2019/10/18

Canopy Basemap from Lidar

I'm always looking for a way to create a better basemap for my cartographic work. One of my favorite tools is the bare Earth model created by stripping canopy data from LiDAR. Sometimes having tree canopy data is useful for cartographic purposes, so here's a quick tutorial on how I've extracted and symbolized that data for use in ArcMap.

Our goal is to end up with a map that looks like this. I have used a hillshade generated from LiDAR and have it set to 50% transparent and the canopy layer is underneath with a color ramp of leaf green for high, apple green for medium, and yucca yellow for low (none). I've added elevation contours, and a water layer created using this tutorial.



To get to this map, you'll need to have two elevation layers rendered from LiDAR. I'm working with data that can be found here. Feel free to download White_2015_16_zLAS.zip and work alongside me. Once you've got all of your zLAS files in a LAS Dataset, add it to the table of contents and zoom in to view an area. You'll also want to turn on the LAS Dataset from the toolbars menu.


Once the LAS Dataset toolbar is open, make sure the drop down menu Filters is set to All, and the drop down menu with colored dots is set to Elevation, as shown below.





It should render out an image that looks like this hot mess. The "static" looking area is what tree canopy looks like when it's made into a TIN (Triangulated irregular network).


Using the LAS Dataset to Raster tool we'll convert what we see above into a raster image to work with. Let's call it elev_w_canopy since it's a combination of elevation and canopy.




Now let's create a bare Earth model (BEM) where we use the LAS Dataset tools to strip away the canopy.



The resulting terrain should look smoother than the terrain with canopy. Let's use the LAS Dataset to Raster tool to make this into a raster also. Let's call it elev.



Once you've created elev, you can create all kinds of wonderful derivative products from it like contours, and hillshade. Since we're making a map in this tutorial go ahead an render out some contours at 100' intervals, and generate a hillshade for use later.

Now for the magic. Since we have a raster of elev and elev_w_canopy, and what we're after is literally the difference between them, we can use the Raster Calculator tool to execute that.



You'll end up with a raster image that looks something like this. Note that if you zoom in, there will be lots of gaps and the image itself appears noisy and grainy.



Let's deal with that noise by using Focal Statistics. Set the neighborhood to circle, the radius to 8 pixels, and the statistics type to maximum as shown below. Let's call the output canopy01.



You should end up with a raster that looks something like this.



Apply a thoughful color ramp to it, and stretch the histogram appropriately (equalize gets rid of the outliers nicely).



Add your hillshade above the canopy layer now and set your transparency to 50%. You should be looking at something that looks like this.




Bartoo Hall Gallery, Tennessee Tech University


It's always cool when my photos get used somewhere. Bartoo Hall on campus at Tennessee Tech is the latest place to take advantage of my regional photos. Below are lots of photos of the images they used with some dork posing beside them. ;)

 









2019/10/11

Topographic Position Index (TPI) as an Alternative to Hypsometric Shading


Hypsometric Shading


Hypsometric Shading is a method that I have been using to generate beautiful basemaps well before I knew what it was called. Sometime during my undergraduate days I had the idea to view a hillshade at 50% transparency and lay it atop a color-ramp-ed elevation layer. The resulting output was already well known to cartographers, and appears to have been first done in 1503 by one of my very favorite historic figures, Leonardo da Vinci.


While I am no Leonardo, I offer these examples of my previous work as a means to better understand what hypsometric shading looks like.



Sparta, White County, Tennessee



Pickett State Park, Tennessee

Topographic Position Index (TPI)


While hypsometric shading is generally pleasing one may need to draw the users attention to other types of features. By using a combination of a hillshade at 50% and a Topographic Position Index (TPI) raster, one could draw attention to ridges and valleys. For example, I offer this map of an area within Scotts Gulf in White County.

Topographic Position Index (TPI) as an Alternative to Hypsometric Shading

The TPI layer draws attention to areas, which are on average lower or higher than their surroundings. I first learned of TPI as an analysis tool through Jenness Enterprises's Land Facet Corridor Designer extension for ArcGIS. As an alternative to that tool I applied some of my Photoshop image processing skills when I realized the nature of TPI. It's unsharp mask. In other words, a gaussian blur is applied to the original image, and then that is subtracted from the original image and a histogram stretch applied. With ArcMap, one can designate the histogram stretch method very specifically without altering the values of the raster, and one can apply a color ramp.

