Typos found by codespell

DimitriPapadopoulos · hjmjohnson · commit ccfcb9285d1d · 2021-09-08T16:47:33.000-05:00
diff --git a/.gitignore b/.gitignore
@@ -34,7 +34,7 @@ CMakeLists.txt.user*
 # Mac System File
 .DS_Store
 
-# A common file writen from vim by accident
+# A common file written from vim by accident
 :w
 
 # Files when cmake builds in the source tree
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -53,14 +53,14 @@ option( BUILD_SHARED_LIBS "Toggle building shared libraries." OFF)
 option(NIFTI_BUILD_APPLICATIONS "Build various utility tools" ON)
 mark_as_advanced(NIFTI_BUILD_APPLICATIONS)
 
-#When including nifti as a subpackage, a prefix is often needed to avoid conflicts with sytem installed libraries.
+#When including nifti as a subpackage, a prefix is often needed to avoid conflicts with system installed libraries.
 set_if_not_defined(NIFTI_PACKAGE_PREFIX "")
 set(PACKAGE_NAME ${NIFTI_PACKAGE_PREFIX}NIFTI)
 set_if_not_defined(NIFTI_INSTALL_EXPORT_NAME ${PACKAGE_NAME}Targets)
 
 # Set default shared library version
 # This library version will be applied to all libraries in the package
-# unless it is not explicitely for a certain lib.
+# unless it is not explicitly for a certain lib.
 set(NIFTI_SHAREDLIB_VERSION ${GIT_REPO_VERSION} )
 if(BUILD_SHARED_LIBS AND NOT NIFTI_LIBRARY_PROPERTIES)
   set(NIFTI_LIBRARY_PROPERTIES ${DEFAULT_SHARED_LIBS}
@@ -179,7 +179,7 @@ endif()
 
 option(USE_FSL_CODE "If OFF, The copyright of this code is questionable for inclusion with nifti." OFF)
 mark_as_advanced(USE_FSL_CODE)
-# the order of add_subdirectory is important! fsliolob has to preceed examples
+# the order of add_subdirectory is important! fsliolob has to precede, examples
 # as otherwise FSLIOLIB_SOURCE_DIR is undefined and hence the examples
 # will fail to compile
 if(USE_FSL_CODE)
diff --git a/Makefile b/Makefile
@@ -205,7 +205,7 @@ tar:
 mention_cmake:
 	@echo ""
 	@echo "---------------------------------------------------------"
-	@echo "This packages has changed to rely more primarly on cmake,"
+	@echo "This packages has changed to rely more primarily on cmake,"
 	@echo "and the Makefile system needs a little love."
 	@echo ""
 	@echo "Consider the steps for cmake, if they would be helpful:"
diff --git a/Makefile.cross_mingw32 b/Makefile.cross_mingw32
@@ -10,7 +10,7 @@
 # Like the other parts of this package, this code is placed into the public
 # domain.
 #
-# The 'devpak' target generates a DevPak suiteable for Dev-Cpp, see:
+# The 'devpak' target generates a DevPak suitable for Dev-Cpp, see:
 # http://www.bloodshed.net/devcpp.html
 #
 # Requirements:
@@ -79,7 +79,7 @@ install-devpak: build-devpak
 	cd $(build_dir) && make install DESTDIR=../
 
 devpak: install-devpak
-	# nifti_tool header is unecessary
+	# nifti_tool header is unnecessary
 	rm $(devpak_dir)/include/nifti/nifti_tool.h
 
 	# generate devpak info file
diff --git a/README.md b/README.md
@@ -16,10 +16,10 @@ hope it is also a useful i/o library.
 `Nifti_clib` code is released into the public domain,
 developers are encouraged to incorporate niftilib code into their applications,
 and, to contribute changes and enhancements to niftilib. Please contact us if
-you would like to contribute additonal functionality to the i/o library.
+you would like to contribute additional functionality to the i/o library.
 
 The main webpage for this project is [hosted on github](https://nifti-imaging.github.io/).
-This web site provde historical information.  Additional informaiton from the [NIFTI DFWG](http://nifti.nimh.nih.gov)
+This web site provde historical information.  Additional information from the [NIFTI DFWG](http://nifti.nimh.nih.gov)
 
 The testing dashboard for monitoring the health of the libraries is at
 [my.cdash.org](https://my.cdash.org/index.php?project=nifti_clib).
diff --git a/Updates.txt b/Updates.txt
@@ -32,8 +32,8 @@ Updates in version 0.4 September 6, 2006
 -----------------------------------------------------------------
 Updates in version 0.5 May 17, 2007
 
