Photogrammetry has incredible potential in archaeological research and education. However, despite Agisoft PhotoScan’s relatively simple initial workflow, things get complicated pretty quickly. Those of us using the program tend to learn by solving problems as they occur, but this is a very piecemeal, time-consuming, and often frustrating process. Currently, anyone getting started with the program must either go through the same thing, or find someone to offer guidance.

In this series I will assemble all the separate tips that I have learned or found into a step-by-step guide on the basic process (posted weekly). I do not consider myself an expert in PhotoScan. If you are familiar with the program and have any corrections or additions, please let me know. Each week, the previous step will be edited to include any comments and placed under the “Resources” menu to serve as a guide for beginners.

The previous steps can be found here.

Step 4: Cleaning the Sparse Point Cloud

Once processing is complete, you will have what is called a sparse point cloud. This is essentially a rough sketch before you ink the lines in during Step 5.

Hopefully, you will be able to make out the shape of your subject, though there will be a lot of points you either do not want, or do not make sense. If you hit the camera icon on your toolbar some blue squares will pop up with the name of your photos attached to each. These are your camera positions in relation the the subject when you took that photo. Pretty neat!

Checking Alignment

photo-alignment
The photo in the top-right did not align and is not being used by the program. (Image by author)

Before proceeding with the cleanup, scroll through your photos and make sure there is a green check mark in the top-right corner of each. This mark tells us that PhotoScan successfully aligned that picture (at least it thinks it did). If a photo failed to align then the program could not figure out where it was supposed to go. This is almost always a result of an out of focus picture, bad lighting, or not enough overlap between photos.

To fix this try right-clicking the offending photo, select “Reset Camera Alignment,” right click it again, and select “Align Selected Cameras.” This is a long shot, but it does work occasionally. If the photo still will not align, you can try messing around with placing markers, but you might be better off just removing or retaking the photos.

Gradual Selection

The first thing you should do to clean up your model is to use the “Gradual Selection” tool. This process is pulled directly from dinsaurpaleo’s blog and boy does it make a big difference. His description is a little hard to follow, so I will include it here again.

  1. Critical! Right click your “Chunk” on the left and select “Duplicate Chunk.” Make sure the “Copy of Chunk” is in bold text before proceeding (this tells you which chunk you are working on).
    copy-of-chunk

This way you will keep the original sparse cloud unaltered in case something goes wrong.

2. Under the “Edit” drop-down menu, select “Gradual Selection…” and a window will appear.

3. In the window, click the drop-down menu next to “Criterion” and select
“Reconstruction Uncertainty”

4. Next to “Level” enter “10” and select “Okay.”gradual-selection-window

You will see that a lot of the points in your sparse cloud turned pink. That means they are selected.

5. Hit your “Delete” key and those pink dots will disappear. (Yes, I’m serious. You won’t be sorry!)

gs-hack
You are better off without all those points. (Image by author)

6. Repeat numbers 2-5 one more time.

optomize-camera7. Open your “Tools” drop-down menu and select “Optimize Cameras…” and a window will pop up.

8. Select all checkboxes except for the last two (I admit to having no idea what these really do) and click the “Okay” button.

This will take a few minutes to reset your photos without the inaccurate points you just deleted. If you deleted a lot of points you might get a “Some cameras have insufficient number of projections and will be reset. Continue?” If you get this popup, click “yes” and the program will try to reset the photos based on the remaining points.

9. Now, go back to your “Gradual Selection…” window and the “Reproduction Error” option should already be selected next to “Criterion.”

10. If the slider total is less than “1” you can skip to number 15.

11. Otherwise, set the “Level” to “1” and select “Okay.”

12. Hit your “Delete” key to delete the selected points.

13. Open your “Tools” drop-down menu again and select “Optimize Cameras.”

14. Your previous setting should still be selected. Click the “Okay” button.

15. Go back to your “Gradual Selection…” window one more time and choose the “Projection Accuracy” option next to “Criterion.”

16. Play around with the number until about 10% of your points are selected and click “Okay.”

17. Hit your “Delete” key.

And you are done! Hopefully, your sparse cloud looks a lot more like the object you were trying to model. I have, occasionally, had this process be too aggressive with a weak sparse point cloud, resulting in big holes in the next step. That is why we made a duplicate!

All that is left to do is some last tidying up. Spin your model around and use your “Freeform Selection Tool” on your toolbar to select and delete any leftover points that you do not want to model. This includes background points and the inevitable nonsense points floating around your model.

freeform-tool-and-resize-tool
The “Freeform” (red), “Resize” (blue), and the “Rotate” (green) tools. Useful Tip: Quickly swap between these tools and your cursor with the spacebar. (Image by author)

Once everything is cleaned up to your satisfaction, use the “Resize Region” and “Rotate Region” tools to manipulate the box surrounding you subject until it is just bigger than what you want to model. This reduces the area PhotoScan has to process and speeds everything up.

Step 4 is done! This part is by far the most involved because it will define the quality of the rest of your model. Things are simpler from here on out.

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