From f667a9be13a2d2035ce2074d3e054c038ba0a2d8 Mon Sep 17 00:00:00 2001 From: albert-github Date: Sat, 22 Mar 2025 14:10:18 +0100 Subject: [PATCH 1/4] DOC: Spelling corrections Spelling corrections --- CMake/ITKSetStandardCompilerFlags.cmake | 4 +- CMake/ITKSoftwareGuideExternalData.cmake | 2 +- CMake/PreventInBuildInstalls.cmake | 2 +- CMake/PreventInSourceBuilds.cmake | 2 +- ...rMacroCheckExternalProjectDependency.cmake | 2 +- CMakeLists.txt | 2 +- CONTRIBUTING.md | 2 +- Common.cmake | 2 +- Latex/Insight.bib | 44 +++++++++---------- Latex/Insight.sty | 2 +- README.md | 2 +- SoftwareGuide/Art/CMakeLists.txt | 4 +- SoftwareGuide/CMakeLists.txt | 2 +- SoftwareGuide/Examples/CMakeLists.txt | 4 +- SoftwareGuide/Examples/ParseCxxExamples.py | 4 +- SoftwareGuide/Examples/RunExamples.py | 4 +- SoftwareGuide/LaTeXWrapper.sh.in | 2 +- .../Latex/Appendices/GitWorkflow.tex | 2 +- .../ConfidenceConnectedOnBrainWeb.tex | 2 +- .../DesignAndFunctionality/Optimizers.tex | 2 +- .../DesignAndFunctionality/Registration.tex | 2 +- .../DesignAndFunctionality/Segmentation.tex | 2 +- .../DesignAndFunctionality/Transforms.tex | 2 +- ...ualizingDeformationFieldsUsingParaview.tex | 2 +- .../WatershedSegmentation.tex | 2 +- .../DevelopmentGuidelines/CreateAModule.tex | 10 ++--- .../Latex/Introduction/Installation.tex | 2 +- SoftwareGuide/Latex/README.md | 2 +- SuperBuild/External_ITK.cmake | 4 +- SuperBuild/External_RunExamples.cmake | 4 +- TODO | 16 +++---- 31 files changed, 70 insertions(+), 70 deletions(-) diff --git a/CMake/ITKSetStandardCompilerFlags.cmake b/CMake/ITKSetStandardCompilerFlags.cmake index 053c1437..bd2a4089 100644 --- a/CMake/ITKSetStandardCompilerFlags.cmake +++ b/CMake/ITKSetStandardCompilerFlags.cmake @@ -88,7 +88,7 @@ function(check_compiler_warning_flags c_warning_flags_var cxx_warning_flags_var) #-wd1419 #Needed for Intel compilers with remark #1419: external declaration in primary source file #-wd1572 #Needed for Intel compilers with remark #1572: floating-point equality and inequality comparisons are unreliable #-wd2259 #Needed for Intel compilers with remark #2259: non-pointer conversion from "itk::SizeValueType={unsigned long}" to "double" may lose significant bits - #-wd1268 #Needed for Intel compliers with warning #1268: support for exported templates is disabled + #-wd1268 #Needed for Intel compilers with warning #1268: support for exported templates is disabled else() set(VerboseWarningsFlag -Wall ) endif () @@ -209,7 +209,7 @@ macro(check_compiler_platform_flags) if("${${listname}}" MATCHES ".*-fopenmp.*") string(REPLACE "-fopenmp" "" tmpFlags "${${listname}}") set(${listname} "${tmpFlags}") - message("-fopenmp causes incorrect compliation of HDF, removing from ${listname}") + message("-fopenmp causes incorrect compilation of HDF, removing from ${listname}") endif() endforeach() diff --git a/CMake/ITKSoftwareGuideExternalData.cmake b/CMake/ITKSoftwareGuideExternalData.cmake index 2eebe17e..8bbc4b3a 100644 --- a/CMake/ITKSoftwareGuideExternalData.cmake +++ b/CMake/ITKSoftwareGuideExternalData.cmake @@ -2,7 +2,7 @@ get_filename_component(_ITKExternalData_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) include(${_ITKExternalData_DIR}/ExternalData.cmake) ## The user can specify an environmental variable for shared locations of -## of object files to prevent continous downloading of common objects. +## of object files to prevent continuous downloading of common objects. if(NOT ExternalData_OBJECT_STORES) # Use ExternalData_OBJECT_STORES from environment as default. set(ExternalData_OBJECT_STORES_DEFAULT "") diff --git a/CMake/PreventInBuildInstalls.cmake b/CMake/PreventInBuildInstalls.cmake index e693f1b2..6ef78a0c 100644 --- a/CMake/PreventInBuildInstalls.cmake +++ b/CMake/PreventInBuildInstalls.cmake @@ -1,4 +1,4 @@ -# Adapated from ITKv4/CMake/PreventInBuildInstalls.cmake +# Adapted from ITKv4/CMake/PreventInBuildInstalls.cmake string(TOLOWER "${CMAKE_INSTALL_PREFIX}" _PREFIX) string(TOLOWER "${${CMAKE_PROJECT_NAME}_BINARY_DIR}" _BUILD) if("${_PREFIX}" STREQUAL "${_BUILD}") diff --git a/CMake/PreventInSourceBuilds.cmake b/CMake/PreventInSourceBuilds.cmake index 4e65ce5e..ae10f747 100644 --- a/CMake/PreventInSourceBuilds.cmake +++ b/CMake/PreventInSourceBuilds.cmake @@ -1,4 +1,4 @@ -# Adapated from ITKv4/CMake/PreventInSourceBuilds.cmake +# Adapted from ITKv4/CMake/PreventInSourceBuilds.cmake # # This function will prevent in-source builds function(AssureOutOfSourceBuilds PROJECT_NAME) diff --git a/CMake/SlicerMacroCheckExternalProjectDependency.cmake b/CMake/SlicerMacroCheckExternalProjectDependency.cmake index 6712bb55..22cb0105 100644 --- a/CMake/SlicerMacroCheckExternalProjectDependency.cmake +++ b/CMake/SlicerMacroCheckExternalProjectDependency.cmake @@ -31,7 +31,7 @@ endmacro() macro(ProjectDependancyPop