-    - fixed duplication of incuding utils directory for CMake
-    - syncronized with developments in ITK to prepare for building and
+    - fixed duplication of including utils directory for CMake
+    - synchronized with developments in ITK to prepare for building and
       tar/rpm/dmg packaging with new versions of cmake
     - added more typecasting to remove compiler warnings
     - fslio.c: check for NULL return from nifti_image_read()
@@ -136,4 +136,4 @@ Updated in version 3.0.0 July 16, 2020
 Updated in version 3.0.1 Aug 07, 2020
     - JL made fix for cmake config add example usage and a test for it
     - JL changed default behavior to not build manpages
-    - RR made a fix for the make build and added a suggestion to use the cmake
+    - RR made a fix for the make build and added a suggestion to use the cmake
diff --git a/cifti/afni_xml_io.c b/cifti/afni_xml_io.c
@@ -521,7 +521,7 @@ static int64_t text_to_i64(int64_t * result, const char * text, int64_t nvals)
    int64_t * rptr, val;
    int64_t   nread;
 
-   *result = 0; /* Initialize to zero incase of failure */
+   *result = 0; /* Initialize to zero in case of failure */
    if( ! text || ! result) return 1;
    if( nvals <= 0 )        return 0;
 
diff --git a/cifti/cifti_tool.c b/cifti/cifti_tool.c
@@ -410,7 +410,7 @@ int ax_show_names(FILE * fp, afni_xml_t * ax, int depth)
 }
 
 /*----------------------------------------------------------------------
- *! display data in hexidecimal, on one line
+ *! display data in hexadecimal, on one line
  *
  *  if mesg is set, print the message first
  *  if fp is not set, print to stdout
diff --git a/cmake/nifti_common.cmake b/cmake/nifti_common.cmake
@@ -425,7 +425,7 @@ while(NOT dashboard_done)
       dashboard_hook_test()
     endif()
     ctest_test(${CTEST_TEST_ARGS} RETURN_VALUE test_return)
-    set(safe_message_skip 1) # Block furhter messages
+    set(safe_message_skip 1) # Block further messages
 
     if(dashboard_do_coverage)
       if(COMMAND dashboard_hook_coverage)
diff --git a/docs/Doxyfile.ORIG b/docs/Doxyfile.ORIG
@@ -139,7 +139,7 @@ STRIP_CODE_COMMENTS    = YES
 # file names in lower case letters. If set to YES upper case letters are also
 # allowed. This is useful if you have classes or files whose names only differ
 # in case and if your file system supports case sensitive file names. Windows
-# users are adviced to set this option to NO.
+# users are advised to set this option to NO.
 
 CASE_SENSE_NAMES       = YES
 
@@ -165,7 +165,7 @@ SHOW_INCLUDE_FILES     = YES
 # will interpret the first line (until the first dot) of a JavaDoc-style
 # comment as the brief description. If set to NO, the JavaDoc
 # comments  will behave just like the Qt-style comments (thus requiring an
-# explict @brief command for a brief description.
+# explicit @brief command for a brief description.
 
 JAVADOC_AUTOBRIEF      = NO
 
@@ -410,7 +410,7 @@ DISABLE_INDEX          = NO
 
 ENUM_VALUES_PER_LINE   = 4
 
-# If the GENERATE_TREEVIEW tag is set to YES, a side pannel will be
+# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
 # generated containing a tree-like index structure (just like the one that
 # is generated for HTML Help). For this to work a browser that supports
 # JavaScript and frames is required (for instance Netscape 4.0+
@@ -515,7 +515,7 @@ COMPACT_RTF            = NO
 RTF_HYPERLINKS         = NO
 
 # Load stylesheet definitions from file. Syntax is similar to doxygen's
-# config file, i.e. a series of assigments. You only have to provide
+# config file, i.e. a series of assignments. You only have to provide
 # replacements, missing definitions are set to their default value.
 
 RTF_STYLESHEET_FILE    =
diff --git a/nifti2/nifti1.h b/nifti2/nifti1.h
@@ -873,7 +873,7 @@ typedef struct { unsigned char r,g,b; } rgb_byte ;
      as a displacement field or vector:
        - dataset must have a 5th dimension
        - intent_code must be NIFTI_INTENT_DISPVECT
-       - dim[5] must be the dimensionality of the displacment
+       - dim[5] must be the dimensionality of the displacement
          vector (e.g., 3 for spatial displacement, 2 for in-plane) */
 
