DOC: Render examples in the CookBook

Documentation/Cookbook/CMakeLists.txt

@@ -117,10 +117,15 @@ file(COPY ${RST_SOURCE_DIR}  DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 
 file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/Art DESTINATION  ${RST_BINARY_DIR})
 
+# Create symlinks to otb-data/Output and otb-data/Input in the rst build directory
+# Used for including figures and images in the CookBook
+execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink "${OTB_DATA_ROOT}/Output" "${RST_BINARY_DIR}/Output")
+execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink "${OTB_DATA_ROOT}/Input" "${RST_BINARY_DIR}/Input")
+
 set(SPHINX_CONF_DIR ${CMAKE_CURRENT_BINARY_DIR})
 
 string(TIMESTAMP OTB_COPYRIGHT_YEAR  "%Y")
-set(OTB_COPYRIGHT_TEXT "${OTB_COPYRIGHT_YEAR} CNES.The OTB CookBook is licensed under a Creative Commons Attribution-ShareAlike 4.0 International license (CC-BY-SA)")
+set(OTB_COPYRIGHT_TEXT "${OTB_COPYRIGHT_YEAR} CNES. The OTB CookBook is licensed under a Creative Commons Attribution-ShareAlike 4.0 International license (CC-BY-SA).")
 
 configure_file(${RST_SOURCE_DIR}/conf.py.in ${SPHINX_CONF_DIR}/conf.py @ONLY)
 
@@ -130,7 +135,16 @@ add_custom_target(generate_otbapps_rst
   COMMAND ${SH_INTERP} ${CMAKE_CURRENT_BINARY_DIR}/RunApplicationsRstGenerator.sh
   ${RST_BINARY_DIR}
   WORKING_DIRECTORY ${RST_BINARY_DIR}
-  COMMENT "Auto-generating Application Reference Documentation in RST"
+  COMMENT "Auto-generating Application Documentation in RST"
+  DEPENDS OTBSWIGWrapper-all
+  )
+
+add_custom_target(generate_examples_rst
+  COMMAND "python3" ${CMAKE_CURRENT_SOURCE_DIR}/Scripts/otbGenerateExamplesRstDoc.py
+  ${RST_BINARY_DIR}
+  ${CMAKE_SOURCE_DIR}
+  WORKING_DIRECTORY ${RST_BINARY_DIR}
+  COMMENT "Auto-generating Examples in RST"
   DEPENDS OTBSWIGWrapper-all
   )
 
@@ -152,6 +166,7 @@ add_custom_target(CookBookHTML
   -c ${SPHINX_CONF_DIR}
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
   DEPENDS generate_otbapps_rst
+  DEPENDS generate_examples_rst
   COMMENT "Building RST documentation in html")
 
 add_custom_target(CookBookArchive

Documentation/Cookbook/Scripts/RunExamples.py

+#!/usr/bin/env python3
+#
+# Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
+#
+# This file is part of Orfeo Toolbox
+#
+#     https://www.orfeo-toolbox.org/
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import argparse
+import glob
+import subprocess
+import os
+from os.path import join
+import re
+
+def run_example(otb_root, otb_data, name, dry_run):
+    """
+    Run an example by name
+    Assumes the current working directory is an OTB build
+    """
+
+    # Find binary in bin/
+    binary_names = glob.glob(join("bin", name))
+    if len(binary_names) == 0:
+        raise RuntimeError("Can't find binary for {}".format(name))
+    if len(binary_names) > 1:
+        raise RuntimeError("Found {} binaries for {}".format(len(binary_names), name))
+    binary = os.path.abspath(binary_names[0])
+
+    # Find source file in otb_root/Examples/<tag>/name
+    sources_files = glob.glob(join(otb_root, "Examples/*/" + name + ".cxx"))
+    if len(sources_files) == 0:
+        raise RuntimeError("Can't find source file for {}".format(name))
+    if len(sources_files) > 1:
+        raise RuntimeError("Found {} source files for {}".format(len(sources_files), name))
+    filename = os.path.abspath(sources_files[0])
+
+    # Extract example usage command arguments
+    usage_rx = r"\/\* Example usage:\n\.\/[a-zA-Z]+ (.*?)\*\/"
+    match = re.search(usage_rx, open(filename).read(), flags = re.MULTILINE | re.DOTALL)
+
+    if not match:
+        raise RuntimeError("Can't find example usage in {}".format(filename))
+
+    example_args = match.group(1).replace("\\\n", "").split()
+
+    # Make sure Output dir exists
+    os.makedirs(join(otb_data, "Output"), exist_ok=True)
+
+    print("$ " + binary + " " + " ".join(example_args))
+
+    if dry_run:
+        return
+
+    # Execute the example with otb_data as working directory,
+    # because paths are given relative to otb_data in the example usage
+    subprocess.check_call([binary, *example_args], cwd=otb_data)
+
+# TODO handle examples with multiple usage (Examples/BasicFilters/DEMToRainbowExample.cxx)
+
+def main():
+    parser = argparse.ArgumentParser(usage="Run one or all OTB cxx examples")
+    parser.add_argument("otb_root", help="Path to otb repository")
+    parser.add_argument("otb_data", help="Path to otb-data repository")
+    parser.add_argument("--name", type=str, help="Run only one example with then given name")
+    parser.add_argument("-n", "--dry-run", action='store_true', help="Dry run, only print commands")
+    parser.add_argument("-k", "--keep-going", action='store_true', help="Keep going after failing examples")
+    args = parser.parse_args()
+
+    if args.name:
+        run_example(args.otb_root, args.otb_data, args.name, dry_run=args.dry_run)
+    else:
+        list_of_examples =[os.path.splitext(os.path.basename(f))[0] for f in glob.glob(join(args.otb_root, "Examples/*/*.cxx"))]
+        for name in list_of_examples:
+            try:
+                run_example(args.otb_root, args.otb_data, name, dry_run=args.dry_run)
+            except Exception as e:
+                if args.keep_going:
+                    print("Warning:", e)
+                else:
+                    raise
+
+if __name__ == "__main__":
+    main()

Documentation/Cookbook/Scripts/otbGenerateExamplesRstDoc.py

+#!/usr/bin/env python3
+#
+# Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
+#
+# This file is part of Orfeo Toolbox
+#
+#     https://www.orfeo-toolbox.org/
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import argparse
+import os
+import os.path
+from os.path import join
+from collections import defaultdict
+import re
+import glob
+
+from rst_utils import rst_section, RstPageHeading
+
+def generate_examples_index(rst_dir, list_of_examples):
+
+    # Compute dictionary of tag -> (list of examples)
+    tag_files = defaultdict(list)
+    for filename in list_of_examples:
+        tag = filename.split("/")[1]
+        name, _ = os.path.splitext(filename.split("/")[2])
+
+        tag_files[tag].append(join(tag, name + ".rst"))
+
+    # Render index file and tag index files
+    os.makedirs(join(rst_dir, "Examples"), exist_ok=True)
+    index_f = open(join(rst_dir, "Examples.rst"), "w")
+    index_f.write(RstPageHeading("Examples", 3, ref="cpp-examples"))
+
+    for tag, examples_filenames in tag_files.items():
+        tag_filename = join("Examples", tag + ".rst")
+        index_f.write("\t" + tag_filename + "\n")
+
+        with open(join(rst_dir, tag_filename), "w") as tag_f:
+            tag_f.write(RstPageHeading(tag, 3))
+
+            for examples_filename in examples_filenames:
+                tag_f.write("\t" + examples_filename + "\n")
+
+def indent(str):
+    return "\n".join(["    " + line for line in str.split("\n")])
+
+def cpp_uncomment(code):
+    # Strip '//  '
+    return "\n".join([line[4:] for line in code.split("\n")])
+
+def render_example(filename, otb_root):
+    "Render a cxx example to rst"
+
+    # Read the source code of the cxx example
+    code = open(join(otb_root, filename)).read()
+
+    # Don't show the license header to make it nicer,
+    # and the cookbook is already under a CC license
+    examples_license_header = open("templates/examples_license_header.txt").read()
+    code = code.replace(examples_license_header, "")
+
+    # Extract usage
+    # TODO handle multiple usage
+    rx_usage = r"\/\* Example usage:\n(\.\/[a-zA-Z]+ (.*?))\*\/"
+    usage_match = re.search(rx_usage, code, flags = re.MULTILINE | re.DOTALL)
+    if usage_match is None:
+        print("Warning: no usage found for example " + filename)
+        example_usage = ""
+    else:
+        example_usage = open("templates/example_usage.rst").read().format(indent(usage_match.group(1).strip()))
+
+    # Don't show usage in example source
+    code = re.sub(rx_usage, "", code, flags = re.MULTILINE | re.DOTALL)
+
+    # Make the link to the source code
+    link_name = os.path.basename(filename)
+    link_href = "https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb/raw/develop/" + filename + "?inline=false"
+
+    # Read the description from the example .rst file if it exists
+    example_rst_file = join(otb_root, filename.replace(".cxx", ".rst"))
+    if os.path.isfile(example_rst_file):
+        rst_description = open(example_rst_file).read()
+    else:
+        rst_description = ""
+
+    # Render the template
+    template_example = open("templates/example.rst").read()
+    output_rst = template_example.format(
+        label="example-" + root,
+        heading=rst_section(name, "="),
+        description=rst_description,
+        usage=example_usage,
+        code=indent(code.strip()),
+        link_name=link_name,
+        link_href=link_href
+    )
+
+    return output_rst
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(usage="Export examples to rst")
+    parser.add_argument("rst_dir", help="Directory where rst files are generated")
+    parser.add_argument("otb_root", help="OTB repository root")
+    args = parser.parse_args()
+
+    # Get list of cxx examples as relative paths from otb_root
+    list_of_examples = [os.path.relpath(p, start=args.otb_root) for p in glob.glob(join(args.otb_root, "Examples/*/*.cxx"))]
+    print("Generating rst for {} examples".format(len(list_of_examples)))
+
+    # Generate example index and tag indexes
+    generate_examples_index(join(args.rst_dir, "C++"), list_of_examples)
+
+    # Generate examples rst
+    for filename in list_of_examples:
+        name = os.path.basename(filename)
+        tag = filename.split("/")[1]
+        root, ext = os.path.splitext(name)
+
+        os.makedirs(join(args.rst_dir, "C++", "Examples", tag), exist_ok=True)
+        with open(join(args.rst_dir, "C++", "Examples", tag, root + ".rst"), "w") as output_file:
+            output_file.write(render_example(filename, args.otb_root))

Documentation/Cookbook/Scripts/otbGenerateWrappersRstDoc.py

@@ -29,6 +29,8 @@ from otbApplication import ParameterType_Bool, ParameterType_Int, ParameterType_
 
 from otb_warnings import application_documentation_warnings
 
+from rst_utils import rst_section, RstPageHeading
+
 linesep = os.linesep
 
 def EncloseString(s):
@@ -179,17 +181,6 @@ def render_choice(app, key):
         choices=choice_entries,
     )
 
-def rst_section(text, delimiter, ref=None):
-    "Make a rst section title"
-
-    output = ""
-
-    if ref is not None:
-        output += ".. _" + ref + ":\n\n"
-
-    output += text + "\n" + delimiter * len(text) + "\n\n"
-    return output
-
 def rst_parameter_value(app, key):
     "Render a parameter value to rst"
 
@@ -400,13 +391,6 @@ def GetApplicationTags(appname):
      app = otbApplication.Registry.CreateApplication(appname)
      return app.GetDocTags()
 
