Merge branch 'master' into native-template-dev

.gitignore

@@ -0,0 +1,4 @@
+.*
+*.tmp
+*.swp
+docs/build/

WMH_extraction/TemplateClasses/AbstractTemplate.m

@@ -1,36 +1,37 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % AbstractTemplate.m
-% 
-% To add a new template, create a new class
-% which inherits from AbstractTemplate
-% and fills out the specified properties
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 classdef (Abstract) AbstractTemplate < matlab.mixin.Copyable
+    % Base class for to be used for templates
+    % 
+    % To add a new template, create a new class
+    % which inherits from AbstractTemplate
+    % and fills out the specified properties
+
     properties (Abstract)
-        % Name, for compatibility with legacy code
         name
-
-        % Brain Mask
+        % Name, for compatibility with original code
         brain_mask
-
-        % Probability Maps
+        % path to the binary brain mask for this template
         gm_prob
+        % path to grey matter probability map
         wm_prob
+        % path to white matter probability map
         csf_prob
-
-        % Thresholded (p >= 0.8) Probability Maps
+        % path to CSF probability map
         gm_prob_thr
+        % path to thresholded grey matter probability map
         wm_prob_thr
-
-        % Ventricle Distance
+        % path to thresholded white matter probability map
         ventricles
-
-        % Arterial and Lobar templates
+        % path to ventricle distance map
         lobar
+        % path to lobar segmentation mask
         arterial
-
+        % path to arterial segmentation mask
+        space
         % For convenience, perhaps we store
         % the 'space' of this template?
-        space
+        % ... I don't think this is currently used
     end
 end

docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/requirements.txt

@@ -0,0 +1,2 @@
+sphinxcontrib-matlabdomain
+sphinx_rtd_theme

docs/source/code/TemplateClasses.rst

@@ -0,0 +1,18 @@
+TemplateClasses
+===============
+
+.. automodule:: WMH_extraction.TemplateClasses
+
+:mod:`WMH_extraction.TemplateClasses` is a collection of classes used to provide information and paths relavent to the Template they help implement.
+
+AbstractTemplate
+----------------
+.. autoclass:: WMH_extraction.TemplateClasses.AbstractTemplate
+    :show-inheritance:
+    :members:
+
+CohortTemplate
+--------------
+.. autoclass:: WMH_extraction.TemplateClasses.CohortTemplate
+    :show-inheritance:
+    :members:

docs/source/conf.py

@@ -0,0 +1,207 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# 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.
+#
+import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = u'CNS'
+copyright = u'2019, Jiyang Jiang, Forrest Koch, Wei Wen'
+author = u'Jiyang Jiang, Forrest Koch, Wei Wen'
+
+# The short X.Y version
+version = u''
+# The full version, including alpha/beta/rc tags
+release = u''
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.todo',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.githubpages',
+    'sphinxcontrib.matlab'
+]
+
+matlab_src_dir=os.path.abspath('/home/forrest/Documents/MATLAB/CNS/')
+primary_domain='mat'
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'CNSdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'CNS.tex', u'CNS Documentation',
+     u'Jiyang Jiang, Forrest Koch, Wei Wen', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'cns', u'CNS Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'CNS', u'CNS Documentation',
+     author, 'CNS', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+html_theme = "sphinx_rtd_theme"
+html_theme_options = {
+    'canonical_url': '',
+    'analytics_id': 'UA-139625346-1',  #  Provided by Google in your dashboard
+    'logo_only': False,
+    'display_version': False,
+    'prev_next_buttons_location': 'bottom',
+    'style_external_links': False,
+    'vcs_pageview_mode': '',
+    'style_nav_header_background': 'white',
+    # Toc options
+    'collapse_navigation': False,
+    'sticky_navigation': True,
+    'navigation_depth': 4,
+    'includehidden': True,
+    'titles_only': False
+}

docs/source/index.rst

@@ -0,0 +1,50 @@
+.. CNS documentation master file, created by
+   sphinx-quickstart on Mon May  6 14:06:08 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+CHeBA Neuroimaging Software!
+===============================
+UBO Detector
+------------
+
+UBO Detector is a cluster-based white matter hyperintensity (WMH) extraction pipeline based on k-nearest neighbors (k-NN) algorithm, using T1-weighted and Fluid Attenuation Inversion Recovery (FLAIR) MRI sequences.
+
+System Requirements
+--------------------
+
+UBO Detector has been tested on both CentOS release 6.8 and macOS Sierra with the following software/toolboxes installed:
+
+- SPM12
+- FSL v5.0
+- MATLAB R2016a or above with the following toolboxes installed\:
+
+    - Image Processing Toolbox (ver 9.5 tested)
+    - Statistics and Machine Learning Toolbox (ver 11.0 tested)
+    - Parallel Computing Toolbox (ver 6.9 tested)
+
+Citation
+---------
+
+If you use UBO Detector, please cite:
+
+*Jiang, J., Liu, T., Zhu, W., Koncz, R., Liu, H., Lee, T., Sachdev, P.S., Wen, W. UBO Detector – A cluster-based, fully automated pipeline for extracting white matter hyperintensities. NeuroImage, doi.org/10.1016/j.neuroimage.2018.03.050 (2018).*
+
+If you use TOPMAL, please cite:
+
+*Jiang, J., Paradise, M., Liu, T., Armstrong, N. J., Zhu, W., Kochan, N. A., Brodaty, H., Sachdev, P. S., Wen, W. The association of regional white matter lesions with cognition in a community-based cohort of older individuals, NeuroImage: Clinical 19:14-21, doi.org/10.1016/j.nicl.2018.03.035 (2018).*
+
+.. toctree::
+   :hidden:
+   :maxdepth: 2
+   :glob:
+   :caption: Contents:
+
+   install/install
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`

docs/source/install/install.rst

@@ -0,0 +1,7 @@
+How To Install
+==============
+
+TODO
+-----------
+
+Include Install Instructions