/inverse_grog.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_tgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_cgsense.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_grappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/__init__.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_mdgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_pars.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/primefac_grog_cardiac.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/primefac_grog.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_hpgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/use_memmap.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_grappaop.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_radialgrappaop.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/bart_pars.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/7t_knee_data.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_vcgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_nlgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/tikhonov_regularization.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_ttgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/bart_kspa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_ncgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_seggrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_sense1d.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_cgrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_igrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    copying pygrappa/examples/basic_slicegrappa.py -> build/lib.linux-x86_64-3.6/pygrappa/examples
    running build_ext
    customize UnixCCompiler
    customize UnixCCompiler using build_ext
    customize UnixCCompiler
    customize UnixCCompiler using build_ext
    building 'pygrappa.cgrappa' extension
    compiling C++ sources
    C compiler: x86_64-linux-gnu-g++ -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
    
    creating build/temp.linux-x86_64-3.6/src
    compile options: '-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I./src/ -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c'
    x86_64-linux-gnu-g++: ./src/cgrappa.cpp
    x86_64-linux-gnu-g++: ./src/get_sampling_patterns.cpp
    error: Command "x86_64-linux-gnu-g++ -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I./src/ -I/usr/local/lib/python3.6/dist-packages/numpy/core/include -I/usr/include/python3.6m -c ./src/cgrappa.cpp -o build/temp.linux-x86_64-3.6/src/cgrappa.o -MMD -MF build/temp.linux-x86_64-3.6/src/cgrappa.o.d" failed with exit status 127
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3.6 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-c7s46can/pygrappa/setup.py'"'"'; __file__='"'"'/tmp/pip-install-c7s46can/pygrappa/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-7hvszict/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.6/pygrappa Check the logs for full command output.

I find it very hard to read and I am wondering whether this error rings a bell for anyone.

This is the singularity recipe file I used:

Bootstrap: docker
From: ubuntu:16.04


%help
    Singularity container for GRAPPA.

%post
  apt update -y
  apt install software-properties-common curl -y
  apt update -y
  add-apt-repository ppa:deadsnakes/ppa -y
  apt update -y
  apt install python3.6 python3.6-dev -y
  curl https://bootstrap.pypa.io/get-pip.py | python3.6
  pip3 install numpy
  pip3 install pygrappa

Build problem on M2 Mac with Meson 1.3.2

Please add the line
version = "0.26.1" to the [project] section of your pyproject.toml file

When I try to install your package using pip I get the following error:
pip install ./pygrappa
Processing ./pygrappa
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [53 lines of output]
+ meson setup /Users/doug/Documents/Development/Python/pygrappa /Users/doug/Documents/Development/Python/pygrappa/.mesonpy-mjp94sf1 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/Users/doug/Documents/Development/Python/pygrappa/.mesonpy-mjp94sf1/meson-python-native-file.ini
The Meson build system
Version: 1.3.2
Source dir: /Users/doug/Documents/Development/Python/pygrappa
Build dir: /Users/doug/Documents/Development/Python/pygrappa/.mesonpy-mjp94sf1
Build type: native build
Project name: pygrappa
Project version: 0.26.1
C compiler for the host machine: cc (clang 15.0.0 "Apple clang version 15.0.0 (clang-1500.1.0.2.5)")
C linker for the host machine: cc ld64 1022.1
C++ compiler for the host machine: c++ (clang 15.0.0 "Apple clang version 15.0.0 (clang-1500.1.0.2.5)")
C++ linker for the host machine: c++ ld64 1022.1
Host machine cpu family: aarch64
Host machine cpu: aarch64
Program cython found: YES (/private/var/folders/rf/h90r9kfj6gj7qtt8csjzlhgc0000gn/T/pip-build-env-5xrqw7ue/overlay/bin/cython)
Program python found: YES (/opt/homebrew/Caskroom/miniforge/base/bin/python3.10)
Found pkg-config: YES (/opt/homebrew/bin/pkg-config) 0.29.2
Run-time dependency python found: YES 3.10
Program pygrappa/utils/cythoner.py found: YES (/opt/homebrew/Caskroom/miniforge/base/bin/python3.10 /Users/doug/Documents/Development/Python/pygrappa/pygrappa/utils/cythoner.py)
Compiler for C supports arguments -Wno-maybe-uninitialized: NO
Compiler for C supports arguments -Wno-discarded-qualifiers: NO
Compiler for C supports arguments -Wno-empty-body: YES
Compiler for C supports arguments -Wno-implicit-function-declaration: YES
Compiler for C supports arguments -Wno-parentheses: YES
Compiler for C supports arguments -Wno-switch: YES
Compiler for C supports arguments -Wno-unused-label: YES
Compiler for C supports arguments -Wno-unused-variable: YES
Compiler for C++ supports arguments -Wno-cpp: YES
Compiler for C++ supports arguments -Wno-deprecated-declarations: YES
Compiler for C++ supports arguments -Wno-class-memaccess: NO
Compiler for C++ supports arguments -Wno-format-truncation: NO
Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES
Compiler for C++ supports arguments -Wno-sign-compare: YES
Compiler for C++ supports arguments -Wno-switch: YES
Compiler for C++ supports arguments -Wno-terminate: NO
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES
Compiler for C++ supports arguments -Wno-unused-function: YES
Compiler for C++ supports arguments -Wno-unused-local-typedefs: YES
Compiler for C++ supports arguments -Wno-unused-variable: YES
Compiler for C++ supports arguments -Wno-int-in-bool-context: YES
Build targets in project: 4