CACHE_LIST TVAR) list(GET ${CACHE_LIST} -1 ${TVAR}) list(REMOVE_AT ${CACHE_LIST} -1) - #message(STATUS "POPING ${${TVAR}} from ${CACHE_LIST}: --> ${${CACHE_LIST}}") + #message(STATUS "POPPING ${${TVAR}} from ${CACHE_LIST}: --> ${${CACHE_LIST}}") endmacro() macro(SlicerMacroCheckExternalProjectDependency proj) diff --git a/CMakeLists.txt b/CMakeLists.txt index f710f5de..b1101d71 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -6,7 +6,7 @@ set(PRIMARY_PROJECT_NAME ITKSoftwareGuide) ## NOTE THERE SHOULD BE NO PROJECT STATEMENT HERE! ## This file acts as a simple switch to initiate -## two completely independant CMake build environments. +## two completely independent CMake build environments. #----------------------------------------------------------------------------- # Superbuild Option - Enabled by default diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 89334385..73b88a47 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -49,7 +49,7 @@ description for the patch. Type a more detailed description of the patch after a blank line. Submit the patch for peer review by running the `git review-push` command. -This will provide a summary message that inclues a URL to view the changes. If +This will provide a summary message that includes a URL to view the changes. If you are logged into [GitHub], there will also be a green button to create a [Pull Request]. diff --git a/Common.cmake b/Common.cmake index 7982303e..63a369a9 100644 --- a/Common.cmake +++ b/Common.cmake @@ -84,7 +84,7 @@ else() # Release, or anything else endif() #----------------------------------------------------------------------------- -# Add needed flag for gnu on linux like enviroments to build static common libs +# Add needed flag for gnu on linux like environments to build static common libs # suitable for linking with shared object libs. if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64") if(NOT "${CMAKE_CXX_FLAGS}" MATCHES "-fPIC") diff --git a/Latex/Insight.bib b/Latex/Insight.bib index ee3df521..b5814d27 100644 --- a/Latex/Insight.bib +++ b/Latex/Insight.bib @@ -298,9 +298,9 @@ @Book{Beaumont1987 @Book{Berestovskij1993, Author = "V. N. Berestovskij and I. G. Nikilaev", - Title = "Multidimensional Generalised Riemannian Spaces", + Title = "Multidimensional Generalized Riemannian Spaces", Publisher = "Springer Verlag", - Series = "Enciclopaedia of Mathematical Sciences", + Series = "Encyclopaedia of Mathematical Sciences", year = 1993, } @@ -604,7 +604,7 @@ @Article{Chan2001 @Book{CPPStandard1998, Author = "ANSI-ISO", Title = "Programming Languages - C++", - Publisher = "American National Standards Institue", + Publisher = "American National Standards Institute", year = 1998, } @@ -823,7 +823,7 @@ @TechReport{Deriche1993 Derivatives ", Institution = "Unite de recherche INRIA Sophia-Antipolis", Number = "1893", - Note = "Research Repport", + Note = "Research Report", annote = "https://www.inria.fr", year = 1993, month = "avril", @@ -923,7 +923,7 @@ @InProceedings{Duta1999 @Article{RimonBurdick2, Author = "Rimon E. and Burdick J.W.", - Title = "Mobility of Bodies in Contact - Part 2: How Froces are + Title = "Mobility of Bodies in Contact - Part 2: How Forces are Generated by Curvature Effects", Journal = "IEEE Transactions on Robotics and Automation", Volume = "15", @@ -1037,7 +1037,7 @@ @Article{Farouki1995 @InProceedings{Reveilles3D, Author = "O. Figueiredo and J-P Reveilles", Title = "A Contribution to 3D Digital Lines", - BookTitle = "Procedings 5th Discrete Geometry and Computer Imagery", + BookTitle = "Proceedings 5th Discrete Geometry and Computer Imagery", Pages = "187-189", Address = "Clermont-Ferrand", year = 1995, @@ -1130,7 +1130,7 @@ @Article{Fritsch1994 @InProceedings{Fritsch1997, Author = "D. Fritsch and S. Pizer and L. Yu and V. Johnson and E. Chaney", - Title = "Localisation and Segmentation of Medical Image Objects + Title = "Segmentation of Medical Image Objects using Deformable Shape Loci", BookTitle = "Information Processing in Medical Imaging 1997 (IPMI'97)", @@ -1501,7 +1501,7 @@ @Article{Hau2002 @Article{Heath, Author = "M. Heath and S. Sarkar and T. Sanoki and K. Bowyer", - Title = "Comparision of Edge Detectors. A Methodology and + Title = "Comparison of Edge Detectors. A Methodology and Initial Study", Journal = "Computer Vision and Image Understanding", Volume = "69", @@ -1772,7 +1772,7 @@ @InProceedings{Ib @Article{Ib'{a}~{n}ezLines, Author = "L. Ib'{a}~{n}ez and C. Hamitouche and C. Roux", - Title = "A Vectorial Algorithm for Tracing Discrete Straigh + Title = "A Vectorial Algorithm for Tracing Discrete Straight Lines in N-Dimensional Generalized Grids", Journal = "IEEE Transactions on Visualization and Computer Graphics", @@ -1932,7 +1932,7 @@ @InProceedings{Jolly2003 @Book{Kaandorp1994, Author = "J.A. Kaandorp", - Title = "Fractal Modelling. Growth and From in Bilogy", + Title = "Fractal Modelling. Growth and Fxprom in Biology", Publisher = "Springer Verlag", year = 1994, } @@ -1998,7 +1998,7 @@ @Article{Kaufman3DScan @InProceedings{Kaufman, Author = "A. E. Kaufman", Title = "Volume Synthesis", - BookTitle = "Procedings 6th International Workshop Discrete + BookTitle = "Proceedings 6th International Workshop Discrete Geometry for Computer Imagery DGCI'96", Editor = "Springer Verlag", Series = "Lecture Notes in Computer Science", @@ -3058,7 +3058,7 @@ @InProceedings{Pelleg1999 @Article{Penney1998, Author = "G. P. Penney and J. Weese and J. A. Little and P. Desmedt and D. L. G. Hill and D. J. Hawkes", - Title = "A comparision of similarity measures for use in 2D-3D + Title = "A comparison of similarity measures for use in 2D-3D Medical image registration", Journal = "IEEE Transactions on Medical Imaging", Volume = "17", @@ -3279,7 +3279,7 @@ @Book{Reshetnyak1993 @PhdThesis{ReveillesThese, Author = "J-P. Reveilles", - Title = "Geometrie discrete, calculs en nombres entiers et + Title = "Geometrie discrete, calcul en nombres entiers et algorithmique", School = "Universite Louis Pasteur ", Address = "Strasbourg", @@ -3380,7 +3380,7 @@ @Book{Roman1992 @InProceedings{Rosch2000, Author = "P. Rosch and T. Netsch and M. Quist and G. P. Penney - and D. L. G. Hill adn J. Weese", + and D. L. G. Hill and J. Weese", Title = "Robust 3D Deformation Field Estimation by Template Propagation", BookTitle = "International Conference on Medical Image Computing @@ -3807,7 +3807,7 @@ @Article{Thirion1998 @Book{Thom1977, Author = "R. Thom", - Title = "Stabilite Structurelle et Mofphogenese. Essai d'une + Title = "Stabilite Structurelle et Morphogenese. Essai d'une theorie generale des modeles", Publisher = "InterEditions", Edition = "Deuxieme", @@ -3947,7 +3947,7 @@ @Article{Unsgaard2003 Author = "G. Unsgaard and S. Ommedal and T. Muller and A. Gronningsaeter and T.A. Nagelhus Hernes", Title = "Neuronavigation by intraoperative 3D ultrasound, - initial experiences durin brain tumor resections. + initial experiences during brain tumor resections. Clinical study", Journal = "Neurosurgery", year = 2003, @@ -4134,8 +4134,8 @@ @InProceedings{Weickert1996 } @InCollection{Weinans, - Author = "H. Weinans and D. Summer", - Title = "Finite Element Analyes to Study Periprosthetic Bone + Author = "H. Weinans and D. Sumner", + Title = "Finite Element Analyses to Study Periprosthetic Bone Adaptation", BookTitle = "Bone Research in Biomechanics", Publisher = "IOS Press", @@ -4414,7 +4414,7 @@ @InProceedings{Yao2000 @InProceedings{Yezzi1999, Author = "A. Yezzi and A. Tsai and A. Willsky", Title = "A statistical approach to snakes for bimodal and trimodal imagery", - BookTitle = "Internation Conf. Computer Vision", + BookTitle = "International Conf. Computer Vision", Volume = 2, Pages = "898-903", year = 1999, @@ -4506,7 +4506,7 @@ @Article{wolpert96 @article{hornoptflow, AUTHOR = "D.K.P. Horn and B.G. Schunck", TITLE = "Determining Optical Flow", - JOURNAL = "Artifical Intelligence", + JOURNAL = "Artificial Intelligence", VOLUME = "17", YEAR = "1981", NUMBER = "1-3", @@ -4519,7 +4519,7 @@ @incollection{ mumford-bayesian booktitle = "Geometry-driven diffusion in Computer Vision", pages = {141--153}, publisher="Kluwer Academic", - editer = "B. Romeny", + editor = "B. Romeny", year = 1994} @@ -4827,7 +4827,7 @@ @TechReport{DICOMStandard Title = "The DICOM Standard", Institution = "NEMA", Address = "http://medial.nema.org/", - Publisher = "National Electical Manufacturers Association", + Publisher = "National Electrical Manufacturers Association", Year = 2013 } diff --git a/Latex/Insight.sty b/Latex/Insight.sty index e5499c0e..76160181 100644 --- a/Latex/Insight.sty +++ b/Latex/Insight.sty @@ -1,5 +1,5 @@ % -% Insight.sty for the Insight docummentation [works only with with Latex2e] +% Insight.sty for the Insight documentation [works only with with Latex2e] % \NeedsTeXFormat{LaTeX2e}[1995/12/01] diff --git a/README.md b/README.md index d5bcac38..d8d7f54c 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ For more detailed instructions, see the [CONTRIBUTING.md](CONTRIBUTING.md) file. Building with Docker -------------------- -All the dependencies described belowe are available pre-installed in a [Docker] +All the dependencies described below are available pre-installed in a [Docker] image. This is the easiest way to build and contribute to The Software Guide. diff --git a/SoftwareGuide/Art/CMakeLists.txt b/SoftwareGuide/Art/CMakeLists.txt index f80378f9..3b7acdcc 100644 --- a/SoftwareGuide/Art/CMakeLists.txt +++ b/SoftwareGuide/Art/CMakeLists.txt @@ -15,11 +15,11 @@ if(NOT IMAGEMAGICK_CONVERT_EXECUTABLE) endif() # Convert