298 Update PyDesigner for Official v1.0.0 Release (#299)

* Update license information

* Update gitignore to avoid builds

* Update documentation

* Update Dockerfiles for latest FSL installer

* Remove AKC from standard processing

* Update docs

Author: TheJaeger

.gitignore

@@ -6,6 +6,7 @@ __pycache__/
 *.egg-info
 .vscode/
 /docs/build/
+dist/
 
 # Files to ignore
 .DS_Store

CHANGELOG.rst

@@ -7,7 +7,7 @@ page
 `v1.0.0`_
 ------------
 
-Jul 8, 2022
+Jan 13, 2023
 
 **Added**
 
@@ -16,6 +16,7 @@ Jul 8, 2022
 * ODF computations and spherical harmonic expansion for DTI and DKI
 * Option to add user-defined map for tractography stopping criteria
 * Added option to import multiple custom maps into DSI studio file
+* PyDesigner can now be pulled from PyPI with `pip install pydesigner`
 
 **Changed**
 

README.rst

@@ -30,6 +30,11 @@ PyDesigner makes this easy, and you will love it!
    :target: https://pydesigner.readthedocs.io/en/latest/
    :alt: Click here to view documentation
 
+.. image:: https://img.youtube.com/vi/mChQFuQqX3k/maxresdefault.jpg
+    :width: 512pt
+    :alt: PyDesigner Walkthrough Video: Software Setup & Usage
+    :target: https://www.youtube.com/watch?v=mChQFuQqX3k
+
 Notable Features
 ================
 
@@ -48,6 +53,7 @@ Notable Features
 - Works with **DTI**, **DKI**, **WMTI**, **FBI**, or **FBWM** datasets
 - Supports **multi-TE** dataset processing
 - **Tractography ready:** Computes ODF spherical harmonic expansion for MRtrix3, and .fib files for DSI Studio
+- Installable modules for **Python or Jupyter Notebook scripting** of custom workflows
 
 
 We welcome all DTI/DKI researchers to evaluate this software and pass

designer/info.py

@@ -28,7 +28,7 @@
 __maintainer__ = 'Siddhartha Dhiman'
 __email__ = 'bridge@musc.edu'
 __url__ = 'https://github.com/m-ama/PyDesigner'
-__license__='MPL 2.0'
+__license__='CUSTOM'
 __description__ = ('Python Port of NYU\'s Designer pipeline for dMRI '
                 'processing')
 # Gets folder name where this file resides
@@ -63,7 +63,7 @@
     'Programming Language :: Python :: 3.7',
     'License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)',
     'Operating System :: OS Independent',
-    'Topic :: Scientific/Engineering :: Bio-Informatics'
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
     'Topic :: Scientific/Engineering :: Information Analysis',
     'Topic :: Scientific/Engineering :: Mathematics',
     'Topic :: Scientific/Engineering :: Physics'

designer/pydesigner.py

@@ -153,8 +153,10 @@ def main():
                         '(requires --denoise to generate a noisemap).')
     parser.add_argument('--nofit', action='store_true', default=False,
                         help='Do not fit DTI or DKI tensors.')
-    parser.add_argument('--noakc', action='store_true', default=False,
-                        help='Do not brute force K tensor outlier rejection.')
+    parser.add_argument('--akc', action='store_true', default=False,
+                        help='Brute force K tensor outlier rejection. Applies '
+                        'a median filter to tensor voxels that exhibit AKC '
+                        'values of less than 2 and more than 10.')
     parser.add_argument('--nooutliers', action='store_true', default=False,
                         help='Do not perform outlier correction on kurtosis '
                         'fitting metrics.')
@@ -322,7 +324,7 @@ def main():
     # Can't do WMTI if no fit
     if args.nofit:
         stdmsg='--nofit given but '
-        if args.noakc:
+        if not args.akc:
             warningmsg+=msgstart+stdmsg+'--noakc'+override+'tensor fitting.\n'
             args.nofit = False
         if args.nooutliers:
@@ -949,7 +951,7 @@ def main():
                     suffix=None,
                     ext=ext,
                     irlls=not args.nooutliers,
-                    akc=not args.noakc,
+                    akc=args.akc,
                     l_max=args.l_max,
                     res=args.t_res,
                     n_fibers=args.t_fibers,
@@ -967,7 +969,7 @@ def main():
                 suffix=None,
                 ext=ext,
                 irlls=not args.nooutliers,
-                akc=not args.noakc,
+                akc=args.akc,
                 l_max=args.l_max,
                 rectify = fbi_rectify,
                 res=args.t_res,

docker/Dockerfile_develop

@@ -74,7 +74,7 @@ RUN echo "alias pip=pip3" >> ~/.bashrc && source ~/.bashrc
 
 # Install FSL
 RUN curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py -o /tmp/fslinstaller.py
-RUN echo "/usr/local/fsl" | python2 /tmp/fslinstaller.py -V 6.0.3
+RUN python /tmp/fslinstaller.py -V 6.0.6 -d /usr/local/fsl
 
 # Configure FSL Environment
 ENV FSLDIR=/usr/local/fsl

docker/Dockerfile_release

@@ -67,15 +67,15 @@ RUN rm /bin/sh && ln -s /bin/bash /bin/sh
 # Clone PyDesigner
 ADD install_pydesigner_release /tmp/install_pydesigner_release
 RUN sed -i 's/\r//g' /tmp/install_pydesigner_release
+RUN pip3 install cmake==3.22.0
 RUN chmod +x /tmp/install_pydesigner_release && bash /tmp/install_pydesigner_release
-RUN pip3 install cmake
 RUN cd /tmp/PyDesigner && pip3 install .
 RUN echo "alias python=python3" >> ~/.bashrc && source ~/.bashrc
 RUN echo "alias pip=pip3" >> ~/.bashrc && source ~/.bashrc
 
 # Install FSL
 RUN curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py -o /tmp/fslinstaller.py
-RUN echo "/usr/local/fsl" | python2 /tmp/fslinstaller.py -V 6.0.3
+RUN python /tmp/fslinstaller.py -V 6.0.6 -d /usr/local/fsl
 
 # Configure FSL Environment
 ENV FSLDIR=/usr/local/fsl

docs/source/installation/pydesigner.rst

@@ -4,6 +4,23 @@ PyDesigner
 PyD is an installable Python package deisgned to perform pre- and
 post- processing of dMRI acquisitions. 
 
+Easy Install
+------------
+PyDesigner can be installed using the PyPI package manager using the command
+
+.. code-block:: console
+
+    $ pip install pydesigner
+
+**Note**:
+    Remember to switch to your conda environement before parsing this
+    command.
+
+That's it, you're done!
+
+Instructions on installing PyDesigner manually from the GitHub repository
+are list below.
+
 Download
 --------
 You may clone the main `PyDesigner repository`_ for the latest build,