Fwd: Re: OpenJUMP HoRAE - Different OpenJUMP versions

[Stefan Steiniger]

Hi Steve,

(will cc this to email to user list in case someone else has similar
questions)

on the wiki:
Yes, I made a link to a restored wiki page, but I think it still misses
some info there that I got on the original wiki. For instance about a
comparison with HRT (see below) - which is, however, now also part of
the manual. Thanks for stopping buy on the new wiki.

On working with OpenJUMP 1.7.1:
Yes as well. In theory it is as simple as copying the Horae jar file
(movantools_mar2013.jar) that can be found in openjumps /lib/ext folder
into the same folder of the 1.7.1 version.
Now, there is no guarantee that it works because in OJ 1.7 there was a
bug with loading files/rasters on MacOSX, and furthermore, there have
been some changes on the raster-file libraries used to load and dsiplay
files. Means: I haven't done any testing, but you are free to check. The
easy way to do this is:
(a) calculate a density grid
(b) calculate a home range polygon for that grid (for comparison later on)
(c) save this grid as (as TIFF file)
(d) eliminate/delete the grid layer
(e) load this grid file
(f) apply again the home range polygon calculation

questions to answer now:
(Q1): Did loading of the raster in step (e) work?
(Q2): Did calculation of the home range polygon work on the reloaded
density grid?
(Q3): Are the calculated polygon from (b) and (f) the same?

I also hope to be able to do this check this week, maybe on friday.

cheers,
stefan



===
Comparability of HoRAE Results with Home Range Tools (HRT) Results:

Thanks to Christine Richter (Göttingen, GER), we got aware of the fact
that results calculated with the Home Range Tools for ArcGIS10 by A.R.
Rodgers and J.G. Kie cannot be directly compared with results calculated
with OpenJUMP HoRAE. If you use the same bandwidth parameter h for HRT
and OpenJUMP HoRAE, then the results (i.e. contours) will be much more
detailed than those from HRT. HRT generated contours will be much
smoother. However, if you take the bandwidth parameter from HRT (e.g.
63m) and multiply it with about 2.78 (e.g. 2.78 * 63 = 175m) and use
this value (i.e. 175m) for HoRAE, then the contours should be about the
same. The reason for these differences and the need to multiply the
values is that in ArcGIS/HRT such multiplication of href is performed.
This is done, as the general href equation is an estimate for a Gaussian
function/kernel that is applied to a bi- weight Kernel (in HRT). As you
can see in HoRAE and on Wikipedia11, both kernel functions have
different maximum values and properties. Internally HoRAE does not
perform a scaling so one can directly compare density results. The
multiplication with the value of 2.78 for the Gaussian-based href value
that will be used with a bi-weight kernel will, however, result in
comparable density estimates (see Silverman 1986).
===

