memory error

[ModiShrushti]

I am using circuitscape toolbox in ArcGIs and getting the error
cs_arc.py failed. Details follow
Python error on line 236 of cs_arc.py version 2013-05-29 memory error
Failed to execute circuitscape.
How to solve this issue

[ranjanan]

I'm afraid that that version of the ArcGIS toolbox is currently deprecated. Could you export your maps and just run Circuitscape on it?

[ModiShrushti]

I have tried to run Circuitscape 4 (GUI version) but it is not responding after few seconds running the program. Also I tried to run Circuitscape 5 using julia but again I am not well acquainted with it and could not follow the instruction
julia> compute("path/to/config/file.ini")

[ranjanan]

Circuitscape works by taking in an "INI file" which is a set of options and paths (look at the tests). One way to generate it to use INIBuilder (check docs). Alternatively, you can simply copy and paste one of those test files and change the paths and the options you want to use.

[ranjanan]

Feel free to post questions here. I'm happy to guide you through the process. Once we figure it out, I'm happy to add any documentation you think is useful for this use case.

[ModiShrushti]

Hi, I was able to successfully run Circuitscape julia and I was using the same resistance file for optimisation in ResistanceGA. After fixing everything I realised that I am getting the opposite results from what has been expected. I am getting higher resistance for favourable habitat and vice-versa based on the ecology of my species. After some reading I realised the issue can be with the resistance surface . This is the sequence which I used for generation of input resistance surface for Circuitscape. Please correct me if I am wrong. 1. Convert all the files into raster format 2. Reclassify the categories using *reclassify tool in ArcGIS* 3. Make all the resistance surface with similar resolution and convert into .asc format using "*export to circuitscape"* tool in ArcGIS 4. Use *Gnarly toolbox* for final input and adding the resistance and habitat quality value for each category Thanks Shrushti Shrushti Modi Ph.D. Scholar, Dept. of Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun Ph: +917088383245 Email Address: ***@***.***, ***@***.***

…

On Thu, May 27, 2021 at 8:17 PM Ranjan Anantharaman < ***@***.***> wrote: Feel free to post questions here. I'm happy to guide you through the process. Once we figure it out, I'm happy to add any documentation you think is useful for this use case. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#292 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUFH5JSYT6S5KX6GMGCK4SDTPZLP5ANCNFSM45JAA7ZQ> .

[ranjanan]

Could you check whether your resistance file is regarded as resistances or conductances? In your INI file, there should be an option like the following: https://github.com/Circuitscape/Circuitscape.jl/blob/master/test/input/raster/pairwise/1/sgVerify1.ini#L40 Basically, if the resistance file you’re feeding Circuitscape contains resistances, that flag should be true. And false if it’s conductances. From: ModiShrushti ***@***.***> Sent: Tuesday, June 29, 2021 1:44 PM To: Circuitscape/Circuitscape.jl ***@***.***> Cc: Ranjan Anantharaman ***@***.***>; Comment ***@***.***> Subject: Re: [Circuitscape/Circuitscape.jl] memory error (#292) Hi, I was able to successfully run Circuitscape julia and I was using the same resistance file for optimisation in ResistanceGA. After fixing everything I realised that I am getting the opposite results from what has been expected. I am getting higher resistance for favourable habitat and vice-versa based on the ecology of my species. After some reading I realised the issue can be with the resistance surface . This is the sequence which I used for generation of input resistance surface for Circuitscape. Please correct me if I am wrong. 1. Convert all the files into raster format 2. Reclassify the categories using *reclassify tool in ArcGIS* 3. Make all the resistance surface with similar resolution and convert into .asc format using "*export to circuitscape"* tool in ArcGIS 4. Use *Gnarly toolbox* for final input and adding the resistance and habitat quality value for each category Thanks Shrushti Shrushti Modi Ph.D. Scholar, Dept. of Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun Ph: +917088383245 Email Address: ***@***.*** <mailto:***@***.***> , ***@***.*** <mailto:***@***.***>

