# SynopFrame
Multiscale Time-dependent Visual Abstraction Framework for Exploratory Analysis of DNA Nanotechnology Simulations

Case study video: https://youtu.be/Hu0tfpS7JBk

Feedback form: https://forms.gle/MH2F7mkDQVHpfNUv6

# GRSI reproducibility 

Following [this installation guide](https://github.com/nanovis/SynopFrame/blob/main/Install-Win.md),
one can find `icosahedron_cndo_10Frames.hipnc`
under `SynopFrame\demo_icosahedron10Frames` (from Step 4 in "Download SynopFrame" in [the installation guide](https://github.com/nanovis/SynopFrame/blob/main/Install-Win.md))
opening it should give visuals very similar to **Fig. 1** in our paper. 
Opening the other two mentioned files (from the same Step 4 in "Download SynopFrame" in [the installation guide](https://github.com/nanovis/SynopFrame/blob/main/Install-Win.md)) should give visuals very similar to **Fig. 5， 7， 8** and **Fig. D.11** in the appendix. One will need to move the time slider and move the camera (mentioned in [Cheat-Sheet-Win](https://github.com/nanovis/SynopFrame/blob/main/Cheat-Sheet-Win.md)) to get closer to the exact figure. But the very exact visual is not intended as the tool is a dynamic analysis tool, which means that spotting insights by navigating in the system is more important.

# Hardware 

The software has been tested on Windows and Max; however, because a high-end MacBook Pro cannot maintain an interactive frame rate, we do not recommend using SynopFrame on MacBooks.

# Installation

Windows installation [guide](https://github.com/nanovis/SynopFrame/blob/main/Install-Win.md). 

For Linux users, the installation process should be similar to Windows. We are happy to guide you through the process. 

## Known issues for Linux users

1. In case you cannot launch Houdini after installation, and the error message is similar to 

```
Crash report from <YourName>; Houdini FX Version 19.5.493 [linux-x86_64-gcc9.3]
Uptime 2 seconds
Tue Feb 14 11:41:13 2023
Caught signal 11

Traceback from 14123 ThreadId=0x7fc00cfb5e80
AP_Interface::coreDumpChaser(UTsignalHandlerArg) <libHoudiniUI.so>
AP_Interface::si_CrashHandler::chaser(UTsignalHandlerArg) <libHoudiniUI.so>
signalCallback(UTsignalHandlerArg) <libHoudiniUT.so>
UT_Signal::UT_ComboSignalHandler::operator()(int, siginfo_t*, void*) const <libHoudiniUT.so>
UT_Signal::processSignal(int, siginfo_t*, void*) <libHoudiniUT.so>
__funlockfile <libpthread.so.0>
```

As suggested [here](https://www.sidefx.com/forum/topic/81386/?page=4#post-358280), you may run `sudo apt-get install lsb-core` and try again. 

2. You will need to find the Houdini preference folder (on Windows, it is `C:\Users\<Your_User_Name>\Documents\houdini19.5`). It is likely under your home foler. 

# Load your own data

To run SynopFrame for your own dataset, you need to create a folder with the following contents. 

```bash
└─<case_folder_name>
  ├─input
  │  ├─design.oxdna.dat
  │  ├─design.oxdna.top
  │  ├─design.synopspace.hb
  │  ├─mean.oxdna.dat
  │  ├─trajectory_run.synopspace.hb
  │  ├─trajectory_run.synopspace.pca_coords
  │  └─trajectory_run_aligned_to_mean.oxdna.dat
  └─<structure_name>.hipnc # this is copied from e.g. `demo_cube.hipnc`
```

Check the [Input-Specification](https://github.com/nanovis/SynopFrame/blob/main/Input-Specification.md) for the meaning of each file. 

After all the files are prepared, open `<structure_name>.hipnc`, go to the `IO_and_Controller` panel, the `IO` tab, change the `print_conf_interval` accordingly. And then click `Cache All`. After the data is cached, you dataset is then at the same state as the demo dataset and is ready to analyze. 

# Feedback and questions 

Please use the GitHub Issues.