From 2a3321459e26342fd4aaab12f9eb14aed9497865 Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Tue, 6 Dec 2022 19:10:12 +0100 Subject: [PATCH] Fix spaces * Remove trailing spaces at end-of-line * Add missing newline at end-of-file --- README.md | 10 +++++----- build_process.md | 2 +- requirements.yml | 2 +- setup.cfg | 2 +- submission.md | 12 ++++++------ tests/__init__.py | 2 +- tests/test_slicing.py | 2 +- 7 files changed, 16 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index a60d7f3..b2337aa 100644 --- a/README.md +++ b/README.md @@ -8,15 +8,15 @@ 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: ``` @@ -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')] @@ -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. \ No newline at end of file +This port is released under the MIT licence and no credit is sought for its use. diff --git a/build_process.md b/build_process.md index 8ce10fc..3c8a818 100644 --- a/build_process.md +++ b/build_process.md @@ -6,4 +6,4 @@ 5. git clean -fdx 6. python setup.py sdist 7. python setup.py bdist_wheel -8. python -m twine upload dist/* \ No newline at end of file +8. python -m twine upload dist/* diff --git a/requirements.yml b/requirements.yml index bfa4abb..3013b31 100644 --- a/requirements.yml +++ b/requirements.yml @@ -8,4 +8,4 @@ dependencies: - pyyaml - pytest - h5py - - six \ No newline at end of file + - six diff --git a/setup.cfg b/setup.cfg index 8236469..0569845 100644 --- a/setup.cfg +++ b/setup.cfg @@ -18,4 +18,4 @@ exclude = .git, __pycache__, .vscode, -max-line-length=120 \ No newline at end of file +max-line-length=120 diff --git a/submission.md b/submission.md index 30aef0d..dcde943 100644 --- a/submission.md +++ b/submission.md @@ -1,6 +1,6 @@ -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: william.clarke@ndcn.ox.ac.uk, www.win.ox.ac.uk/people/william-clarke \ No newline at end of file +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: william.clarke@ndcn.ox.ac.uk, www.win.ox.ac.uk/people/william-clarke diff --git a/tests/__init__.py b/tests/__init__.py index eedc48e..ba0a8b5 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -1,4 +1,4 @@ """ Created by shahdloo 22/09/2020 -""" \ No newline at end of file +""" diff --git a/tests/test_slicing.py b/tests/test_slicing.py index 67b3aa5..4de78cc 100644 --- a/tests/test_slicing.py +++ b/tests/test_slicing.py @@ -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]) \ No newline at end of file + assert np.allclose(np.squeeze(twixObj.image[1000:2000,0:32:4, :, :, :, :, :, :,1,:]),fulldata[1000:2000,0:32:4,1])