an image from some file format to EPS for inclusion in Latex using # ImageMagick. This image is an input image. A separate macro is necessary -# because input images do not have any dependecies +# because input images do not have any dependencies set(EPS_INPUT_CONVERT_FLAGS) set(EPS_OUTPUT_CONVERT_FLAGS) if( PDF_QUALITY_LEVEL STREQUAL "Printer" ) - # Upsample to satify the printer + # Upsample to satisfy the printer set( EPS_INPUT_CONVERT_FLAGS -density 72 ) set( EPS_OUTPUT_CONVERT_FLAGS -density 72 -scale 4194304@ ) endif() diff --git a/SoftwareGuide/CMakeLists.txt b/SoftwareGuide/CMakeLists.txt index b3ca88e2..aac6e5e5 100644 --- a/SoftwareGuide/CMakeLists.txt +++ b/SoftwareGuide/CMakeLists.txt @@ -13,7 +13,7 @@ # directory containing the Insight executables. Specify ITK data paths. # The default data path inferred is ITK/Examples/Data. This should suffice # for building the SoftwareGuide. Should more paths be need add them in a colon -# seperated list. +# separated list. # # Make # diff --git a/SoftwareGuide/Examples/CMakeLists.txt b/SoftwareGuide/Examples/CMakeLists.txt index c8b475db..8924b12e 100644 --- a/SoftwareGuide/Examples/CMakeLists.txt +++ b/SoftwareGuide/Examples/CMakeLists.txt @@ -250,11 +250,11 @@ set(ITK_FLIP_IMG # END FLIP_INPUTS LIST # Convert an image from some file format to EPS for inclusion in Latex using # ImageMagick. This image is an input image. A separate macro is necessary -# because input images do not have any dependecies +# because input images do not have any dependencies set(EPS_INPUT_CONVERT_FLAGS) set(EPS_OUTPUT_CONVERT_FLAGS) if( \"${PDF_QUALITY_LEVEL}\" STREQUAL \"Printer\" ) - # Upsample to satify the printer + # Upsample to satisfy the printer set( EPS_INPUT_CONVERT_FLAGS -density 72 ) set( EPS_OUTPUT_CONVERT_FLAGS -density 72 -scale 4194304@ ) endif() diff --git a/SoftwareGuide/Examples/ParseCxxExamples.py b/SoftwareGuide/Examples/ParseCxxExamples.py index 3410bbdd..343e76b9 100755 --- a/SoftwareGuide/Examples/ParseCxxExamples.py +++ b/SoftwareGuide/Examples/ParseCxxExamples.py @@ -124,8 +124,8 @@ def ParseOneFile(sourceFile): def GetPreambleString(examplefilename): - # The following message is a warning writen on the generated .tex - # files for preventing them from being manualy edited. + # The following message is a warning written on the generated .tex + # files for preventing them from being manually edited. preamble = f""" % Please do NOT edit this file. % It has been automatically generated diff --git a/SoftwareGuide/Examples/RunExamples.py b/SoftwareGuide/Examples/RunExamples.py index 7db6535e..d7bdd08f 100644 --- a/SoftwareGuide/Examples/RunExamples.py +++ b/SoftwareGuide/Examples/RunExamples.py @@ -94,7 +94,7 @@ def AreOutputsNewer(self): if os.path.exists(o): this_output_time = os.path.getmtime(o) if self.verbose: - print(f"This Ouptut Time: {this_output_time}") + print(f"This Output Time: {this_output_time}") if this_output_time < oldest_output: oldest_output = this_output_time else: @@ -285,7 +285,7 @@ def __init__(self, itkSourceDir, itkExecutablesDir, itkBuildDir, SWGuidBaseOutpu self.outPicDir = self.outPicDir.rstrip("/") mkdir_p(self.outPicDir) - # HACK: Need beter search criteria + # HACK: Need better search criteria searchPaths = f"{itkBuildDir}/ExternalData/Testing/Data/Input#{itkBuildDir}/ExternalData/Examples/Data/BrainWeb#{itkBuildDir}/Testing/Temporary#{itkBuildDir}/Modules/Nonunit/Review/test#{itkBuildDir}/ExternalData/Modules/Segmentation/LevelSetsv4/test/Baseline#{itkBuildDir}/ExternalData/Modules/IO/GE/test/Baseline#{itkBuildDir}/ExternalData/Examples/Filtering/test/Baseline#{itkBuildDir}/Examples/Segmentation/test#{SWGuidBaseOutput}/Art/Generated#{itkSourceDir}/Examples/Data" dirtyDirPaths = searchPaths.split("#") diff --git a/SoftwareGuide/LaTeXWrapper.sh.in b/SoftwareGuide/LaTeXWrapper.sh.in index a4639ed1..56dd54c3 100755 --- a/SoftwareGuide/LaTeXWrapper.sh.in +++ b/SoftwareGuide/LaTeXWrapper.sh.in @@ -3,6 +3,6 @@ TEXINPUTS=$TEXINPUTS:${ITK_TEXINPUTS} export TEXINPUTS -# NOTE: Run 3 times just to get all dependancies resolved. +# NOTE: Run 3 times just to get all dependencies resolved. ${LATEX_COMPILER} -shell-escape "$@" diff --git a/SoftwareGuide/Latex/Appendices/GitWorkflow.tex b/SoftwareGuide/Latex/Appendices/GitWorkflow.tex index 465942e6..7d4ba891 100644 --- a/SoftwareGuide/Latex/Appendices/GitWorkflow.tex +++ b/SoftwareGuide/Latex/Appendices/GitWorkflow.tex @@ -3058,7 +3058,7 @@ \subsubsection{Local} One of Git's standard whitespace checks is to reject trailing whitespace on lines that were added or modified. Many people consider extra space characters at the end of a line to be an unprofessional style (including Git's own -developers), but some don ot care. Text editors typically have a mode to +developers), but some don't care. Text editors typically have a mode to highlight trailing whitespace: \begin{itemize} diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/ConfidenceConnectedOnBrainWeb.tex b/SoftwareGuide/Latex/DesignAndFunctionality/ConfidenceConnectedOnBrainWeb.tex index 25eba60d..7ce88d22 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/ConfidenceConnectedOnBrainWeb.