dmsenter89 / meshmerizeme

Software to create 2D geometry for IBAMR and IB2D

Hi there 👋

I’m an Research Statistician Developer at SAS Institute, Inc. I have a PhD in mathematics from the University of North Carolina at Chapel Hill where I worked on computational fluid dynamics as part of the Miller Lab Group, now at UA. I have broad interests in scientific computing and data analysis. Feel free to check out my GitHub pages site.

meshmerizeme's Issues

Check Vertices for Uniqueness

If the SVG defines multiple paths, it is possible that two paths overlap. In particular, if a path is handdrawn or coded, it may be that the end point of one path coincides with the beginning of a second. MeshmerizeMe does not currently check if this is the case, and would create two identical vertices. This will lead to the simulation failing in IB2D/IBAMR.

Proposed solution: Prior to writing the vertex file, check for duplicate vertices. If any duplicates are found, remove one of them.
For this fix to work the comparison, or at least equality operation '==', will need to be added to the Vertex class.

Create Log

Have the software print and save a log file. One of the key elements of the log file should be to identify which of the vertices correspond to paths from the svg. Initial and final position could be printed to help users identify the paths.

Out of Bounds

SVG Allows for coordinate markers to be outside of the viewbox. MeshmerizeMe will dutifully create these vertices outside of the domain for the simulation without complaint. I can see two ways of handling this problem:

1. Throw error, abort simulation.
2. Eliminate all vertices that that are out of bounds simply by cutting them from the list of vertex points prior to writing.

While the first might be more honest, I think the second might be the way to go, since I've noticed inkscape does occasionaly produce coordinates that are out-of-bounds, without the users intention.

ContourizeMe crashes on macOS when you attempt to zoom on the image with the scroll-wheel.

I do not see this issue on Ubuntu or Windows.

Vertex files are plotted upside-down in Matplotlib

The origin of SVG images is in the top-left corner, but the origin of the current Matplotlib plots is in the bottom-left, causing the mesh points to look upside-down.

This is easy enough to fix within the Matplotlib plots, but do we need to also flip the mesh points within the exported vertex files before using them in IB2D?

Allow for Non-Pixel Sized SVGs

The SVG format allows the height and width of an SVG to be specified in units other than pixels, such as milimeters. This seems like a very useful feature to support for converting image data to for simulation. Currently MeshmerizeMe requires the height and width to be given in pixels, and does not contain any code to handle coordinate transforms within the SVG. We should add a feature that allows for SVGs with height/width specified in units other than pixels.