Force::isDisabled -->> Force::appliesForce

.travis.yml

@@ -10,7 +10,7 @@ matrix:
   include:
     - os: linux
       compiler: clang
-      env: BTYPE=RelWithDebInfo WRAP=on  DOXY=on  NPROC=1 DEPLOY=no # (TEMP bintray not working) yes
+      env: BTYPE=RelWithDebInfo WRAP=on  DOXY=on  NPROC=2 DEPLOY=no # (TEMP bintray not working) yes
     - os: linux
       compiler: gcc
       env: BTYPE=RelWithDebInfo WRAP=off DOXY=off NPROC=3 DEPLOY=no

Applications/Analyze/CMakeLists.txt

@@ -1,4 +1,6 @@
-OpenSimAddApplication(NAME analyze)
+if(OPENSIM_BUILD_INDIVIDUAL_APPS)
+    OpenSimAddApplication(NAME analyze)
+endif()
 
 if(BUILD_TESTING)
     subdirs(test)

Applications/CMC/CMakeLists.txt

@@ -1,4 +1,6 @@
-OpenSimAddApplication(NAME cmc)
+if(OPENSIM_BUILD_INDIVIDUAL_APPS)
+    OpenSimAddApplication(NAME cmc)
+endif()
 
 if(BUILD_TESTING)
     subdirs(test)

Applications/CMakeLists.txt

@@ -1,14 +1,13 @@
-if(OPENSIM_BUILD_INDIVIDUAL_APPS)
-    # Basically, don't install the old applications on Linux or OSX, where
-    # they conflict with system executables like "id".
-    add_subdirectory(Analyze)
-    add_subdirectory(Forward)
-    add_subdirectory(Scale)
-    add_subdirectory(IK)
-    add_subdirectory(ID)
-    add_subdirectory(CMC)
-    add_subdirectory(RRA)
-    add_subdirectory(versionUpdate)
-endif()
+# If NOT OPENSIM_BUILD_INDIVIDUAL_APPS, then we will not build the old
+# applications like "id". However, we still need to include those folders to
+# build the tests for the tools.
+add_subdirectory(Analyze)
+add_subdirectory(Forward)
+add_subdirectory(Scale)
+add_subdirectory(IK)
+add_subdirectory(ID)
+add_subdirectory(CMC)
+add_subdirectory(RRA)
+add_subdirectory(versionUpdate)
 
 add_subdirectory(opensim-cmd)

Applications/Forward/CMakeLists.txt

@@ -1,4 +1,6 @@
-OpenSimAddApplication(NAME forward)
+if(OPENSIM_BUILD_INDIVIDUAL_APPS)
+    OpenSimAddApplication(NAME forward)
+endif()
 
 if(BUILD_TESTING)
     subdirs(test)

Applications/ID/CMakeLists.txt

@@ -1,4 +1,6 @@
-OpenSimAddApplication(NAME id)
+if(OPENSIM_BUILD_INDIVIDUAL_APPS)
+    OpenSimAddApplication(NAME id)
+endif()
 
 if(BUILD_TESTING)
     subdirs(test)

Applications/IK/CMakeLists.txt

@@ -1,4 +1,6 @@
-OpenSimAddApplication(NAME ik)
+if(OPENSIM_BUILD_INDIVIDUAL_APPS)
+    OpenSimAddApplication(NAME ik)
+endif()
 
 if(BUILD_TESTING)
     subdirs(test)

Applications/RRA/CMakeLists.txt

@@ -1,4 +1,6 @@
-OpenSimAddApplication(NAME rra)
+if(OPENSIM_BUILD_INDIVIDUAL_APPS)
+    OpenSimAddApplication(NAME rra)
+endif()
 
 if(BUILD_TESTING)
     subdirs(test)

Applications/Scale/CMakeLists.txt

@@ -1,4 +1,6 @@
-OpenSimAddApplication(NAME scale)
+if(OPENSIM_BUILD_INDIVIDUAL_APPS)
+    OpenSimAddApplication(NAME scale)
+endif()
 
 if(BUILD_TESTING)
     subdirs(test)

