Python wrappers for external BART computational imaging tools and internal libraries

Related tags

Image Processing python wrapper mri recon imaging
Overview

bartpy

BART-logo

Python bindings for BART.

Overview

This repo contains code to generate an updated Python wrapper for the Berkeley Advance Reconstruction Toolbox. The repo aims to expose command line tools and internal library functions to Python users.

The command line tools can be listed by running bart from the command line:

tools

Each of these has been exposed to the command-line via the bartpy.tools library:

code img

For users looking to integrate BART functions into existing Python workflows, and work fluidly with Numpy, SigPy, or other scientific packages, bartpy.tools should suffice!

[In Development] For developers looking to build Python tools using BART's internal C functions, the internal library functions expose BART's development libraries to the user. This is currently under production and not accessible via the master branch.

Requirements

BART version 0.7.00. It is important that running a bart command with the --interface option is successful. For example, you should see something like the following for running bart fft --interface:

interface

Ensure you have Python >= 3.6 and run pip install -r requirements.txt to install necessary dependencies.

Installation.

Once BART and the required libraries are installed, clone this repo.

To support the growth of BART with minimal overhead, the Python code is autogenerated from a user's BART installation. Run python3 setup.py install to build the tools library and install it. If successful, you should be able to import bartpy.tools and interface with the tutorials located in the demos folder.

Before working with the demos folder, unzip data.zip; this file contains the necessary datasets for the demos.

For Developers

The build_tools folder contains the necessary code for generating the tools wrappers.

Low-Level

Documentation on SWIG exists in the doc/ folder along with several links to SWIG documentation for developers interested in working with the experimental wrappers.

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Comments
  • Installation not working

    Installation not working

    Hi,

    Thank you for making bart more accassible by wrapping it for python! Unfortunately, I cant install it though. It seems that some code that is pulled during python setup.py install is erroneous

    SyntaxError: duplicate argument 'llambda' in function definition The file the duplicate definition of llambda is /miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/tools/tools.py", line 3286.

    Full stacktrace 
    [INFO] Complete
[INFO] Installing Library
running install
running build
running build_py
creating build
creating build/lib
creating build/lib/bartpy
copying bartpy/__init__.py -> build/lib/bartpy
creating build/lib/bartpy/utils
copying bartpy/utils/__init__.py -> build/lib/bartpy/utils
copying bartpy/utils/md_utils.py -> build/lib/bartpy/utils
copying bartpy/utils/cfl.py -> build/lib/bartpy/utils
creating build/lib/bartpy/tools
copying bartpy/tools/__init__.py -> build/lib/bartpy/tools
copying bartpy/tools/tools.py -> build/lib/bartpy/tools
creating build/lib/bartpy/wrapper
copying bartpy/wrapper/__init__.py -> build/lib/bartpy/wrapper
copying bartpy/wrapper/bart.py -> build/lib/bartpy/wrapper
running install_lib
copying build/lib/bartpy/__init__.py -> /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy
copying build/lib/bartpy/utils/__init__.py -> /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/utils
copying build/lib/bartpy/utils/md_utils.py -> /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/utils
copying build/lib/bartpy/utils/cfl.py -> /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/utils
copying build/lib/bartpy/wrapper/__init__.py -> /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/wrapper
copying build/lib/bartpy/wrapper/bart.py -> /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/wrapper
copying build/lib/bartpy/tools/__init__.py -> /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/tools
copying build/lib/bartpy/tools/tools.py -> /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/tools
byte-compiling /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/__init__.py to __init__.cpython-38.pyc
byte-compiling /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/utils/__init__.py to __init__.cpython-38.pyc
byte-compiling /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/utils/md_utils.py to md_utils.cpython-38.pyc
byte-compiling /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/utils/cfl.py to cfl.cpython-38.pyc
byte-compiling /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/wrapper/__init__.py to __init__.cpython-38.pyc
byte-compiling /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/wrapper/bart.py to bart.cpython-38.pyc
byte-compiling /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/tools/__init__.py to __init__.cpython-38.pyc
byte-compiling /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/tools/tools.py to tools.cpython-38.pyc
File "/home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy/tools/tools.py", line 3286
  def reconet(kspace, sensitivities, weights, ref_out, train=None, eval=None, apply=None, gpu=None, load=None, batch_size=None, iterations=None, normalize=None, network=None, resnet_block=None, varnet_block=None, unet=None, data_consistency=None, initial_reco=None, shared_weights=None, no_shared_weights=None, llambda=None, llambda=None, rss_norm=None, trajectory=None, pattern=None, adjoint=None, psf=None, export=None, mask=None, valid_data=None, train_loss=None, valid_loss=None, train_algo=None, adam=None, iPALM=None, load_memory=None, lowmem=None, test=None, export_graph=None, B=None):
  ^
SyntaxError: duplicate argument 'llambda' in function definition

