Commit ceff97aa authored by Antoine Regimbeau's avatar Antoine Regimbeau
Browse files

Merge branch 'develop' into ci_hidden_key

parents 84b16d03 dbf88cdf
...@@ -64,25 +64,29 @@ if __name__ == "__main__": ...@@ -64,25 +64,29 @@ if __name__ == "__main__":
sha1 = env['CI_COMMIT_SHA'] sha1 = env['CI_COMMIT_SHA']
# are we in a merge_request pipeline ? # are we in a merge_request pipeline ?
if 'CI_MERGE_REQUEST_IID' in env.keys(): 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) 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]:") wip_regex = re.compile("^[Ww][Ii][Pp]:")
# is it a "WIP" merge request ? # is it a "WIP" merge request ?
if wip_regex.search(mrInfo["title"]): if wip_regex.search(mrInfo["title"]):
# Yes: cancel the current pipeline # Yes: cancel the current pipeline
print("Cancel current pipeline "+env['CI_PIPELINE_ID']) print("Cancel current pipeline "+env['CI_PIPELINE_ID'])
GitlabRequest('pipelines/'+env['CI_PIPELINE_ID']+'/cancel', data={}, \ 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) time.sleep(180)
print("Error: this pipeline should have been canceled") print("Error: this pipeline should have been canceled")
sys.exit(1) sys.exit(1)
else: else:
# No: cancel any previous "normal" pipeline on the same SHA1 # 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: for item in jres:
if item["id"] < int(env['CI_PIPELINE_ID']) and item["status"] == "running": if item["id"] < int(env['CI_PIPELINE_ID']) and item["status"] == "running":
print("Cancel pipeline "+str(item["id"])) print("Cancel pipeline "+str(item["id"]))
jres2 = GitlabRequest('pipelines/'+str(item["id"])+'/cancel', data={}, \ 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'])
...@@ -55,8 +55,7 @@ OTB_USE_SSE_FLAGS:BOOL=ON ...@@ -55,8 +55,7 @@ OTB_USE_SSE_FLAGS:BOOL=ON
OTB_MPIEXEC_OPT:STRING=--allow-run-as-root") OTB_MPIEXEC_OPT:STRING=--allow-run-as-root")
set (otb_wrap_option set (otb_wrap_option
"OTB_WRAP_JAVA:BOOL=ON "OTB_WRAP_PYTHON:BOOL=ON")
OTB_WRAP_PYTHON:BOOL=ON")
set (otb_data_option set (otb_data_option
"OTB_DATA_USE_LARGEINPUT:BOOL=OFF "OTB_DATA_USE_LARGEINPUT:BOOL=OFF
......
...@@ -165,9 +165,6 @@ endif() ...@@ -165,9 +165,6 @@ endif()
if(NOT OTB_INSTALL_PYTHON_DIR) if(NOT OTB_INSTALL_PYTHON_DIR)
set(OTB_INSTALL_PYTHON_DIR "${OTB_INSTALL_LIBRARY_DIR}/otb/python") set(OTB_INSTALL_PYTHON_DIR "${OTB_INSTALL_LIBRARY_DIR}/otb/python")
endif() 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) if(NOT OTB_INSTALL_DATA_DIR)
set(OTB_INSTALL_DATA_DIR "share/otb") set(OTB_INSTALL_DATA_DIR "share/otb")
endif() endif()
...@@ -533,7 +530,6 @@ foreach(otb_option ...@@ -533,7 +530,6 @@ foreach(otb_option
CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS
${option_list} ${option_list}
OTB_WRAP_PYTHON OTB_WRAP_PYTHON
OTB_WRAP_JAVA
OTB_DATA_ROOT OTB_DATA_ROOT
OTB_USE_OPENMP OTB_USE_OPENMP
OTB_USE_SSE_FLAGS OTB_USE_SSE_FLAGS
......
...@@ -5,7 +5,6 @@ ...@@ -5,7 +5,6 @@
<name>TestApplication</name> <name>TestApplication</name>
<descr>This application helps developers to test parameters types</descr> <descr>This application helps developers to test parameters types</descr>
<doc> <doc>
<name>Test</name>
<longdescr>The purpose of this application is to test parameters types.</longdescr> <longdescr>The purpose of this application is to test parameters types.</longdescr>
<authors>OTB-Team</authors> <authors>OTB-Team</authors>
<limitations>None</limitations> <limitations>None</limitations>
......