Applications/opensim-cmd/CMakeLists.txt

@@ -5,30 +5,13 @@
 # docopt_DIR.
 find_package(docopt 0.6.1
              HINTS "${OPENSIM_DEPENDENCIES_DIR}/docopt/lib/cmake/docopt")
-if(WIN32)
-    # Back out the directory containing docopt.dll
-    # The docopt-config.cmake file does not define a variable containing
-    # the docopt installation directory.
-    # The location of docopt-config.cmake within the docopt installation is
-    # lib/cmake/docopt.
-    # docopt_DIR is the path to the docopt-config.cmake file.
-    # So we remove the last two directories from docopt_DIR.
-    get_filename_component(docopt_lib_dir ${docopt_DIR} PATH)
-    get_filename_component(docopt_lib_dir ${docopt_lib_dir} PATH)
-    CopyDependencyDLLsForWin(docopt ${docopt_lib_dir})
-endif()
 
 if(NOT docopt_FOUND)
     message(FATAL_ERROR "Dependency 'docopt' not found, but is needed for \
             command-line argument parsing; see the related CMake Warning.\
             Follow the Superbuild instructions in README.md to obtain docopt.")
 endif()
 
-
-# We put "-cli" in the name of the executable in the build directory; the name
-# "opensim" would conflict with the "OpenSim" folder in the build directory (on
-# case-insensitive filesystems). However, the executable is renamed to
-# "opensim" when it is installed.
 OpenSimAddApplication(NAME opensim-cmd
     SOURCES opensim-cmd_run-tool.h
             opensim-cmd_print-xml.h
@@ -37,7 +20,7 @@ OpenSimAddApplication(NAME opensim-cmd
             parse_arguments.h
     )
 
-target_link_libraries(opensim-cmd docopt)
+target_link_libraries(opensim-cmd docopt_s)
 
 if(BUILD_TESTING)
     subdirs(test)

Bindings/Java/Matlab/examples/wiringInputsAndOutputsWithTableReporter.m

@@ -0,0 +1,99 @@
+% ----------------------------------------------------------------------- %
+% The OpenSim API is a toolkit for musculoskeletal modeling and           %
+% simulation. See http://opensim.stanford.edu and the NOTICE file         %
+% for more information. OpenSim is developed at Stanford University       %
+% and supported by the US National Institutes of Health (U54 GM072970,    %
+% R24 HD065690) and by DARPA through the Warrior Web program.             %
+%                                                                         %
+% Copyright (c) 2005-2016 Stanford University and the Authors             %
+% Author(s): Christopher Dembia                                           %
+%                                                                         %
+% 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.                          %
+% ----------------------------------------------------------------------- %
+
+% This example shows how to wire inputs and outputs by reporting the position
+% of the system's center of mass. We also illustrate that input-output
+% connections are stored in model (.osim) files.
+% The model contains just one body, a free joint, and the table reporter.
+
+import org.opensim.modeling.*;
+
+
+modelFilename = 'wiring_inputs_and_outputs_with_TableReporter.osim';
+
+%% Create and print the model to a .osim file.
+% --------------------------------------------
+model = Model();
+model.setName('model');
+
+% Create a body with name 'body', mass of 1 kg, center of mass at the
+% origin of the body, and unit inertia (Ixx = Iyy = Izz = 1 kg-m^2).
+body = Body('body', 1.0, Vec3(0), Inertia(1));
+
+% Create a free joint (all 6 degrees of freedom) with Ground as the parent
+% body and 'body' as the child body.
+joint = FreeJoint('joint', model.getGround(), body);
+
+% Add the body and joint to the model.
+model.addComponent(body);
+model.addComponent(joint);
+
+% Create a TableReporter to save quantities to a file after simulating.
+reporter = TableReporterVec3();
+reporter.setName('reporter');
+reporter.set_report_time_interval(0.1);
+% Report the position of the origin of the body.
+reporter.updInput().connect(body.getOutput('position'));
+% For comparison, we will also get the center of mass position from the
+% Model, and we can check that the two outputs are the same for our
+% one-body system. The (optional) second argument is an alias for the name
+% of the output; it is used as the column label in the table.
+reporter.updInput().connect(model.getOutput('com_position'), 'com_pos');
+% Display what input-output connections look like in XML (in .osim files).
+disp('Reporter input-output connections in XML:');
+disp(reporter.dump());
+
+model.addComponent(reporter);
+
+model.print(modelFilename);
+
+
+%% Load the model file and simulate.
+% ----------------------------------
+deserializedModel = Model(modelFilename);
+state = deserializedModel.initSystem();
+
+% We can fetch the TableReporter from within the deserialized model.
+reporter = TableReporterVec3.safeDownCast(...
+        deserializedModel.getComponent('reporter'));
+% We can access the names of the outputs that the reporter is connected to.
+disp('Outputs connected to the reporter:');
+for i = 0:(reporter.getInput('inputs').getNumConnectees() - 1)
+    disp(reporter.getInput('inputs').getConnecteeName(i));
+end
+
+% Simulate the model.
+manager = Manager(deserializedModel);
+manager.setInitialTime(0);
+manager.setFinalTime(1.0);
+manager.integrate(state);
+
+% Now that the simulation is done, get the table from the TableReporter and
+% write it to a file.
+% This returns the TimeSeriesTableVec3 that holds the history of positions.
+table = reporter.getTable();
+% Create a FileAdapter, which handles writing to (and reading from) .sto files.
+sto = STOFileAdapterVec3();
+sto.write(table, 'wiring_inputs_and_outputs_with_TableReporter.sto');
+% You can open the .sto file in a text editor and see that both outputs
+% (position of body's origin, and position of system mass center) are the same.
+