 #define NIFTI_INTENT_DISPVECT  1006   /* specifically for displacements */
diff --git a/nifti2/nifti2_io.c b/nifti2/nifti2_io.c
@@ -42,7 +42,7 @@ static char const * const gni1_history[] =
   "     (FMRIB Centre, University of Oxford, UK)\n"
   "   - Mainly adding low-level IO and changing things to allow gzipped\n"
   "     files to be read and written\n"
-  "   - Full backwards compatability should have been maintained\n"
+  "   - Full backwards compatibility should have been maintained\n"
   "\n",
   "0.2  16 Nov 2004 [rickr]\n"
   "     (Rick Reynolds of the National Institutes of Health, SSCC/DIRP/NIMH)\n"
@@ -265,7 +265,7 @@ static char const * const gni1_history[] =
   "1.12b 25 August 2005 [rickr] - changes by Hans Johnson\n",
   "1.13  25 August 2005 [rickr]\n",
   "   - finished changes by Hans for Insight\n"
-  "   - added const in all appropraite parameter locations (30-40)\n"
+  "   - added const in all appropriate parameter locations (30-40)\n"
   "     (any pointer referencing data that will not change)\n"
   "   - shortened all string constants below 509 character limit\n"
   "1.14  28 October 2005 [HJohnson]\n",
@@ -1154,7 +1154,7 @@ int valid_nifti_brick_list(nifti_image * nim , int64_t nbricks,
 
    if( nim->dim[0] < 3 ){
       if( disp_error || g_opts.debug > 1 )
-        fprintf(stderr,"** NIFTI: cannot read explict brick list from %" PRId64
+        fprintf(stderr,"** NIFTI: cannot read explicit brick list from %" PRId64
                 "-D dataset\n", nim->dim[0]);
       return 0;
    }
@@ -2615,7 +2615,7 @@ mat33 nifti_mat33_polar( mat33 A )
 }
 
 /*---------------------------------------------------------------------------*/
-/*! compute the (closest) orientation from a 4x4 ijk->xyz tranformation matrix
+/*! compute the (closest) orientation from a 4x4 ijk->xyz transformation matrix
 
    <pre>
    Input:  4x4 matrix that transforms (i,j,k) indexes to (x,y,z) coordinates,
@@ -2799,7 +2799,7 @@ void nifti_dmat44_to_orientation( nifti_dmat44 R ,
    *icod = i ; *jcod = j ; *kcod = k ; }
 
 /*---------------------------------------------------------------------------*/
-/*! compute the (closest) orientation from a 4x4 ijk->xyz tranformation matrix
+/*! compute the (closest) orientation from a 4x4 ijk->xyz transformation matrix
 
    <pre>
    Input:  4x4 matrix that transforms (i,j,k) indexes to (x,y,z) coordinates,
@@ -2993,7 +2993,7 @@ void nifti_mat44_to_orientation( mat44 R , int *icod, int *jcod, int *kcod )
 /*! swap each byte pair from the given list of n pairs
  *
  *  Due to alignment of structures at some architectures (e.g. on ARM),
- *  stick to char varaibles.
+ *  stick to char variables.
  *  Fixes http://bugs.debian.org/446893   Yaroslav <debian@onerussian.com>
  *
 *//*--------------------------------------------------------------------*/
@@ -3725,7 +3725,7 @@ char * nifti_findhdrname(const char* fname)
 
    /* note: efirst is 0 in the case of ".img" */
 
-   /* if the user passed an uppercase entension (.IMG), search for uppercase */
+   /* if the user passed an uppercase extension (.IMG), search for uppercase */
    if( eisupper ) {
       make_uppercase(elist[0]);
       make_uppercase(elist[1]);
@@ -4062,11 +4062,11 @@ int nifti_set_filenames( nifti_image * nim, const char * prefix, int check,
     - if type 1, expect .nii (and names must match)
 
     \param nim       given nifti_image
-    \param show_warn if set, print a warning message for any mis-match
+    \param show_warn if set, print a warning message for any mismatch
 
     \return
         -   1 if the values seem to match
-        -   0 if there is a mis-match
+        -   0 if there is a mismatch
         -  -1 if there is not sufficient information to create file(s)
 
     \sa NIFTI_FTYPE_* codes in nifti1_io.h
@@ -4118,7 +4118,7 @@ int nifti_type_and_names_match( nifti_image * nim, int show_warn )
       errs++;
    }
 
-   if( errs ) return 0;   /* do not proceed, but this is just a mis-match */
+   if( errs ) return 0;   /* do not proceed, but this is just a mismatch */
 
    /* general tests */
    if( (nim->nifti_type == NIFTI_FTYPE_NIFTI1_1) ||
@@ -7294,7 +7294,7 @@ nifti_1_header * nifti_make_new_n1_header(const int64_t arg_dims[],
 /*! basic creation of a nifti_image struct
 
    Create a nifti_image from the given dimensions and data type.
-   Optinally, allocate zero-filled data.
+   Optionally, allocate zero-filled data.
 