...@@ -25,7 +25,7 @@ import argparse ...@@ -25,7 +25,7 @@ import argparse
import re import re
import otbApplication 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 from otb_warnings import application_documentation_warnings
...@@ -202,7 +202,6 @@ def rst_parameter_value(app, key): ...@@ -202,7 +202,6 @@ def rst_parameter_value(app, key):
values.update({ParameterType_InputImageList: "image1 image2..."}) values.update({ParameterType_InputImageList: "image1 image2..."})
values.update({ParameterType_InputVectorDataList: "vectorfile1 vectorfile2..."}) values.update({ParameterType_InputVectorDataList: "vectorfile1 vectorfile2..."})
values.update({ParameterType_InputFilenameList: "filename1 filename2..."}) values.update({ParameterType_InputFilenameList: "filename1 filename2..."})
values.update(dict.fromkeys([ParameterType_InputProcessXML, ParameterType_OutputProcessXML], "filename.xml"))
if type in values: if type in values:
return values[type] return values[type]
...@@ -356,10 +355,17 @@ def make_links(text, allapps): ...@@ -356,10 +355,17 @@ def make_links(text, allapps):
rep = {appname: ":ref:`{}`".format(appname) for appname in allapps} rep = {appname: ":ref:`{}`".format(appname) for appname in allapps}
return multireplace(text, rep) 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): def render_application(appname, allapps):
"Render app to rst" "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 # TODO: remove this when bug 440 is fixed
app.Init() app.Init()
...@@ -368,6 +374,7 @@ def render_application(appname, allapps): ...@@ -368,6 +374,7 @@ def render_application(appname, allapps):
output = template_application.format( output = template_application.format(
label=appname, label=appname,
deprecation_string=render_deprecation_string(app),
heading=rst_section(app.GetName(), '='), heading=rst_section(app.GetName(), '='),
description=app.GetDescription(), description=app.GetDescription(),
longdescription=make_links(app.GetDocLongDescription(), allapps), longdescription=make_links(app.GetDocLongDescription(), allapps),
...@@ -381,8 +388,9 @@ def render_application(appname, allapps): ...@@ -381,8 +388,9 @@ def render_application(appname, allapps):
return output return output
def GetApplicationTags(appname): def GetApplicationTags(appname):
app = otbApplication.Registry.CreateApplication(appname) # Create the application without logger to avoid the deprecation warning log
return app.GetDocTags() app = otbApplication.Registry.CreateApplicationWithoutLogger(appname)
return app.GetDocTags()
def GenerateRstForApplications(rst_dir): def GenerateRstForApplications(rst_dir):
"Generate .rst files for all applications" "Generate .rst files for all applications"
...@@ -404,9 +412,12 @@ def GenerateRstForApplications(rst_dir): ...@@ -404,9 +412,12 @@ def GenerateRstForApplications(rst_dir):
for appName in appNames: for appName in appNames:
# Get application first tag # 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: if not tags or len(tags) == 0:
raise RuntimeError("No tags for application: " + appName) raise RuntimeError("No tags for application: " + appName)
tag = tags[0] tag = tags[0]
tag_ = tag.replace(" ", "_") tag_ = tag.replace(" ", "_")
......
...@@ -158,9 +158,6 @@ parameters: ...@@ -158,9 +158,6 @@ parameters:
- ``ParameterType_InputVectorDataList`` : parameter storing a list of - ``ParameterType_InputVectorDataList`` : parameter storing a list of
input vector data. input vector data.
- ``ParameterType_InputProcessXML`` : parameter storing an input XML
file name.
- ``ParameterType_OutputFilename`` : parameter storing an output file - ``ParameterType_OutputFilename`` : parameter storing an output file
name. name.
...@@ -169,9 +166,6 @@ parameters: ...@@ -169,9 +166,6 @@ parameters:
- ``ParameterType_OutputVectorData`` : parameter storing an output - ``ParameterType_OutputVectorData`` : parameter storing an output
vector data. vector data.