Bindings/Java/Matlab/tests/CMakeLists.txt

@@ -74,6 +74,8 @@ OpenSimAddMatlabTest(TugOfWar ../examples/OpenSimCreateTugOfWarModel.m)
 OpenSimAddMatlabTest(ConnectorsInputsOutputs testConnectorsInputsOutputs.m)
 OpenSimAddMatlabTest(AccessSubcomponents testAccessSubcomponents.m)
 OpenSimAddMatlabTest(Simbody testSimbody.m)
+OpenSimAddMatlabTest(wiringInputsAndOutputsWithTableReporter
+    ../examples/wiringInputsAndOutputsWithTableReporter.m)
 
 # Copy resources.
 file(COPY "${OPENSIM_SHARED_TEST_FILES_DIR}/arm26.osim"

Bindings/Java/Matlab/tests/testConnectorsInputsOutputs.m

@@ -43,7 +43,7 @@
 end
 
 % Access (and iterate through) a component's connectees as objects.
-expectedNames = {'ground', 'block'};
+expectedNames = {'block', 'ground'};
 for i = 0:(names.size() - 1)
     obj = joint.getConnectee(names.get(i)); % this is an object.
     assert(strcmp(obj.getName(), expectedNames{i+1}));
@@ -80,7 +80,7 @@
 % --------
 % Access AbstractChannels.
 assert(strcmp(coord.getOutput('speed').getChannel('').getPathName(), ...
-              '/leg/pin/pin_coord_0/speed'));
+              '/leg/pin/pin_coord_0|speed'));
 
 % Access the value of a concrete Channel.
 % TODO Concrete channels are not wrapped yet.
@@ -92,7 +92,7 @@
 % ==========================
 % Only need the abstract types in order to connect.
 rep.updInput('inputs').connect(coord.getOutput('value'));
-% With annotation:
+% With alias:
 rep.updInput('inputs').connect(coord.getOutput('speed'), 'target');
 % These commands use the AbstractChannel.
 rep.updInput('inputs').connect(source.getOutput('column').getChannel('c1'));
@@ -105,15 +105,19 @@
 
 % Access (and iterate through) the AbstractInputs, using names.
 names = rep.getInputNames();
-expectedAnnos = {'value', 'target', 'c1', 'second_col'};
+expectedAliases = {'', 'target', '', 'second_col'};
+expectedLabels  = {'/leg/pin/pin_coord_0|value', 'target', ...
+                   '/leg/source|column:c1', 'second_col'};
 for i = 0:(names.size() - 1)
     % Actually, there is only one Input, named 'inputs'.
     % We connected it to 4 channels.
     numConnectees = rep.getInput(names.get(i)).getNumConnectees();
     assert(numConnectees == 4);
     for j = 0:(numConnectees - 1)
-        assert(strcmp(rep.getInput(names.get(i)).getAnnotation(j), ...
-                      expectedAnnos{j+1}));
+        assert(strcmp(rep.getInput(names.get(i)).getAlias(j), ...
+                      expectedAliases{j+1}));
+        assert(strcmp(rep.getInput(names.get(i)).getLabel(j), ...
+                      expectedLabels{j+1}));
     end
 end
 

