Fixed segfault bug with error checking messages with invalid number of arguments

git-svn-id: https://simtk.org/svn/opensim/Trunk@8167 551e70df-b0f6-0310-80ee-9b1508f7454c
GUI: module to import Collada files. So far it creates bodies, extract mass and mass_center. Files to hook module into default build are not included for now

git-svn-id: https://simtk.org/svn/opensim/Trunk@8168 551e70df-b0f6-0310-80ee-9b1508f7454c
First check-in of a new ClutchedPathSpring actuator based on popular demand at the DARPA WW workshop.
It is based on discussions with Sherm and Matt D. and it maintains an internal stretch state, which is only affected when the clutch is engaged. Otherwise the dynamics of the stretch are such that it relaxes to zero quickly when the clutch is disengaged. A control signal > 0 engages the clutch and scales the tension.

testClutchedPathSpring is now a test in testActuators and it verifies that that the clutch is dis/engaged, the spring tension scales with different control values, can have a multiple point path, and de/serializes correctly. Discovered that PiecewiseConstantFunction function was not in list of registerTypes and so it was added.

Made minor changes to PathSpring so that it is consistent with ClutchedPathSpring's use of stretch instead of strain since the change in length is not being normalized in both cases.

All tests are passing except for:  27 - testSerializeOpenSimObjects (SEGFAULT) which appears to be related to recent changes (rev 8166) to testSerializeOpenSimObjects made by Ayman. Need to confirm.


git-svn-id: https://simtk.org/svn/opensim/Trunk@8169 551e70df-b0f6-0310-80ee-9b1508f7454c
Scripts: Fix editPtoperties script to use SimTK::Vec3 directly rather than ArrayDouble. Based on Jen's updated version.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8170 551e70df-b0f6-0310-80ee-9b1508f7454c
Changes based on Jen's feedback (no algorithmic changes though - just infrastructure design):

(1) Changed name of probes to adhere to OpenSim convention:
MuscleMetabolicPowerProbeUmberger2010 --> MuscleMetabolicsUmberger2010Probe
MuscleMetabolicPowerProbeBhargava2004 --> MuscleMetabolicsBhargave2004Probe

Please adjust accordingly in your model files!!!!!

(2) Added references for each probe. (another bookkeeping convention we introduced when implementing components based on literature publications).
(3) Disabled exception if muscle is not found in model. Now it is just simply ignored.
(4) Moved MetabolicParameter class doxygen to the main probe doxygen. This is in anticipation of making the MetabolicParameter classes private.


I have not:
1) Made any classes private.
2) Swigged anything

git-svn-id: https://simtk.org/svn/opensim/Trunk@8171 551e70df-b0f6-0310-80ee-9b1508f7454c
Replaced the Newton iteration non-convergence warning with an exception. Checked that this exception will be caught in the forward tool - it integrates within a try/catch statement.
We throw an exception here because there is no point integrating a muscle velocity that is invalid. Nothing can be learned from allowing the simulation to proceed in terms of debugging a simulation -- and furthermore, it will produce invalid fiber lengths and cause misleading numerical problems down the track when trying to debug. The idea is to produce an exception and catch this early before it can wreak havoc with the simulation.

Also converted tabs to spaces.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8172 551e70df-b0f6-0310-80ee-9b1508f7454c
GUI: remove now unused EditMusclesAction

git-svn-id: https://simtk.org/svn/opensim/Trunk@8173 551e70df-b0f6-0310-80ee-9b1508f7454c
Remove code that tries to access member variables too early. Same code already exists in connectToModel as it should.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8174 551e70df-b0f6-0310-80ee-9b1508f7454c
Test: fix test case testSerializeOpenSimObjects to serialize/deserialize all model components in the object registry. test case passes.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8175 551e70df-b0f6-0310-80ee-9b1508f7454c
Wrapping: Update SWIG interface, cxx and java files to be in sync. with latest source.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8176 551e70df-b0f6-0310-80ee-9b1508f7454c
GUI: Make parsing of ArrayDouble more robust by handling tabs as well as spaces for arrays. Came up during parsing Collada exported files during the workshop

git-svn-id: https://simtk.org/svn/opensim/Trunk@8177 551e70df-b0f6-0310-80ee-9b1508f7454c
First check-in of the InducedAccelerationsSolver.
It passes a simple double pendulum test was added to testInducedAccelerations virtually identical to the analytical test of the InducedAccelerations analysis.
TODO: add feature to replace the external force (or contact) with user supplied constraint and make the analysis use the solver.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8178 551e70df-b0f6-0310-80ee-9b1508f7454c
Rename of MuscleMetabolicsProbes.
Added renameType only for Umberger2010MuscleMetabolicsProbe so that WW teams can still load their models  from theWW workshop.
TODO: rename MetabolicMuscleParameter to MetabolicMuscleParameters since it contains parameters.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8179 551e70df-b0f6-0310-80ee-9b1508f7454c
GUI: Make explorer node for object selected when corresponding pathPoints are selected regardless of whether it's a muscle.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8180 551e70df-b0f6-0310-80ee-9b1508f7454c
GUI Script: Changed the scripting shell panel to improve efficiency and code maintainability. Merged back the 30 fix that didn't get backported. Did a whole bunch of refactoring for extensibility of code. 

git-svn-id: https://simtk.org/svn/opensim/Trunk@8181 551e70df-b0f6-0310-80ee-9b1508f7454c
GUI Scripts: Forgot to add this new class.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8182 551e70df-b0f6-0310-80ee-9b1508f7454c
Completing and testing the implementation of the InducedAccelerationsSolver interface to getInducedCoordinateAcceleration, getInducedBodyAcceleration, and getInducedMassCenterAcceleration.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8183 551e70df-b0f6-0310-80ee-9b1508f7454c
Improved visualization of muscles in the visualizer.
1) muscle lines are made a little bit thicker
2) intersection of path lines are not small spheres colored by activation, rather than little white crosses.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8184 551e70df-b0f6-0310-80ee-9b1508f7454c
Update includes to new MuscleMetabolicsProbe names for Java wrapping.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8185 551e70df-b0f6-0310-80ee-9b1508f7454c
Updated #includes of MuscleMetabolicsProbes in javaWrapOpenSim.i that were missed in previous check in.

git-svn-id: https://simtk.org/svn/opensim/Trunk@8186 551e70df-b0f6-0310-80ee-9b1508f7454c