-def RstPageHeading(text, maxdepth, ref=None):
-    output = rst_section(text, "=", ref=ref)
-    output += ".. toctree::" + linesep
-    output += "\t:maxdepth: " + maxdepth + linesep
-    output += linesep + linesep
-    return output
-
 def GenerateRstForApplications(rst_dir):
     "Generate .rst files for all applications"
 

Documentation/Cookbook/Scripts/rst_utils.py

+
+def rst_section(text, delimiter, ref=None):
+    "Make a rst section title"
+
+    output = ""
+
+    if ref is not None:
+        output += ".. _" + ref + ":\n\n"
+
+    output += text + "\n" + delimiter * len(text) + "\n\n"
+    return output
+
+def RstPageHeading(text, maxdepth, ref=None):
+    output = rst_section(text, "=", ref=ref)
+    output += ".. toctree::\n"
+    output += "\t:maxdepth: {}\n\n\n".format(maxdepth)
+    return output
+

Documentation/Cookbook/rst/C++.rst

+.. _cpp-api:
+
+C++ API
+=======
+
+.. toctree::
+
+    C++/Examples.rst

Documentation/Cookbook/rst/index_TOC.rst

@@ -13,5 +13,6 @@ Table of Contents
    AdvancedUse
    Recipes
    Applications
+   C++
    FAQ
    Contributors

Documentation/Cookbook/rst/templates/example.rst

+.. _{label}:
+
+{heading}
+
+{description}
+
+{usage}
+
+Example source code (`{link_name} <{link_href}>`_):
+
+.. code-block:: cpp
+
+{code}

Documentation/Cookbook/rst/templates/example_usage.rst

+Example usage:
+
+.. code-block:: bash
+
+{}

Documentation/Cookbook/rst/templates/examples_license_header.txt

+/*
+ * Copyright (C) 2005-2019 Centre National d'Etudes Spatiales (CNES)
+ *
+ * This file is part of Orfeo Toolbox
+ *
+ *     https://www.orfeo-toolbox.org/
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */

Examples/Application/ApplicationExample.cxx

@@ -19,88 +19,57 @@
  */
 
 
+/* Example usage:
+./ApplicationExample Input/QB_Suburb.png Output/ApplicationExample.png
+*/
 
-//  Software Guide : BeginCommandLineArgs
-//    INPUTS: {QB_Suburb.png}
-//    OUTPUTS: {ApplicationExample.png}
-//  Software Guide : EndCommandLineArgs
 
-
-//  Software Guide : BeginLatex
 // This example illustrates the creation of an application.
 // A new application is a class, which derives from \subdoxygen{otb}{Wrapper}{Application} class.
 // We start by including the needed header files.
-//
-//  Software Guide : EndLatex
 
-//  Software Guide : BeginCodeSnippet
 #include "otbWrapperApplication.h"
 #include "otbWrapperApplicationFactory.h"
-//  Software Guide : EndCodeSnippet
 
 namespace otb
 {
 
-//  Software Guide : BeginLatex
 //  Application class is defined in Wrapper namespace.
-//
-//  Software Guide : EndLatex
 
-//  Software Guide : BeginCodeSnippet
 namespace Wrapper
 {
-//  Software Guide : EndCodeSnippet
 
 
-//  Software Guide : BeginLatex
-//
 //  ExampleApplication class is derived from Application class.
-//
-//  Software Guide : EndLatex
 
-//  Software Guide : BeginCodeSnippet
 class ApplicationExample : public Application
-//  Software Guide : EndCodeSnippet
 {
 public:
-  //  Software Guide : BeginLatex
   // Class declaration is followed by \code{ITK} public types for the class, the superclass and
   // smart pointers.
-  // Software Guide : EndLatex
 
-  //  Software Guide : BeginCodeSnippet
-  typedef ApplicationExample Self;
-  typedef Application Superclass;
-  typedef itk::SmartPointer<Self> Pointer;
+  typedef ApplicationExample            Self;
+  typedef Application                   Superclass;
+  typedef itk::SmartPointer<Self>       Pointer;
   typedef itk::SmartPointer<const Self> ConstPointer;
-  // Software Guide : EndCodeSnippet
 
-  //  Software Guide : BeginLatex
   //  Following macros are necessary to respect ITK object factory mechanisms. Please report
   //  to \ref{sec:FilterConventions} for additional information.
-  //  Software Guide : EndLatex
 
-  //  Software Guide : BeginCodeSnippet
   itkNewMacro(Self);
   itkTypeMacro(ExampleApplication, otb::Application);
-  //  Software Guide : EndCodeSnippet
 
 
 private:
-  //  Software Guide : BeginLatex
   //  \doxygen{otb}{Application} relies on three main private methods: \code{DoInit()}, \code{DoUpdate()}, and \code{DoExecute()}.
   //  Section \ref{sec:appArchitecture} gives a description a these methods.
-  //  Software Guide : EndLatex
 
 
-  //  Software Guide : BeginLatex
   //  \code{DoInit()} method contains class information and description, parameter set up, and example values.
-  //  Software Guide : EndLatex
 
   void DoInit() override
   {
 
-    // Software Guide : BeginLatex
     // Application name and description are set using following methods :
     // \begin{description}
     // \item[\code{SetName()}] Name of the application.
@@ -111,44 +80,36 @@ private:
     // \item[\code{SetDocAuthors()}] Set the application Authors. Author List. Format : "John Doe, Winnie the Pooh" \dots
     // \item[\code{SetDocSeeAlso()}] If the application is related to one another, it can be mentioned.
     // \end{description}
-    // Software Guide : EndLatex
 
-    //  Software Guide : BeginCodeSnippet
     SetName("Example");
-    SetDescription("This application opens an image and save it. "
-      "Pay attention, it includes Latex snippets in order to generate "
-      "software guide documentation");
+    SetDescription(
+        "This application opens an image and save it. "
+        "Pay attention, it includes Latex snippets in order to generate "
+        "software guide documentation");
 
     SetDocName("Example");
-    SetDocLongDescription("The purpose of this application is "
-      "to present parameters types,"
-      " and Application class framework. "
-      "It is used to generate Software guide documentation"
-      " for Application chapter example.");
+    SetDocLongDescription(
+        "The purpose of this application is "
+        "to present parameters types,"
+        " and Application class framework. "
+        "It is used to generate Software guide documentation"
+        " for Application chapter example.");
     SetDocLimitations("None");
     SetDocAuthors("OTB-Team");
     SetDocSeeAlso(" ");
-    //  Software Guide : EndCodeSnippet
 
 
-    // Software Guide : BeginLatex
     // \code{AddDocTag()} method categorize the application using relevant tags.
     // The header file \code{otbWrapperTags.h} in OTB sources contains some predefined tags defined in \code{Tags} namespace.
-    // Software Guide : EndLatex
 
-    //  Software Guide : BeginCodeSnippet
     AddDocTag(Tags::Analysis);
     AddDocTag("Test");
-    //  Software Guide : EndCodeSnippet
 
-    // Software Guide : BeginLatex
     // Application parameters declaration is done using \code{AddParameter()} method.
     // \code{AddParameter()} requires the input parameter type
     // (ParameterType\_InputImage, ParameterType\_Int, ParameterType\_Float), its name and description.
     // \subdoxygen{otb}{Wrapper}{Application} class contains methods to set parameters characteristics.
-    // Software Guide : EndLatex
 
-    //  Software Guide : BeginCodeSnippet
     AddParameter(ParameterType_InputImage, "in", "Input Image");
 
     AddParameter(ParameterType_OutputImage, "out", "Output Image");
@@ -181,13 +142,11 @@ private:
     AddChoice("inchoice.choice1", "Choice 1");
     AddChoice("inchoice.choice2", "Choice 2");
     AddChoice("inchoice.choice3", "Choice 3");
-      
-    AddParameter(ParameterType_Float, "inchoice.choice1.floatchoice1"
-                 , "Example of float parameter for choice1");
+
+    AddParameter(ParameterType_Float, "inchoice.choice1.floatchoice1", "Example of float parameter for choice1");
     SetDefaultParameterFloat("inchoice.choice1.floatchoice1", 0.125);
 
-    AddParameter(ParameterType_Float, "inchoice.choice3.floatchoice3"
-                 , "Example of float parameter for choice3");
+    AddParameter(ParameterType_Float, "inchoice.choice3.floatchoice3", "Example of float parameter for choice3");
     SetDefaultParameterFloat("inchoice.choice3.floatchoice3", 5.0);
 
     AddParameter(ParameterType_Group, "ingroup", "Input group");
@@ -195,14 +154,12 @@ private:
     AddParameter(ParameterType_Int, "ingroup.valint", "Example of integer parameter for group");
     MandatoryOff("ingroup.valint");
     AddParameter(ParameterType_Group, "ingroup.images", "Input Images group");
-    AddParameter(ParameterType_InputImage, "ingroup.images.inputimage"
-                 , "Input Image");
+    AddParameter(ParameterType_InputImage, "ingroup.images.inputimage", "Input Image");
     MandatoryOff("ingroup.images.inputimage");
 
     AddParameter(ParameterType_Group, "outgroup", "Output group");
     MandatoryOff("outgroup");
-    AddParameter(ParameterType_OutputImage, "outgroup.outputimage"
-                 , "Output Image");
+    AddParameter(ParameterType_OutputImage, "outgroup.outputimage", "Output Image");
     MandatoryOff("outgroup.outputimage");
     AddParameter(ParameterType_InputImageList, "il", "Input image list");
     MandatoryOff("il");
@@ -220,58 +177,42 @@ private:
     AddParameter(ParameterType_ComplexOutputImage, "cout", "Output complex image");
     MandatoryOff("cin");
     MandatoryOff("cout");
-    //  Software Guide : EndCodeSnippet
 
-    // Software Guide : BeginLatex
     // An example of command-line is automatically generated. Method \code{SetDocExampleParameterValue()} is
     // used to set parameters. Dataset should be located in  \code{OTB-Data/Examples} directory.
-    // Software Guide : EndLatex
 
-    //  Software Guide : BeginCodeSnippet
     SetDocExampleParameterValue("boolean", "true");
     SetDocExampleParameterValue("in", "QB_Suburb.png");
     SetDocExampleParameterValue("out", "Application_Example.png");
-    //  Software Guide : EndCodeSnippet
   }
 
-  // Software Guide : BeginLatex
   // \code{DoUpdateParameters()} is called as soon as a parameter value change. Section \ref{sec:appDoUpdateParameters}
   // gives a complete description of this method.
-  // Software Guide : EndLatex
   //  Software Guide :BeginCodeSnippet
   void DoUpdateParameters() override
   {
   }
-  //  Software Guide : EndCodeSnippet
 
-  // Software Guide : BeginLatex
   // \code{DoExecute()} contains the application core. Section \ref{sec:appDoExecute}
   // gives a complete description of this method.
-  // Software Guide : EndLatex
   //  Software Guide :BeginCodeSnippet
   void DoExecute() override
   {
     FloatVectorImageType::Pointer inImage = GetParameterImage("in");
 
     int paramInt = GetParameterInt("param2");
-    otbAppLogDEBUG( << paramInt << std::endl );
+    otbAppLogDEBUG(<< paramInt << std::endl);
     int paramFloat = GetParameterFloat("param3");
-    otbAppLogINFO( << paramFloat );
+    otbAppLogINFO(<< paramFloat);
 
     SetParameterOutputImage("out", inImage);
   }
   //  Software Guide :EndCodeSnippet
-
-
 };
-}
-}
+} // namespace Wrapper
+} // namespace otb
 
-// Software Guide : BeginLatex
 // Finally \code{OTB\_APPLICATION\_EXPORT} is called:
-// Software Guide : EndLatex
 //  Software Guide :BeginCodeSnippet
 OTB_APPLICATION_EXPORT(otb::Wrapper::ApplicationExample)
 //  Software Guide :EndCodeSnippet
-
-

