Merge branch 'develop' into superbuild_data

.gitlab-ci.yml

@@ -24,10 +24,10 @@ before_script:
   # Provision efficiently the local LFS cache before checkout
   - git lfs fetch origin $CI_COMMIT_SHA
   # Checkout the expected branch
-  - git checkout $CI_COMMIT_REF_NAME
+  - git checkout -f -q $CI_COMMIT_SHA
 
 after_script:
-  - python3 CI/cdash_handler.py $CI_COMMIT_SHA $CI_PROJECT_ID $CI_PROJECT_DIR $K8S_SECRET_CDASH
+  - python3 CI/cdash_handler.py $CI_COMMIT_SHA $CI_PROJECT_ID $CI_PROJECT_DIR $K8S_SECRET_API_TOKEN
 
 stages:
   - precheck

CI/check_twin_pipelines.py

@@ -64,25 +64,29 @@ if __name__ == "__main__":
   sha1 = env['CI_COMMIT_SHA']
   # are we in a merge_request pipeline ?
   if 'CI_MERGE_REQUEST_IID' in env.keys():
-    if not CheckEnvParameters(['K8S_SECRET_TWIN_PIPELINE','CI_PROJECT_ID','CI_PIPELINE_ID']):
+    if not CheckEnvParameters(['K8S_SECRET_API_TOKEN']):
+      print("Make sure you have set a valid acces token for Gitlab API")
+      print("The K8S_SECRET_API_TOKEN environment variable should be set in 'Settings -> CI/CD -> Variables'")
       sys.exit(1)
-    mrInfo = GitlabRequest('merge_requests/'+env['CI_MERGE_REQUEST_IID'],token=env['K8S_SECRET_TWIN_PIPELINE'])
+    if not CheckEnvParameters(['CI_PROJECT_ID','CI_PIPELINE_ID']):
+      sys.exit(1)
+    mrInfo = GitlabRequest('merge_requests/'+env['CI_MERGE_REQUEST_IID'],token=env['K8S_SECRET_API_TOKEN'])
     wip_regex = re.compile("^[Ww][Ii][Pp]:")
     # is it a "WIP" merge request ?
     if wip_regex.search(mrInfo["title"]):
       # Yes: cancel the current pipeline
       print("Cancel current pipeline "+env['CI_PIPELINE_ID'])
       GitlabRequest('pipelines/'+env['CI_PIPELINE_ID']+'/cancel', data={}, \
-        project=env['CI_PROJECT_ID'], token=env['K8S_SECRET_TWIN_PIPELINE'])
+        project=env['CI_PROJECT_ID'], token=env['K8S_SECRET_API_TOKEN'])
       time.sleep(180)
       print("Error: this pipeline should have been canceled")
       sys.exit(1)
     else:
       # No: cancel any previous "normal" pipeline on the same SHA1
-      jres = GitlabRequest('pipelines?sha='+sha1, project=env['CI_PROJECT_ID'], token=env['K8S_SECRET_TWIN_PIPELINE'])
+      jres = GitlabRequest('pipelines?sha='+sha1, project=env['CI_PROJECT_ID'], token=env['K8S_SECRET_API_TOKEN'])
       for item in jres:
         if item["id"] < int(env['CI_PIPELINE_ID']) and item["status"] == "running":
           print("Cancel pipeline "+str(item["id"]))
           jres2 = GitlabRequest('pipelines/'+str(item["id"])+'/cancel', data={}, \
-            project=env['CI_PROJECT_ID'], token=env['K8S_SECRET_TWIN_PIPELINE'])
+            project=env['CI_PROJECT_ID'], token=env['K8S_SECRET_API_TOKEN'])
 

CI/configure_options.cmake

@@ -55,8 +55,7 @@ OTB_USE_SSE_FLAGS:BOOL=ON
 OTB_MPIEXEC_OPT:STRING=--allow-run-as-root")
 
 set (otb_wrap_option
-"OTB_WRAP_JAVA:BOOL=ON
-OTB_WRAP_PYTHON:BOOL=ON")
+"OTB_WRAP_PYTHON:BOOL=ON")
 
 set (otb_data_option
 "OTB_DATA_USE_LARGEINPUT:BOOL=OFF

CMakeLists.txt

@@ -165,9 +165,6 @@ endif()
 if(NOT OTB_INSTALL_PYTHON_DIR)
   set(OTB_INSTALL_PYTHON_DIR "${OTB_INSTALL_LIBRARY_DIR}/otb/python")
 endif()
-if(NOT OTB_INSTALL_JAVA_DIR)
-  set(OTB_INSTALL_JAVA_DIR "${OTB_INSTALL_LIBRARY_DIR}/otb/java")
-endif()
 if(NOT OTB_INSTALL_DATA_DIR)
   set(OTB_INSTALL_DATA_DIR "share/otb")
 endif()
@@ -533,7 +530,6 @@ foreach(otb_option
     CMAKE_CXX_FLAGS
     ${option_list}
     OTB_WRAP_PYTHON
-    OTB_WRAP_JAVA
     OTB_DATA_ROOT
     OTB_USE_OPENMP
     OTB_USE_SSE_FLAGS

