Blog Archives

SDM re-projected for Google Earth, OSM with gdal2tile

I think I have stumbled upon the solution for tiling the png image.
To re-project the PNG image, we can geo-reference the images with GDAL, then warp the geo-referenced image to the correct projection, also with GDAL.
The process is described here:
First, enter “gdalinfo Abies_fraseri.png” into terminal to get the bounds of the PNG image.
This yields the following output:
Corner Coordinates:
Upper Left  (    0.0,    0.0)
Lower Left  (    0.0, 1302.0)
Upper Right ( 2899.0,    0.0)
Lower Right ( 2899.0, 1302.0)
Center      ( 1449.5,  651.0)
A template and implementation for our PNG files is demonstrated here:
Template:
gdal_translate -of VRT -a_srs EPSG:4326 -gcp 0 0 ULlong ULlat -gcp UPPERRIGHTPx 0 URlong URlat -gcp LOWERRIGHTPx LOWERRIGHTPy LRlong LRlat Abies_fraseri.png Abies_fraseri.vrt
Implementation: 
gdal_translate -of VRT -a_srs EPSG:4326 -gcp 0 0 -84.000683874 35.7889383688 -gcp 2899.0 0 -83.0424855 35.7889383688 -gcp 2899.0 1302.0 -83.0424855 35.426963641 Abies_fraseri.png Abies_fraseri.vrt

For “ULlong” (Upper Left Long) and so forth I used a bounding box tool (http://boundingbox.klokantech.com) to determine the following bounds of the PNG – however, if there is a more “official” known boundary, it would be wise to use that instead.
                                35.426963641,-84.000683874 – bottom left / lower left
                                35.426963641,-83.0424855 bottom right / lower right
                                35.7889383688,-83.0424855 – top right / upper right
                                35.7889383688,-84.000683874 – top left / upper left
Next, take the .vrt file and warp it:
    gdalwarp -of VRT -t_srs EPSG:4326 Abies_fraseri.vrt Abies_fraseri_2.vrt
This creates a folder with tiles for a KML network link.
see “doc.kml” in the attached zip folder which you may open in Google Earth.
There is also an Open Map Layers HTML page in the attached zip folder.
To add trails in Google Earth
My opinion is it would be more interesting and informative to have the species occurrences added as a separate layer.  Therefore, I would prefer to create placemarkers / waypoints for species locations rather than black squares on the images.  Is it possible to generate PNG images with the likely distribution but not the black squares?  If so, would that take a long time to re-do to make these tiled overlays?
Also, although I “hacked” the PNG bounds, I’m still worried it the overlay’s georeferencing be “off” a bit and would love to use a more trustworthy set of coordinates than those derived from my best judgement and http://boundingbox.klokantech.com.
From here, I think it would be smart to document a workflow for doing a lot of PNG to VRT to KML at a time.  I haven’t tried processing a whole directory of images at once yet – just playing with the Abies_fraseri.png for now.
The doc.kml and virtual raster dataset work with Google Map API and Open Layers map.  I think they both run on Javascript.
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Request for File – DataONE users


From: Jessel, Tanner Monroe
Sent: Wednesday, November 14, 2012 6:22 PM
To: Dave Vieglais; Mitchell, Chad Matthew
Cc: Amber E Budden
Subject: Request for File – DataONE users

Hello Dave,

I’m a Masters candidate in Information Science at UT-Knoxville working as a GRA on the DataONE project with Dr. Tenopir.

I’m working on a research question regarding social networks and influence within the DataONE user community.

Poking around on the DataONE docs.dataone.org site, I found a document you’d created in October of 2011 that I believe will be helpful in exploring this topic.

It’s called “List of DataONE users and groups” and apparently was created using a python script.

The exact filename is 2011025_dataone_users.xls

I found this file under “Project Information” <https://docs.dataone.org/member-area/project-information> on the main navigation menu of the DataONE docs site.

The download URL for the document is located on this page: https://docs.dataone.org/member-area/project-information/d1_users.xls/view, along with this description:

This spreadsheet lists members of DataONE, their group memberships and mailing list memberships. It is generated by the python script located in subversion software/tools/trunk/listusers/listusers.py executed with the command: python listusers.py -x file_name

I’m interested in this file as a view of historic membership of the DataONE community, but I’m also interested in re-creating the file to reflect current membership on the docs.dataone.org site.