Examples/BasicFilters/BandMathFilterExample.cxx

@@ -18,20 +18,18 @@
  * limitations under the License.
  */
 
+/* Example usage:
+./BandMathFilterExample Input/qb_RoadExtract.tif Output/RoadExtractBandMath.tif Output/qb_BandMath-pretty.jpg
+*/
 
 
-//  Software Guide : BeginCommandLineArgs
-//    INPUTS: {qb_RoadExtract.tif}
-//    OUTPUTS: {RoadExtractBandMath.tif}, {qb_BandMath-pretty.jpg}
-//  Software Guide : EndCommandLineArgs
-
-//  Software Guide : BeginLatex
+//  Software Guide : BeginDescription
 //
-//  This filter is based on the mathematical parser library muParser.
-//  The built in functions and operators list is available at:
-//  \url{http://muparser.sourceforge.net/mup_features.html}.
+// This filter is based on the mathematical parser library muParser.
+// The built in functions and operators list is available at:
+// http://muparser.sourceforge.net/mup_features.html.
 //
-//  In order to use this filter, at least one input image should be
+// In order to use this filter, at least one input image should be
 // set. An associated variable name can be specified or not by using
 // the corresponding SetNthInput method. For the nth input image, if
 // no associated variable name has been specified, a default variable
@@ -40,9 +38,9 @@
 //
 // The next step is to set the expression according to the variable
 // names. For example, in the default case with three input images the
-// following expression is valid : "(b1+b2)*b3".
+// following expression is valid: ``(b1+b2)*b3``.
 //
-//  Software Guide : EndLatex
+// Software Guide : EndDescription
 
 #include "itkMacro.h"
 #include <iostream>
@@ -55,66 +53,39 @@
 #include "itkCastImageFilter.h"
 #include "otbVectorImageToImageListFilter.h"
 
-//  Software Guide : BeginLatex
-//
 // We start by including the required header file.
 // The aim of this example is to compute the Normalized Difference Vegetation Index (NDVI)
 // from a multispectral image and then apply a threshold to this
 // index to extract areas containing a dense vegetation canopy.
-//
-//  Software Guide : EndLatex
-
-// Software Guide : BeginCodeSnippet
 #include "otbBandMathImageFilter.h"
-// Software Guide : EndCodeSnippet
 
-int main( int argc, char* argv[])
+int main(int argc, char* argv[])
 {
   if (argc != 4)
-    {
+  {
     std::cerr << "Usage: " << argv[0] << " inputImageFile ";
     std::cerr << " outputImageFile ";
     std::cerr << " outputPrettyImageFile" << std::endl;
     return EXIT_FAILURE;
-    }
+  }
 
-//  Software Guide : BeginLatex
-//
-//  We start by the classical \code{typedef}s needed for reading and
-//  writing the images. The \doxygen{otb}{BandMathImageFilter} class
-//  works with \doxygen{otb}{Image} as input, so we need to define additional
-//  filters to extract each layer of the multispectral image.
-//
-//  Software Guide : EndLatex
-
-// Software Guide : BeginCodeSnippet
-  typedef double                                                          PixelType;
-  typedef otb::VectorImage<PixelType, 2>                                  InputImageType;
-  typedef otb::Image<PixelType, 2>                                        OutputImageType;
-  typedef otb::ImageList<OutputImageType>                                 ImageListType;
-  typedef otb::VectorImageToImageListFilter<InputImageType, ImageListType>
-  VectorImageToImageListType;
-  typedef otb::ImageFileReader<InputImageType>                            ReaderType;
-  typedef otb::ImageFileWriter<OutputImageType>                           WriterType;
-// Software Guide : EndCodeSnippet
-
-//  Software Guide : BeginLatex
-//
-//  We can now define the type for the filter:
-//
-//  Software Guide : EndLatex
+  // We start by the typedef needed for reading and
+  // writing the images. The BandMathImageFilter class
+  // works with Image as input, so we need to define additional
+  // filters to extract each layer of the multispectral image.
 
-// Software Guide : BeginCodeSnippet
-  typedef otb::BandMathImageFilter<OutputImageType>   FilterType;
-// Software Guide : EndCodeSnippet
+  typedef double                                                           PixelType;
+  typedef otb::VectorImage<PixelType, 2>                                   InputImageType;
+  typedef otb::Image<PixelType, 2>                                         OutputImageType;
+  typedef otb::ImageList<OutputImageType>                                  ImageListType;
+  typedef otb::VectorImageToImageListFilter<InputImageType, ImageListType> VectorImageToImageListType;
+  typedef otb::ImageFileReader<InputImageType>                             ReaderType;
+  typedef otb::ImageFileWriter<OutputImageType>                            WriterType;
 
-//  Software Guide : BeginLatex
-//
-//  We instantiate the filter, the reader, and the writer:
-//
-//  Software Guide : EndLatex
+  // We can now define the type for the filter:
+  typedef otb::BandMathImageFilter<OutputImageType> FilterType;
 
-// Software Guide : BeginCodeSnippet
+  // We instantiate the filter, the reader, and the writer:
   ReaderType::Pointer reader = ReaderType::New();
   WriterType::Pointer writer = WriterType::New();
 
@@ -123,20 +94,12 @@ int main( int argc, char* argv[])
   writer->SetInput(filter->GetOutput());
   reader->SetFileName(argv[1]);
   writer->SetFileName(argv[2]);
-// Software Guide : EndCodeSnippet
 
   reader->UpdateOutputInformation();
 
-
-//  Software Guide : BeginLatex
-//
-//  We now need to extract each band from the input \doxygen{otb}{VectorImage},
-//  it illustrates the use of the \doxygen{otb}{VectorImageToImageList}.
-//  Each extracted layer is an input to the \doxygen{otb}{BandMathImageFilter}:
-//
-//  Software Guide : EndLatex
-
-// Software Guide : BeginCodeSnippet
+  // We now need to extract each band from the input \doxygen{otb}{VectorImage},
+  // it illustrates the use of the \doxygen{otb}{VectorImageToImageList}.
+  // Each extracted layer is an input to the \doxygen{otb}{BandMathImageFilter}:
   VectorImageToImageListType::Pointer imageList = VectorImageToImageListType::New();
   imageList->SetInput(reader->GetOutput());
 
@@ -144,72 +107,48 @@ int main( int argc, char* argv[])
 
   const unsigned int nbBands = reader->GetOutput()->GetNumberOfComponentsPerPixel();
 
-  for(unsigned int j = 0; j < nbBands; ++j)
-      {
-      filter->SetNthInput(j, imageList->GetOutput()->GetNthElement(j));
-      }
-// Software Guide : EndCodeSnippet
+  for (unsigned int j = 0; j < nbBands; ++j)
+  {
+    filter->SetNthInput(j, imageList->GetOutput()->GetNthElement(j));
+  }
 
-//  Software Guide : BeginLatex
-//
-//  Now we can define the mathematical expression to perform on the layers (b1, b2, b3, b4).
-//  The filter takes advantage of the parsing capabilities of the muParser library and
-//  allows setting the expression as on a digital calculator.
-//
-//  The expression below returns 255 if the ratio $(NIR-RED)/(NIR+RED)$ is greater than 0.4 and 0 if not.
-//
-//  Software Guide : EndLatex
-
-// Software Guide : BeginCodeSnippet
+  // Now we can define the mathematical expression to perform on the layers (b1, b2, b3, b4).
+  // The filter takes advantage of the parsing capabilities of the muParser library and
+  // allows setting the expression as on a digital calculator.
+  //
+  // The expression below returns 255 if the ratio $(NIR-RED)/(NIR+RED)$ is greater than 0.4 and 0 if not.
   filter->SetExpression("if((b4-b3)/(b4+b3) > 0.4, 255, 0)");
-  
-  #ifdef OTB_MUPARSER_HAS_CXX_LOGICAL_OPERATORS
+
+#ifdef OTB_MUPARSER_HAS_CXX_LOGICAL_OPERATORS
   filter->SetExpression("((b4-b3)/(b4+b3) > 0.4) ? 255 : 0");
-  #else
+#else
   filter->SetExpression("if((b4-b3)/(b4+b3) > 0.4, 255, 0)");
-  #endif
-  
-// Software Guide : EndCodeSnippet
-
-//  Software Guide : BeginLatex
-//
-//  We can now plug the pipeline and run it.
-//
-//  Software Guide : EndLatex
+#endif
 
-// Software Guide : BeginCodeSnippet
+  // We can now plug the pipeline and run it.
   writer->Update();
-// Software Guide : EndCodeSnippet
-
-//  Software Guide : BeginLatex
-//
-//  The muParser library also provides the possibility to extend existing built-in functions. For example,
-//  you can use the OTB expression "ndvi(b3, b4)" with the filter. In this instance, the mathematical expression would be 
-//  \textit{if($ndvi(b3, b4)>0.4$, 255, 0)}, which would return the same result.
-//
-//  Software Guide : EndLatex
-
-//  Software Guide : BeginLatex
-//
-// Figure~\ref{fig:BandMathImageFilter} shows the result of the threshold applied to the NDVI index
-// of a Quickbird image.
-// \begin{figure}
-// \center
-// \includegraphics[width=0.45\textwidth]{qb_ExtractRoad_pretty.eps}
-// \includegraphics[width=0.45\textwidth]{qb_BandMath-pretty.eps}
-// \itkcaption[Band Math]{From left to right:
-// Original image, thresholded NDVI index.}
-// \label{fig:BandMathImageFilter}
-// \end{figure}
-//
-// Software Guide : EndLatex
 
-  typedef otb::Image<unsigned char, 2>                                      OutputPrettyImageType;
-  typedef otb::ImageFileWriter<OutputPrettyImageType>            PrettyImageFileWriterType;
+  // The muParser library also provides the possibility to extend existing built-in functions. For example,
+  // you can use the OTB expression "ndvi(b3, b4)" with the filter. In this instance, the mathematical expression would be
+  // \textit{if($ndvi(b3, b4)>0.4$, 255, 0)}, which would return the same result.
+
+  // Figure~\ref{fig:BandMathImageFilter} shows the result of the threshold applied to the NDVI index
+  // of a Quickbird image.
+  // \begin{figure}
+  // \center
+  // \includegraphics[width=0.45\textwidth]{qb_ExtractRoad_pretty.eps}
+  // \includegraphics[width=0.45\textwidth]{qb_BandMath-pretty.eps}
+  // \itkcaption[Band Math]{From left to right:
+  // Original image, thresholded NDVI index.}
+  // \label{fig:BandMathImageFilter}
+  // \end{figure}
+
+  typedef otb::Image<unsigned char, 2>                                 OutputPrettyImageType;
+  typedef otb::ImageFileWriter<OutputPrettyImageType>                  PrettyImageFileWriterType;
   typedef itk::CastImageFilter<OutputImageType, OutputPrettyImageType> CastImageFilterType;
 
   PrettyImageFileWriterType::Pointer prettyWriter = PrettyImageFileWriterType::New();
-  CastImageFilterType::Pointer caster = CastImageFilterType::New();
+  CastImageFilterType::Pointer       caster       = CastImageFilterType::New();
   caster->SetInput(filter->GetOutput());
 
   prettyWriter->SetInput(caster->GetOutput());

Examples/BasicFilters/BandMathXImageFilterExample.cxx

@@ -19,14 +19,11 @@
  */
 
 
+/* Example usage:
+./BandMathXImageFilterExample Input/qb_RoadExtract.tif Output/qb_BandMath-res1.tif Output/qb_BandMath-res2.tif Output/context.txt
+*/
 
