Improve latex typography

.gitignore

@@ -0,0 +1 @@
+/Utilities/.chktexrc

Common.cmake

@@ -16,7 +16,6 @@ endif()
 #-----------------------------------------------------------------------------
 # Build option(s)
 #-----------------------------------------------------------------------------
-option(USE_OPTION1           "Build OPTION1"           ON)
 
 #-----------------------------------------------------------------------------
 # Update CMake module path

ITKSoftwareGuide.cmake

@@ -11,7 +11,8 @@ set(CMAKE_MODULE_PATH
   )
 
 #-----------------------------------------------------------------------------
-find_package(ITK REQUIRED)
+set(MINIMUM_ITK_VERSION 5)
+find_package(ITK ${MINIMUM_ITK_VERSION} REQUIRED)
 if(Slicer_BUILD_${PROJECT_NAME})
   set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1) # Incorporate with Slicer nicely
 endif()

SoftwareGuide/Art/CMakeLists.txt

@@ -9,8 +9,8 @@
 file(GLOB PNGandJPG_IMAGES *.jpg *.png)
 file(GLOB EPS_IMAGES *.eps)
 
-find_package(ImageMagick REQUIRED)
-if(NOT IMAGEMAGICK_CONVERT_EXECUTABLE)
+find_package(ImageMagick 6 COMPONENTS convert REQUIRED)
+if(NOT ImageMagick_convert_EXECUTABLE)
   message("ImageMagick convert utility was not found. Please pass to advanced mode and provide its full path")
 endif()
 # Convert an image from some file format to EPS for inclusion in Latex using
@@ -30,7 +30,7 @@ foreach(ImageFile ${PNGandJPG_IMAGES})
   set(OutputEPSFile "${OutputEPSFilePath}/${ImageFileNoExt}.eps")
   add_custom_command(
     OUTPUT    ${OutputEPSFile}
-    COMMAND   ${IMAGEMAGICK_CONVERT_EXECUTABLE}
+    COMMAND   ${ImageMagick_convert_EXECUTABLE}
               ${EPS_INPUT_CONVERT_FLAGS}
               ${ImageFile}
               ${EPS_OUTPUT_CONVERT_FLAGS}

SoftwareGuide/Cover/Source/CMakeLists.txt

@@ -3,7 +3,7 @@ cmake_policy(VERSION 3.10.2)
 
 project( VWSegmentation )
 
-find_package( ITK REQUIRED )
+find_package( ITK 5 REQUIRED )
 include( ${ITK_USE_FILE} )
 
 set( operations

SoftwareGuide/Examples/CMakeLists.txt

@@ -21,7 +21,7 @@ endforeach()
 #
 # First make a directory to store generated images
 set(ART_GENERATED_FOLDER "${SoftwareGuide_BINARY_DIR}/Art/Generated" )
-make_directory( "${ART_GENERATED_FOLDER}" )
+file(MAKE_DIRECTORY "${ART_GENERATED_FOLDER}" )
 
 #
 # Rebuild the Software Guide figures
@@ -37,8 +37,8 @@ set(RUN_EXAMPLES_SCRIPT "${SoftwareGuide_SOURCE_DIR}/Examples/RunExamples.py" CA
 # This is used to convert image formats
 #
 #include(${CMAKE_ROOT}/Modules/FindImageMagick.cmake)
-find_package(ImageMagick REQUIRED)
-if(NOT IMAGEMAGICK_CONVERT_EXECUTABLE)
+find_package(ImageMagick 6 COMPONENTS convert REQUIRED)
+if(NOT ImageMagick_convert_EXECUTABLE)
   message("ImageMagick convert utility was not found. Please pass to advanced mode and provide its full path")
 endif()
 
@@ -269,7 +269,7 @@ macro(CONVERT_INPUT_IMG SOME_IMG EPS_IMG IMAGEMAGICK_FLAGS)
   if( NOT DEFINED \${EPS_IMG}_HAS_CUSTOM_COMMAND)
     message(STATUS \"Converting \${SOME_IMG}\")
     execute_process(
-        COMMAND \"${IMAGEMAGICK_CONVERT_EXECUTABLE}\" \${FLAGS} -quality 100 \${EPS_INPUT_CONVERT_FLAGS} \"\${SOME_IMG}\" \${EPS_OUTPUT_CONVERT_FLAGS} \"\${EPS_IMG}\"
+        COMMAND \"${ImageMagick_convert_EXECUTABLE}\" \${FLAGS} -quality 100 \${EPS_INPUT_CONVERT_FLAGS} \"\${SOME_IMG}\" \${EPS_OUTPUT_CONVERT_FLAGS} \"\${EPS_IMG}\"
         OUTPUT_FILE ${CMAKE_CURRENT_BINARY_DIR}/ConvertImagesToEPSOutput.txt
 	ERROR_FILE ${CMAKE_CURRENT_BINARY_DIR}/ConvertImagesToEPSError.txt
 	RESULT_VARIABLE _result