I’m working with Chad Mitchell, another Masters candidate and research assistant at
UT-Knoxville.

He has some experience with python and I’m curious as well – if it’s possible for you to share, we’d like to learn how to generate a new file reflecting current membership.

Is this something that we or someone on the Dev team would have access to?

Barring re-creating your methods, we’d appreciate if you could supply us with a 2012 version of the d1_users.xls file.

Thanks for any help,

Tanner

Tanner Jessel
Graduate Research Assistant:
Data Observation Network for Earth (DataONE)
http://www.dataone.org

Center for Information and Communication Studies
The University of Tennessee
Mail: 1345 Circle Park Drive, Suite 420
Physical: Hoskins 5, Room 5-H
865-974-7931 (voice)
865-974-7973 (fax)
tjessel@utk.edu

Discipline Classification Survey Instrument & Informed Consent

Hi Dr. Allard,

Here is an attempt at a survey instrument for discipline classification, two sections and 8 questions total.

Section I includes questions about role and work environment.

Questions 1 and 2 derived from Arsev’s PhD dissertation (8 primary subject disciplines; 11 work settings).

Question 3, current job titles, is synthesized from the actual job titles of 284 DataONE.org members’ linkedIN profiles "Job Title" section, that I aggregated and merged into 17 main classifications. I expect the list could be honed further; or expanded, I would love to use the U.S. Census Bureaus list of Job Titles but I think people would get frustrated finding their desired title out of so many options, then quit the survey.

Of the options I provided, I am concerned about "Director" and "Manager;" "Research Fellow" and "Post Doctoral Researcher" and "Research Associate / Assistant." Perhaps I don’t understand these well enough.

Question 4 and Question 5 are about total career and "in discipline" career.

Section II contains demographics – credentials and degrees first, plus year obtained, and finally age / gender.

"Education" and "Computer Science" include special degrees – Doctor of Education, Education Specialist, and Doctor of Engineering, respectively. I don’t know if you want these homogenized as "Doctorate" or not.

There is an "other" in case there is a problem where a respondent does not see what they expect.

Let me know what the next steps are and if you have any questions.

Thanks,

Tanner

DataONE_Discipline_Survey-Informed-Consent.docx

DataONE_Discipline_Survey-Instrument.docx

Test 3: Network Visualization with NESCENT GeoPhyloBuilder

Hi Chad,

FYI because it’s cool, and also because I want to note it for future possible use on the network visualization project.

https://www.nescent.org/wg_EvoViz/Main_Page

https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder

-Tanner

Test 4: Network Visualization with NESCENT GeoPhyloBuilder

Hi Chad,

FYI because it’s cool, and also because I want to note it for future possible use on the network visualization project.

https://www.nescent.org/wg_EvoViz/Main_Page

https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder

-Tanner

Test 3: Network Visualization with NESCENT GeoPhyloBuilder

From: Jessel, Tanner Monroe
Sent: Wednesday, July 17, 2013 10:16 PM
To:
Subject: FW: Evolution Visualization Tools – GeoPhyloBuilder

status.draft

From: Jessel, Tanner Monroe
Sent: Monday, February 11, 2013 4:51 PM
To: Mitchell, Chad Matthew
Subject: Evolution Visualization Tools – GeoPhyloBuilder

Hi Chad,

FYI because it’s cool, and also because I want to note it for future possible use on the network visualization project.

https://www.nescent.org/wg_EvoViz/Main_Page

https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder

-Tanner

Network Visualization with NESCENT GeoPhyloBuilder

status.draft

From: Jessel, Tanner Monroe
Sent: Monday, February 11, 2013 4:51 PM
To: Mitchell, Chad Matthew
Subject: Evolution Visualization Tools – GeoPhyloBuilder

Hi Chad,

FYI because it’s cool, and also because I want to note it for future possible use on the network visualization project.

https://www.nescent.org/wg_EvoViz/Main_Page

https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder

-Tanner

Network Visualization with NESCENT GeoPhyloBuilder

From: Jessel, Tanner Monroe
Sent: Monday, February 11, 2013 4:51 PM
To: Mitchell, Chad Matthew
Subject: Evolution Visualization Tools – GeoPhyloBuilder

Hi Chad,

FYI because it’s cool, and also because I want to note it for future possible use on the network visualization project.

https://www.nescent.org/wg_EvoViz/Main_Page

https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder

-Tanner