Specific Format Settings

Image based (gif, jpeg, quicktime mov) and text based (spreadsheet csv) export formats will display an additional dialog when the 'start export' button is pressed. The dialog displays additional controls that alter the appearance or structure of the final export file. Point/Polygon based (vtk, ucd) formats have no additional dialogue.

Image Based (gif, jpeg, quicktime mov) settings dialog

• Encoding Format setting will be 'JPEG' for jpeg image and QuickTime movies. The setting will be 'GIF' for gif images.
• File Compression slider is enabled for jpeg and QuickTime formats. Moving the slider to any position other than 'lossless' will create smaller export files at the expense of image quality. The slider is disabled for GIF image export as that format always uses 'lossless' compression.
• Variables Display Composition is enabled if more than 1 variable has been chosen for export. The 'Separate' button tells the exporter to create a separate export file for each variable chosen to export. The 'Combined' button tells the exporter to create a 'montage' of all the variable images in one export file.
• QuickTime Format is enabled for QuickTime format type. The 'Regular' button creates a normal QuickTime movie, 1 image for each frame of the movie. The 'QTVR' button will tell the exporter to create a specially format export file readable by QuickTime players. This format allows the player to display multiple images at each movie time point controllable by the user (see Apple QuickTime QTVR) for more information).
• Volume Var Membrane Outline Thickness is always enabled. Setting the slider to 'Hide' will disable the rendering of a membrane outline to the slice plane being exported. Numerical slider values will cause the rendering of membrane outlines the same way as they are viewed in the Slice Data Viewer.
• Variables Mirroring is always enabled. For settings other than 'No mirroring', tells the exported to copy and 'flip' each image along the selected axis. This setting is a convenience to create 'whole' images from partial simulation geometries that were defined by the user to take advantage of spatial symmetries.
• Image Size Scaling is always enabled. If 'from View Data zoom' is chosen the exported images will be the same as the View Data display. Otherwise exported images horizontal and vertical axes will be stretched by the scaling value chosen.
• Membrane Variable Thickness is enabled when membrane variables are being exported. The slider sets the size in pixels of the rendered membrane in a slice.
• Movie Duration (seconds) is enables when QuickTime mov format is chosen. Sets the amount of time the movie will take to do one complete play-through.
• Particle Mode is enabled when a 'particle' variable is chosen to export. Selecting 'Particles' will cause an image of 'spheres' rendered at their location in space for the exported slice and times. 'Histogram' exports an image where each slice pixel is colored according to how many particles where at the corresponding point in the mesh for each time
• Continue... will display a summary of the settings you have chosen and give information about the resulting export file size.

• Variable values Saves file as comma separated text of simulation data values. For 'slice' exports, the values will be arranged in a row/column grid corresponding to the x,y values of the slice. For 'User ROI' exports, the values are saved as a row of values sampled by the ROI.
• Particle data Enabled for 'Spatial Stochastic (smoldyn solver)' simulation data. Saves file as comma separated text of the x,y,z location of each 'particle' for each simulation timepoint. GUI reference (Simulations tab->Edit Simulation button->Solver tab->integrator menu-button->smoldyn, then under 'advanced solver options' check box 'save particle files'). See 'Settings for Spatial Stochastic Solver' in Simulation Editor.
• switch rows/columns Transpose the ordering of data values in the output file.
• Export multiple simulations together Enabled if the 'MathModel' or 'BioModel application' parent of the simulation contains other simulations. Select check-box, click 'Select simulations', choose additional simulations. Data will be exported from the additional simulations and saved in the export file using the same settings for the current export. Check-box CSV Time-Sim-Var is used to change the ordering of simulation data in the export file. Time-Sim-Var ordering may be preferable depending on the users needs.
• Export parameter scans together
Enabled if the simulation has any parameter scans defined. Select check-box, click 'Select Param Scans...', choose scans. Exports all selected parameter scan data together in the same file using the current export settings. See 'Parameters' in Simulation Editor for a description of parameter scans.