For a more indepth look into the workings of DGM, please read our software paper.
Input/output
Application use
Input/output
Supported mapping systems
For several known mapping systems, we provide a preprocessor to convert the default file to our LAT format. Currently DGM is tested to work with the systems and versions below
| Mapping system | Version | File extension |
|---|---|---|
| CARTO | V7.1.80.33 | _car.txt and .mesh |
| RHYTHMIA | SW 3 (Lumipoint), SW 4 (Autotag) and later | .mat |
Please check the examples page on how to export CARTO and RHYTHMIA to your computer.
Input files
The default input for DGM is an LAT_p{n}.txt file, with n the amount of nodes. Currently, we provide automatic preprocessing of CARTO and RHYTHMIA files into the correct DGM file. Please check the above examples.
Each line consists of the node index, followed by its coordinates and a list of local activation times (LAT).
index : x y z [LATs]
0 : 7.02 -30.454 43.253 117.030048 467.266549 794.072015 1110.443573 1426.511669 1742.023554
1 : -19.809 -28.381 76.222 196.978161 553.421788 873.160412 1189.729673 1505.395787 1821.126171
2 : 14.553 -37.11 80.147 268.712687 617.652994 943.853217 1261.895495 1576.255179 1892.253029
...
If you want to visualize additional nodes, for example ablation or ppi in a simulation, you can load a custom .txt file using the icon in the top bar. Then you can simply toggle the nodes of your file with the custom checkbox.
Each line should consist of x, y, z coordinates followed by a color.
Supported colors are red, orange, yellow, green, blue, purple, pink, white, grey, black
x,y,z,color
12.8304,-6.62596,118.946,purple
-27.7116,27.6031,130.075,green
3.87938,1.83967,138.014,yellow
Output
In all output files, nodes represents the amount of nodes, time represents the time of rendering. For periodic data, a single file of each type is generated with time = 0. For non-periodic data, a file of each type is generated for each step in the time interval.
| Filename | Description |
|---|---|
| result_loops_t{time}.csv | Resulting loops |
| result_focal_t{time}.csv | Resulting focal sources |
| front_t{time}_p{nodes}.csv | The complete wavefront |
| loopband_t{time}_p{nodes}.csv | The wave region around the detected loops |
| mesh_t0_p0.csv | Unaltered mesh |
File format
| Filename | Content |
|---|---|
| result_loops_t{time}.csv | x, y, z, amount, core variance, intervariability, range, length, direction, [key, phase pair for each node in the loop] |
| Each row of this files provides detailed information about the different reentry cycles which are visualized in the GUI. The first 3 columns correspond with the location of core of the reentry loop. Amount is a measure for the number of different cycles which are detected by DGM and belong to the same reentry loop. Variance is a measure for the uniformity of the reentry. Intervariability is the absolute value of the maximal deviation of the LATs from the straight line used to calculate the variance. Length is the accumulative length of the reentry by taking the sum of the euclidean distances between the nodes. Next follows a series of indices and their corresponding LAT which belong to the chosen cycle. Each electrode or node has a unique index. | |
| result_focal_t{time}.csv | x, y, z, amount, core variance, intervariability, range, length, direction, [key, phase pair for each node in the loop] |
| Each row determines represents an arrow which contributes to the visualization of the focal beats. For easy implementation, we copied the same format as the loops. However, only index0 and index1 are used as each row represents a directed arrow from index0 to index1. | |
| front_t{time}_p{nodes}.csv | color, scalar, x, y, z, x_dirs, y_dirs, z_dirs |
| Each row in this file represents a single arrow of our wavefront. The wavefront is a collective of arrows which gives a visual representation of the electrical flow. Color represents a time associated to the arrow which is a value larger than the time t upon the directed network is created. Scalar is the normalized size of the arrow and should always be one. x, y and z is the 3D spatial location of the starting point of the arrow whilst x_dir, y_dir and z_dir is the normalized direction of the wave arrow. Drawing all these arrows creates a wavefront generated by DGM. | |
| loopband_t{time}_p{nodes}.csv | color, scalar, x, y, z, x_dirs, y_dirs, z_dirs |
| Each row in this file represents an arrow in the loopband in the same format as the previously described wavefront. The loopband creates an easy-to-interpret visualization of a region around the detected loops. | |
| mesh_t0_p0.csv | x, y, z |
| This file represents the mesh which was used for the visualization, which can be used in other visualization tools (e.g. Paraview). It contains the spatial coordinates of the mesh nodes. The top line is also included in the mesh file. | |
Application use
Settings
File > Settings
File selection
Open dialog for input file selection on startupAdvanced layout
Open application in advanced layout (versus basic layout)Delete output
Delete DGM generated input and output on file selection and closing of the applicationDebug logging
Set if you want to see debug output on top of the default info messages
Application startup settings
View
Advanced layout
Toggle advanced/basic layout
Help
Documentation
Link to this webpageAbout
General application info such as version number. You can also find the software licence here
Layouts
There are two main layouts which the user can toggle between from the main menu. The basic layout tries to keep things as simple as possible by providing several preset rendering templates to quickly show a specific result. Calculations will be done using the current set of parameters. In the advanced layout, users can alter parameters and have large control over what the visualization should look like.
Templates
Preset visualization schemes to quickly show different results
| Template | Description |
|---|---|
| loops | DGM loops in spectrum color scheme |
| focal | DGM focal sources |
| loopband | Band showing the region of the wave around the found loops |
| wavefront | The entire wavefront |
| ablation | Ablation point (if file is present) together with loopband |
Parameters
The following parameters can be set to further optimize your result
| Parameter | Description |
|---|---|
| Minimal arrow count | Minimum required amount of arrows in a loop |
| Variance | Maximal allowed variance |
| Intervariability | Maximum allowed intervariability |
| Distance (mm) | Maximum allowed distance between neighbours |
| Focal threshold | Threshold for dividing cycle length into bins for detection of focal sources |
| CV min (mm/ms) | Minimum allowed conduction velocity |
| CV max (mm/ms) | Maximum allowed conduction velocity |
| Merge jump | Maximum difference (ms) for merging graphs |
| Core separator | Threshold (mm) to distinguish different loops by comparing the centre of each loop |
Visualization
Main rendering
| Tab | Settings |
|---|---|
| Nodes | Set nodesize for different groups of nodes |
| Mesh | Set mesh opacity and color scheme |
| Arrows | Set size and color scheme of loopband and wavefront arrows |
| Source | Set variance threshold for loops |
| Visualization | Select which elements to show in the rendering |
Icon bar
The first two icons in this bar - photo and video camera - allow you to take a screenshot or movie of the current rendering. When creating a video, the rendering will loop over the set time interval. You can save your video as either .ogg or .mp4.
The next icon of coloured nodes allows you to upload a custom node file as described under input.
Finally the time interval slider allows you to manually loop through the different time steps.