Without invoking the tool, one can use focal statistics in place of the gaussian blur, and use raster calculator to subtract the focal statistics layer. In other words, it would look like this:



All this is just to say, "Hey, this may look cool." Let me know if and how you use it. :)

2019/10/01

Tennessee Mississippian Strata - Fossils - St Louis, Warsaw, and Salem Limestones

St Louis, Warsaw, and Salem Limestones

collection_no identified_name identified_rank accepted_name accepted_rank early_interval max_ma min_ma
64639 Naticopsis (Naticopsis ?) n. sp. buttsi species Naticopsis (Naticopsis) buttsi species Meramecian 345 336
Bellerophon cf. scissile species Bellerophon scissile species Meramecian 345 336
133416 Stethacanthus altonensis species Stethacanthus altonensis species Visean 346.7 330.9
40773 Meekopora cf. clausa species Meekopora genus Meramecian 345 336
162328 Beyrichiella confluens species Beyrichiella genus Osagean 353.8 342.8
Cytherella glandella species Cytherella genus Osagean 353.8 342.8
Glyptopleura costata species Glyptopleura genus Osagean 353.8 342.8
Paraparchites carbonaria species Paraparchites genus Osagean 353.8 342.8
Paraparchites nicklesi species Paraparchites nicklesi species Osagean 353.8 342.8
Savagella lindahli species Savagella genus Osagean 353.8 342.8
Data Provider The Paleobiology Database
Data Source The Paleobiology Database
Data License Creative Commons CC-BY
License URL http://creativecommons.org/licenses/by/4.0/
Documentation URL http://paleobiodb.org/data1.2/occs/list_doc.html
Data URL http://paleobiodb.org/data1.2/occs/list.csv?datainfo&rowcount&strat=St.%20Louis%20limestone
Data URL http://paleobiodb.org/data1.2/occs/list.csv?datainfo&rowcount&strat=warsaw%20limestone
Access Time Mon 2018-02-12 17:04:28 GMT
Title PBDB Data Service

Longwave Light on Cave Formations

Last year I purchased a handheld longwave light in the hopes that it would assist in non-destructive mineral identification in caves. The model I purchased was Convoy S2+ Nichia 365nm UV LED 1Mode OP Reflector Flashlight since it ran on 18650 rechargeable batteries and seemed of rugged construction. After having been caving with it for more than a year I've found it to be rugged enough for my typical caving trip, though I generally carry it in a pelican case with my camera. It is lightweight, and doesn't seem to drain the battery quickly, though I use it only for a handful of minutes on any given caving trip.

To no one's surprise calcite is the dominant mineral in the caves of Middle Tennessee that I frequent. Trace impurities within calcite which can color it dramatically in visible light do not significantly change the phosphorescent color spectra. Other minerals present in caves of Middle Tennessee include chert (which does not phosphoress), dolomite (which reflects purple under longwave), and gypsum (which with phosphoress green the same as calcite).

Example 1: Flowstone in Blowhole Cave

Painted light from my headlamp (white balance adjusted)

Flowstone, A Passage, Blowhole Cave, Cannon County, Tennessee

Actively painting the formation with the longwave light
Longwave light, Flowstone, A Passage, Blowhole Cave, Cannon County, Tennessee

Phosphorescence from mineral after turning off longwave light
Phosphorescent light, Flowstone, A Passage, Blowhole Cave, Cannon County, Tennessee

The top image being what one sees in the "natural" colored light of one's headlamp, or if we were standing outside holding it under sunlight. The following image is where the mineral is being actively excited by the longwave light. The final image is the afterglow (captured small bit by small bit in numerous photos stacked in Photoshop), which is the most diagnostic of the three images in terms of mineral identification. Note the location of red color in natural light is slightly visible in the other images.



Example 2: Dolomite vugs in the Bangor Limestone in Gourdneck Cave

Illuminated by an external camera flash
Dolomite vugs, Gourdneck Cave, Gourdneck Cave Preserve, Marion County, Tennessee

Actively painting vugs with the longwave light
Dolomite vugs in longwave light, Gourdneck Cave, Gourdneck Cave Preserve, Marion County, Tennessee

The lack of phosphorescence in this example is what I believe to be so striking.