-//  Software Guide : BeginCommandLineArgs
-//    INPUTS: {qb_RoadExtract.tif}
-//    OUTPUTS: {qb_BandMath-res1.tif}, {qb_BandMath-res2.tif}, {context.txt}
-//  Software Guide : EndCommandLineArgs
 
-//  Software Guide : BeginLatex
-//
 //  This filter is based on the mathematical parser library muParserX.
 //  The built in functions and operators list is available at:
 //  \url{http://articles.beltoforion.de/article.php?a=muparserx}.
@@ -39,8 +36,6 @@
 // corresponding input index plus one (for instance, im1 is related to the first input).
 // If the jth input image is multidimensional, then the variable imj represents a vector whose components are related to its bands.
 // In order to access the kth band, the variable observes the following pattern : imjbk.
-//
-//  Software Guide : EndLatex
 
 #include "itkMacro.h"
 #include <iostream>
@@ -49,233 +44,138 @@
 #include "otbImageFileReader.h"
 #include "otbImageFileWriter.h"
 
-//  Software Guide : BeginLatex
-//
 // We start by including the needed header files.
-//
-//  Software Guide : EndLatex
 
-// Software Guide : BeginCodeSnippet
 #include "otbVectorImage.h"
 #include "otbImageFileReader.h"
 #include "otbImageFileWriter.h"
 #include "otbBandMathXImageFilter.h"
-// Software Guide : EndCodeSnippet
 
-int main( int argc, char* argv[])
+int main(int argc, char* argv[])
 {
 
   if (argc != 5)
-    {
+  {
     std::cerr << "Usage: " << argv[0] << " inputImageFile ";
     std::cerr << " outputImageFile ";
     std::cerr << " outputImageFile2";
     std::cerr << " context.txt" << std::endl;
     return EXIT_FAILURE;
-    }
+  }
 
-//  Software Guide : BeginLatex
-//
-//  Then, we set the classical \code{typedef}s needed for reading and
-//  writing the images. The \doxygen{otb}{BandMathXImageFilter} class
-//  works with \doxygen{otb}{VectorImage}.
-//
-//  Software Guide : EndLatex
+  //  Then, we set the classical \code{typedef}s needed for reading and
+  //  writing the images. The \doxygen{otb}{BandMathXImageFilter} class
+  //  works with \doxygen{otb}{VectorImage}.
 
-// Software Guide : BeginCodeSnippet
-  typedef double                                                PixelType;
-  typedef otb::VectorImage<PixelType, 2>                         ImageType;
-  typedef otb::ImageFileReader<ImageType>                        ReaderType;
-  typedef otb::ImageFileWriter<ImageType>                        WriterType;
-// Software Guide : EndCodeSnippet
+  typedef double                          PixelType;
+  typedef otb::VectorImage<PixelType, 2>  ImageType;
+  typedef otb::ImageFileReader<ImageType> ReaderType;
+  typedef otb::ImageFileWriter<ImageType> WriterType;
 
 
-//  Software Guide : BeginLatex
-//
-//  We can now define the type for the filter:
-//
-//  Software Guide : EndLatex
+  //  We can now define the type for the filter:
 
-// Software Guide : BeginCodeSnippet
-  typedef otb::BandMathXImageFilter<ImageType>                  FilterType;
-// Software Guide : EndCodeSnippet
+  typedef otb::BandMathXImageFilter<ImageType> FilterType;
 
-//  Software Guide : BeginLatex
-//
-//  We instantiate the filter, the reader, and the writer:
-//
-//  Software Guide : EndLatex
+  //  We instantiate the filter, the reader, and the writer:
 
-// Software Guide : BeginCodeSnippet
   ReaderType::Pointer reader = ReaderType::New();
   WriterType::Pointer writer = WriterType::New();
   FilterType::Pointer filter = FilterType::New();
-// Software Guide : EndCodeSnippet
 
-//  Software Guide : BeginLatex
-//
-//  The reader and the writer are parametrized with usual settings:
-//
-//  Software Guide : EndLatex
+  //  The reader and the writer are parametrized with usual settings:
 
-// Software Guide : BeginCodeSnippet
   reader->SetFileName(argv[1]);
   writer->SetFileName(argv[2]);
-// Software Guide : EndCodeSnippet
 
 
-//  Software Guide : BeginLatex
-//
-//  The aim of this example is to compute a simple high-pass filter.
-//  For that purpose, we are going to perform the difference between the original signal
-//  and its averaged version. The definition of the expression that follows is only suitable for a 4-band image.
-//  So first, we must check this requirement:
-//
-//  Software Guide : EndLatex
+  //  The aim of this example is to compute a simple high-pass filter.
+  //  For that purpose, we are going to perform the difference between the original signal
+  //  and its averaged version. The definition of the expression that follows is only suitable for a 4-band image.
+  //  So first, we must check this requirement:
 
-// Software Guide : BeginCodeSnippet
- reader->UpdateOutputInformation();
- if (reader->GetOutput()->GetNumberOfComponentsPerPixel() !=4)
+  reader->UpdateOutputInformation();
+  if (reader->GetOutput()->GetNumberOfComponentsPerPixel() != 4)
     itkGenericExceptionMacro(<< "Input image must have 4 bands." << std::endl);
-// Software Guide : EndCodeSnippet
 
-//  Software Guide : BeginLatex
-//
-//  Now, we can define the expression. The variable im1 represents a pixel (made of 4 components) of the input image.
-//  The variable im1b1N5x5 represents a neighborhood of size 5x5 around this pixel (and so on for each band).
-//  The last element we need is the operator 'mean'. By setting its inputs with four neigborhoods, we tell this operator to process the four related bands.
-//  As output, it will produce a vector of four components; this is consistent with the fact that we wish to perform a difference with im1.
-//
-//  Thus, the expression is as follows:
+  //  Now, we can define the expression. The variable im1 represents a pixel (made of 4 components) of the input image.
+  //  The variable im1b1N5x5 represents a neighborhood of size 5x5 around this pixel (and so on for each band).
+  //  The last element we need is the operator 'mean'. By setting its inputs with four neigborhoods, we tell this operator to process the four related bands.
+  //  As output, it will produce a vector of four components; this is consistent with the fact that we wish to perform a difference with im1.
+  //
+  //  Thus, the expression is as follows:
 
-//
-//  Software Guide : EndLatex
 
-// Software Guide : BeginCodeSnippet
- filter->SetExpression("im1-mean(im1b1N5x5,im1b2N5x5,im1b3N5x5,im1b4N5x5)");
-// Software Guide : EndCodeSnippet
+  filter->SetExpression("im1-mean(im1b1N5x5,im1b2N5x5,im1b3N5x5,im1b4N5x5)");
 
-//  Software Guide : BeginLatex
-//
-//  Note that the importance of the averaging is driven by the names of the neighborhood variables.
-//  Last thing we have to do, is to set the pipeline:
-//
-//  Software Guide : EndLatex
+  //  Note that the importance of the averaging is driven by the names of the neighborhood variables.
+  //  Last thing we have to do, is to set the pipeline:
 
-// Software Guide : BeginCodeSnippet
- filter->SetNthInput(0,reader->GetOutput());
- writer->SetInput(filter->GetOutput());
- writer->Update();
-// Software Guide : EndCodeSnippet
+  filter->SetNthInput(0, reader->GetOutput());
+  writer->SetInput(filter->GetOutput());
+  writer->Update();
 
-//  Software Guide : BeginLatex
-//
-// Figure~\ref{fig:BandMathXImageFilter} shows the result of our high-pass filter.
-// \begin{figure}
-// \center
-// \includegraphics[width=0.45\textwidth]{qb_ExtractRoad_pretty.eps}
-// \includegraphics[width=0.45\textwidth]{qb_BandMath-res1.eps}
-// \itkcaption[Band Math X]{From left to right:
-// Original image, high-pass filter output.}
-// \label{fig:BandMathXImageFilter}
-// \end{figure}
-//
-// Software Guide : EndLatex
+  // Figure~\ref{fig:BandMathXImageFilter} shows the result of our high-pass filter.
+  // \begin{figure}
+  // \center
+  // \includegraphics[width=0.45\textwidth]{qb_ExtractRoad_pretty.eps}
+  // \includegraphics[width=0.45\textwidth]{qb_BandMath-res1.eps}
+  // \itkcaption[Band Math X]{From left to right:
+  // Original image, high-pass filter output.}
+  // \label{fig:BandMathXImageFilter}
+  // \end{figure}
 
 
-//  Software Guide : BeginLatex
-//
-//  Now let's see a little bit more complex example.
-//  The aim now is to give the central pixel a higher weight. Moreover :
-//  - we wish to use smaller neighborhoods
-//  - we wish to drop the 4th band
-//  - we wish to add a given number to each band.
-//
-//  First, we instantiate new filters to later make a proper pipeline:
-//
-//  Software Guide : EndLatex
+  //  Now let's see a little bit more complex example.
+  //  The aim now is to give the central pixel a higher weight. Moreover :
+  //  - we wish to use smaller neighborhoods
+  //  - we wish to drop the 4th band
+  //  - we wish to add a given number to each band.
+  //
+  //  First, we instantiate new filters to later make a proper pipeline:
 
-// Software Guide : BeginCodeSnippet
   ReaderType::Pointer reader2 = ReaderType::New();
   WriterType::Pointer writer2 = WriterType::New();
   FilterType::Pointer filter2 = FilterType::New();
 
   reader2->SetFileName(argv[1]);
   writer2->SetFileName(argv[3]);
-// Software Guide : EndCodeSnippet
 
-//  Software Guide : BeginLatex
-//
-//  We define a new kernel (rows are separated by semi-colons, whereas their elements are separated by commas):
-//
-//  Software Guide : EndLatex
+  //  We define a new kernel (rows are separated by semi-colons, whereas their elements are separated by commas):
 
-// Software Guide : BeginCodeSnippet
-  filter2->SetMatrix("kernel","{ 0.1 , 0.1 , 0.1; 0.1 , 0.2 , 0.1; 0.1 , 0.1 , 0.1 }");
-// Software Guide : EndCodeSnippet
+  filter2->SetMatrix("kernel", "{ 0.1 , 0.1 , 0.1; 0.1 , 0.2 , 0.1; 0.1 , 0.1 , 0.1 }");
 
-//  Software Guide : BeginLatex
-//
-//  We then define a new constant:
-//
-//  Software Guide : EndLatex
+  //  We then define a new constant:
 
-// Software Guide : BeginCodeSnippet
-  filter2->SetConstant("cst",1.0);
-// Software Guide : EndCodeSnippet
+  filter2->SetConstant("cst", 1.0);
 
-//  Software Guide : BeginLatex
-//
-//  We now set the expression (note the use of 'dotpr' operator, as well as the 'bands' operator which is used as a band selector):
-//
-//  Software Guide : EndLatex
+  //  We now set the expression (note the use of 'dotpr' operator, as well as the 'bands' operator which is used as a band selector):
 
-// Software Guide : BeginCodeSnippet
   filter2->SetExpression("bands(im1,{1,2,3})-dotpr(kernel,im1b1N3x3,im1b2N3x3,im1b3N3x3) + {cst,cst,cst}");
-// Software Guide : EndCodeSnippet
 
-//  Software Guide : BeginLatex
-//
-//  It is possible to export these definitions to a txt file (they will be reusable later thanks to the method ImportContext):
-//
-//  Software Guide : EndLatex
+  //  It is possible to export these definitions to a txt file (they will be reusable later thanks to the method ImportContext):
 
-// Software Guide : BeginCodeSnippet
   filter2->ExportContext(argv[4]);
-// Software Guide : EndCodeSnippet
 
