Mostly just stuff I am doing to help the planet
This artificial shag roost in Hobson Bay was constructed by Auckland Council to mitigate the effects of a boardwalk being constructed next to an existing shag roost. Nesting materials and a plywood decoy has been added but the birds are yet to show interest in it.
I’m experimenting with mapping the seafloor for restoration projects. This is what I have done so far:
ArgiSoft Metashape worked much better than using Adobes photo stitching software (Photoshop & Lightroom) on the same data. But I need more overlapping images as all the software packages were not able to match all of any of the four test sequences I did.
I’m going to test shooting in video next. The frames will be smaller 2704×1520 (if I stick with linear to avoid extra processing for lens distortion) instead of 4000×3000 with the time-lapse but I’m hopping all the extra frames will more than compensate (2FPS=>24FPS).
In theory an ROV will be better but I don’t think there are any on the market that know where they are based on what they can see. All the work arounds for knowing where you are underwater are expensive, here are two UWIS & Nimrod. I want to see if we can do this with divers and no location data. I don’t think towing a GPS will be accurate enough to match up the photos but it does seem to work with drones taking images of bigger scenes (I want this to work in 50cm visibility). I expect if I want large complete images the diver will need to follow another diver who has left a line on the seafloor. One advantage of this is that the line could have a scale on it, but I’m hoping to avoid it as the lines will be ugly š So far I can do only two turns before it fails. There are three patterns that might work (Space invaders, Spirals and Pick up sticks). For my initial trials I am focusing on Space invaders.
Video provides lots more frames and the conversion is easy. A land based test with GPS disabled, multiple turns, 2500 photos, 2704 x 2028 linear, space invader pattern at 1.2m from the ground worked perfectly. However I cant get it to work underwater. In every test so far Metashape will only align 50-100 frames. I tried shooting on a sunny day which was terrible as the reflection of the waves dancing on the seafloor confuses the software. But two follow up shoots also failed, when I look at the frames Metashape cant match I just don’t see why its can’t align them. Theses two images are in sequence, one gets aligned and the next one is dropped!
Here is what the test footage looks like, I have increased the contrast.
I have also tried exporting the frames at 8fps to see if the alignment errors are happening because the images are too similar but got similar results (faster).
Detailed advice from Metashape:
Since you are using Sequential pre-selection, you wouldn’t get matching points for the images from the different lines of “space invader” or “pick up sticks” scenarios or from different radius of “spiral” scenario.
If you are using “space invader” scenario and have hundreds or thousands of images, it may be reasonable to align the data in two iterations: with sequential preselection and then with estimated preselection, providing that most of the cameras are properly aligned.
As for the mesh reconstruction – using Sparse Cloud source would give you very rough model, so you may consider building the model from the depth maps with medium/high quality in Arbitrary mode. As for the texture reconstruction, I can suggest to generate it in Generic mode and then in the model view switch the view from Perspective to Orthographic, then orient the viewpoint in the desired way and use Capture View option get a kind of planar orthomosaic projection for your model.
Align ‘sequential’ only ever gets about 5% of the shots. Repeating the alignment procedure on ‘estimated’ picks up the rest but the camera alignment gets curved. I think I have calibrated the cameras to 24mm (it’s hard to see if that has been applied) but it doesn’t seem to change things.
I tried an above water test and made a two minute video of the MÄori fish dams at Tahuna Torea. I used the same settings as above, but dropped the quality down to medium. It looks great!
The differences between above and below water are: Camera distance to subject, flotsam, visibility / image quality and colour range. If the footage I am gathering is too poor for Metashape to align it might mean we need less suspended sediment in the water to make the images. That’s a problem as the places I want to map are suffering from suspended sediment ā which is why they would benefit from shellfish restoration.
The Agisoft support team are awesome. They processed my footage with f = 1906 in the camera calibration, align photos without using preselection and a 10,00 tie point limit. The alignment took 2.5 days but worked perfectly (click on the image below). There are a few glitches but I think the result is good enough for mapping life on the seafloor. I will refine the numbers a bit and post them in a seperate blog post, wahoo!
Update Jul 2022: Great paper explaining the process with more sophisticated hardware
Final method
Here is my photogrammetry process / settings for GoPro underwater. I am updating them as I learn more. Please let me know if you discover an improvement. Thanks to Vanessa Maitland for her help refining the process.
Step 1: Make a video of the seafloor using a GoPro
Step 2: Edit your video
Step 3: Install and launch Agisoft Metashape Standard.