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/ConfidenceConnectedOnBrainWeb.tex @@ -6,7 +6,7 @@ \subsubsection{Application of the Confidence Connected filter on the Brain Web D The previous code was used in this example replacing the image dimension by 3. Gradient Anistropic diffusion was applied to smooth the image. The filter used 2 iterations, a time step of 0.05 and a conductance value of 3. The smoothed volume was then segmented using the Confidence Connected approach. Five seed points were used at coordinate locations (118,85,92), (63,87,94), (63,157,90), (111,188,90), (111,50,88). The ConfidenceConnnected filter used the parameters, a neighborhood radius of 2, 5 iterations and an $f$ of 2.5 (the same as in the previous example). The results were then rendered using VolView. -Figure \ref{fig:3DregionGrowingScreenshot1} shows the rendered volume. Figure \ref{fig:SlicesBrainWeb} shows an axial, saggital and a coronal slice of the volume. +Figure \ref{fig:3DregionGrowingScreenshot1} shows the rendered volume. Figure \ref{fig:SlicesBrainWeb} shows an axial, sagittal and a coronal slice of the volume. \begin{figure} \centering diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/Optimizers.tex b/SoftwareGuide/Latex/DesignAndFunctionality/Optimizers.tex index ef84e7ea..5d6e586e 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/Optimizers.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/Optimizers.tex @@ -124,7 +124,7 @@ in N (initially orthogonal) directions. This optimizer is described in~\cite{Press1992}. (\doxygen{PowellOptimizerv4}). -\item \textbf{Exhausive Optimizer}: Fully samples a grid on the parameteric space. +\item \textbf{Exhaustive Optimizer}: Fully samples a grid on the parametric space. This optimizer is equivalent to an exahaustive search in a discrete grid defined over the parametric space. The grid is centered on the initial position. The subdivisions of the grid along each one of the dimensions of the parametric space diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/Registration.tex b/SoftwareGuide/Latex/DesignAndFunctionality/Registration.tex index d768d5b7..ad4cbb2f 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/Registration.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/Registration.tex @@ -597,7 +597,7 @@ \subsection{General heuristics for parameter fine-tunning} Once you identify the anatomical structures in the histogram, then rerun that same program with less - and less number of bins, until you reach the minimun + and less number of bins, until you reach the minimum number of bins for which all the tissues that are important for your application, are still distinctly differentiated in the histogram. At that point, take that number of bins and diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/Segmentation.tex b/SoftwareGuide/Latex/DesignAndFunctionality/Segmentation.tex index 24a97b1a..918a46af 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/Segmentation.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/Segmentation.tex @@ -90,7 +90,7 @@ \section{Level Set Segmentation} \input{DesignAndFunctionality/LevelSetsSegmentation.tex} -%HACK: TODO Review what happended to these. +%HACK: TODO Review what happened to these. %REMOVED PATENTED: \section{Hybrid Methods} %REMOVED PATENTED: \label{sec:HybridSegmentationMethods} %REMOVED PATENTED: diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/Transforms.tex b/SoftwareGuide/Latex/DesignAndFunctionality/Transforms.tex index 867c34f8..4ba22b14 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/Transforms.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/Transforms.tex @@ -70,7 +70,7 @@ \subsection{Geometrical Representation} Additional uses of the \doxygen{Point}, \doxygen{Vector} and \doxygen{CovariantVector} classes have been discussed in the Data -Representation chaper of Book 1. Each one of these classes behaves +Representation chapter of Book 1. Each one of these classes behaves differently under spatial transformations. It is therefore quite important to keep their distinction clear. Figure \ref{fig:GeometricalObjects} illustrates the differences between these concepts. diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/VisualizingDeformationFieldsUsingParaview.tex b/SoftwareGuide/Latex/DesignAndFunctionality/VisualizingDeformationFieldsUsingParaview.tex index 4b7a59e1..3f003464 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/VisualizingDeformationFieldsUsingParaview.