 
-//  Software Guide : BeginLatex
-//
-//  And finally, we set the pipeline:
-//
-//  Software Guide : EndLatex
+  //  And finally, we set the pipeline:
 
-// Software Guide : BeginCodeSnippet
- filter2->SetNthInput(0,reader2->GetOutput());
- writer2->SetInput(filter2->GetOutput());
- writer2->Update();
-// Software Guide : EndCodeSnippet
+  filter2->SetNthInput(0, reader2->GetOutput());
+  writer2->SetInput(filter2->GetOutput());
+  writer2->Update();
 
-//  Software Guide : BeginLatex
-//
-// Figure~\ref{fig:BandMathXImageFilter2} shows the result of the second filter.
-// \begin{figure}
-// \center
-// \includegraphics[width=0.45\textwidth]{qb_ExtractRoad_pretty.eps}
-// \includegraphics[width=0.45\textwidth]{qb_BandMath-res2.eps}
-// \itkcaption[Band Math X]{From left to right:
-// Original image, second filter output.}
-// \label{fig:BandMathXImageFilter2}
-// \end{figure}
-//
-// Software Guide : EndLatex
+  // Figure~\ref{fig:BandMathXImageFilter2} shows the result of the second filter.
+  // \begin{figure}
+  // \center
+  // \includegraphics[width=0.45\textwidth]{qb_ExtractRoad_pretty.eps}
+  // \includegraphics[width=0.45\textwidth]{qb_BandMath-res2.eps}
+  // \itkcaption[Band Math X]{From left to right:
+  // Original image, second filter output.}
+  // \label{fig:BandMathXImageFilter2}
+  // \end{figure}
 
-//  Software Guide : BeginLatex
-//
-// Finally, it is strongly recommended to take a look at the cookbook, where additional information and examples can be found (http://www.orfeo-toolbox.org/packages/OTBCookBook.pdf).
-//
-//  Software Guide : EndLatex
+  // Finally, it is strongly recommended to take a look at the cookbook, where additional information and examples can be found
+  // (http://www.orfeo-toolbox.org/packages/OTBCookBook.pdf).
 
 
   return EXIT_SUCCESS;

Examples/BasicFilters/DEMToRainbowExample.cxx

@@ -19,24 +19,21 @@
  */
 
 
+/* Example usage:
+./DEMToRainbowExample Output/DEMToRainbowImageGenerator.png 6.5 45.5 500 500 0.002 -0.002 Input/DEM_srtm
+*/
 
-//  Software Guide : BeginCommandLineArgs
-//  OUTPUTS: {DEMToRainbowImageGenerator.png}
-//  6.5 45.5 500 500 0.002 -0.002 ${OTB_DATA_ROOT}/Input/DEM_srtm
-//  Software Guide : EndCommandLineArgs
 
-//  Software Guide : BeginCommandLineArgs
-//  OUTPUTS: {DEMToHotImageGenerator.png}
-//  6.5 45.5 500 500 0.002 -0.002 ${OTB_DATA_ROOT}/Input/DEM_srtm hot
-//  Software Guide : EndCommandLineArgs
+/* Example usage:
+./DEMToRainbowExample Output/DEMToHotImageGenerator.png 6.5 45.5 500 500 0.002 -0.002 Input/DEM_srtm hot
+*/
+
+
+/* Example usage:
+./DEMToRainbowExample Output/DEMToReliefImageGenerator.png 6.5 45.5 500 500 0.002 -0.002 Input/DEM_srtm relief
+*/
 
-//  Software Guide : BeginCommandLineArgs
-//  OUTPUTS: {DEMToReliefImageGenerator.png}
-//  6.5 45.5 500 500 0.002 -0.002 ${OTB_DATA_ROOT}/Input/DEM_srtm relief
-//  Software Guide : EndCommandLineArgs
 
-// Software Guide : BeginLatex
-//
 // In some situation, it is desirable to represent a gray scale image in color for easier
 // interpretation. This is particularly the case if pixel values in the image are used
 // to represent some data such as elevation, deformation map,
@@ -48,8 +45,6 @@
 // combined with the \doxygen{otb}{ScalarToRainbowRGBPixelFunctor}. You can refer to the
 // source code or to section \ref{sec:ReadDEM} for the DEM conversion to image,
 // we will focus on the color conversion part here.
-//
-// Software Guide : EndLatex
 
 #include "otbImageFileReader.h"
 #include "otbImageFileWriter.h"
@@ -59,24 +54,22 @@
 #include "otbDEMToImageGenerator.h"
 #include "otbReliefColormapFunctor.h"
 
-int main(int argc, char * argv[])
+int main(int argc, char* argv[])
 {
 
   if (argc < 9)
-    {
-    std::cout << argv[0] <<
-    " <output_filename> <Longitude Output Origin point>";
-    std::cout <<
-    " <Latitude Output Origin point> <X Output Size> <Y Output size>";
-    std::cout << " <X Spacing> <Y Spacing> <DEM folder path>"  << std::endl;
+  {
+    std::cout << argv[0] << " <output_filename> <Longitude Output Origin point>";
+    std::cout << " <Latitude Output Origin point> <X Output Size> <Y Output size>";
+    std::cout << " <X Spacing> <Y Spacing> <DEM folder path>" << std::endl;
     return EXIT_FAILURE;
-    }
+  }
 
-  typedef double                                      PixelType;
-  typedef unsigned char                               UCharPixelType;
-  typedef itk::RGBPixel<UCharPixelType>               RGBPixelType;
-  typedef otb::Image<PixelType, 2>                    ImageType;
-  typedef otb::Image<RGBPixelType, 2>                 RGBImageType;
+  typedef double                             PixelType;
+  typedef unsigned char                      UCharPixelType;
+  typedef itk::RGBPixel<UCharPixelType>      RGBPixelType;
+  typedef otb::Image<PixelType, 2>           ImageType;
+  typedef otb::Image<RGBPixelType, 2>        RGBImageType;
   typedef otb::ImageFileWriter<RGBImageType> WriterType;
 
   WriterType::Pointer writer = WriterType::New();
@@ -86,9 +79,9 @@ int main(int argc, char * argv[])
 
   DEMToImageGeneratorType::Pointer demToImage = DEMToImageGeneratorType::New();
 
-  typedef DEMToImageGeneratorType::SizeType       SizeType;
-  typedef DEMToImageGeneratorType::SpacingType    SpacingType;
-  typedef DEMToImageGeneratorType::PointType      PointType;
+  typedef DEMToImageGeneratorType::SizeType    SizeType;
+  typedef DEMToImageGeneratorType::SpacingType SpacingType;
+  typedef DEMToImageGeneratorType::PointType   PointType;
 
   otb::DEMHandler::Instance()->OpenDEMDirectory(argv[8]);
 
@@ -110,99 +103,77 @@ int main(int argc, char * argv[])
 
   demToImage->SetOutputSpacing(spacing);
 
-  // Software Guide : BeginLatex
-  //
   // As in the previous example, the \doxygen{itk}{ScalarToRGBColormapImageFilter} is
   // the filter in charge of calling the functor we specify to do the work for
   // each pixel. Here it is the \doxygen{otb}{ScalarToRainbowRGBPixelFunctor}.
-  //
-  // Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
-  typedef itk::ScalarToRGBColormapImageFilter<ImageType,
-      RGBImageType> ColorMapFilterType;
-  ColorMapFilterType::Pointer colormapper = ColorMapFilterType::New();
+  typedef itk::ScalarToRGBColormapImageFilter<ImageType, RGBImageType> ColorMapFilterType;
+  ColorMapFilterType::Pointer                                          colormapper = ColorMapFilterType::New();
   colormapper->UseInputImageExtremaForScalingOff();
 
   if (argc == 9)
-    {
-    typedef otb::Functor::ScalarToRainbowRGBPixelFunctor<PixelType,
-        RGBPixelType>
-    ColorMapFunctorType;
-    ColorMapFunctorType::Pointer colormap = ColorMapFunctorType::New();
+  {
+    typedef otb::Functor::ScalarToRainbowRGBPixelFunctor<PixelType, RGBPixelType> ColorMapFunctorType;
+    ColorMapFunctorType::Pointer                                                  colormap = ColorMapFunctorType::New();
     colormap->SetMinimumInputValue(0);
     colormap->SetMaximumInputValue(4000);
     colormapper->SetColormap(colormap);
-    }
-  // Software Guide : EndCodeSnippet
+  }
 
   else
-    {
+  {
     if (strcmp(argv[9], "hot") == 0)
-      {
-      typedef itk::Function::HotColormapFunction<PixelType,
-          RGBPixelType>
-      ColorMapFunctorType;
-      ColorMapFunctorType::Pointer colormap = ColorMapFunctorType::New();
+    {
+      typedef itk::Function::HotColormapFunction<PixelType, RGBPixelType> ColorMapFunctorType;
+      ColorMapFunctorType::Pointer                                        colormap = ColorMapFunctorType::New();
       colormap->SetMinimumInputValue(0);
       colormap->SetMaximumInputValue(4000);
       colormapper->SetColormap(colormap);
-      }
+    }
     else
-      {
-      typedef otb::Functor::ReliefColormapFunctor<PixelType,
-          RGBPixelType>
-      ColorMapFunctorType;
-      ColorMapFunctorType::Pointer colormap = ColorMapFunctorType::New();
+    {
+      typedef otb::Functor::ReliefColormapFunctor<PixelType, RGBPixelType> ColorMapFunctorType;
+      ColorMapFunctorType::Pointer                                         colormap = ColorMapFunctorType::New();
       colormap->SetMinimumInputValue(0);
       colormap->SetMaximumInputValue(4000);
       colormapper->SetColormap(colormap);
-      }
     }
-  // Software Guide : BeginLatex
-  //
+  }
   // And we connect the color mapper filter with the filter producing
   // the image of the DEM:
-  //
-  // Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
   colormapper->SetInput(demToImage->GetOutput());
-  // Software Guide : EndCodeSnippet
 
   writer->SetInput(colormapper->GetOutput());
 
   try
-    {
+  {
     writer->Update();
-    }
+  }
   catch (itk::ExceptionObject& excep)
-    {
+  {
     std::cerr << "Exception caught !" << std::endl;
     std::cerr << excep << std::endl;
-    }
+  }
   catch (...)
-    {
+  {
     std::cout << "Unknown exception !" << std::endl;
     return EXIT_FAILURE;
-    }
+  }
 
-  // Software Guide : BeginLatex
-  //
   // Figure~\ref{fig:RAINBOW_FILTER} shows the effect of applying the filter to
   // a gray scale image.
   //
-// \begin{figure}
-// \center
-// \includegraphics[width=0.44\textwidth]{pretty_DEMToImageGenerator.eps}
-// \includegraphics[width=0.44\textwidth]{DEMToRainbowImageGenerator.eps}
-// \includegraphics[width=0.44\textwidth]{DEMToHotImageGenerator.eps}
-// \includegraphics[width=0.44\textwidth]{DEMToReliefImageGenerator.eps}
-// \itkcaption[Grayscale to color]{The gray level DEM extracted from SRTM
-// data (top-left) and the same area represented in color.}
-// \label{fig:RAINBOW_FILTER}
-// \end{figure}
-//  Software Guide : EndLatex
+  // \begin{figure}
+  // \center
+  // \includegraphics[width=0.44\textwidth]{pretty_DEMToImageGenerator.eps}
+  // \includegraphics[width=0.44\textwidth]{DEMToRainbowImageGenerator.eps}
+  // \includegraphics[width=0.44\textwidth]{DEMToHotImageGenerator.eps}
+  // \includegraphics[width=0.44\textwidth]{DEMToReliefImageGenerator.eps}
+  // \itkcaption[Grayscale to color]{The gray level DEM extracted from SRTM
+  // data (top-left) and the same area represented in color.}
+  // \label{fig:RAINBOW_FILTER}
+  // \end{figure}
 
   return EXIT_SUCCESS;
 }

Examples/BasicFilters/FrostImageFilter.cxx

@@ -19,15 +19,11 @@
  */
 
 
+/* Example usage:
+./FrostImageFilter Input/GomaSmall.png Output/GomaSmallFrostFiltered.png 5 0.1
+*/
 