    \param dims      : optional dim[8]   (default {3,1,1,1,0,0,0,0})
    \param datatype  : optional datatype (default DT_FLOAT32)
@@ -7646,7 +7646,7 @@ int nifti_copy_extensions(nifti_image * nim_dest, const nifti_image * nim_src)
       /* data length is size-8, as esize includes space for esize and ecode */
       data = (char *)calloc(size-8,sizeof(char));      /* maybe size > old */
       if( !data ){
-         fprintf(stderr,"** NIFTI: failed to alloc %d bytes for extention\n",
+         fprintf(stderr,"** NIFTI: failed to alloc %d bytes for extension\n",
                  size);
          if( c == 0 ) { free(nim_dest->ext_list); nim_dest->ext_list = NULL; }
          /* otherwise, keep what we have (a.o.t. deleting them all) */
@@ -8966,7 +8966,7 @@ compute_strides(int64_t *strides,const int64_t *size,int nbyper)
 /*---------------------------------------------------------------------------*/
 /*! read an arbitrary subregion from a nifti image
 
-    This function may be used to read a single arbitary subregion of any
+    This function may be used to read a single arbitrary subregion of any
     rectangular size from a nifti dataset, such as a small 5x5x5 subregion
     around the center of a 3D image.
 
diff --git a/nifti2/nifti2_io.h b/nifti2/nifti2_io.h
@@ -50,7 +50,7 @@ extern "C" {
 
       Mainly adding low-level IO and changing things to allow gzipped files
       to be read and written
-      Full backwards compatability should have been maintained
+      Full backwards compatibility should have been maintained
 
    ......................................................................
    Modified by: Rick Reynolds (SSCC/DIRP/NIMH, National Institutes of Health)
@@ -65,7 +65,7 @@ extern "C" {
 
       Converted to be based on nifti_2_header.
 
-      ** NOT BACKWARD COMPATABLE **
+      ** NOT BACKWARD COMPATIBLE **
 
       These routines will read/write both NIFTI-1 and NIFTI-2 image files,
       but modification to the _calling_ routies is necessary, since:
diff --git a/nifti2/nifti_regress_test/README_regress b/nifti2/nifti_regress_test/README_regress
@@ -11,13 +11,13 @@ be fast and easy.
 
 The test consists of command scripts that were written before.  The
 scripts are executed, and the output is compared with the output of
-an older execution.  The should ususally be identical.
+an older execution.  The should usually be identical.
 
 ---------------------------------------------------------------------------
 
 To perform regression testing, one needs the data (via 'make regress_data').
 Given that, only the @test and @show_diffs are needed (sample commands are
-shown with a preceeding prompt, '> ').
+shown with a preceding prompt, '> ').
 
     1. Run the regression testing script.  It goes through the steps:
 
diff --git a/nifti2/nifti_regress_test/cmake_testscripts/c21_b_cifti_in.sh b/nifti2/nifti_regress_test/cmake_testscripts/c21_b_cifti_in.sh
@@ -176,7 +176,7 @@ else
 echo === good: diff_hdr2 showed a difference
 fi
 
-echo "============== swap hdr as NIFTI (failes for N-2, but still debug)"
+echo "============== swap hdr as NIFTI (fails for N-2, but still debug)"
 if $NT -swap_as_nifti -debug 3 -infiles ${infile} -prefix ${prefix}.05.swap.nii
 then
 echo === swap_as_nifti incorrectly succeeded
diff --git a/nifti2/nifti_regress_test/commands/b20.mod.hdr b/nifti2/nifti_regress_test/commands/b20.mod.hdr
@@ -1,7 +1,7 @@
 #!/bin/tcsh
 
 # written in the format of the bash scripts under cmake_testscripts
-# (this is not meant to be run along with the c* scritps here)
+# (this is not meant to be run along with the c* scripts here)
 
 if ( $#argv < 2 ) then
    echo "** missing nifti tool and data directory name"
diff --git a/nifti2/nifti_tool.c b/nifti2/nifti_tool.c
diff --git a/nifticdf/nifticdf.c b/nifticdf/nifticdf.c
diff --git a/niftilib/nifti1.h b/niftilib/nifti1.h
diff --git a/niftilib/nifti1_io.c b/niftilib/nifti1_io.c
diff --git a/niftilib/nifti1_io.h b/niftilib/nifti1_io.h
diff --git a/niftilib/nifti1_tool.c b/niftilib/nifti1_tool.c
diff --git a/niftilib/nifti_tester001.c b/niftilib/nifti_tester001.c
diff --git a/real_easy/Demonstrations.md b/real_easy/Demonstrations.md

Original file line number	Diff line number	Diff line change
`@@ -410,7 +410,7 @@ int ax_show_names(FILE * fp, afni_xml_t * ax, int depth)`
`410`	`410`	`}`
`411`	`411`
`412`	`412`	`/*----------------------------------------------------------------------`
`413`		`- *! display data in hexidecimal, on one line`
	`413`	`+ *! display data in hexadecimal, on one line`
`414`	`414`	`*`
`415`	`415`	`* if mesg is set, print the message first`
`416`	`416`	`* if fp is not set, print to stdout`