Data/Baseline/OTB-Applications/Files/apTvClTrainVectorRegressionModel.1.txt

+io.mse: 0.003289417131

Data/Baseline/OTB-Applications/Files/apTvClTrainVectorRegressionModel.txt

+io.mse: 0.001359587419

Data/Baseline/OTB-Applications/Files/apTvTestApplicationOutputXML_All.xml

@@ -5,7 +5,6 @@
         <name>TestApplication</name>
         <descr>This application helps developers to test parameters types</descr>
         <doc>
-            <name>Test</name>
             <longdescr>The purpose of this application is to test parameters types.</longdescr>
             <authors>OTB-Team</authors>
             <limitations>None</limitations>

Documentation/Cookbook/Scripts/otbGenerateWrappersRstDoc.py

@@ -25,7 +25,7 @@ import argparse
 import re
 
 import otbApplication
-from otbApplication import ParameterType_Bool, ParameterType_Int, ParameterType_Radius, ParameterType_RAM, ParameterType_Float, ParameterType_String, ParameterType_StringList, ParameterType_InputFilename, ParameterType_OutputFilename, ParameterType_InputImage, ParameterType_OutputImage, ParameterType_InputVectorData, ParameterType_OutputVectorData, ParameterType_Directory, ParameterType_Choice, ParameterType_InputImageList, ParameterType_InputVectorDataList, ParameterType_InputFilenameList, ParameterType_InputProcessXML, ParameterType_OutputProcessXML, ParameterType_ListView, ParameterType_Group
+from otbApplication import ParameterType_Bool, ParameterType_Int, ParameterType_Radius, ParameterType_RAM, ParameterType_Float, ParameterType_String, ParameterType_StringList, ParameterType_InputFilename, ParameterType_OutputFilename, ParameterType_InputImage, ParameterType_OutputImage, ParameterType_InputVectorData, ParameterType_OutputVectorData, ParameterType_Directory, ParameterType_Choice, ParameterType_InputImageList, ParameterType_InputVectorDataList, ParameterType_InputFilenameList, ParameterType_ListView, ParameterType_Group
 
 from otb_warnings import application_documentation_warnings
 
@@ -202,7 +202,6 @@ def rst_parameter_value(app, key):
     values.update({ParameterType_InputImageList: "image1 image2..."})
     values.update({ParameterType_InputVectorDataList: "vectorfile1 vectorfile2..."})
     values.update({ParameterType_InputFilenameList: "filename1 filename2..."})
-    values.update(dict.fromkeys([ParameterType_InputProcessXML, ParameterType_OutputProcessXML], "filename.xml"))
 
     if type in values:
         return values[type]
@@ -356,10 +355,17 @@ def make_links(text, allapps):
     rep = {appname: ":ref:`{}`".format(appname) for appname in allapps}
     return multireplace(text, rep)
 
+def render_deprecation_string(app):
+    if app.IsDeprecated():
+        return "This application is deprecated and will be removed in a future release."
+    else:
+        return ""
+
 def render_application(appname, allapps):
     "Render app to rst"
 
-    app = otbApplication.Registry.CreateApplication(appname)
+    # Create the application without logger to avoid the deprecation warning log
+    app = otbApplication.Registry.CreateApplicationWithoutLogger(appname)
 
     # TODO: remove this when bug 440 is fixed
     app.Init()
@@ -368,6 +374,7 @@ def render_application(appname, allapps):
 
     output = template_application.format(
         label=appname,
+        deprecation_string=render_deprecation_string(app),
         heading=rst_section(app.GetName(), '='),
         description=app.GetDescription(),
         longdescription=make_links(app.GetDocLongDescription(), allapps),
@@ -381,8 +388,9 @@ def render_application(appname, allapps):
     return output
 
 def GetApplicationTags(appname):
-     app = otbApplication.Registry.CreateApplication(appname)
-     return app.GetDocTags()
+    # Create the application without logger to avoid the deprecation warning log
+    app = otbApplication.Registry.CreateApplicationWithoutLogger(appname)
+    return app.GetDocTags()
 
 def GenerateRstForApplications(rst_dir):
     "Generate .rst files for all applications"
@@ -404,9 +412,12 @@ def GenerateRstForApplications(rst_dir):
     for appName in appNames:
 