SoftwareGuide/LaTeXWrapper.sh.in

@@ -3,6 +3,9 @@
 TEXINPUTS=$TEXINPUTS:${ITK_TEXINPUTS}
 export TEXINPUTS
 
-# NOTE: Run 3 times just to get all dependencies resolved. 
-${LATEX_COMPILER} -shell-escape "$@"
+# Prevent console and log outputs from latex from wrapping at 80 characters.
+export max_print_line=10000
+export error_line=254
+export half_error_line=238
 
+${LATEX_COMPILER} -shell-escape "$@"

SoftwareGuide/Latex/00-Preamble-Common.tex

@@ -1,3 +1,4 @@
+\usepackage[T1]{fontenc}
 \usepackage[dvips]{graphicx}
 \usepackage{times}
 \usepackage[table]{xcolor}
@@ -13,6 +14,9 @@
 %\usepackage{siunitx}
 \usepackage[papersize={7.5in,9.25in},margin=1in]{geometry}
 \usepackage[utf8]{inputenc}
+\usepackage{csquotes}
+
+\newcommand{\shelldblquotes}[1]{\textquotedbl{}#1\textquotedbl{}}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %
@@ -94,7 +98,7 @@
 %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \ifitkPrintedVersion
-\usepackage[dvips,
+\usepackage[
 pdfencoding=auto,
 psdextra,
 pdfpagemode={UseOutlines},
@@ -104,7 +108,7 @@
 colorlinks,linkcolor={black},citecolor={black},urlcolor={black},
 ]{hyperref}
 \else
-\usepackage[dvips,
+\usepackage[
 pdfencoding=auto,
 psdextra,
 pdfpagemode={UseOutlines},

SoftwareGuide/Latex/01-PrintedPreamble-Book1.tex

@@ -1,6 +1,6 @@
 \begin{minipage}[t][1.0cm][b]{\textwidth}
 \begin{center}
 Printed and produced in the United States of America.\\
-\bf{ISBN 978-1-930934-35-1}
+\textbf{ISBN 978-1-930934-35-1}
 \end{center}
 \end{minipage}

SoftwareGuide/Latex/01-PrintedPreamble-Book2.tex

@@ -1,6 +1,6 @@
 \begin{minipage}[t][1.0cm][b]{\textwidth}
 \begin{center}
 Printed and produced in the United States of America.\\
-\bf{ISBN 978-1-930934-36-8}
+\textbf{ISBN 978-1-930934-36-8}
 \end{center}
 \end{minipage}

SoftwareGuide/Latex/02-Cover-Book2.tex

@@ -4,7 +4,8 @@
 \chapter*{About the Cover}
 
 The cover image consists of a photograph of ABS plastic anatomical objects
-printed with a MakerBot Replicator 2X 3D printer. Mesh STL files were generated from the images with VTK.
+printed with a \verb|MakerBot Replicator 2X 3D| printer.
+Mesh STL files were generated from the images with VTK.
 
 \begin{description}
 

SoftwareGuide/Latex/03-Abstract-Common.tex

@@ -2,12 +2,12 @@ \chapter*{Abstract}
 \noindent
 The National Library of Medicine Insight Segmentation and Registration Toolkit,
 shortened as the Insight Toolkit \href{https://itk.org}{(ITK)}, is an
-open-source software toolkit for performing registration and
-segmentation. \emph{Segmentation} is the process of identifying and
+open-source software toolkit for performing registration and segmentation.
+\emph{Segmentation} is the process of identifying and
 classifying data found in a digitally sampled
 representation. Typically the sampled representation is an image
-acquired from such medical instrumentation as CT or MRI
-scanners. \emph{Registration} is the task of aligning or developing
+acquired from such medical instrumentation as CT or MRI scanners.
+\emph{Registration} is the task of aligning or developing
 correspondences between data. For example, in the medical environment,
 a CT scan may be aligned with a MRI scan in order to combine the
 information contained in both.

SoftwareGuide/Latex/04-Contributors.tex

@@ -16,65 +16,64 @@ \chapter*{Contributors}
 guide and their contributions.
 
 
-{\bf Luis Ib\'{a}\~{n}ez} is principal author of this text.
+\textbf{Luis Ib\'{a}\~{n}ez} is principal author of this text.
 He assisted in the design and layout of the text, implemented the bulk of
 the \LaTeX{} and CMake build process, and was responsible for the bulk of
 the content. He also developed most of the example code found in the
 \code{Insight/Examples} directory.
 
-{\bf Will Schroeder} helped design and establish the organization
+\textbf{Will Schroeder} helped design and establish the organization
 of this text and the \code{Insight/Examples} directory. He is principal
 content editor, and has authored several chapters.
 