Step 4: Use GPU.
Step 5: Import video
Step 6: Camera calibration
Step 7: Align photos
If 100% of cameras are not aligned then try Step 8 otherwise skip to Step 9.
Step 8: Align photos (again)
Now all the photos should be aligned, if not repeat step 7 & 8 with higher settings and check ‘Reset current alignment’ on step 7 only. I have been happy with models that have 10% of photos not aligned.
Step 9: Tools / Optimize Camera Locations
Just check the check boxes below (default settings):
Leave the other checkboxes (including Advanced settings) unchecked.
Step 10: Resize region
Use the region editing tools in the graphical menu make sure that the region covers all the photos you want to turn into a 3D mesh. You can change what is being displayed in the viewport under ‘Model’, ‘Show/Hide Items’.
Step 11: Build dense cloud
Step 12: Build mesh
Step 13: Build texture
Step 14: Export orthomosaic
You can orientate the view using the tools in the graphical menu. Make sure the view is in orthographic before you export the image (5 on the keypad). Then chose ‘View’, ‘Capture View’ from the menu. The maximum pixel dimensions are 16,384 x 16,384. Alternatively you can export the texture.
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Let me know if you have experimented converting timelaspe / hyperlapse video to photogrammetry. There may be some advantages.
As communities get increasingly worried about the declining quality of their waterways there is more interest stream health assessments. I am a huge fan of the Waicare Invertebrate Monitoring Protocol (WIMP) which is simple enough that school students can use it. However the Waicare programme has been largely defunded by Auckland Council and there is no way for the public to share WIMP data. NIWA and Federated Farmers of New Zealand have put together https://nzwatercitizens.co.nz/ based on the New Zealand Stream Health Monitoring and Assessment Kit (SHMAK). It is great but incredibly hard to use, the manual is horrific. I believe this is being addressed but will take years. To help, the science learning hub has made this great guide for teachers and students. NIWA have put together some videos. They are not published together anywhere online so I have posted the list below:
I really like this list of alternative words for environmental terms, offered by George Monbiot & Ralph Steadman. I have rebuilt it in HTML with some additions and deletions, I plan to evolve it over time.
| Existing terms | What’s wrong with it | Alternative terms |
| Environment | Cold, technical Seen as seperate | The natural world |
| Global warming | Warm sounds pleasant | Global overheating |
| Biodiversity | Inaccessible | Wildlife |
| Ecosystem services | Anthropocentric and reductive | Life support systems |
| Nature reserve | ‘reserve’ suggests coldness | Wildlife refuge |
| Habitat destruction Deforestation Biodiversity loss | Sounds like they are happening to themselves | Ecocide |
| Conservation | Preserving what little is left rather than rebuilding living systems (New Zealand needs a department of Restoration) | Restoration |
| Clean rivers / seas | Sounds too hygienic, is blind to waters as habitats | Thriving rivers / seas |
| Fossil fuels | Suggests redundancy | Dirty fuels |
| Sustainable development | Green growth is an oxymoron | Regenerative development |
| Photopollution | Too technical, doesn’t indicate what is being impacted | Ecological light pollution |
| Stormwater | Suggests that the water is unwanted, unnecessary or unsavoury | Rainwater |
| MARINE | ||
| Fish stocks | Suggests fish are here to serve us | Wild fish populations |
| Biofoul, foul, foul ground | Suggests there is something ugly about biogenic habitats | Sea life, seafloor life, benthic epifauna |
| Fishing | Casual everyday activity | Killing native wildlife |
| Bait fish | Implies the fish exist to be bait | Small schooling fish / forage fish / small pelagic fish / shoaling fish |
| Bait ball | Implies the fish exist to be bait | Tight ball of fish |
| Seaweeds | Pest connotations | Ocean plants |
| Mobile bottom contact fishing | Implies a light touch | (Mobile) Bottom impact fishing |
Please include a network of safe places for shorebirds to roost and nest in parks adjacent to the TÄmaki Estuary. The areas that are important to shorebirds have been mapped in the attached document Shorebirds-of-the-Tamaki-Estuary-by-Shaun-Lee.pdf detailed evidence for the preservation of the shorebird roosting and nesting habitat can be found in PE-Development-Full-Evidence-Shaun Lee.pdf and PE-Development-Futher-Evidence-Shaun-Lee.pdf also attached. Since the Point England Development Enabling Bill has passed the stock have been removed from Point England. Despite our best efforts with mowing productivity has declined dramatically. I suggest we return the stock, feel free to contact me or Council biodiversity staff if you would like to see the breeding reports.