On Thu, May 27, 2021 at 8:17 PM Ranjan Anantharaman < ***@***.*** <mailto:***@***.***> > wrote: Feel free to post questions here. I'm happy to guide you through the process. Once we figure it out, I'm happy to add any documentation you think is useful for this use case. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#292 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUFH5JSYT6S5KX6GMGCK4SDTPZLP5ANCNFSM45JAA7ZQ> .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <#292 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFOAQN25EPM6NQGDJVW3Q3TVIA5TANCNFSM45JAA7ZQ> . <https://github.com/notifications/beacon/ACFOAQIUVGCBHIW5EXENVO3TVIA5TA5CNFSM45JAA7Z2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOGPTTVUA.gif>

[ModiShrushti]

I have rechecked it is regarded as resistance file only. On Wed, 30 Jun 2021, 2:09 am Ranjan Anantharaman, ***@***.***> wrote:

…

Could you check whether your resistance file is regarded as resistances or conductances? In your INI file, there should be an option like the following: https://github.com/Circuitscape/Circuitscape.jl/blob/master/test/input/raster/pairwise/1/sgVerify1.ini#L40 Basically, if the resistance file you’re feeding Circuitscape contains resistances, that flag should be true. And false if it’s conductances. From: ModiShrushti ***@***.***> Sent: Tuesday, June 29, 2021 1:44 PM To: Circuitscape/Circuitscape.jl ***@***.***> Cc: Ranjan Anantharaman ***@***.***>; Comment ***@***.***> Subject: Re: [Circuitscape/Circuitscape.jl] memory error (#292) Hi, I was able to successfully run Circuitscape julia and I was using the same resistance file for optimisation in ResistanceGA. After fixing everything I realised that I am getting the opposite results from what has been expected. I am getting higher resistance for favourable habitat and vice-versa based on the ecology of my species. After some reading I realised the issue can be with the resistance surface . This is the sequence which I used for generation of input resistance surface for Circuitscape. Please correct me if I am wrong. 1. Convert all the files into raster format 2. Reclassify the categories using *reclassify tool in ArcGIS* 3. Make all the resistance surface with similar resolution and convert into .asc format using "*export to circuitscape"* tool in ArcGIS 4. Use *Gnarly toolbox* for final input and adding the resistance and habitat quality value for each category Thanks Shrushti Shrushti Modi Ph.D. Scholar, Dept. of Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun Ph: +917088383245 Email Address: ***@***.*** <mailto:***@***.***> , ***@***.*** <mailto:***@***.***> On Thu, May 27, 2021 at 8:17 PM Ranjan Anantharaman < ***@***.*** <mailto:***@***.***> > wrote: > Feel free to post questions here. I'm happy to guide you through the > process. Once we figure it out, I'm happy to add any documentation you > think is useful for this use case. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > < #292 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AUFH5JSYT6S5KX6GMGCK4SDTPZLP5ANCNFSM45JAA7ZQ > > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub < #292 (comment)> , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ACFOAQN25EPM6NQGDJVW3Q3TVIA5TANCNFSM45JAA7ZQ> . < https://github.com/notifications/beacon/ACFOAQIUVGCBHIW5EXENVO3TVIA5TA5CNFSM45JAA7Z2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOGPTTVUA.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#292 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUFH5JXOHALCJMUWT4XCPF3TVIVQLANCNFSM45JAA7ZQ> .