Example 3. Gypsum crust in Cumberland Caverns

Painted light from my headlamp (white balance adjusted)
Gypsum crust, Cumberland Caverns, Warren County, Tennessee

Actively painting the formation with the longwave light
Gypsum crust, longwave light, Cumberland Caverns, Warren County, Tennessee

Composite of the previous two photographs
Gypsum crust, longwave blend, Cumberland Caverns, Warren County, Tennessee

This sequence shows that only a portion of the gypsum is phosphorescent, but I have no explanation why other than perhaps there is a patina on the surrounding gypsum blocking the longwave from exciting the mineral. This would suggest that older formations don't phosphoress where the younger ones do.

The research leaves me with more questions than answers.

2019/06/05

Biggest Building in Tennessee

What is the biggest building in Tennessee?

Obviously, this blog post will be dated at some point, likely in the not-so-far future. But I have at my disposal, after several hours of processing a huge geojson of data, courtesy of Microsoft, the building footprints for Tennessee in an easily digestible GIS format.

It turns out the GM Spring Hill Plant is the largest building, weighing in at approximately 5,942,799 square feet. Or, in other words, 0.21 square miles.

2019/04/18

Rescue at Mill Pond

I am surfing on the receding limb of a media wave that swept around the globe, gradually slowing. In this story I am not the protagonist or the antagonist, but simply someone near. As such, the knowledge that comes from perspective may be useful to someone now, or in the future, or perhaps never at all. This story will find its way to the surface likely long after the media cycle and the world has forgotten about little Jackson County, Tennessee. This story is for cavers, and for the locals who call the Upper Cumberland home. This story is for you.

This story is disconnected. It's disconnected from direct involvement with any of the exploration, and disconnected from the rescue. But these are events that originated from a disconnect, a moment where the dive line which held the diver's life separated. As you know, all things are connected, and so in this story I will attempt to connect all the lose bits.


On November 12th, 2016 my friend showed me a beautiful spring in her backyard. This property had long been in her husband's family's ownership, and he informed me that the spring was used to drive a mill once upon a time. They called it Mill Pond. Recognizing what I saw as a cave entrance (and one within the structure of the meteor impact site at Flynn Creek, making this especially interesting), I negotiated for access for a diver to check the lead.


Somewhere along the way I brought Gerald Moni to the spring and submitted to the Tennessee Cave Survey, Mill Pond. In Gerald's inimitable way, he said "It's not a pond survey." And thus it became Mill Pond Cave.


Mill Pond, Jackson County, Tennessee


Surprisingly the landowners were excited that someone else appreciated their little bit of heaven and were thrilled to allow access. First exploration took place a week later on November 19th, 2016. Thorn Walthall, our local cave diver was interested to see what was there. After a short dive he surfaced and conveyed what he saw.


Mill Pond, Jackson County, Tennessee 2


The dimensions were large, but it was a silty environment. This means that it's easy to stir up sediment which can linger and cloud visibility for long periods of time. In addition, several large trees had fallen down into the passage of the cave which obstructed safe progress. Over the next few months the landowners and he worked to remove these trees and grant access.


Thorn re-entered the cave a few more times, but was concerned to proceed further. I played "surface watch" for him once or twice, and each time was concerned, and proud that he knew his own limitations. I would rather have this lingering curiosity than the alternative.


Noted cave diver Jason Richards entered the cave on August 27, 2017, and made a line plot which documented 434' of cave. Where he turned around was a large air pocket.






Mill Pond Cave - a curiosity.

The morning of the Spring Presentation meeting of the Tennessee Cave Survey found cavers from around TAG (Tennessee, Alabama, Georgia for you non-cavers) congregated in one room hearing about such things as "Going Digital: Paperless Cave Surveying" by Jon Zetterberg, 'Karst Hydrogeology of the western Great Smoky Mountains" by Ben Miller, and "The Redcoats and Redneck Tennessee Collaboration: Surveying Mountain Eye" by Rostam Namaghi.


"Redcoat" Rostam is a medical doctor, and a caver from the UK. He and about two dozen of his friends are on expedition to the United States to explore and map caves.