The roosting and nesting shorebirds. Numbers of shorebirds in the parks have greatly reduced over the last few decades and some species are now locally extinct. We need to do a better job of looking after them as some species are going extinct globally. The most important parks in the Maungakiekie-TÄmaki area are the Point England Reserve and Mt Wellington War Memorial Reserve.
Can you tell us what you donāt like about the park(s) in your local board area? Please include the name or location of the parks, if possible.
There is no space dedicated to shorebirds. This means they are regularly disturbed by golf practice, frisbee, casual ball play, jogging, walking, drone flying, kite-surfing, kite flying, picnicking, dog walking and much more. Disturbance in parks is increasing with population density. Key roosting and nesting areas are threatened with development. Minor things like paths, lighting and even trees can negatively impact shorebird habitat.
Is there anything else youād like to tell us about parks in your area? Please share any other thoughts about local parks here.
Please make sure decision makers are aware of the status of threatened and conservation dependant species that use Maungakiekie-TÄmaki Local Parks, then they can make good decisions and start to restore habitats and associated abundance and diversity.
These graphs from the Hauraki Gulf 2020 State of Our Environment Report show how some New Zealand fish populations are managed very poorly.
You can see that Fisheries New Zealand has no intention managing these ‘stocks’ to the target. Instead they manage populations to the limit where action is required. This is like driving a car at the speed limit the whole time and slamming your brakes on at the corners. Some people may drive like that, but New Zealand should have better attitudes to managing its native marine biodiversity.
Auckland Council has just installed this sign I designed for shorebirds at Tahuna Torea. It will be interesting to hear if the ‘sleeping zone’ idea gets through to the general public.
UPDATE 30 JULY 2020
I have been asked for this sign to be used at other locations. Here is a PDF of the sign with a text that mentions dogs, a more refined illustration and space for logos. Feel free to use it without asking, but I would love to know when it does get used.
UPDATE 22 MARCH 2023
On the night of the 5th of April 2020 I noticed emergency services lights at Point England. Today I counted three areas of previously un-mowed grass on the south-eastern end that had been burnt and two partially forested areas on the northern end. The fires look like intentional arson to me, with drought conditions over hopefully we wont see any more burning. I’m very disappointed to loose some of the trees I planted. Damage to fences (including an area removed by emergency services) needs to be fixed before the dotterel breeding season begins (Auckland Council reference: 8110308091). I’m grateful to emergency services for managing the fire risk and to the mowers who have kept the tinder dry grass very short.
This is completely off topic but I have to blog it somewhere just incase it helps others.
For the last twenty years I have suffered from Repetitive strain injury (RSI) or Occupational overuse syndrome (OOS). It has always affected how much time I can spend working on the computer. It started in my forearm then eventually moved to my bicep which was quite debilitating.
These are the things I have tried that helped a little:
Here are the things I tried that did not work:
I now have it 100% under control and it has very little impact on my life as long as I:
These things all help with increasing blood flow to the areas where the pain was coming from. I think lack of blood flow was causing my pain.
It’s nearly one week into the Covid 19 lockdown. Council were not able to retrieve dying and dead birds from the pond at Tahuna Torea. The birds have been dying from avian botulism which paralyse them (its a horrible way to go). I took a pied stilt to the vet but it did not make it and cleaned up other dead and dying geese and mallards.
While I was there I noticed a lot of trash that had become exposed, as the water was the lowest it’s been in at least 10 years. Going back to pick it up I found it was mostly bread bags taken to the pond to feed the birds. I understand the commonly known reasons for not feeding birds. But I had no idea how much plastic goes into the water as byproduct of the practice. Light can not penetrate the dark pond waters and the plastic doesn’t break down. Sediment settles on top and where ever I dug into the dried mud I found plastic.
I’ll spend a few more hours gathering it but I’ll never get it all. I’m sure other ponds are similar if not worse. As long as we keep selling bread in plastic, bird feeding will be contributing to our plastic legacy.
UPDATE: 5 April
After removing three black sacks of dead birds and soft plastics I was rewarded with seeing this secretive bird feeding right where I had been cleaning up š
UPDATE: 12 April
So far I have retrieved two geese, four mallards, one juvenile black-backed gull and four black sacks full of plastic, mostly bread bags.