Digital Archaeology in Nova Scotia

Methods and Applications from Nova Scotia

Project maintained by Wesley Weatherbee Hosted on GitHub Pages — Theme by mattgraham

Photogrammetry 3 ─ How to increase the quality and decrease resolution of your archaeological 3D models.

In our last post on photogrammetry, we covered how applying masks to photos can help in point cloud alignment. We also discovered that applying masks to Tie Points increases the speed of producing an artifact model. Faster production can increase the quantity of 3D models you can produce in a given time, but what about quality?

I’m really excited to share a workflow that covers just that: quality.

For many practitioners of photogrammetry, geometric accuracy will be the important measure 3D reconstruction quality. Here we will be exploring a workflow that can help to increase geometric accuracy. Once again in Metashape.

Geometric accuracy is a measure of how closely a reconstruction represents the physical geometry of the object. As usual, accuracy is limited by precision a.k.a resolution. Today we’re only going to be simply visually evaluating geometric accuracy. Below we can see the product of todays post.

Visualization of a raw (before) and refined (after) mesh using multidirectional hillshade in ArcGIS with a 10x relief exaggeration. Scaled using measurements collected by digital caliper.

The refined mesh shows a noticable reduction in noise and increase in detail. The comparison becomes more interesting realizing that the raw mesh has 9.5 million triangular faces and the refined mesh only 722 thousand faces. Reducing the number of mesh faces equals dramatically reduced output file size at face value. Smaller file sizes present an opportunity for us to better communicate archaeological data through more accessible visualizations.

Resolution vs. Quality

Bad puns aside, I often worried about how I would share my 3D models until uncovering the following workflow. The worry stems from the fact that until recently, the quality of a model produced in agisoft was highly correlated to resolution. If I created a highly accurate model I can easily share it. However, it might not be accessible as high resolution models bog down the majority of consumer computers, and mobile devices.

Ultimately, this is less than effective communication. So why bother?

My typical response is to slightly smooth, then decimate the mesh to my desired face-count for sharing the model. This blob of a representation is then given a high resolution image texture, and combined with materials and lighting effects in the sketchfab 3D viewer.

As much as I have appreciated using this workflow to share something that people can interactively view. I’ve always been a bit anxious when sharing because so much detail is lost unless accesibility is comprimised.

When decimating a model you lose important geometric detail, and there is no guarantee the software will filter out only noise. It seems like a lose-lose situation. Lowering the resolution AND quality of the model.

"Metashape's Photoconsistent Refine Mesh Tool!"

I’ve recently stumbled upon a tool that subtley came onto the scene in October 2017: Refine Mesh. In my experience using the tool, it does a great job at smoothing noise while retaining important geometric details. The process even adds geometric detail from the photos that was too small to be captured in the mesh, but can be identified within your photos.

According to Agisoft Metashape’s user manual, for whom I’ve graciously fixed a typo:

"Metashape allows to refine already reconstructed mesh with respect to camera photos. This is [an] iterative process that can further recover details on surface. For example it can recover bas-relief or ditch."

So let’s take a look at before and after results of using the tool.

LEFT: High resolution mesh after processing, no mesh refinement. RIGHT: High resolution mesh after 1 iteration using *Refine Mesh*.

The results above aren’t incredibly exciting. The tool definitely has potential, but the results led me to believe that I would need to take steps to reduce the reflectivity of my object because the noise is still a prominent feature in the mesh. You can likely see why I wasn’t incredibly interested in the Refine Mesh tool when it was originally released in 2017.

I recently decided to revisit Refine Mesh as a tool to help retain geometric features as part of a slow, iterative process lowering 3D model resolution. The goal was to create a low resolution 3D model preserving more geometric detail than the refine mesh tool. To my surprise, I actually ended up with a low resolution output that was higher quality than my original high resolution input. You can see the difference below.

LEFT: High resolution mesh (9.5 million faces) after processing, no mesh refinement. RIGHT: Low resolution mesh (25 thousand faces) after integrating Refine Mesh into this workflow.

In the images above, it is apparent that a smoother low-resolution model still retaining detail, such as large flake scars, is produced by this workflow. I do still have issues with the result and its rounded edges, but it definitely does a great job at improving on the original in both accesibility and quality.

I noticed there seems to be a ‘sweetspot’ for how many times you apply this workflow. The workflow was repeated on the model above 8 times before decimating to the 25 thousand faces needed for accessible viewing. In the case of this object, it was 5 iterations that produced the best result. Check it out below.

Mesh after 5 iterations of the workflow integrating Refine Mesh.

The above mesh is definitely superior to the 25 thousand face mesh shown prior to this, and is definitely a huge improvement on the original output. This is due in part to the higher resolution of the mesh.

