gidili

First time they open the main page (the petri dish one):
- [ ] we need to have customizable text snippets appearing in the right panel 
- [ ] the only button that will be visible will be a "next" button (arrow same as in the previous flow) to go to the next tutorial message
- [ ] at the end of the flow simulation buttons will start appearing as they are introduced to the user
- [ ] once the user finishes the flow all the simulation buttons are visible and we need to persist that they have done so

Post Tutorial flow: 
-  [ ] simulation buttons always show
-  [ ] after this flow is completed we can show random tips / facts as text (from a list) and the user can go to the next / prev 

gidili

Objects in the file:
/  (Group)
/time  (Dataset)
/wormsim  (Group)
/wormsim/mechanical  (Group)
/wormsim/mechanical/VISUALIZATION_TREE  (Group)
/wormsim/mechanical/VISUALIZATION_TREE/transformation  (Dataset)
/wormsim/muscle_0  (Group)
/wormsim/muscle_0/mechanical  (Group)
/wormsim/muscle_0/mechanical/SIMULATION_TREE  (Group)

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scene = new THREE.Scene();

// setup lighting etc.

load('/org.wormsim.frontend/resources/files/cuticleNotBent.dae');
load("/org.wormsim.frontend/resources/files/muscles.dae");
load("/org.wormsim.frontend/resources/files/neurons.dae");

function load(daeLocation){
    var manager = new THREE.LoadingManager();

gidili

/* Ismael Celis 2010
Simplified WebSocket events dispatcher (no channels, no users)

var socket = new FancyWebSocket();

// bind to server events
socket.bind('some_event', function(data){
  alert(data.name + ' says: ' + data.message)
});

gidili

// set activation signal buffer to test contraction
float[] signals = new float[_elasticBundlesCount];
for(int i = 0; i < _elasticBundlesCount; i++)
{
  signals[i] = 0.9f;
}
	
this.setActivationSignal(signals);

gidili

SOFA Limitations:
1. not distributed
2. not web-based front-end

SOFA SPH Limitations:
1. SOFA does not support PCISPH
2. SOFA does not support contractile tissue
3. SOFA does not support impermeable membranes

Boyle Model Limitations:

gidili

Writer test_log = null;	
// write txt files
test_log = new FileWriter("test_log.txt");
	
for(int i=0; i<checkpoint_values.neighborMap.size(); i=i+2 )
{
	test_log.write(checkpoint_values.neighborMap.get(i) + "\t" + 
	checkpoint_values.neighborMap.get(i + 1) + "\r\n");
}
	

gidili

__kernel void clearBuffers(
  					   __global float2 * neighborMap,
						   int PARTICLE_COUNT
						   )
{
	int id = get_global_id( 0 );
	if( id >= PARTICLE_COUNT )return;
	
	float2 initVector = (float2)( -1, -1);
	

gidili

// read buffer functions inline declarations in owOpenCLSolver.h

void read_position_b( float * positionBuffer ) { copy_buffer_from_device( positionBuffer, position, PARTICLE_COUNT * sizeof( float ) * 4 ); };
void read_sortedPosition_b( float * sortedPositionBuffer ) { copy_buffer_from_device( sortedPositionBuffer, sortedPosition, PARTICLE_COUNT * sizeof( float ) * 4 * 2 ); };
void read_neighborMap_b( float * neighborMapBuffer ) { copy_buffer_from_device( neighborMapBuffer, neighborMap, PARTICLE_COUNT * sizeof( float ) * 2 ); };
void read_velocity_b( float * velocityBuffer ) { copy_buffer_from_device( velocityBuffer, velocity, PARTICLE_COUNT * sizeof( float ) * 4 ); };
void read_acceleration_b( float * accelerationBuffer ) { copy_buffer_from_device( accelerationBuffer, acceleration, PARTICLE_COUNT * sizeof( float ) * 4 * 2); };
void read_sortedVelocity_b( float * sortedVelocityBuffer ) { copy_buffer_from_device( sortedVelocityBuffer, sortedVelocity, PARTICLE_COUNT * sizeof( float ) * 4 ); };
void read_elastic

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 public synchronized float[] solveWithDeviceMemory() {
  	// Allocate native (device) memory for the input data
	CLBuffer<Float> bufIn = _context.createFloatBuffer(CLMem.Usage.Input, _input.length);
	// Allocate native (device) memory for the output data
	CLBuffer<Float> bufOut = _context.createFloatBuffer(CLMem.Usage.Output, _input.length);

	// Copy input data directly to device memory
	Pointer<Float> ptrIn = bufIn.map(_queue, CLMem.MapFlags.Write);
	ptrIn.setFloats(_input);
	bufIn.unmap(_queue, ptrIn);