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/VisualizingDeformationFieldsUsingParaview.tex @@ -16,7 +16,7 @@ \subsection{Visualizing 2D deformation fields} Load the Deformation field in Paraview. (The deformation field must be capable of handling vector data, such as MetaImages). Paraview shows a color map of the magnitudes of the deformation fields as shown in \ref{fig:ParaviewScreenshot1}. -Covert the deformation field to 3D vector data using a {\it Calculator}. The Calculator may be found in the {\it Filter} pull down menu. A screenshot of the calculator tab is shown in Figure \ref{fig:ParaviewScreenshot2}. Although the deformation field is a 2D vector, we will generate a 3D vector with the third component set to 0 since Paraview generates glyphs only for 3D vectors. You may now apply a glyph of arrows to the resulting 3D vector field by using {\it Glyph} on the menu bar. The glyphs obtained will be very dense since a glyph is generated for each point in the data set. To better visualize the deformation field, you may adopt one of the following approaches. +Convert the deformation field to 3D vector data using a {\it Calculator}. The Calculator may be found in the {\it Filter} pull down menu. A screenshot of the calculator tab is shown in Figure \ref{fig:ParaviewScreenshot2}. Although the deformation field is a 2D vector, we will generate a 3D vector with the third component set to 0 since Paraview generates glyphs only for 3D vectors. You may now apply a glyph of arrows to the resulting 3D vector field by using {\it Glyph} on the menu bar. The glyphs obtained will be very dense since a glyph is generated for each point in the data set. To better visualize the deformation field, you may adopt one of the following approaches. Reduce the number of glyphs by reducing the number in {\it Max. Number of Glyphs} to a reasonable amount. This uniformly downsamples the number of glyphs. Alternatively, you may apply a {\it Threshold} filter to the {\it Magnitude} of the vector dataset and then glyph the vector data that lie above the threshold. This eliminates the smaller deformation fields that clutter the display. You may now reduce the number of glyphs to a reasonable value. diff --git a/SoftwareGuide/Latex/DesignAndFunctionality/WatershedSegmentation.tex b/SoftwareGuide/Latex/DesignAndFunctionality/WatershedSegmentation.tex index 97b5cb5d..b1832eed 100644 --- a/SoftwareGuide/Latex/DesignAndFunctionality/WatershedSegmentation.tex +++ b/SoftwareGuide/Latex/DesignAndFunctionality/WatershedSegmentation.tex @@ -171,7 +171,7 @@ \subsection{Using the ITK Watershed Filter} %\begin{figure} %\centering %\includegraphics[width=0.95\textwidth]{WatershedRendering.eps} -%\itkcaption[Watershed segmenation visualization]{A surface rendering (right) +%\itkcaption[Watershed segmentation visualization]{A surface rendering (right) %of four anatomical structures in the Visible %Female head and neck. A slice of the data from which the segmentation was %created is shown at the left. The right and left optic nerves and chiasm are diff --git a/SoftwareGuide/Latex/DevelopmentGuidelines/CreateAModule.tex b/SoftwareGuide/Latex/DevelopmentGuidelines/CreateAModule.tex index e4af8d2b..d2cc4569 100644 --- a/SoftwareGuide/Latex/DevelopmentGuidelines/CreateAModule.tex +++ b/SoftwareGuide/Latex/DevelopmentGuidelines/CreateAModule.tex @@ -541,8 +541,8 @@ \subsection{Class wrap files} \end{table} Class wrap files call sets of wrapping macros for the class to be wrapped. The -macros are often called in loops over the wrapping variables to instatiate the -desired types. The following example demonstates wrapping the +macros are often called in loops over the wrapping variables to instantiate the +desired types. The following example demonstrates wrapping the \doxygen{ImportImageFilter} class, taken from the \code{ITK/Modules/Core/Common/wrapping/itkImportImageFilter.wrap} file. @@ -759,7 +759,7 @@ \subsubsection{Wrapping Enumerations} which results in access to the class in Python as \code{itk.MathematicalMorphologyEnum}, its \code{Algorithm} enumeration class -being accesible as \code{itk.MathematicalMorphologyEnums.Algorithm}, and its +being accessible as \code{itk.MathematicalMorphologyEnums.Algorithm}, and its enum-list being accessed as \code{itk.MathematicalMorphologyEnums.Algorithm\_BASIC}, \code{itk.MathematicalMorphologyEnums.Algorithm\_HISTO}, etc. @@ -1268,9 +1268,9 @@ \subsection{CMakeList.txt} Optionally, the dependency libraries are added to the \code{\_LIBRARIES} variable. Alternatively, if the module creates -a library, publically link to the dependency libraries. Our +a library, publicly link to the dependency libraries. Our