Bindings/Java/OpenSimJNI/OpenSimContext.h

@@ -125,12 +125,13 @@ OpenSim_DECLARE_CONCRETE_OBJECT(OpenSimContext, Object);
         _model->assemble(*_configState);
     }
     // Forces
-    bool isDisabled(const Force& force) const {
-        return  force.isDisabled(*_configState);
+    bool appliesForce(const Force& force) const {
+        return  force.appliesForce(*_configState);
     }
-    void setDisabled(Force& force, bool disable) const {
-        force.setDisabled(*_configState, disable);
-        _model->getMultibodySystem().realize(*_configState, SimTK::Stage::Position);
+    void setAppliesForce(Force& force, bool applyForce) const {
+        force.setAppliesForce(*_configState, applyForce);
+        _model->getMultibodySystem().realize(*_configState,
+                                             SimTK::Stage::Position);
     }
     // Muscles
     double getActivation(Muscle& act);

Bindings/Java/tests/TestReporter.java

@@ -46,9 +46,9 @@ public static void test_TableReporter_1() throws java.io.IOException {
 
         assert table.getColumnLabels().size()          == 2;
         assert table.getColumnLabel(0).
-                                      equals("/model/table_source/column:col1");
+                                      equals("/model/table_source|column:col1");
         assert table.getColumnLabel(1).
-                                      equals("/model/table_source/column:col2");
+                                      equals("/model/table_source|column:col2");
         assert table.getNumRows()                      == 3;
         assert table.getNumColumns()                   == 2;
         assert table.getRowAtIndex(0).get(0)           == 1;
@@ -67,17 +67,17 @@ public static void test_TableReporter_1() throws java.io.IOException {
             assert table.getNumColumns()               == 0;
             assert table.getColumnLabels().size()      == 2;
             assert table.getColumnLabel(0).
-                                      equals("/model/table_source/column:col1");
+                                      equals("/model/table_source|column:col1");
             assert table.getColumnLabel(1).
-                                      equals("/model/table_source/column:col2");
+                                      equals("/model/table_source|column:col2");
             // Make sure the table reference is still valid.
             assert table.getNumRows()                  == 0;
             assert table.getNumColumns()               == 0;
             assert table.getColumnLabels().size()      == 2;
             assert table.getColumnLabel(0).
-                                      equals("/model/table_source/column:col1");
+                                      equals("/model/table_source|column:col1");
             assert table.getColumnLabel(1).
-                                      equals("/model/table_source/column:col2");
+                                      equals("/model/table_source|column:col2");
 
             state = model.initSystem();
             state.setTime(0.1);
@@ -89,9 +89,9 @@ public static void test_TableReporter_1() throws java.io.IOException {
 
             assert table.getColumnLabels().size()      == 2;
             assert table.getColumnLabel(0).
-                                      equals("/model/table_source/column:col1");
+                                      equals("/model/table_source|column:col1");
             assert table.getColumnLabel(1).
-                                      equals("/model/table_source/column:col2");
+                                      equals("/model/table_source|column:col2");
             assert table.getNumRows()                  == 3;
             assert table.getNumColumns()               == 2;
             assert table.getRowAtIndex(0).get(0)       == 1;

Bindings/Python/examples/build_simple_arm_model.py

@@ -119,9 +119,9 @@
 # We want to write our simulation results to the console.
 reporter = osim.ConsoleReporter()
 reporter.set_report_time_interval(1.0)
-reporter.updInput("inputs").connect(biceps.getOutput("fiber_force"))
+reporter.updInput().connect(biceps.getOutput("fiber_force"))
 elbow_coord = elbow.getCoordinate().getOutput("value")
-reporter.updInput("inputs").connect(elbow_coord, "elbow_angle")
+reporter.updInput().connect(elbow_coord, "elbow_angle")
 arm.addComponent(reporter)
 
 # ---------------------------------------------------------------------------