Visible Progress!

Over the last couple of weeks, my role in the Going Live project increased significantly, and then stopped completely. All of the animated shots had lighting added, and then I added the render layers/passes and started feeding completed shots through the render farm (which was considerably faster than I expected it to be). Sound effects and music were then added by the sound team, creating our finished advert.

It took a long time to get there, and there were problems along the way, but I learned a lot (particularly about rendering and compositing) and I am glad we all got there in the end! Next week, we are due to meet with the company in their London studio and present our finished project - hopefully the feedback will be good!

As for my cell visualisation work, this has been making good progress since my role in Going Live has lessened.

The first data-set I was working with, which represented cells and fibres in 2D space, now has fully working scripts, which are streamlined to work efficiently (or to actually work at all!). I am currently awaiting feedback on the video outcome of this work, so that I can decide where to take this next.

The other data-sets (involving cells, blood vessels, and oxygen density maps) have made even better progress. Again, after optimising my MEL scripts, the amount of data (several million lines of information) has become manageable, although time-consuming to process. I am currently part of the way through 'translating' this data into Maya's 3D environment.

An example render from the cells file can be seen below. This example frame is approximately two thirds of the way through the cell data, and incorporates some 'noise' on the cell surfaces to break up the uniformity (an idea suggested by the mathematician who provided the data);

As for the oxygen density, I decided to continue using a single polygonal plane for this, with grid points in the data having a matching vertex on the 3D geometry. The data then lifts/lowers each grid point/vertex between 0 and 1, where 1 is the most dense area of the oxygen 'clouds'.

The 'look' of these clouds is then controlled using one of two shaders.

Shader 1 ("Clouds") is coloured white, and uses a vertically-aligned ramp shader for it's transparency value, where 0 is fully transparent and 1 is fully visible. This means that as points on the vertex grid are changed in the Y-axis, their transparency is also changed (as they are moved higher, they become more visible).

Shader 2 ("Bands") expands upon this idea, and uses a second ramp for the colour (from blue to red, low to high). The transparency ramp is also 'sliced' into bands which are evenly spaced vertically - this means that only the narrow bands are visible, giving us slices of colour (where the colour is defined by where the slice falls on the colour ramp, rather than a fixed colour). This gives a result similar to the high/low pressure bands which weather presenters often use, but with colour added.

I have included a video below, which better explains these shaders - the white 'cloud' is shader 1, and the coloured 'bands' are shader 2;

Although this video shows a top-down view of the scene, it is important to remember that these effects are generated in 3D - moving forwards, I could include moving camera or changing points of view to highlight particular events.

Also, the oxygen density visuals are considered another 'layer' which I can add to the cells and blood vessels, creating a more complete final output.

I am not sure as to how this final output will look at the moment, as I am still developing the visual elements of each of the data-sets, but progress is good and things are at least working now...

Needs more juice...

Similar to my last blog entry, my efforts are still divided between two main projects;

The Going Live project has been making excellent progress. The team and I have continued improving the visual outcome of the 3D elements. With a texture in place, lighting and rendering have started to progress rapidly. Animated shots are being lit, rendered and composited, so that final testing can take place.

Although I have taken on the role of CG Supervisor, I have been involved in other areas, and responsible for others. I was involved in tracking the camera footage and creating a 3D pre-visualisation of the sequence. I have monitored the 3D pipeline continuously, and offered advice and created fixes for problems - this includes working with others in modeling, texturing, rigging, animation, and lighting. I was responsible for creating a dynamic cloth system which would allow for easier animation, and I have managed the rendering process (involving creating render layers and using the render farm). Finally, I get to pass rendered scenes to the compositing team, who can work their magic... and before I know it, we will have finished the advert!

Returning to my cell visualisation work, I have reached a temporary plateau. I have developed my pipeline/workflow and have implemented new and improved scripts to manage the new data that I have received from my colleagues in the Mathematics division.

However, the vast quantity of data has been as proving difficult to process efficiently. After some development, I have speeded up the process, but this still takes a considerable amount of time to complete. Fortunately, I discussed this with my project supervisor/programme leader, and agreed the use of high-specification computers in the University, where I can process data quickly, making use of round-the-clock facilities. This week, I will begin using these facilities, to start working with this new data that I have received.

It is important that I begin this early, as the sooner the numerical data has been translated into 3D space, the sooner I can begin developing the visual qualities of the mathematical models. Completing this visualisation process becomes even more important, as the mathematical models will be presented as part of a conference in June - giving me a deadline to work towards...

More Data

Over the last couple of weeks, I have had to divide my attention between multiple projects.

The 'Going Live' project has ramped up into production, with modeling and rigging now complete. Animation has started, and texturing is currently underway. My role as CG Supervisor has been demanding, as all of these CG elements have been happening in quick succession. On top of this role, I was also responsible for implementing a customised nCloth dynamics system for our 'character'. This was created alongside the rigging process, to ensure that these components would work together happily, and after resolving a few technical problems, the system is now working nicely. My next task was to create and organise the appropriate render layers in Maya, ready for rendering and then compositing to take place (hopefully late this week or early next). Although I had worked with render layers before, this project requires more variants than I am used to working with, so has taken a bit of time to configure and setup properly. Despite all this work taking up more time than initially expected, the project has made good progress, and continues to do so.

After my meeting with mathematics last week (and several more since), my cell visualisation workload has increased also. I have received new data from both students, and I am currently in the process of writing scripts that will translate these into 3D scenes inside Maya.

The first new data set contains fibres (to be added to cells), which are based on xyz locations and xy rotations. I had not scripted rotation values yet, so this was a good opportunity to expand my knowledge of MEL. I am currently awaiting the full data-set for this part of the visualisation, so will continue to work on this moving forwards.

The other data set adds oxygen density to a scene containing cancer cells and blood vessels. This file contains over 30 million lines of information, and weighs in at around 800mb - making it rather difficult to work with. I have tried different approaches in visualising this data efficiently, such as adjusting transparency on cubes based on the density value or scaling particle clouds. Unfortunately, there are about 10,200 points per frame, so these methods take far too long to calculate. I am currently testing a new method, which creates a single polygonal plane, with the required number of vertices. The script then runs through each vertice, and moves it in the y-axis based on the density value (between 0 and 1). A ramp shader then adjusts the transparency of the plane based on the height (where 0 density is fully transparent). This creates white, cloudy patches where oxygen density is high. Although this still takes a long time to process, it is considerably faster than the other methods.

Most of this work is still on-going, and has 'arrived' at the same time, making it difficult to balance. Fortunately, I have been able to allow extra time in working on these projects, so hopefully the worst of it is over now...

On a more exciting note, three of my videos were used at an event in Dundee on Saturday 12th March. The videos are 3D visualisations of mathematical models which are being used to predict cancer growth and development, and were developed in collabroation with a PhD student in the University's mathematics division. They were shown at an event called "Sensational Women in Science" as part of the Women in Science Festival 2011.

Also, some of the other data I am currently working with will be presented at a large conference later this year (in June), so I have a deadline which I can work towards.