         # Get application first tag
-        tags = GetApplicationTags(appName)
+        tags = list(GetApplicationTags(appName))
+        if "Deprecated" in tags:
+            tags.remove("Deprecated")
         if not tags or len(tags) == 0:
             raise RuntimeError("No tags for application: " + appName)
+
         tag = tags[0]
         tag_ = tag.replace(" ", "_")
 

Documentation/Cookbook/rst/C++/WriteAnApplication.rst

@@ -158,9 +158,6 @@ parameters:
 -  ``ParameterType_InputVectorDataList`` : parameter storing a list of
    input vector data.
 
--  ``ParameterType_InputProcessXML`` : parameter storing an input XML
-   file name.
-
 -  ``ParameterType_OutputFilename`` : parameter storing an output file
    name.
 
@@ -169,9 +166,6 @@ parameters:
 -  ``ParameterType_OutputVectorData`` : parameter storing an output
    vector data.
 
--  ``ParameterType_OutputProcessXML`` : parameter storing an output XML
-   file name.
-
 -  ``ParameterType_RAM`` : parameter storing the maximum amount of RAM
    to be used.
 

Documentation/Cookbook/rst/CliInterface.rst

@@ -123,7 +123,6 @@ example based on the OrthoRectification application:
             -opt.rpc                 <int32>          RPC modeling (points per axis)  (optional, off by default, default value is 10)
             -opt.ram                 <int32>          Available RAM (MB)  (optional, off by default, default value is 128)
             -opt.gridspacing         <float>          Resampling grid spacing  (optional, off by default, default value is 4)
-            -inxml                   <string>         Load parameters from XML  (optional, off by default)
             -progress                <boolean>        Report progress
             -help                    <string list>    Display long help (empty list), or help for given parameters keys
 
@@ -145,11 +144,10 @@ Command-line examples are provided in the chapter :ref:`apprefdoc`.
 Load and save parameters to XML
 -------------------------------
 
-Since OTB 3.20, OTB applications parameters can be export/import to/from
-an XML file using inxml/outxml parameters. Those parameters are
-available in all applications.
-
-An example is worth a thousand words
+OTB application parameters can be saved and loaded to
+an XML file using the special ``-inxml`` and ``-outxml`` parameters.
+Those parameters are available in all applications.
+For example:
 
 ::
 
@@ -177,17 +175,6 @@ time
 In this case it will use as mathematical expression “(im1b1 - im2b1)”
 instead of “abs(im1b1 - im2b1)”.
 
-Finally, you can also launch applications directly from the command-line
-launcher executable using the inxml parameter without having to declare
-the application name. Use in this case:
-
-::
-
-    otbApplicationLauncherCommandLine -inxml saved_applications_parameters.xml
-
-It will retrieve the application name and related parameters from the
-input XML file and launch in this case the BandMath applications.
-
 Parallel execution with MPI
 ---------------------------
 

Documentation/Cookbook/rst/Installation.rst

@@ -152,3 +152,15 @@ following repositories with these command-lines:
     http://download.opensuse.org/repositories/home:/tzotsos/openSUSE_Tumbleweed/ tzotsos
 
 and then add the OTB packages as shown above.
+
+
+Archlinux
+~~~~~~~~~~
+
+Package is in AUR (Arch User Repository).
+You will then need to run (if you use yaourt, you could use trizen instead):
+
+::
+
+    yaourt -S orfeo-toolbox
+

Documentation/Cookbook/rst/PythonAPI.rst

@@ -218,11 +218,34 @@ implementation does not break it, for instance by using an internal
 writer to write intermediate data. In this case, execution should
 still be correct, but some intermediate data will be read or written.
 