My mesh refinement workflow

So I’m going to assume that you already have a mesh to work from. As I mentioned above, the workflow is an iterative process that will bring out details and reduce the resolution of your mesh. The base process has three steps:

  • Smooth Mesh
  • Decimate Mesh
  • Refine Mesh

These three steps will allow you to pull out details in your model and reduce noise. At the end of the process, you will be able to decimate your mesh to an easily accessible size while increasing the quality of the model.

Smoothing and decimating the mesh

The first step is to slightly smooth the model.

A somewhat subjective description. But I mean it to be. Actually, all of the following steps are subjective.

What smoothing in this workflow is intended to do is to smooth some noise to help Refine Mesh produce a more accurate surface when decimating. Smoothing the mesh will help emphasize features larger than the ~0.2mm diameter noise present on the raw, high-resolution mesh shown above. You’ll likely want to save your project or duplicate the 3D model right before running Smooth Mesh. I frequently over-smooth the mesh and have to revisit a previous version to apply a smaller smoothing strength that only removes the noise.

Refining the mesh

After running Smooth Mesh, the next step is running Refine Mesh.

The input parameters in Refine Mesh are Quality, Iterations, and Smoothness.

Refine Mesh dialog box.

Quality refers to the mesh refinement quality, and I reccomend using the highest setting possible for the first few steps in this process. Though it doesn’t directly relate to mesh resolution, the number of mesh faces in the output are correlated with the quality setting chosen.

Iterations refers to the number of times the tool repeats the process on the object. Unfortunately, The actual underlying process isn’t explained by Agisoft’s User Manual, but I’ll hazarded a vague guess. I think the algorithm may incorporate depth maps, colour maps, and edge maps from the highest quality photos to identify features to be excluded from multiple iterations of localized smoothing. The same result could be achived in plenty of other ways, with much more sophisticated algorithms being applied.

Finally, the Smoothing parameter relates to the weight of the smoothing filter applied. Frustratingly, the Agisoft User Manual documents what effect changing the values of the parameter has on the output, but not what the smoothign factor is applied to. It could relate to the size or weight of a localized smoothing filter, the weight of a global smoothing filter, or somethign completely unrelated. Agisoft just doesn’t tell us. I have noticed that decreasing the smoothing value between successive iterations of Refine Mesh seems to work well to produce better results.

Iterations and choosing when to stop

Choosing where to stop depends on what your outcomes are. Assuming you’ve followed along this far, you will have realized that the objective is accesibility of the models, or finding a balance between quality and the obvious loss of geometric accuracy when reducing the face count of a 3D model from 9.5 million to 25k.

Visualizing outputs of the workflow.

For our purposes, subjectivity is key, unless you want to make some measurements with a caliper and really find the optimal parameters for accuracy retention. I didn’t take this route here because my objective was to illustrate this technique.


So to recap, the general workflow is decimate, smooth, and refine, saving your project or duplicating the mesh at every step. In each succesive iteration of this workflow you can gradually reduce the parameter values. Also, smoothing can be dropped from the workflow if there is no noise present in the mesh. You won’t end up with a perfectly accurate 3D representation of the object, but you will get a high quality mesh with a lower resolution for sharing.

However, refine mesh can also be used to simply refine a mesh without first decimating and smoothing. The result is a higher quality mesh of higher, if not only slightly higher resolution than the original mesh. For GIS products, a single use of the Refine Mesh tool might be able to retain geometry while smoothing noise.

Actually I tested this quickly on a model I produced with a set of aerial photos captured by a Phantom 3 Pro. Shown is an orthophoto with raw and refined digital surface models (DSMs) of tire tracks in the fine dirt of a baseball diamond. These tracks barely show in the raw DSM, but after one iteration of Refine Mesh at Ultra high quality, the tire tracks are well defined. The noise on the smooth surface stemming from a lack of highly accurate location information is also reduced. I haven’t done more field testing but I was impressed with this quick experiment.

Left: Orthophoto. Centre: Raw DSM. Right: DSM after running Refine Mesh

Below is the model shown in the examples throughout this post. It is a re-processed model of the Georgetown Flint Projectile Point model shown in the previous blog post on photogrammetry.

Next week I’ll be moving away from photogrammetry to introduce a method I’ve been working on in applying openCV in Python to artifact analyses. I hope that this post helped spawn some ideas about how accessibility of 3D models can be leveraged to better communicate archaeology. If you have any concepts that you would like to see covered in the future, please comment on the social media post that directed you to this blog and I will try to implement them in future posts!

Wesley Weatherbee

Written on February 4, 2020

Creative Commons License
DigitalArchNS by Wesley Weatherbee is licensed under a Creative Commons Attribution 4.0 International License.