-{\bf Lydia Ng} authored the description for the registration framework
+\textbf{Lydia Ng} authored the description for the registration framework
 and its components, the section on the multiresolution framework, and
 the section on deformable registration methods. She also edited the
 section on the resampling image filter and the sections on various
 level set segmentation algorithms.
 
-{\bf Joshua Cates} authored the iterators chapter and the text and examples
+\textbf{Joshua Cates} authored the iterators chapter and the text and examples
 describing watershed segmentation. He also co-authored the level-set
 segmentation material.
 
-{\bf Jisung Kim} authored the chapter on the statistics framework.
+\textbf{Jisung Kim} authored the chapter on the statistics framework.
 
-{\bf Julien Jomier} contributed the chapter on spatial objects and examples on
+\textbf{Julien Jomier} contributed the chapter on spatial objects and examples on
 model-based registration using spatial objects.
 
-{\bf Karthik Krishnan} reconfigured the process for automatically generating
+\textbf{Karthik Krishnan} reconfigured the process for automatically generating
 images from all the examples. Added a large number of new examples and updated
 the Filtering and Segmentation chapters for the second edition.
 
-{\bf Stephen Aylward} contributed material describing spatial objects and
+\textbf{Stephen Aylward} contributed material describing spatial objects and
 their application.
 
-{\bf Tessa Sundaram} contributed the section on deformable registration using
+\textbf{Tessa Sundaram} contributed the section on deformable registration using
 the finite element method.
 
-{\bf Mark Foskey} contributed the examples on the
+\textbf{Mark Foskey} contributed the examples on the
  \doxygen{AutomaticTopologyMeshSource} class.
 
-{\bf Mathieu Malaterre} contributed the entire section on the description and
+\textbf{Mathieu Malaterre} contributed the entire section on the description and
 use of DICOM readers and writers based on the GDCM library. He also contributed
 an example on the use of the VTKImageIO class.
 
-{\bf Gavin Baker} contributed the section on how to write composite filters.
+\textbf{Gavin Baker} contributed the section on how to write composite filters.
 Also known as minipipeline filters.
 
 Since the software guide is generated in part from the ITK source code
 itself, many ITK developers have been involved in updating and
-extending the ITK documentation.  These include {\bf David Doria},
-{\bf Bradley Lowekamp}, {\bf Mark Foskey}, {\bf Ga\"{e}tan Lehmann},
-{\bf Andreas Schuh}, {\bf Tom Vercauteren}, {\bf Cory Quammen}, {\bf Daniel Blezek},
-{\bf Paul Hughett}, {\bf Matthew McCormick}, {\bf Josh Cates}, {\bf Arnaud Gelas},
-{\bf Jim Miller}, {\bf Brad King}, {\bf Gabe Hart}, {\bf Hans Johnson}. 
-
-{\bf Hans Johnson}, {\bf Kent Williams}, {\bf Constantine Zakkaroff}, {\bf
-Xiaoxiao Liu}, {\bf Ali Ghayoor}, and {\bf Matthew McCormick} updated
+extending the ITK documentation.  These include \textbf{David Doria},
+\textbf{Bradley Lowekamp}, \textbf{Mark Foskey}, \textbf{Ga\"{e}tan Lehmann},
+\textbf{Andreas Schuh}, \textbf{Tom Vercauteren}, \textbf{Cory Quammen}, \textbf{Daniel Blezek},
+\textbf{Paul Hughett}, \textbf{Matthew McCormick}, \textbf{Josh Cates}, \textbf{Arnaud Gelas},
+\textbf{Jim Miller}, \textbf{Brad King}, \textbf{Gabe Hart}, \textbf{Hans Johnson}.
+
+\textbf{Hans Johnson}, \textbf{Kent Williams}, \textbf{Constantine Zakkaroff}, \textbf{Xiaoxiao Liu}, \textbf{Ali Ghayoor}, and \textbf{Matthew McCormick} updated
 the documentation for the initial ITK Version 4 release.
 
-{\bf Luis Ib\'{a}\~{n}ez} and {\bf S\'{e}bastien Barr\'{e}} designed the
-original Book 1 cover. {\bf Xiaoxiao Liu}, {\bf Bill Lorensen}, 
-{\bf Luis Ib\'{a}\~{n}ez}, and {\bf Matthew McCormick} created the 3D printed anatomical 
-objects that were photographed by {\bf S\'{e}bastien Barr\'{e}} for the Book 2 cover. 
-{\bf Steve Jordan} designed the layout of the covers.
+\textbf{Luis Ib\'{a}\~{n}ez} and \textbf{S\'{e}bastien Barr\'{e}} designed the
+original Book 1 cover. \textbf{Xiaoxiao Liu}, \textbf{Bill Lorensen},
+\textbf{Luis Ib\'{a}\~{n}ez}, and \textbf{Matthew McCormick} created the 3D printed anatomical
+objects that were photographed by \textbf{S\'{e}bastien Barr\'{e}} for the Book 2 cover.
+\textbf{Steve Jordan} designed the layout of the covers.