- ``ParameterType_OutputProcessXML`` : parameter storing an output XML
file name.
- ``ParameterType_RAM`` : parameter storing the maximum amount of RAM - ``ParameterType_RAM`` : parameter storing the maximum amount of RAM
to be used. to be used.
......
...@@ -123,7 +123,6 @@ example based on the OrthoRectification application: ...@@ -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.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.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) -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 -progress <boolean> Report progress
-help <string list> Display long help (empty list), or help for given parameters keys -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`. ...@@ -145,11 +144,10 @@ Command-line examples are provided in the chapter :ref:`apprefdoc`.
Load and save parameters to XML Load and save parameters to XML
------------------------------- -------------------------------
Since OTB 3.20, OTB applications parameters can be export/import to/from OTB application parameters can be saved and loaded to
an XML file using inxml/outxml parameters. Those parameters are an XML file using the special ``-inxml`` and ``-outxml`` parameters.
available in all applications. Those parameters are available in all applications.
For example:
An example is worth a thousand words
:: ::
...@@ -177,17 +175,6 @@ time ...@@ -177,17 +175,6 @@ time
In this case it will use as mathematical expression “(im1b1 - im2b1)” In this case it will use as mathematical expression “(im1b1 - im2b1)”
instead of “abs(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 Parallel execution with MPI
--------------------------- ---------------------------
......
...@@ -152,3 +152,15 @@ following repositories with these command-lines: ...@@ -152,3 +152,15 @@ following repositories with these command-lines:
http://download.opensuse.org/repositories/home:/tzotsos/openSUSE_Tumbleweed/ tzotsos http://download.opensuse.org/repositories/home:/tzotsos/openSUSE_Tumbleweed/ tzotsos
and then add the OTB packages as shown above. 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
...@@ -218,11 +218,34 @@ implementation does not break it, for instance by using an internal ...@@ -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 writer to write intermediate data. In this case, execution should
still be correct, but some intermediate data will be read or written. 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 Interactions with OTB pipeline
------------------------------ ------------------------------
[Since OTB 6.6]
The application framework has been extended in order to provide ways to The application framework has been extended in order to provide ways to
interact with the pipelines inside each application. It applies only to interact with the pipelines inside each application. It applies only to
applications that use input or output images. Let's check which applications that use input or output images. Let's check which
......
.. _{label}: .. _{label}:
{heading} {heading}
{deprecation_string}
{description} {description}
Description Description
......
...@@ -68,7 +68,6 @@ private: ...@@ -68,7 +68,6 @@ private:
// \begin{description} // \begin{description}
// \item[\code{SetName()}] Name of the application. // \item[\code{SetName()}] Name of the application.
// \item[\code{SetDescription()}] Set the short description of the class. // \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{SetDocLongDescription()}] This methods is used to describe the class.
// \item[\code{SetDocLimitations()}] Set known limitations (threading, invalid pixel type \dots) or bugs. // \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 // \item[\code{SetDocAuthors()}] Set the application Authors. Author List. Format : "John Doe, Winnie the Pooh" \dots
...@@ -81,7 +80,6 @@ private: ...@@ -81,7 +80,6 @@ private:
"Pay attention, it includes Latex snippets in order to generate " "Pay attention, it includes Latex snippets in order to generate "
"software guide documentation"); "software guide documentation");
SetDocName("Example");
SetDocLongDescription( SetDocLongDescription(
"The purpose of this application is " "The purpose of this application is "
"to present parameters types," "to present parameters types,"
......
...@@ -49,7 +49,6 @@ private: ...@@ -49,7 +49,6 @@ private:
SetDescription("Change detection by Multivariate Alteration Detector (MAD) algorithm"); SetDescription("Change detection by Multivariate Alteration Detector (MAD) algorithm");
// Documentation // Documentation
SetDocName("Multivariate Alteration Detector");
SetDocLongDescription("This application performs change detection between two multispectral" SetDocLongDescription("This application performs change detection between two multispectral"
" images using the Multivariate Alteration Detector (MAD) [1]" " images using the Multivariate Alteration Detector (MAD) [1]"
" algorithm.\n\n" " algorithm.\n\n"
......