Am 07.07.14 09:58, schrieb Steve Minta:
> Stefan,
>
> Thanks for the MacOSX Users Short Installation Guide, and the updated
> wiki page.
>
> I successfully followed the installation and noticed that HoRAE is
> bundled with OpenJUMP 1.6.0. It appears I can only use HoRAE with that
> OpenJUMP version.
>
> I had already installed the latest OpenJUMP version 1.7.1 and set it up
> for analyses, and of course I would like to keep up with future OpenJUMP
> versions.
>
> Is there a way to use HoRAE with the latest OpenJUMP versions, or can we
> only use HoRAE with its bundled OpenJUMP 1.6.0 version?
>
> I don't suppose it would be as simple as opening the v.1.7.1 application
> package and copying unique HoRAE resources/files to it within the
> corresponding folders?
>
> Best wishes from coastal Oregon,
> Steve
>
>
>
>> Hi Steve,
>>
>> ..ah well, this is unfortunate indeed. The links are actually internal
>> wiki links to "wiki pages" that I never created in that test wiki.
>>
>> I attach the "MacOSX" text I printed from the internal wiki that is
>> running behind closed university walls. Beginning of next week this
>> wiki should be accessible from outside. Btw. I am not sure if the
>> key-issue, described at the bottom, was actually fixed meanwhile. But
>> don't hesitate to contact me again if you need further assistance.
>>
>> best wishes from Santiago de Chile,
>> stefan
>>
>>
>> Am 01.07.14 08:28, schrieb Steve Minta:
>>> Stefan,
>>>
>>> Thanks for the prompt reply.
>>>
>>> Unfortunately, the documents at your suggested web page,
>>> http://sourceforge.net/projects/mentaer.u/files/moveantools/ojhorae/,
>>> do not contain the documents I need, particularly the "MacOSX Users
>>> Short Installation Guide."
>>>
>>> However, if you click on "OpenJUMP Horae" button on that web page, you
>>> go to the main wiki at
>>> https://sourceforge.net/u/mentaer/horae/wiki/Home/
>>> which does have the documents.
>>>
>>> Note that any document on this wiki page with brackets, such as/[MacOSX
>>> Users Short Installation Guide]/, cannot be downloaded. Looking at the
>>> download urls, they all seem to be formatted wrong.
>>>
>>> Is there another way of obtaining these documents?
>>>
>>> Thanks for the help,
>>> Steve
>>>
>>>
>>>> Dear Steve,
>>>>
>>>> sorry for the inconvenience. We actually had two wikis but both are
>>>> currently down for some reasons. And the link below was never be
>>>> intended to be some official wiki, so if some links do not work, it
>>>> may make sense
>>>>
>>>> Anyway I hope I have one wiki accessible next week (it is up and
>>>> running, by unfortunately accessible only from a university internal
>>>> network). Most of the files for download can be accessed here:
>>>> http://sourceforge.net/projects/mentaer.u/files/moveantools/ojhorae/
>>>>
>>>> Please let me know if you look for something specific. Eg. send me a
>>>> copy of the link, that does not work.
>>>>
>>>> best,
>>>> stefan
>>>>
>>>> Am 30.06.14 11:22, schrieb Andrew Hunter:
>>>>> Hi Stefan
>>>>>
>>>>> Do you have digital copies of the pdfs that you can send to Steve?
>>>>> The links appear to been broken broken.
>>>>>
>>>>> A.
>>>>>
>>>>>
>>>>>
>>>>> Begin forwarded message:
>>>>>
>>>>> From: Steve Minta <mi...@peak.org<mailto:mi...@peak.org>>
>>>>> Subject: OpenJUMP HoRAE - Some documents unavailable for download
>>>>> Date: June 30, 2014 at 8:25:22 AM MDT
>>>>> To: Andrew Hunter <ahu...@ucalgary.ca<mailto:ahu...@ucalgary.ca>>
>>>>>
>>>>> Dear Andrew Hunter,
>>>>>
>>>>> I want to install OpenJUMP HoRAE, but I cannot download several pdf
>>>>> documents from:
>>>>>
>>>>> https://sourceforge.net/u/mentaer/horae/wiki/Home/
>>>>>
>>>>> because downloading attempts produce "Error 403 - Create access
>>>>> required" for documents such as "MacOSX Users Short Installation
>>>>> Guide."
>>>>>
>>>>> Is there another way I can obtain these documents?
>>>>>
>>>>> I'm logged in to sourceforge using latest Firefox browser.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Steve Minta
>>>>> Consultant, UN FAO
>>>>>
>>>>>
>>>>>
>>>>> Andrew Hunter PEng RPSurv PhD
>>>>> Assistant Professor & Associate Head (Undergraduate Studies)
>>>>> Department of Geomatics Engineering
>>>>> Schulich School of Engineering
>>>>> University of Calgary
>>>>>
>>>>> T: +403.220.7377
>>>>> F: +403.284.1980
>>>>> E: ahunter (at) ucalgary (dot) ca
>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>
>>
>>
>> Content-Type: application/pdf;
>> name="OpenJUMP Horae - MacOSX Users Short Installation Guide -
>> stgo.pdf"
>> Content-Disposition: attachment;
>> filename*0="OpenJUMP Horae - MacOSX Users Short Installation Guide
>> - stg";
>> filename*1="o.pdf"
>>
>> Attachment converted: iMac:OpenJUMP Horae - MacOSX Use.pdf (PDF /«IC»)
>> (00DD8AD6)
>
>
>

[Stefan Steiniger]

Hi Steve,

a bit later than expected, but today I tried if saving a density raster
(as tif file) and re-loading (as Sextante Raster) works, and it does.
And also the calculated home range polygon is the same.

Of course, I should properly test each function with OpenJUMP 1.7.1 in
detail, but at the moment I can't think of any other problems that could
appear (except you are using OpenJUMPs new/reworked PostGIS database
connector to load and store tracking locations). Let's hope I find some
time soon to do a new HoRAE release packaged with OJ 1.7.1. The time
consuming part is that I also need to go through the documentation and
updated it where needed.

cheers,
stefan

Am 08.07.14 07:43, schrieb Steve Minta:
> Stefan,
>
> Since I have never used OpenJUMP or HoRAE before, I think I'll wait
> until for your test results with the raster loading issue.
>
> However, I did copy movantools_mar2013.jar from
> openjump_rc16moveantools_mar2013 into OpenJUMP 1.7.1. By the way, I
> noticed only these file differences between the two versions:
>
> In openjump_rc16moveantools_mar2013, the file:
> PostGISPlugIn-1.5.2.jar
> seems to be replaced by two files in OpenJUMP 1.7.1:
> postgis-jdbc-1.3.3.jar
> postgis-stubs-1.3.3.jar
>
> I ran your openjump_rc16moveantools_mar2013 side by side with the
> modified OpenJUMP 1.7.1 (i.e., with added movantools_mar2013.jar) under
> Java 1.6. I used the example in your Mac install guide. Your version 1.6
> is above 1.7.1:
>
> Best,
> Steve

>> Thanks to Christine Richter (Göttingen, GER), we got aware of the fact