-//  Software Guide : BeginCommandLineArgs
-//    INPUTS: {GomaSmall.png}
-//    OUTPUTS: {GomaSmallFrostFiltered.png}
-//    5 0.1
-//  Software Guide : EndCommandLineArgs
 
-// Software Guide : BeginLatex
-//
 // This example illustrates the use of the \doxygen{otb}{FrostImageFilter}.
 // This filter belongs to the family of the edge-preserving smoothing
 // filters which are usually used for speckle reduction in radar
@@ -54,41 +50,31 @@
 // will be highlighted.
 //
 // First, we need to include the header:
-//
-// Software Guide : EndLatex
 
-// Software Guide : BeginCodeSnippet
 #include "otbFrostImageFilter.h"
-// Software Guide : EndCodeSnippet
 
 #include "otbImage.h"
 #include "otbImageFileReader.h"
 #include "otbImageFileWriter.h"
 
-int main(int argc, char * argv[])
+int main(int argc, char* argv[])
 {
 
   if (argc != 5)
-    {
+  {
     std::cerr << "Usage: " << argv[0] << " inputImageFile ";
     std::cerr << " outputImageFile radius deramp" << std::endl;
     return EXIT_FAILURE;
-    }
+  }
 
-  typedef  unsigned char PixelType;
+  typedef unsigned char PixelType;
 
-  typedef otb::Image<PixelType,  2> InputImageType;
-  typedef otb::Image<PixelType,  2> OutputImageType;
+  typedef otb::Image<PixelType, 2> InputImageType;
+  typedef otb::Image<PixelType, 2> OutputImageType;
 
-  //  Software Guide : BeginLatex
-  //
   //  The filter can be instantiated using the image types defined previously.
-  //
-  //  Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
   typedef otb::FrostImageFilter<InputImageType, OutputImageType> FilterType;
-  // Software Guide : EndCodeSnippet
 
   typedef otb::ImageFileReader<InputImageType> ReaderType;
 
@@ -101,22 +87,14 @@ int main(int argc, char * argv[])
   writer->SetInput(filter->GetOutput());
   reader->SetFileName(argv[1]);
 
-  //  Software Guide : BeginLatex
-  //
   //  The image obtained with the reader is passed as input to the
   //  \doxygen{otb}{FrostImageFilter}.
   //
   //  \index{otb::FrostImageFilter!SetInput()}
   //  \index{otb::FileImageReader!GetOutput()}
-  //
-  //  Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
   filter->SetInput(reader->GetOutput());
-  // Software Guide : EndCodeSnippet
 
-  //  Software Guide : BeginLatex
-  //
   //  The method \code{SetRadius()} defines the size of the window to
   //  be used for the computation of the local statistics. The method
   //  \code{SetDeramp()} sets the $K$ coefficient.
@@ -124,22 +102,17 @@ int main(int argc, char * argv[])
   //  \index{otb::FrostImageFilter!SetRadius()}
   //  \index{otb::FrostImageFilter!SetDeramp()}
   //  \index{SetDeramp()!otb::FrostImageFilter}
-  //
-  //  Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
   FilterType::SizeType Radius;
   Radius[0] = atoi(argv[3]);
   Radius[1] = atoi(argv[3]);
 
   filter->SetRadius(Radius);
   filter->SetDeramp(atof(argv[4]));
-  // Software Guide : EndCodeSnippet
 
   writer->SetFileName(argv[2]);
   writer->Update();
 
-  //  Software Guide : BeginLatex
   // Figure~\ref{fig:FROST_FILTER} shows the result of applying the Frost
   // filter to a SAR image.
   // \begin{figure}
@@ -155,8 +128,6 @@ int main(int argc, char * argv[])
   //  \begin{itemize}
   //  \item \doxygen{otb}{LeeImageFilter}
   //  \end{itemize}
-  //
-  //  Software Guide : EndLatex
 
   return EXIT_SUCCESS;
 }

Examples/BasicFilters/HillShadingExample.cxx

@@ -19,14 +19,11 @@
  */
 
 
+/* Example usage:
+./HillShadingExample Output/HillShadingExample.png Output/HillShadingColorExample.png 6.5 45.5 500 500 0.002 -0.002 Input/DEM_srtm
+*/
 
-//  Software Guide : BeginCommandLineArgs
-//  OUTPUTS: {HillShadingExample.png}, {HillShadingColorExample.png}
-//  6.5 45.5 500 500 0.002 -0.002 ${OTB_DATA_ROOT}/Input/DEM_srtm
-//  Software Guide : EndCommandLineArgs
 
-// Software Guide : BeginLatex
-//
 // Visualization of digital elevation models (DEM) is often more intuitive by simulating a
 // lighting source and generating the corresponding shadows. This principle is called
 // hill shading.
@@ -38,8 +35,6 @@
 // \doxygen{otb}{ReliefColormapFunctor} you can easily generate the classic elevation maps.
 //
 // This example will focus on the shading itself.
-//
-// Software Guide : EndLatex
 
 #include "otbImageFileReader.h"
 #include "otbImageFileWriter.h"
@@ -53,26 +48,25 @@
 #include "itkShiftScaleImageFilter.h"
 #include "otbWorldFile.h"
 
-int main(int argc, char * argv[])
+int main(int argc, char* argv[])
 {
 
   if (argc < 10)
-    {
+  {
     std::cout << argv[0] << " <output_filename> <output_color_filename> "
               << " <Longitude Output Origin point> <Latitude Output Origin point>"
               << " <X Output Size> <Y Output size>"
               << " <X Spacing> <Y Spacing> <DEM folder path>"
-              << " [Projection Ref]"
-              << std::endl;
+              << " [Projection Ref]" << std::endl;
     return EXIT_FAILURE;
-    }
-
-  typedef double                                         PixelType;
-  typedef unsigned char                                  UCharPixelType;
-  typedef itk::RGBPixel<UCharPixelType>                  RGBPixelType;
-  typedef otb::Image<PixelType, 2>                       ImageType;
-  typedef otb::Image<RGBPixelType, 2>                    RGBImageType;
-  typedef otb::Image<UCharPixelType, 2>                  ScalarImageType;
+  }
+
+  typedef double                                PixelType;
+  typedef unsigned char                         UCharPixelType;
+  typedef itk::RGBPixel<UCharPixelType>         RGBPixelType;
+  typedef otb::Image<PixelType, 2>              ImageType;
+  typedef otb::Image<RGBPixelType, 2>           RGBImageType;
+  typedef otb::Image<UCharPixelType, 2>         ScalarImageType;
   typedef otb::ImageFileWriter<RGBImageType>    WriterType;
   typedef otb::ImageFileWriter<ScalarImageType> ScalarWriterType;
 
@@ -86,9 +80,9 @@ int main(int argc, char * argv[])
 
   DEMToImageGeneratorType::Pointer demToImage = DEMToImageGeneratorType::New();
 
-  typedef DEMToImageGeneratorType::SizeType       SizeType;
-  typedef DEMToImageGeneratorType::SpacingType    SpacingType;
-  typedef DEMToImageGeneratorType::PointType      PointType;
+  typedef DEMToImageGeneratorType::SizeType    SizeType;
+  typedef DEMToImageGeneratorType::SpacingType SpacingType;
+  typedef DEMToImageGeneratorType::PointType   PointType;
 
   otb::DEMHandler::Instance()->OpenDEMDirectory(argv[9]);
 
@@ -111,69 +105,56 @@ int main(int argc, char * argv[])
   demToImage->SetOutputSpacing(spacing);
   double res = 0;
 
-  if ( argc > 10)
-    {
+  if (argc > 10)
+  {
     demToImage->SetOutputProjectionRef(argv[10]);
     res = spacing[0];
-    }
+  }
   else
-    {
-    //Compute the resolution (Vincenty formula)
+  {
+    // Compute the resolution (Vincenty formula)
     double lon1 = origin[0];
     double lon2 = origin[0] + size[0] * spacing[0];
     double lat1 = origin[1];
     double lat2 = origin[1] + size[1] * spacing[1];
-    double R = 6371; // km
-    double d = std::acos(std::sin(lat1) * std::sin(lat2) +
-                        std::cos(lat1) * std::cos(lat2) * std::cos(lon2 - lon1)) * R;
-    res = d / std::sqrt(2.0);
-    }
-  // Software Guide : BeginLatex
-  //
+    double R    = 6371; // km
+    double d    = std::acos(std::sin(lat1) * std::sin(lat2) + std::cos(lat1) * std::cos(lat2) * std::cos(lon2 - lon1)) * R;
+    res         = d / std::sqrt(2.0);
+  }
   // After generating the DEM image as in the DEMToImageGenerator example, you can declare
   // the hill shading mechanism. The hill shading is implemented as a functor doing some
   // operations in its neighborhood. A convenient filter called \doxygen{otb}{HillShadingFilter}
   // is defined around this mechanism.
-  //
-  // Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
   typedef otb::HillShadingFilter<ImageType, ImageType> HillShadingFilterType;
-  HillShadingFilterType::Pointer hillShading = HillShadingFilterType::New();
+  HillShadingFilterType::Pointer                       hillShading = HillShadingFilterType::New();
   hillShading->SetRadius(1);
   hillShading->SetInput(demToImage->GetOutput());
-  // Software Guide : EndCodeSnippet
 
   hillShading->GetFunctor().SetXRes(res);
   hillShading->GetFunctor().SetYRes(res);
 
   typedef itk::ShiftScaleImageFilter<ImageType, ScalarImageType> RescalerType;
-  RescalerType::Pointer rescaler = RescalerType::New();
+  RescalerType::Pointer                                          rescaler = RescalerType::New();
   rescaler->SetScale(255.0);
   rescaler->SetInput(hillShading->GetOutput());
 
   writer->SetInput(rescaler->GetOutput());
 
-  typedef itk::ScalarToRGBColormapImageFilter<ImageType,
-      RGBImageType> ColorMapFilterType;
-  ColorMapFilterType::Pointer colormapper = ColorMapFilterType::New();
+  typedef itk::ScalarToRGBColormapImageFilter<ImageType, RGBImageType> ColorMapFilterType;
+  ColorMapFilterType::Pointer                                          colormapper = ColorMapFilterType::New();
   colormapper->UseInputImageExtremaForScalingOff();
 
-  typedef otb::Functor::ReliefColormapFunctor<PixelType,
-      RGBPixelType> ColorMapFunctorType;
-  ColorMapFunctorType::Pointer colormap = ColorMapFunctorType::New();
+  typedef otb::Functor::ReliefColormapFunctor<PixelType, RGBPixelType> ColorMapFunctorType;
+  ColorMapFunctorType::Pointer                                         colormap = ColorMapFunctorType::New();
   colormap->SetMinimumInputValue(0);
   colormap->SetMaximumInputValue(4000);
   colormapper->SetColormap(colormap);
 
   colormapper->SetInput(demToImage->GetOutput());
 
-  typedef itk::BinaryFunctorImageFilter<RGBImageType, ImageType, RGBImageType,
-      otb::Functor::
-      HillShadeModulationFunctor<RGBPixelType,
-          PixelType,
-          RGBPixelType> >
-  MultiplyFilterType;
+  typedef itk::BinaryFunctorImageFilter<RGBImageType, ImageType, RGBImageType, otb::Functor::HillShadeModulationFunctor<RGBPixelType, PixelType, RGBPixelType>>
+      MultiplyFilterType;
 