...@@ -65,6 +65,11 @@ otb_create_application( ...@@ -65,6 +65,11 @@ otb_create_application(
SOURCES otbTrainRegression.cxx SOURCES otbTrainRegression.cxx
LINK_LIBRARIES ${${otb-module}_LIBRARIES}) LINK_LIBRARIES ${${otb-module}_LIBRARIES})
otb_create_application(
NAME TrainVectorRegression
SOURCES otbTrainVectorRegression.cxx
LINK_LIBRARIES ${${otb-module}_LIBRARIES})
otb_create_application( otb_create_application(
NAME PredictRegression NAME PredictRegression
SOURCES otbPredictRegression.cxx SOURCES otbPredictRegression.cxx
......
...@@ -62,7 +62,6 @@ private: ...@@ -62,7 +62,6 @@ private:
SetName("ClassificationMapRegularization"); SetName("ClassificationMapRegularization");
SetDescription("Filters the input labeled image using Majority Voting in a ball shaped neighbordhood"); SetDescription("Filters the input labeled image using Majority Voting in a ball shaped neighbordhood");
SetDocName("Classification Map Regularization");
SetDocLongDescription( SetDocLongDescription(
"This application filters the input labeled image (with a maximal class label = 65535) using Majority Voting in a ball shaped neighbordhood." "This application filters the input labeled image (with a maximal class label = 65535) using Majority Voting in a ball shaped neighbordhood."
......
...@@ -109,7 +109,6 @@ private: ...@@ -109,7 +109,6 @@ private:
SetDescription("Computes the confusion matrix of a classification"); SetDescription("Computes the confusion matrix of a classification");
// Documentation // Documentation
SetDocName("Confusion matrix Computation");
SetDocLongDescription("This application computes the confusion matrix of a classification map relative to a ground truth dataset. " 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 " "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: " "from NoData are handled in the calculation of the confusion matrix. The confusion matrix is organized the following way: "
......
...@@ -48,7 +48,6 @@ private: ...@@ -48,7 +48,6 @@ private:
void DoInit() override void DoInit() override
{ {
SetName("ComputeImagesStatistics"); SetName("ComputeImagesStatistics");
SetDocName("Compute Images second order statistics");
SetDescription("Computes global mean and standard deviation for each band " SetDescription("Computes global mean and standard deviation for each band "
"from a set of images and optionally saves the results in an XML file."); "from a set of images and optionally saves the results in an XML file.");
SetDocLongDescription("This application computes a global mean and standard deviation " SetDocLongDescription("This application computes a global mean and standard deviation "
......
...@@ -51,7 +51,6 @@ private: ...@@ -51,7 +51,6 @@ private:
SetName("ComputeOGRLayersFeaturesStatistics"); SetName("ComputeOGRLayersFeaturesStatistics");
SetDescription("Compute statistics of the features in a set of OGR Layers"); 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."); 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."); SetDocLimitations("Experimental. For now only shapefiles are supported.");
SetDocAuthors("David Youssefi during internship at CNES"); SetDocAuthors("David Youssefi during internship at CNES");
......
...@@ -97,7 +97,6 @@ private: ...@@ -97,7 +97,6 @@ private:
{ {
SetName("FusionOfClassifications"); SetName("FusionOfClassifications");
SetDescription("Fuses several classifications maps of the same image on the basis of class labels."); SetDescription("Fuses several classifications maps of the same image on the basis of class labels.");
SetDocName("Fusion of Classifications");
SetDocLongDescription("This application allows you to fuse several classification maps and produces a single more robust classification map. " SetDocLongDescription("This application allows you to fuse several classification maps and produces a single more robust classification map. "
"Fusion is done either by mean of Majority Voting, or with the Dempster Shafer combination method on class labels.\n\n" "Fusion is done either by mean of Majority Voting, or with the Dempster Shafer combination method on class labels.\n\n"
" - MAJORITY VOTING: for each pixel, the class with the highest number of votes is selected.\n" " - MAJORITY VOTING: for each pixel, the class with the highest number of votes is selected.\n"
......
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