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* Remove trailing spaces at end-of-line
* Add missing newline at end-of-file
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DimitriPapadopoulos committed Dec 6, 2022
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10 changes: 5 additions & 5 deletions README.md
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Python port of the Matlab mapVBVD tool for reading Siemens raw data 'twix' (.dat) files.

## Installation
`conda install -c conda-forge pymapvbvd`
or
`conda install -c conda-forge pymapvbvd`
or
`pip install pymapvbvd`

## Use

I have attempted to replicate the syntax of the original matlab code, but there are a few differences due to differing variable types.

This package contains a demo Jupyter notebook 'Demo.ipynb' which can be run on the demo data found in tests/test_data. There is unsuppressed water SVS MRS, from both a 7T VB scanner and a VE Prisma. There is also imaging data (3D GRE and EPI) from the [ISMRMRD test dataset](https://doi.org/10.5281/zenodo.33166).
This package contains a demo Jupyter notebook 'Demo.ipynb' which can be run on the demo data found in tests/test_data. There is unsuppressed water SVS MRS, from both a 7T VB scanner and a VE Prisma. There is also imaging data (3D GRE and EPI) from the [ISMRMRD test dataset](https://doi.org/10.5281/zenodo.33166).

Run using the following:
```
Expand All @@ -43,7 +43,7 @@ To retrieve the data in an unsorted format (i.e. Col,Cha,NAcq) use `twixObj.imag

Header information is contained in a dict `twixObj.hdr`
`twixObj.hdr.keys()` provides a list of the data containers.
Access them manually using e.g. `twixObj.hdr['MeasYaps']` or `twixObj.hdr.MeasYaps`.
Access them manually using e.g. `twixObj.hdr['MeasYaps']` or `twixObj.hdr.MeasYaps`.
These objects are in turn a final level of dictionaries. The actual data values can be accessed either manually using tuples of key values e.g.
```
twixObj.hdr.MeasYaps[('sTXSPEC','asNucleusInfo','0','tNucleus')]
Expand Down Expand Up @@ -75,4 +75,4 @@ This code is a port of Philipp Ehses' original Matlab code. I am incredibly grat

More recent thanks to Mo Shahdloo and Aaron Hess for edits.

This port is released under the MIT licence and no credit is sought for its use.
This port is released under the MIT licence and no credit is sought for its use.
2 changes: 1 addition & 1 deletion build_process.md
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5. git clean -fdx
6. python setup.py sdist
7. python setup.py bdist_wheel
8. python -m twine upload dist/*
8. python -m twine upload dist/*
2 changes: 1 addition & 1 deletion requirements.yml
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- pyyaml
- pytest
- h5py
- six
- six
2 changes: 1 addition & 1 deletion setup.cfg
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.git,
__pycache__,
.vscode,
max-line-length=120
max-line-length=120
12 changes: 6 additions & 6 deletions submission.md
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Developer: William Clarke
Name of the software: pymapVBVD
Abstract: A python port of the Matlab mapVBVD tool for reading Siemens Twix files.
Language: Python
Credit: No credit is required for the use of this code.
Contact: [email protected], www.win.ox.ac.uk/people/william-clarke
Developer: William Clarke
Name of the software: pymapVBVD
Abstract: A python port of the Matlab mapVBVD tool for reading Siemens Twix files.
Language: Python
Credit: No credit is required for the use of this code.
Contact: [email protected], www.win.ox.ac.uk/people/william-clarke
2 changes: 1 addition & 1 deletion tests/__init__.py
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"""
Created by shahdloo
22/09/2020
"""
"""
2 changes: 1 addition & 1 deletion tests/test_slicing.py
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Expand Up @@ -29,4 +29,4 @@ def test_vb():

twixObj.image.squeeze = False
assert twixObj.image[0:2000,0:32:4, :, :, :, :, :, :,0:2,:].shape == (2000,8, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1)
assert np.allclose(np.squeeze(twixObj.image[1000:2000,0:32:4, :, :, :, :, :, :,1,:]),fulldata[1000:2000,0:32:4,1])
assert np.allclose(np.squeeze(twixObj.image[1000:2000,0:32:4, :, :, :, :, :, :,1,:]),fulldata[1000:2000,0:32:4,1])

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