Thorn approached me indicating that the Brits had asked him to show them some dive leads. At his request I rattled off a few dives I was aware of where they may get the coveted "cave booty" aka virgin passage. Among that list was my nagging curiosity, Mill Pond Cave.




Everything was fine, until it wasn't.

The morning of April 17th, 2019 I received a text message from my friend, the landowner at Mill Pond Cave. It read, "Thought I would let you know that last night some guys (friends of Thorn) were here diving and one guy had a line break. He didn't come back out so they are hoping he is in an air pocket. We have sheriff and rescue here now. Hamilton County [Cave and Cliff Rescue] got here just a big ago. I will let you know how it turns out." Subsequent text messages revealed him to not be a local, but one of the British divers on expedition.


I visited my friend that morning, the cave being a hundred feet from her house. I think anyone else would have been ruminating on liability issues, angry at anyone for the situation. My friend was desperate, hopeful, and only concerned with the man's safety. At this point, I still did not know his identity. I walked to the Mill Pond and touched the dive line leading into the cave. A story came to mind about a silver cord.


Outside of the property, rescue had setup their command station. A Twin Lakes utility truck lingered nearby, presumably working on communications within the rural valley. I spoke with some of the real heroes of this story, Jackson County rescue, and the Hamilton County Cave and Cliff Rescue Team led by Brian Krebs. The consensus was that this experienced diver would have found his way to the air bell in the back of the cave and could safely remain there for sometime in his (Thorn's) drysuit.


The plan was that expert cave divers, one from Florida, and another from Arkansas would arrive around 5pm to make the rescue. It had crossed my mind that this may be a recovery, though at times like these I don't speak such thoughts aloud.


Mill Pond Rescue 5



A long wait

At approximately 4pm Jackson County held a press brief to communicate the situation to the public. The time of the dive was pushed back to around 6pm.




At 6:44pm I received a text from the landowner saying "Diver went down about 40 minutes ago. We are waiting".


At 6:53pm I jumped from my chair on Jason Collard's porch and hugged both Jason and Rebecca - the text read "He's out and alive!!!!". Inquiring about his health she said, "They are checking his vitals now, but he walked out of that water like it was nothing!"


I posted to Facebook this update. I didn't immediately notice the religious imagery behind a man, thought to be dead, emerging from a cave alive a few days before Easter. What happier ending to a story can there be than, "He is out. And he is alive."?






Postscript






2019/02/22

NSS 2019 Convention Datasets

Glad you have found your way here! Below are a few datasets of local attractions that I think will help you get better acquainted with the Upper Cumberland (though some of the data is for the whole state!). 

KMZ and GPX are GPS file formats for use on GPSs and on your GPS enabled cell phone. As an Android user, I am fond of Locus Pro as a GPS app. For the Apple users, I would recommend Gaia. These aren't the only programs you can use, so if you're comfortable with other software feel free to use that instead.


Dataset NameAuthorKMZGPX

Tennessee Landforms

Tom Dunigan

Arches
Balds
Lakes
Lookout Towers
Peaks
Rocks
Sinkholes
Waterfalls
Water AccessBen DruryWaterAccess.kmz
Breweries, Wineries, and DistilleriesChuck SutherlandAlcohol.kmz
Local FoodChuck SutherlandLocalFood.kmz
-->

Ament Resurgence

Ament resurgence is the name of Cookeville's largest natural storm water drain (also known as a cave). A resurgence is a spring, a place where water returns to the surface from the subsurface.

Two springs can be found at this place. Pigeon Roost Spring, which sits somewhat higher in elevation above the Ament resurgence is only a short distance away and drains to the same location (in the video below, it's the waterfall coming from the left). From this place where they meet approximately 3800 acres are drained, all within the city of Cookeville.

Many of the tributary streams begin above ground, go underground, resurface, and go underground again before coming out at this location.


After a large rain on 2/20/2019 I visited the spring to find the spring like this.





For comparison, here is another high water event that I recorded on 2/16/2018.



Using GIS I was able to tease out the area which drains to this spot, or the watershed. Curious about how the land was used in that region I further analysed it and produced this map.


Ament Resurgence Watershed, Putnam County, Tennessee