   MultiplyFilterType::Pointer multiply = MultiplyFilterType::New();
   multiply->SetInput1(colormapper->GetOutput());
@@ -182,20 +163,20 @@ int main(int argc, char * argv[])
   writer2->SetInput(multiply->GetOutput());
 
   try
-    {
+  {
     writer->Update();
     writer2->Update();
-    }
+  }
   catch (itk::ExceptionObject& excep)
-    {
+  {
     std::cerr << "Exception caught !" << std::endl;
     std::cerr << excep << std::endl;
-    }
+  }
   catch (...)
-    {
+  {
     std::cout << "Unknown exception !" << std::endl;
     return EXIT_FAILURE;
-    }
+  }
 
   otb::WorldFile::Pointer worldFile = otb::WorldFile::New();
   worldFile->SetLonOrigin(origin[0]);
@@ -208,8 +189,6 @@ int main(int argc, char * argv[])
   worldFile->SetImageFilename(argv[2]);
   worldFile->Update();
 
-  // Software Guide : BeginLatex
-  //
   // Figure~\ref{fig:HILL_SHADING} shows the hill shading result from SRTM data.
   //
   // \begin{figure}
@@ -220,7 +199,6 @@ int main(int argc, char * argv[])
   // the color representation (right)}
   // \label{fig:HILL_SHADING}
   // \end{figure}
-  //  Software Guide : EndLatex
 
   return EXIT_SUCCESS;
 }

Examples/BasicFilters/IndexedToRGBExample.cxx

@@ -19,14 +19,11 @@
  */
 
 
+/* Example usage:
+./IndexedToRGBExample Input/buildingExtractionIndexed.tif Output/buildingExtractionRGB.png Output/buildingExtractionIndexed_scaled.png
+*/
 
-//  Software Guide : BeginCommandLineArgs
-//    INPUTS: {buildingExtractionIndexed.tif}
-//    OUTPUTS: {buildingExtractionRGB.png}, {buildingExtractionIndexed_scaled.png}
-//  Software Guide : EndCommandLineArgs
 
-//  Software Guide : BeginLatex
-//
 //  Some algorithms produce an indexed image as output. In such images,
 // each pixel is given a value according to the region number it belongs to.
 // This value starting at 0 or 1 is usually an integer value.
@@ -39,8 +36,6 @@
 // such conversion, it is important to ensure that neighborhood region, which are
 // likely to have consecutive number have easily dicernable colors. This is done
 // randomly using a hash function by the \doxygen{itk}{ScalarToRGBPixelFunctor}.
-//
-//  Software Guide : EndLatex
 
 #include "otbImage.h"
 #include "otbImageFileReader.h"
@@ -50,65 +45,55 @@
 
 #include "itkRescaleIntensityImageFilter.h"
 
-int main(int argc, char * argv[])
+int main(int argc, char* argv[])
 {
   if (argc != 4)
-    {
+  {
     std::cerr << "Usage: " << argv[0] << " <inputImageFile> ";
     std::cerr << " <outputRGBImageFile> <outputScaledImageFile>" << std::endl;
     return EXIT_FAILURE;
-    }
-  const char * inputFilename  = argv[1];
-  const char * outputRGBFilename = argv[2];
-  const char * outputScaledFilename = argv[3];
+  }
+  const char* inputFilename        = argv[1];
+  const char* outputRGBFilename    = argv[2];
+  const char* outputScaledFilename = argv[3];
 
   typedef otb::Image<unsigned long, 2>                ImageType;
   typedef otb::Image<itk::RGBPixel<unsigned char>, 2> RGBImageType;
 
   typedef otb::ImageFileReader<ImageType> ReaderType;
-  ReaderType::Pointer reader = ReaderType::New();
+  ReaderType::Pointer                     reader = ReaderType::New();
 
   reader->SetFileName(inputFilename);
 
-  //  Software Guide : BeginLatex
-  //
   //  The \doxygen{itk}{UnaryFunctorImageFilter} is the filter in charge of
   // calling the functor we specify to do the work for each pixel. Here it is the
   // \doxygen{itk}{ScalarToRGBPixelFunctor}.
-  //
-  //  Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
-  typedef itk::Functor::ScalarToRGBPixelFunctor<unsigned long>
-  ColorMapFunctorType;
-  typedef itk::UnaryFunctorImageFilter<ImageType, RGBImageType,
-      ColorMapFunctorType> ColorMapFilterType;
-  ColorMapFilterType::Pointer colormapper = ColorMapFilterType::New();
+  typedef itk::Functor::ScalarToRGBPixelFunctor<unsigned long>                       ColorMapFunctorType;
+  typedef itk::UnaryFunctorImageFilter<ImageType, RGBImageType, ColorMapFunctorType> ColorMapFilterType;
+  ColorMapFilterType::Pointer                                                        colormapper = ColorMapFilterType::New();
 
   colormapper->SetInput(reader->GetOutput());
-  // Software Guide : EndCodeSnippet
 
   typedef otb::ImageFileWriter<RGBImageType> WriterType;
-  WriterType::Pointer writer = WriterType::New();
+  WriterType::Pointer                        writer = WriterType::New();
   writer->SetFileName(outputRGBFilename);
   writer->SetInput(colormapper->GetOutput());
 
   writer->Update();
 
-  //The following is just to produce the input image for the software guide
-  typedef otb::Image<unsigned char, 2> OutputImageType;
-  typedef itk::RescaleIntensityImageFilter<ImageType,
-      OutputImageType> RescalerType;
-  RescalerType::Pointer rescaler = RescalerType::New();
+  // The following is just to produce the input image for the software guide
+  typedef otb::Image<unsigned char, 2>                                 OutputImageType;
+  typedef itk::RescaleIntensityImageFilter<ImageType, OutputImageType> RescalerType;
+  RescalerType::Pointer                                                rescaler = RescalerType::New();
   rescaler->SetInput(reader->GetOutput());
 
   typedef otb::ImageFileWriter<OutputImageType> UCharWriterType;
-  UCharWriterType::Pointer writer2 = UCharWriterType::New();
+  UCharWriterType::Pointer                      writer2 = UCharWriterType::New();
   writer2->SetFileName(outputScaledFilename);
   writer2->SetInput(rescaler->GetOutput());
   writer2->Update();
 
-  //  Software Guide : BeginLatex
   // Figure~\ref{fig:INDEXTORGB_FILTER} shows the result of the conversion
   // from an indexed image to a color image.
   // \begin{figure}
@@ -119,8 +104,6 @@ int main(int argc, char * argv[])
   // conversion to color image.}
   // \label{fig:INDEXTORGB_FILTER}
   // \end{figure}
-  //
-  //  Software Guide : EndLatex
 
   return EXIT_SUCCESS;
 }

Examples/BasicFilters/LeeImageFilter.cxx

@@ -19,171 +19,66 @@
  */
 
 
+/* Example usage:
+./LeeImageFilter Input/GomaSmall.png Output/GomaSmallLeeFiltered.png 3 1
+*/
 
-//  Software Guide : BeginCommandLineArgs
-//    INPUTS: {GomaSmall.png}
-//    OUTPUTS: {GomaSmallLeeFiltered.png}
-//    3 1
-//  Software Guide : EndCommandLineArgs
-
-// Software Guide : BeginLatex
-//
-// This example illustrates the use of the \doxygen{otb}{LeeImageFilter}.
-// This filter belongs to the family of the edge-preserving smoothing
-// filters which are usually used for speckle reduction in radar
-// images. The Lee filter \cite{LeeFilter} aplies a linear regression
-// which minimizes the mean-square error in the frame of a
-// multiplicative speckle model.
-//
-//
-// The first step required to use this filter is to include its header file.
-//
-// Software Guide : EndLatex
-
-// Software Guide : BeginCodeSnippet
 #include "otbLeeImageFilter.h"
-// Software Guide : EndCodeSnippet
 
 #include "otbImage.h"
 #include "otbImageFileReader.h"
 #include "otbImageFileWriter.h"
 
-int main(int argc, char * argv[])
+int main(int argc, char* argv[])
 {
-
   if (argc != 5)
-    {
+  {
     std::cerr << "Usage: " << argv[0] << " inputImageFile ";
     std::cerr << " outputImageFile radius NbLooks" << std::endl;
     return EXIT_FAILURE;
-    }
-
-  //  Software Guide : BeginLatex
-  //
-  //  Then we must decide what pixel type to use for the image.
-  //
-  //  Software Guide : EndLatex
-
-  // Software Guide : BeginCodeSnippet
-  typedef  unsigned char PixelType;
-  // Software Guide : EndCodeSnippet
-
-  //  Software Guide : BeginLatex
-  //
-  //  The images are defined using the pixel type and the dimension.
-  //
-  //  Software Guide : EndLatex
-
-  // Software Guide : BeginCodeSnippet
-  typedef otb::Image<PixelType,  2> InputImageType;
-  typedef otb::Image<PixelType,  2> OutputImageType;
-  // Software Guide : EndCodeSnippet
-
-  //  Software Guide : BeginLatex
-  //
-  //  The filter can be instantiated using the image types defined above.
-  //
-  //  Software Guide : EndLatex
-
-  // Software Guide : BeginCodeSnippet
+  }
+
+  typedef unsigned char PixelType;
+
+  // The images are defined using the pixel type and the dimension.
+  typedef otb::Image<PixelType, 2> InputImageType;
+  typedef otb::Image<PixelType, 2> OutputImageType;
+
+  // The filter can be instantiated using the image types defined above.
   typedef otb::LeeImageFilter<InputImageType, OutputImageType> FilterType;
-  // Software Guide : EndCodeSnippet
 
-  //  Software Guide : BeginLatex
-  //
-  //  An \doxygen{otb}{ImageFileReader} class is also instantiated in order to read
+  //  An ImageFileReader class is also instantiated in order to read
   //  image data from a file.
-  //
-  //  Software Guide : EndLatex
-
-  // Software Guide : BeginCodeSnippet
   typedef otb::ImageFileReader<InputImageType> ReaderType;
-  // Software Guide : EndCodeSnippet
 
-  //  Software Guide : BeginLatex
-  //
   // An \doxygen{otb}{ImageFileWriter} is instantiated in order to write the
   // output image to a file.
-  //
-  //  Software Guide : EndLatex
-
-  // Software Guide : BeginCodeSnippet
   typedef otb::ImageFileWriter<OutputImageType> WriterType;
-  // Software Guide : EndCodeSnippet
 
-  //  Software Guide : BeginLatex
-  //
   //  Both the filter and the reader are created by invoking their \code{New()}
   //  methods and assigning the result to SmartPointers.
-  //
-  //  Software Guide : EndLatex
-
-  // Software Guide : BeginCodeSnippet
   ReaderType::Pointer reader = ReaderType::New();
   FilterType::Pointer filter = FilterType::New();
-  // Software Guide : EndCodeSnippet
 
   WriterType::Pointer writer = WriterType::New();
   writer->SetInput(filter->GetOutput());
   reader->SetFileName(argv[1]);
 