ITKVideoBridgeOpenCV module example creates its own library, named -\code{ITKVideoBridgeOpenCV}, and publically links to the OpenCV libraries. +\code{ITKVideoBridgeOpenCV}, and publicly link to the OpenCV libraries. \code{CMakeLists.txt}: \begin{minted}[baselinestretch=1,fontsize=\footnotesize,linenos=false,bgcolor=ltgray]{cmake} diff --git a/SoftwareGuide/Latex/Introduction/Installation.tex b/SoftwareGuide/Latex/Introduction/Installation.tex index 8d3a3a65..8178841a 100644 --- a/SoftwareGuide/Latex/Introduction/Installation.tex +++ b/SoftwareGuide/Latex/Introduction/Installation.tex @@ -305,7 +305,7 @@ \subsection{Advanced Module Configuration} \code{ITKGroup\_\{group name\}} variables for group module selection are visible when \code{ITK\_BUILD\_DEFAULT\_MODULES} is \code{OFF}. The ITK source code tree -is organized in such way that a group of modules characterised by close +is organized in such way that a group of modules characterized by close relationships or similar functionalities stay in one subdirectory. Currently there are 11 groups (excluding the External and Remote groups). The CMake \code{ITKGroup\_\{group name\}} options are created for the convenient enabling diff --git a/SoftwareGuide/Latex/README.md b/SoftwareGuide/Latex/README.md index 71a45111..c764b2d3 100644 --- a/SoftwareGuide/Latex/README.md +++ b/SoftwareGuide/Latex/README.md @@ -18,7 +18,7 @@ Style Guidelines for the ITK Software Guide `\subdoxygen{}`. Subsequent references to the class name should just use plain text (do not - use `\code{}` or `\doxygen{}`). This is for readibility (too much font + use `\code{}` or `\doxygen{}`). This is for readability (too much font changing drives the reader nuts). 3. `\code{}` - Method names (which should have a trailing `()`, e.g., diff --git a/SuperBuild/External_ITK.cmake b/SuperBuild/External_ITK.cmake index dd4ec552..e1172b08 100644 --- a/SuperBuild/External_ITK.cmake +++ b/SuperBuild/External_ITK.cmake @@ -1,4 +1,4 @@ -# Make sure this file is included only once by creating globally unique varibles +# Make sure this file is included only once by creating globally unique variables # based on the name of this included file. get_filename_component(CMAKE_CURRENT_LIST_FILENAME ${CMAKE_CURRENT_LIST_FILE} NAME_WE) if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED) @@ -6,7 +6,7 @@ if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED) endif() set(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED 1) -## External_${extProjName}.cmake files can be recurisvely included, +## External_${extProjName}.cmake files can be recursively included, ## and cmake variables are global, so when including sub projects it ## is important make the extProjName and proj variables ## appear to stay constant in one of these files. diff --git a/SuperBuild/External_RunExamples.cmake b/SuperBuild/External_RunExamples.cmake index e0b02e1f..09384b2a 100644 --- a/SuperBuild/External_RunExamples.cmake +++ b/SuperBuild/External_RunExamples.cmake @@ -1,4 +1,4 @@ -# Make sure this file is included only once by creating globally unique varibles +# Make sure this file is included only once by creating globally unique variables # based on the name of this included file. get_filename_component(CMAKE_CURRENT_LIST_FILENAME ${CMAKE_CURRENT_LIST_FILE} NAME_WE) if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED) @@ -6,7 +6,7 @@ if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED) endif() set(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED 1) -## External_${extProjName}.cmake files can be recurisvely included, +## External_${extProjName}.cmake files can be recursively included, ## and cmake variables are global, so when including sub projects it ## is important make the extProjName and proj variables ## appear to stay constant in one of these files. diff --git a/TODO b/TODO index 4f533d13..dcaf37f1 100644 --- a/TODO +++ b/TODO @@ -10,9 +10,9 @@ Get output images only produced in BINARY_DIR. -- Remove "CenteredTransforms" from all examples in book. -- Remove redundant information. -- Describe Modularization as part of a ITKv3->ITKv4 transition appendix --- Update Acknowledgements +-- Update Acknowledgments -- Test clean builds --- Suport "USE_SYSTEM_ITK" +-- Support "USE_SYSTEM_ITK" ========================================================== This is a list of potential topics to be added to the Software Guide. @@ -161,7 +161,7 @@ Chapter 6 Filtering (5) - 6.2.1 Casting filters (low priority) - spliting CastImageFilter into 4 separate .cxx + splitting CastImageFilter into 4 separate .cxx and check if we have other casting filters... @@ -263,7 +263,7 @@ Chapter 6 Filtering ...maybe add an example... https://www.itk.org/Insight/Doxygen/html/classitk_1_1ReinitializeLevelSetImageFilter.html - Check with Lydia (Brain