+Load and save parameters to XML
+-------------------------------
+
+As with a the `command line interface` you can save application parameters
+to an xml file:
+
+.. code-block:: python
+
+    # Save application parameters to XML
+    app = otb.Registry.CreateApplication('BandMath')
+    app.SetParameterStringList("il", ["image1.tif", "image2.tif"], True)
+    app.SetParameterString("out", out, True)
+    app.SetParameterString("exp", "cos(im1b1)+im2b1*im1b1", True)
+    app.SaveParametersToXML("parameters.xml")
+
+And load them later for execution:
+
+.. code-block:: python
+
+    # Load application parameters from XML
+    app = otb.Registry.CreateApplication("BandMath")
+    app.LoadParametersFromXML("parameters.xml")
+    app.ExecuteAndWriteOutput()
+
+
 Interactions with OTB pipeline
 ------------------------------
 
-[Since OTB 6.6]
-
 The application framework has been extended in order to provide ways to
 interact with the pipelines inside each application. It applies only to
 applications that use input or output images. Let's check which  

Documentation/Cookbook/rst/templates/application.rst

 .. _{label}:
 
 {heading}
+
+{deprecation_string}
+
 {description}
 
 Description

Examples/Application/ApplicationExample.cxx

@@ -68,7 +68,6 @@ private:
     // \begin{description}
     // \item[\code{SetName()}] Name of the application.
     // \item[\code{SetDescription()}] Set the short description of the class.
-    // \item[\code{SetDocName()}] Set long name of the application (that can be displayed \dots).
     // \item[\code{SetDocLongDescription()}] This methods is used to describe the class.
     // \item[\code{SetDocLimitations()}] Set known limitations (threading, invalid pixel type \dots) or bugs.
     // \item[\code{SetDocAuthors()}] Set the application Authors. Author List. Format : "John Doe, Winnie the Pooh" \dots
@@ -81,7 +80,6 @@ private:
         "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,"

Modules/Applications/AppChangeDetection/app/otbMultivariateAlterationDetector.cxx

@@ -49,7 +49,6 @@ private:
     SetDescription("Change detection by Multivariate Alteration Detector (MAD) algorithm");
 
     // Documentation
-    SetDocName("Multivariate Alteration Detector");
     SetDocLongDescription("This application performs change detection between two multispectral"
                           " images using the Multivariate Alteration Detector (MAD) [1]"
                           " algorithm.\n\n"

Modules/Applications/AppClassification/app/CMakeLists.txt

@@ -65,6 +65,11 @@ otb_create_application(
   SOURCES        otbTrainRegression.cxx
   LINK_LIBRARIES ${${otb-module}_LIBRARIES})
 
+otb_create_application(
+  NAME           TrainVectorRegression
+  SOURCES        otbTrainVectorRegression.cxx
+  LINK_LIBRARIES ${${otb-module}_LIBRARIES})
+
 otb_create_application(
   NAME           PredictRegression
   SOURCES        otbPredictRegression.cxx

Modules/Applications/AppClassification/app/otbClassificationMapRegularization.cxx

@@ -62,7 +62,6 @@ private:
     SetName("ClassificationMapRegularization");
     SetDescription("Filters the input labeled image using Majority Voting in a ball shaped neighbordhood");
 
-    SetDocName("Classification Map Regularization");
 
     SetDocLongDescription(
         "This application filters the input labeled image (with a maximal class label = 65535) using Majority Voting in a ball shaped neighbordhood."

Modules/Applications/AppClassification/app/otbComputeConfusionMatrix.cxx

@@ -109,7 +109,6 @@ private:
   SetDescription("Computes the confusion matrix of a classification");
 
   // Documentation
-  SetDocName("Confusion matrix Computation");
   SetDocLongDescription("This application computes the confusion matrix of a classification map relative to a ground truth dataset. "
       "This ground truth can be given as a raster or a vector data. Only reference and produced pixels with values different "
       "from NoData are handled in the calculation of the confusion matrix. The confusion matrix is organized the following way: "

Modules/Applications/AppClassification/app/otbComputeImagesStatistics.cxx

@@ -48,7 +48,6 @@ private:
   void DoInit() override
   {
     SetName("ComputeImagesStatistics");
-    SetDocName("Compute Images second order statistics");
     SetDescription("Computes global mean and standard deviation for each band "
       "from a set of images and optionally saves the results in an XML file.");
     SetDocLongDescription("This application computes a global mean and standard deviation "

Modules/Applications/AppClassification/app/otbComputeOGRLayersFeaturesStatistics.cxx

@@ -51,7 +51,6 @@ private:
     SetName("ComputeOGRLayersFeaturesStatistics");
     SetDescription("Compute statistics of the features in a set of OGR Layers");
 
-    SetDocName("ComputeOGRLayersFeaturesStatistics");
     SetDocLongDescription("Compute statistics (mean and standard deviation) of the features in a set of OGR Layers, and write them in an XML file. This XML file can then be used by the training application.");
     SetDocLimitations("Experimental. For now only shapefiles are supported.");
     SetDocAuthors("David Youssefi during internship at CNES");