-  //  Software Guide : BeginLatex
-  //
   //  The image obtained with the reader is passed as input to the
-  //  \doxygen{otb}{LeeImageFilter}.
-  //
-  //  \index{otb::LeeImageFilter!SetInput()}
-  //  \index{otb::FileImageReader!GetOutput()}
-  //
-  //  Software Guide : EndLatex
-
-  // Software Guide : BeginCodeSnippet
+  //  LeeImageFilter.
   filter->SetInput(reader->GetOutput());
-  // Software Guide : EndCodeSnippet
-
-  //  Software Guide : BeginLatex
-  //
-  //  The method \code{SetRadius()} defines the size of the window to
-  //  be used for the computation of the local statistics. The method
-  //  \code{SetNbLooks()} sets the number of looks of the input
-  //  image.
-  //
-  //  \index{otb::LeeImageFilter!SetRadius()}
-  //  \index{otb::LeeImageFilter!SetNbLooks()}
-  //  \index{SetNbLooks()!otb::LeeImageFilter}
-  //
-  //  Software Guide : EndLatex
-
-  // Software Guide : BeginCodeSnippet
+
+  // The method SetRadius() defines the size of the window to
+  // be used for the computation of the local statistics. The method
+  // SetNbLooks() sets the number of looks of the input
+  // image.
   FilterType::SizeType Radius;
   Radius[0] = atoi(argv[3]);
   Radius[1] = atoi(argv[3]);
 
   filter->SetRadius(Radius);
   filter->SetNbLooks(atoi(argv[4]));
-  // Software Guide : EndCodeSnippet
 
   writer->SetFileName(argv[2]);
   writer->Update();
-
-  //  Software Guide : BeginLatex
-  // Figure~\ref{fig:LEE_FILTER} shows the result of applying the Lee
-  // filter to a SAR image.
-  // \begin{figure}
-  // \center
-  // \includegraphics[width=0.44\textwidth]{GomaSmall.eps}
-  // \includegraphics[width=0.44\textwidth]{GomaSmallLeeFiltered.eps}
-  // \itkcaption[Lee Filter Application]{Result of applying the
-  // \doxygen{otb}{LeeImageFilter} to a SAR image.}
-  // \label{fig:LEE_FILTER}
-  // \end{figure}
-  //
-  //  \relatedClasses
-  //  \begin{itemize}
-  //  \item \doxygen{otb}{FrostImageFilter}
-  //  \end{itemize}
-  //
-  //  Software Guide : EndLatex
-
-  return EXIT_SUCCESS;
 }

Examples/BasicFilters/LeeImageFilter.rst

+This example illustrates the use of the LeeImageFilter.
+This filter belongs to the family of the edge-preserving smoothing
+filters which are usually used for speckle reduction in radar
+images. The LeeFilter aplies a linear regression
+which minimizes the mean-square error in the frame of a
+multiplicative speckle model.
+
+.. figure:: /Input/GomaSmall.png
+
+.. figure:: /Output/GomaSmallLeeFiltered.png
+
+    Result of applying the Lee filter to a SAR image.

Examples/BasicFilters/MeanShiftSegmentationFilterExample.cxx

@@ -19,15 +19,20 @@
  */
 
 
+/* Example usage:
+./MeanShiftSegmentationFilterExample Input/ROI_QB_MUL_1.png \
+                                     Output/MSLabeledOutput.tif \
+                                     Output/MSClusteredOutput.tif \
+                                     Output/MSLabeledOutput-pretty.png \
+                                     Output/MSClusteredOutput-pretty.png \
+                                     16 \
+                                     16 \
+                                     100 \
+                                     100 \
+                                     0.1
+*/
 
-//  Software Guide : BeginCommandLineArgs
-//    INPUTS: {ROI_QB_MUL_1.png}
-//    OUTPUTS: {MSLabeledOutput.tif}, {MSClusteredOutput.tif}, {MSLabeledOutput-pretty.png}, {MSClusteredOutput-pretty.png}
-//    16 16 100 100 0.1
-//  Software Guide : EndCommandLineArgs
 
-//  Software Guide : BeginLatex
-//
 //  This example demonstrates the use of the
 //  \doxygen{otb}{MeanShiftSegmentationFilter} class which implements
 //  filtering and clustering using the mean shift algorithm
@@ -37,8 +42,6 @@
 //  then computed and the algorithm iterates with this new spatial and
 //  color center. The Mean Shift can be used for edge-preserving
 //  smoothing, or for clustering.
-//
-//  Software Guide : EndLatex
 
 #include "otbVectorImage.h"
 #include "otbImageFileReader.h"
@@ -49,43 +52,32 @@
 #include "itkScalarToRGBPixelFunctor.h"
 #include "itkUnaryFunctorImageFilter.h"
 
-//  Software Guide : BeginLatex
-//
 //  We start by including the needed header file.
-//
-//  Software Guide : EndLatex
 
-// Software Guide : BeginCodeSnippet
 #include "otbMeanShiftSegmentationFilter.h"
-// Software Guide : EndCodeSnippet
-int main(int argc, char * argv[])
+int main(int argc, char* argv[])
 {
   if (argc != 11)
-    {
+  {
     std::cerr << "Usage: " << argv[0] << " infname labeledfname clusteredfname labeledpretty clusteredpretty "
-        << "spatialRadius rangeRadius minRegionSize maxiter thres" << std::endl;
+              << "spatialRadius rangeRadius minRegionSize maxiter thres" << std::endl;
     return EXIT_FAILURE;
-    }
-
-  const char * infname             = argv[1];
-  const char * labeledfname        = argv[2];
-  const char * clusteredfname      = argv[3];
-  const char * labeledpretty       = argv[4];
-  const char * clusteredpretty     = argv[5];
-  const unsigned int spatialRadius = atoi(argv[6]);
-  const double rangeRadius         = atof(argv[7]);
-  const unsigned int minRegionSize = atoi(argv[8]);
-  const unsigned int maxiter       = atoi(argv[9]);
-  const double thres               = atof(argv[10]);
-
-  //  Software Guide : BeginLatex
-  //
+  }
+
+  const char*        infname         = argv[1];
+  const char*        labeledfname    = argv[2];
+  const char*        clusteredfname  = argv[3];
+  const char*        labeledpretty   = argv[4];
+  const char*        clusteredpretty = argv[5];
+  const unsigned int spatialRadius   = atoi(argv[6]);
+  const double       rangeRadius     = atof(argv[7]);
+  const unsigned int minRegionSize   = atoi(argv[8]);
+  const unsigned int maxiter         = atoi(argv[9]);
+  const double       thres           = atof(argv[10]);
+
   //  We start by the classical \code{typedef}s needed for reading and
   //  writing the images.
-  //
-  //  Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
   const unsigned int Dimension = 2;
 
   typedef float                        PixelType;
@@ -96,80 +88,50 @@ int main(int argc, char * argv[])
   typedef otb::Image<LabelPixelType, Dimension>  LabelImageType;
   typedef otb::Image<ColorPixelType, Dimension>  RGBImageType;
 
-  typedef otb::ImageFileReader<ImageType>               ReaderType;
+  typedef otb::ImageFileReader<ImageType>      ReaderType;
   typedef otb::ImageFileWriter<ImageType>      WriterType;
   typedef otb::ImageFileWriter<LabelImageType> LabelWriterType;
 
   typedef otb::MeanShiftSegmentationFilter<ImageType, LabelImageType, ImageType> FilterType;
-  // Software Guide : EndCodeSnippet
 
-  //  Software Guide : BeginLatex
-  //
   //  We instantiate the filter, the reader, and 2 writers (for the
   //  labeled and clustered images).
-  //
-  //  Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
-  FilterType::Pointer filter = FilterType::New();
-  ReaderType::Pointer reader = ReaderType::New();
-  WriterType::Pointer writer1 = WriterType::New();
+  FilterType::Pointer      filter  = FilterType::New();
+  ReaderType::Pointer      reader  = ReaderType::New();
+  WriterType::Pointer      writer1 = WriterType::New();
   LabelWriterType::Pointer writer2 = LabelWriterType::New();
-  // Software Guide : EndCodeSnippet
 
-  //  Software Guide : BeginLatex
-  //
   //  We set the file names for the reader and the writers:
-  //
-  //  Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
   reader->SetFileName(infname);
   writer1->SetFileName(clusteredfname);
   writer2->SetFileName(labeledfname);
-  // Software Guide : EndCodeSnippet
 
-  //  Software Guide : BeginLatex
-  //
   //  We can now set the parameters for the filter. There are 3 main
   //  parameters: the spatial radius used for defining the neighborhood,
   //  the range radius used for defining the interval in the color space
   //  and the minimum size for the regions to be kept after clustering.
-  //
-  //  Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
   filter->SetSpatialBandwidth(spatialRadius);
   filter->SetRangeBandwidth(rangeRadius);
   filter->SetMinRegionSize(minRegionSize);
-  // Software Guide : EndCodeSnippet
-  //  Software Guide : BeginLatex
-  //
   // Two another parameters can be set  : the maximum iteration number, which defines maximum number of iteration until convergence.
   //  Algorithm iterative scheme will stop if convergence hasn't been reached after the maximum number of iterations.
-  //  Threshold parameter defines mean-shift vector convergence value. Algorithm iterative scheme will stop if mean-shift vector is below this threshold or if iteration number reached maximum number of iterations.
-  //  Software Guide : EndLatex
+  //  Threshold parameter defines mean-shift vector convergence value. Algorithm iterative scheme will stop if mean-shift vector is below this threshold or if
+  //  iteration number reached maximum number of iterations.
 
-  // Software Guide : BeginCodeSnippet
   filter->SetMaxIterationNumber(maxiter);
   filter->SetThreshold(thres);
-  // Software Guide : EndCodeSnippet
-  //  Software Guide : BeginLatex
-  //
   //  We can now plug the pipeline and run it.
-  //
-  //  Software Guide : EndLatex
 
-  // Software Guide : BeginCodeSnippet
   filter->SetInput(reader->GetOutput());
   writer1->SetInput(filter->GetClusteredOutput());
   writer2->SetInput(filter->GetLabelOutput());
 
   writer1->Update();
   writer2->Update();
-  // Software Guide : EndCodeSnippet
 
-  //  Software Guide : BeginLatex
   // Figure~\ref{fig:MeanShiftSegmentationFilter} shows the result of applying the mean shift
   // to a Quickbird image.
   // \begin{figure}
@@ -182,16 +144,15 @@ int main(int argc, char * argv[])
   // mean shift after clustering , and labeled image.}
   // \label{fig:MeanShiftSegmentationFilter}
   // \end{figure}
-  // Software Guide : EndLatex
 
   typedef otb::PrintableImageFilter<ImageType> PrintableFilterType;
-  PrintableFilterType::Pointer printableImageFilter = PrintableFilterType::New();
+  PrintableFilterType::Pointer                 printableImageFilter = PrintableFilterType::New();
 
   printableImageFilter->SetChannel(1);
   printableImageFilter->SetChannel(2);
   printableImageFilter->SetChannel(3);
 
-  typedef PrintableFilterType::OutputImageType OutputImageType;
+  typedef PrintableFilterType::OutputImageType  OutputImageType;
   typedef otb::ImageFileWriter<OutputImageType> PrettyWriterType;
 
   PrettyWriterType::Pointer prettyWriter = PrettyWriterType::New();
@@ -206,9 +167,9 @@ int main(int argc, char * argv[])
   LabelRGBWriterType::Pointer labelRGBWriter = LabelRGBWriterType::New();
 
   // Label to RGB image
-  typedef itk::Functor::ScalarToRGBPixelFunctor<LabelPixelType> FunctorType;
+  typedef itk::Functor::ScalarToRGBPixelFunctor<LabelPixelType>                   FunctorType;
   typedef itk::UnaryFunctorImageFilter<LabelImageType, RGBImageType, FunctorType> ColorLabelFilterType;
-  ColorLabelFilterType::Pointer labelToRGB = ColorLabelFilterType::New();
+  ColorLabelFilterType::Pointer                                                   labelToRGB = ColorLabelFilterType::New();
 
   labelToRGB->SetInput(filter->GetLabelOutput());