Fix HDF5 issues in Docker build (#258)

* Add `echotime` function

* Add TE awareness to DWIParser

* Add `dwiextract` function

Extracts DWI volumes from star:end index

* Add filename dictionary

* Adjust tensor type thresholds

* Add maxFBIBval() method

* Fine tune tensor type thresolhds

* Add fit regime function

Eases full automation of pipeline

* Fix #232 by mitigating large values

* Incorporate fit regime into main

* Fix #255 by introducing overflow mitigation

* Introduce proper indexing of b-value shells in FBI/FBWM

* Add more proper handling of b-value shells

* Add multi-TE support to main

* Minor documentation changes

* Disable B0 exclusion in IRLLS

* Update version to RC10

* Update filenaming algorithm

* Add doc files

* Update CHANGELOG

* Remove unused print statement

* Add `--no_rectify` flag

* Update CHANGELOG

* Update documentation

* Remove unused doc files

* Update PyDesigner Logo

* Update Sphinx documentation

* Update Dockerfiles to include HDF5

Author: TheJaeger

CHANGELOG.rst

@@ -5,7 +5,7 @@ All notable changes to this project will be documented in this file or
 page
 
 `v1.0-RC10`_
------------
+------------
 
 Jun 29, 2021
 
@@ -143,7 +143,7 @@ Oct 26, 2020
 **Changed**:
 
 * Fixed issue where eddy correction would attempt
- to QC and fail despite parsing the ``--noqc`` flag.
+  to QC and fail despite parsing the ``--noqc`` flag.
 * SNR plotting works in very specific scenarious when
   input DWIs are of the same same dimensions. A try/except
   loop now ensure that the entire pipeline doesn't halt

README.rst

@@ -33,8 +33,8 @@ PyDesigner makes this easy, and you will love it!
 
 .. _NYU's DESIGNER: https://github.com/NYU-DiffusionMRI/DESIGNER
 
-.. image:: https://imgur.com/Anc33XI.png
-   :width: 256pt
+.. image:: https://i.imgur.com/YeCvz8s.png
+   :width: 512pt
    :target: https://pydesigner.readthedocs.io/en/latest/
    :alt: Click here to view documentation
 
@@ -54,6 +54,7 @@ Notable Features
 - **Quality control metrics** to evaluate data integrity – SNR graphs, outlier voxels, and head motion
 - Uses the **latest techniques** from DTI/DKI/FBI literature
 - Works with **DTI**, **DKI**, **WMTI**, **FBI**, or **FBWM** datasets
+- Supports **multi-TE** dataset processing
 
 We welcome all DTI/DKI researchers to evaluate this software and pass
 on their feedback or issues through the `Issues`_ page of this

docker/Dockerfile_develop

@@ -55,7 +55,8 @@ RUN apt-get install -y --no-install-recommends \
       libgl1-mesa-dev \
       libfftw3-dev \
       libtiff5-dev \
-      libomp-dev
+      libomp-dev \
+      libhdf5-serial-dev
 
 RUN rm /bin/sh && ln -s /bin/bash /bin/sh
 

docker/Dockerfile_release

@@ -55,7 +55,8 @@ RUN apt-get install -y --no-install-recommends \
       libgl1-mesa-dev \
       libfftw3-dev \
       libtiff5-dev \
-      libomp-dev
+      libomp-dev \
+      libhdf5-serial-dev
 
 RUN rm /bin/sh && ln -s /bin/bash /bin/sh
 

docs/source/api/designer.system.rst

@@ -15,16 +15,17 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath('../'))
+# sys.path.insert(0, os.path.abspath('../../'))
 
 # -- Project information -----------------------------------------------------
 
 project = 'PyDesigner'
-copyright = '2020, MUSC Advanced MRI Analysis (MAMA)'
+copyright = '2021, MUSC Advanced MRI Analysis (MAMA)'
 author = 'Siddhartha Dhiman, Joshua Teves, Kayti Keith'
 
 # The full version, including alpha/beta/rc tags
-release = 'v1.0-RC1'
+release = 'v1.0-RC10'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/api/designer.system.systemtools.rst

@@ -35,8 +35,8 @@
 
 .. .. _NYU's DESIGNER: https://github.com/NYU-DiffusionMRI/DESIGNER
 
-.. .. image:: images/PyDesigner-Logo.png
-..    :width: 384pt
+.. .. image:: https://i.imgur.com/YeCvz8s.png
+..    :width: 512pt
 
 .. Notable Features
 .. ================