Linkage Mapper Error: before step 1

[Nino Pierantonio]

Dear all,
I am fairly new to linkage mapper so my question might sound redundant.
I am running the toolbox on ArcMap 10.3 and Win 10 (64bit) OS. After running the test exampleto chech t5hat everything was ok (and it was), I have started running trial analysis with my onw data. I keep getting the following errors after a few seconds of computation wile processing step 1. I can't figure out where the problem is (as far as I understand,it has something to do with Java). Any help is most wellcome.

Regards
N

Executing: MapLinkages C:\LinkMapperTest Critical_areas Code friction_rec5 true true "Cost-Weighted & Euclidean" # true true true 1 Euclidean true true 10000 100000 40000
Start Time: Fri Nov 18 15:50:47 2016
Running script MapLinkages...
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A record of run settings and messages can be found in your log directory:
C:\LinkMapperTest\run_history\log
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********************************************************
NOTE: Linkage Mapper tools often work best when run from ArcCatalog instead of ArcMap.


Linkage Mapper Version 1.1.0
on ArcGIS Desktop 10.3 Service Pack N/A
Setting data frame spatial reference to that of core area feature class.

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Starting at step 1.

Making temporary copy of resistance raster for this run.

Making temporary raster of core file for this run.

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Running script s1_getAdjacencies.py
Adjacency files will be written to C:\LinkMapperTest\datapass\adj
Reducing processing area using bounding circle plus buffer of 10000.0 map units

Calculating cost-weighted distance adjacency

Reduced resistance raster extracted using bounding circle.
That took 1 seconds.

Starting cost-weighted distance allocation...
Processing cell size: 0.016666666667

Building output statistics and pyramids for CWD raster.
Cost-weighted distance allocation done.
That took 13 seconds.

Calculating adjacencies crossing allocation boundaries...
That took 12 seconds.

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Python error on **line 481** of lm_util.py in Linkage Mapper Version 1.1.0:
IndexError: index 0 is out of bounds for axis 0 with size 0

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****Failed in step 1. Details follow.****
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Python error on **line 199** of s1_getAdjacencies.py in Linkage Mapper Version 1.1.0:
SystemExit: 1

---------------------------------
****Failed in step 1. Details follow.****
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Python error on **line 99** of s1_getAdjacencies.py in Linkage Mapper Version 1.1.0:
SystemExit: 1
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Python error on **line 174** of lm_master.py in Linkage Mapper Version 1.1.0:
SystemExit: 1
---------------------------------
A record of run settings and messages can be found in your log directory:
C:\LinkMapperTest\run_history\log
---------------------------------

Completed script MapLinkages...
Failed to execute (MapLinkages).
Failed at Fri Nov 18 15:51:21 2016 (Elapsed Time: 33.40 seconds)

[Brad McRae]

Hi Nino,

It might be your core ID field. Is it only positive integers? If not
email me directly please and we'll figure it out.

Also an observation- it doesn't look like you are running with meters
as your spatial unit in your input layers. I'd recommend
re-projecting, as we have tested only in meter-based systems and it
also aids in interpretation down the road (by relating CWD units and
cutoffs to euclidean distances).

Best,
Brad

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[Nino Pierantonio]

Hi Brad,

Thank you for your quick answer. My bad, I totally forgot to change the projection system of my project. Now the tool is running smoothly and I am trying out a few options and settings.
I have got a couple of further questions regarding the resistance map. I have created it by inverting a habitat suitability model generated by Maximum Enthropy Models. To invert my species distribution model I have used the SDM Toolbox (http://sdmtoolbox.org/) that, as stated in the tool itself, creates friction layer. Would a friction map equal a resistance map (as far as I understand, at least conceptually, yes)? If not, is there a way I could generate my resistance map from a friction layer or from a species distribution model (would this last opttion make sense at all?)?. Does the resistance range of values have to be between 1 and 100 or any other range, say 1-10, would work?
Thank you very much for your support.
Regards,

N

[Brad McRae]

Hi Nino,

Conceptually they are probably the same, but I'm not familiar with the
SDM toolbox. There are few hard and fast rules about resistance
modeling, but there are some tips in the user guide (or in the Gnarly
Landscape Utilities user guide, I forget which). The range is up to
you, although we recommend starting with 1 as representing 'ideal'
movement habitat and increasing values from there.

Here are some papers that might be helpful:
https://dl.dropboxusercontent.com/u/1340127/CONNECTIVITY_READINGS.zip

Best,
Brad

On Mon, Nov 21, 2016 at 4:30 AM, Nino Pierantonio