  pygrappa 0.26.1

    User defined options
      Native files: /Users/doug/Documents/Development/Python/pygrappa/.mesonpy-mjp94sf1/meson-python-native-file.ini
      buildtype   : release
      b_ndebug    : if-release
      b_vscrt     : md

  Found ninja-1.11.1.git.kitware.jobserver-1 at /private/var/folders/rf/h90r9kfj6gj7qtt8csjzlhgc0000gn/T/pip-build-env-5xrqw7ue/overlay/bin/ninja

  ('\x1b[31m',)meson-python: error: Required "project.version" field is missing and not declared as dynamic
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Adding the version line to my local copy allows the build to proceed.

Thanks.

Numpy required to install

Because cython needs location of numpy includes, numpy is imported by setup.py. This means installation will fail when numpy is not previously installed.

Python compatability

Currently setup.py enforces python version >= 3.6, could be lower.

ENH: revamp cgrappa

Need a better C++ implementation

Lack of template support locks users into complex128 (see #79)
Not well documented
Strange bugs with hacked fixes

Slow performance of mdgrappa

Hi,

Thank you for making this awesome project! Its has exactly the parts I missed for my project.
Unfortunately, I noticed mdgrappa to be quite slow even on a powerful pc.

Would it be possible to accelerate this function by making use of mkl or openblas?

Benchmarking/testing with real data

Create a database of real data to make sure performance is as expected
Run against existing implementations (e.g., Gadgetron)

Aliasing artifacts

Hi,
so I was trying to use grappa which worked as intented at first. But as soon as I started to create error images abs(reconstructed_image - reference_image) , I realized that grappa is producing aliasing artifacts.
The error is also reproducible with the example provided in examples/basic_grappa.py. Therefore you only have to add the following code at the end of the example:

reference_img = np.zeros((2*N, 2*N))
kk = 0
for idx in np.ndindex((2, 2)):
    ii, jj = idx[:]
    reference_img[ii*N:(ii+1)*N, jj*N:(jj+1)*N] = abs(imspace[..., kk])
    kk += 1
plt.imshow(abs(reference_img-res0), cmap='gray')
plt.show()

Before using pygrappa I was using PULSAR which is a grappa implementation for matlab and aliasing artifacts weren't a problem.
So my question is, am I missing something or is this a bug.

(I also tried using cgrappa and mdgrappa which led to the same results.)

Even kernel sizes break cgrappa implementation

I think it has to do with get_sampling_patterns.cpp implementation. Not giving expected size patterns back,