Allen Institue) and/or Josh Cates (Utah) + Check with Lydia (Brain Allen Institute) and/or Josh Cates (Utah) [Status: Done] [Added Insight/Code/BasicFilters/itkSignedDanielssonDistanceMapImageFilter.hxx, @@ -296,7 +296,7 @@ Chapter 7 IO (1) Karthik - Update Figure 7.3 to add all the known fileformats -- Add a table withh all the fileformat from the FAQ in Wiki. +- Add a table with all the fileformat from the FAQ in Wiki. [Status: Done] [ToDo: Update figure InsightDocuments/Art/SoftwareGuideImageIOFactoriesClassDiagram.fig in CVS] @@ -361,7 +361,7 @@ Chapter 7 IO describe Zion. (check about multithreading). (1) Karthik (add them to the list, not making new examples). - - Secion 8.4 Add the other MI metrics + - Section 8.4 Add the other MI metrics - Kullback Leibler MI @@ -598,7 +598,7 @@ Chapter 9 Segmentation run the Plugins in VolView. [Status: Done Added a 3D example for ConfidenceConnected filter - Some images and segemented white matter with Volview. + Some images and segmented white matter with Volview. ToDo: cvs add 3DregionGrowingScreenshot1.eps cvs add SlicesBrainWebConfidenceConnected.eps @@ -622,7 +622,7 @@ Chapter 9 Segmentation (2) (Luis) Outsource to Sayan - - Add example for KLMRegionGrowing (Ceck with Sayan). + - Add example for KLMRegionGrowing (Check with Sayan). & fix Doxygen documentation. From the Doxygen page on Groups, remove the helper classes used in the KLM filter (e.g. border & region). From 77818f6a6490cf8fd0f78c8a9c18adb5956d4bb5 Mon Sep 17 00:00:00 2001 From: albert-github Date: Sun, 23 Mar 2025 10:48:17 +0100 Subject: [PATCH 2/4] DOC: Spelling corrections review: Spelling corrections --- Latex/Insight.bib | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Latex/Insight.bib b/Latex/Insight.bib index b5814d27..7019b14d 100644 --- a/Latex/Insight.bib +++ b/Latex/Insight.bib @@ -120,9 +120,9 @@ @InProceedings{VoxelTraversal } @PhdThesis{AndresThese, - Author = "E. Andres", - Title = "Cercles discrets et rotations discretes", - School = "Universite Louis Pasteur ", + Author = "{\'E}. Andres", + Title = "Cercles discrets et rotations discr{\`e}tes", + School = "Universit{\'e} Louis Pasteur ", Address = "Strasbourg", year = 1992, } @@ -1932,7 +1932,7 @@ @InProceedings{Jolly2003 @Book{Kaandorp1994, Author = "J.A. Kaandorp", - Title = "Fractal Modelling. Growth and Fxprom in Biology", + Title = "Fractal Modelling. Growth and From in Biology", Publisher = "Springer Verlag", year = 1994, } @@ -2242,7 +2242,7 @@ @Book{Langton1995 @Book{Larsen1997, Author = "W. J. Larsen ", Title = "Embryologie Humaine", - Publisher = "DeBoeck Universite", + Publisher = "DeBoeck Universit{\'e}", year = 1997, } @@ -3278,10 +3278,10 @@ @Book{Reshetnyak1993 } @PhdThesis{ReveillesThese, - Author = "J-P. Reveilles", - Title = "Geometrie discrete, calcul en nombres entiers et + Author = "J-P. Reveill{\`e}s", + Title = "G{\'e}om{\'e}trie discr{\`e}te, calcul en nombres entiers et algorithmique", - School = "Universite Louis Pasteur ", + School = "Universit{\'e} Louis Pasteur ", Address = "Strasbourg", annote = "Departement d'Informatique", year = 1991, From be0b8e3352c05a4eea1bd1f5265d13ae2cfa19cd Mon Sep 17 00:00:00 2001 From: albert-github Date: Sun, 23 Mar 2025 16:29:19 +0100 Subject: [PATCH 3/4] DOC: Spelling corrections review: Spelling corrections --- Latex/Insight.bib | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Latex/Insight.bib b/Latex/Insight.bib index 7019b14d..fd2b2ad4 100644 --- a/Latex/Insight.bib +++ b/Latex/Insight.bib @@ -1932,7 +1932,7 @@ @InProceedings{Jolly2003 @Book{Kaandorp1994, Author = "J.A. Kaandorp", - Title = "Fractal Modelling. Growth and From in Biology", + Title = "Fractal Modelling. Growth and Form in Biology", Publisher = "Springer Verlag", year = 1994, } @@ -3807,10 +3807,10 @@ @Article{Thirion1998 @Book{Thom1977, Author = "R. Thom", - Title = "Stabilite Structurelle et Morphogenese. Essai d'une - theorie generale des modeles", + Title = "Stabilit{\'e} Structurelle et Morphog{\'e}n{\`e}se. Essai d'une + th{\'e}orie generale des mod{\`e}les", Publisher = "InterEditions", - Edition = "Deuxieme", + Edition = "Deuxi{\`}me", year = 1977, } From 5849c78a1d2d3955e9a29f1e570db2c16e4a0fb7 Mon Sep 17 00:00:00 2001 From: albert-github Date: Mon, 24 Mar 2025 09:40:49 +0100 Subject: [PATCH 4/4] DOC: Spelling corrections review: Spelling corrections --- Latex/Insight.bib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Latex/Insight.bib b/Latex/Insight.bib index fd2b2ad4..01a4479c 100644 --- a/Latex/Insight.bib +++ b/Latex/Insight.bib @@ -3810,7 +3810,7 @@ @Book{Thom1977 Title = "Stabilit{\'e} Structurelle et Morphog{\'e}n{\`e}se. Essai d'une th{\'e}orie generale des mod{\`e}les", Publisher = "InterEditions", - Edition = "Deuxi{\`}me", + Edition = "Deuxi{\`e}me", year = 1977, }