Added some documentation.
Sometimes, it is quite difficult to follow the growth and degradation of single rectants because the circles showing the concentration or number of molecules of them present in the system at a certain point of time do sometimes overlap, Therefore, I added the possibility to create an initial graph view (with all nodes at minimum size, so that the topology of the network can be clearly seen) beside every image that is written to file, when recording is activated. This option can be activated in the Settings menu of SimWiz.
In order to identify the start within a looping animation, the first image written out is now a simple start image. The parameter file is changed in a way that a gif animation created with convert, using the delay values in the parameter file will now show the start image for 1 second before the simulation frames are shown.
When capturing animation frames, SimWiz now writes a parameter file (parameters.txt) containing the time delay values which are needed to produce
delays between the images in an animation sequence and thus, to get a realistic impression of the temporal behaviour of the
simulation. The format used is -delay d1 image000000.png -delay d2 image000001.png ... . This can be used
by the ImageMagick convert program in the following way (Unix shell command):
convert `cat parameters.txt` animation-file.gif
The numbers d1, d2, ... specify factors for 1/100th of a second.
Depending on which animation mode the images are written out the delay information is grabbed from different sources.
It is now possible to export all animation frames and thus, to create a "film" which can be viewed independantly from running SimWiz. Clicking on the camera symbol
(which turns to red when activated and grey when inactivated) in the main menu, the user is asked to specify a directory where to write the image files to. After
activating the export, all frames which are created in an animation process (either between starting and stopping the animation or single steppping through it)
are written to file. The file are named imageXXXXXX.png where XXXXXX represents a number, starting with 000000. BEWARE!!!: The animation process slows
down substantailly when images are written to file.
In order to create a "film" the images must now be postprocessed. I created some
animated gif examples
using ImageMagick with the following command (for the first example file):
convert -delay 10 *.png glyco.gif
This command converts the png images in the right order to gif and combines them in an anmiated gif file which loops forever and which should show 10 frames per
second (delay factor is given in multiples of 1/100 sec).
However, creating a film using the parameters file, you must be aware of the fact, that actions like pressing the rewind button or scrolling within the timeline slider,
can produce unwanted behaviour.
Of course, when using a stochastic simulation, the relative time differences between the frames are not preserved. In order to use them when creating e.g. an
animated gif they have to be written out as well. This will be the next thing to be finished.