running install_egg_info
Removing /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy-1.0-py3.8.egg-info
Writing /home/lukas/miniconda3/envs/cs/lib/python3.8/site-packages/bartpy-1.0-py3.8.egg-info```

</details>
    opened by lukasfolle 2
  • Typo and none check

    Typo and none check

    Hi Max,

    I took a look at your (really great!) notebooks and was surprised by the quality of the result in the Non-Cartesian notebook, especially compared to the Matlab example (image here). I found one typo, where you assign to trad_rad2 instead of overwriting traj_rad2. Fixing this gets rid of the ugly part at the bottom of the phantom.

    Additionally, I think that is not None is more common in the python community. But feel free to regard this if you don't like it.

    All the best, Christian

    opened by hcmh 0
  • Update to pics broke wrapper

    Update to pics broke wrapper

    I'm not sure if this project is still in active development, but I just wanted to submit an issue as a couple of recent changes in BART broke this wrapper

    The first change I'm aware of was 2bf1f14. This change only affected the pics tool, which will either fail silently and return incorrect output, or with a FileNotFound-error.

    Using, set_debug(True) I can see the following command to bart

    bart pics -t /tmp/tmpgm0hxcp9t /tmp/tmpgm0hxcp9kspace /tmp/tmpgm0hxcp9sensitivities /tmp/tmpgm0hxcp9output /tmp/tmpgm0hxcp9psf_export

    Manually running this command gives the following error

    ERROR: cmdline: too few or too many arguments

    MWE:

    import bartpy.tools as bart
import numpy as np

traj = bart.traj(x=256, y=144, r=True)
ksp = bart.phantom(t=traj, s=8)
img = bart.nufft(traj, ksp, i=True, t=True)
cart_ksp = bart.fft(img, u=True, bitmask=7)
sens, _ = bart.ecalib(cart_ksp, m=1)
pics_out = bart.pics(ksp, sens, t=traj, r=0.01)

print(np.array_equal(cart_ksp, pics_out))

    The final check (array_equal) will return True. This highlights an issue related to https://github.com/malits/bartpy/issues/3 Since temp file names are global, and the files are not cleared, any tool can fail silently but still return an output that was created by another tool. In this case, pics returns the output of bart.fft.

    The second change was 5393516 which breaks the wrapper completely and gives this error on import.

    File "/content/bartpy/bartpy/tools/tools.py", line 1717
def ictv(input, llambda, flags, flags, i=None, u=None):
SyntaxError: duplicate argument 'flags' in function definition
    opened by fyrdahl 0
  • Tempfile cleanup

    Tempfile cleanup

    Problem: It appears that temp files are accumulating when repeatedly running scripts using bartpy. This behavior is different from the "old" Python wrapper found within BART.

    Expected outcome: The wrapper should delete temp files

    Observed outcome: Temp files are not deleted

    Proposed solution: Either using context managers or keeping track of created files and deleting manually. I believe the latter is how the old wrapper does it. I would be happy to work on a patch for this, but I felt like it may involve some substantial changes, so I decided to open an issue for potential discussions first.

    MWE:

    import bartpy.tools as bart
phantom = bart.phantom()

    du -sh /tmp
for i in {1..100}
do
    python3 test.py
done
du -sh /tmp

    Output:

    264K    /tmp
14M     /tmp

    The same problem does not occur if using the "old" Python wrapper:

    from bart import bart
phantom = bart(1,'phantom')

    Output:

    264K    /tmp
264K    /tmp
    opened by fyrdahl 0
Owner
Max Litster
Berkeley CS + Math
Max Litster
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