[ranjanan]

I see, would you mind attaching your inputs in a google drive file? I’ll take a look. From: ModiShrushti ***@***.***> Sent: Tuesday, June 29, 2021 11:03 PM To: Circuitscape/Circuitscape.jl ***@***.***> Cc: Ranjan Anantharaman ***@***.***>; Comment ***@***.***> Subject: Re: [Circuitscape/Circuitscape.jl] memory error (#292) I have rechecked it is regarded as resistance file only. On Wed, 30 Jun 2021, 2:09 am Ranjan Anantharaman, ***@***.*** <mailto:***@***.***> > wrote:

Could you check whether your resistance file is regarded as resistances or conductances? In your INI file, there should be an option like the following: https://github.com/Circuitscape/Circuitscape.jl/blob/master/test/input/raster/pairwise/1/sgVerify1.ini#L40 Basically, if the resistance file you’re feeding Circuitscape contains resistances, that flag should be true. And false if it’s conductances. From: ModiShrushti ***@***.*** <mailto:***@***.***> > Sent: Tuesday, June 29, 2021 1:44 PM To: Circuitscape/Circuitscape.jl ***@***.*** <mailto:***@***.***> > Cc: Ranjan Anantharaman ***@***.*** <mailto:***@***.***> >; Comment ***@***.*** <mailto:***@***.***> > Subject: Re: [Circuitscape/Circuitscape.jl] memory error (#292) Hi, I was able to successfully run Circuitscape julia and I was using the same resistance file for optimisation in ResistanceGA. After fixing everything I realised that I am getting the opposite results from what has been expected. I am getting higher resistance for favourable habitat and vice-versa based on the ecology of my species. After some reading I realised the issue can be with the resistance surface . This is the sequence which I used for generation of input resistance surface for Circuitscape. Please correct me if I am wrong. 1. Convert all the files into raster format 2. Reclassify the categories using *reclassify tool in ArcGIS* 3. Make all the resistance surface with similar resolution and convert into .asc format using "*export to circuitscape"* tool in ArcGIS 4. Use *Gnarly toolbox* for final input and adding the resistance and habitat quality value for each category Thanks Shrushti Shrushti Modi Ph.D. Scholar, Dept. of Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun Ph: +917088383245 Email Address: ***@***.*** <mailto:***@***.***> <mailto:***@***.***> , ***@***.*** <mailto:***@***.***> <mailto:***@***.***> On Thu, May 27, 2021 at 8:17 PM Ranjan Anantharaman < ***@***.*** <mailto:***@***.***> <mailto:***@***.***> > wrote: > Feel free to post questions here. I'm happy to guide you through the > process. Once we figure it out, I'm happy to add any documentation you > think is useful for this use case. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > < #292 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AUFH5JSYT6S5KX6GMGCK4SDTPZLP5ANCNFSM45JAA7ZQ > > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub < #292 (comment)> , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ACFOAQN25EPM6NQGDJVW3Q3TVIA5TANCNFSM45JAA7ZQ> . < https://github.com/notifications/beacon/ACFOAQIUVGCBHIW5EXENVO3TVIA5TA5CNFSM45JAA7Z2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOGPTTVUA.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#292 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUFH5JXOHALCJMUWT4XCPF3TVIVQLANCNFSM45JAA7ZQ> .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <#292 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFOAQISC4JEXX74TUHTSZTTVKCMPANCNFSM45JAA7ZQ> . <https://github.com/notifications/beacon/ACFOAQP3TL2TSEPCLWGK5WTTVKCMPA5CNFSM45JAA7Z2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOGPVVDRI.gif>

[ModiShrushti]

Sure. Please find attached the .asc files, I have used for the analysis. I have used two different sets one with considering the resistance value during reclassification and second using reclassification without resistance values. Thanks Shrushti Shrushti Modi Ph.D. Scholar, Dept. of Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun Ph: +917088383245 Email Address: ***@***.***, ***@***.*** On Wed, Jun 30, 2021 at 7:44 PM Ranjan Anantharaman < ***@***.***> wrote:

…

I see, would you mind attaching your inputs in a google drive file? I’ll take a look. From: ModiShrushti ***@***.***> Sent: Tuesday, June 29, 2021 11:03 PM To: Circuitscape/Circuitscape.jl ***@***.***> Cc: Ranjan Anantharaman ***@***.***>; Comment ***@***.***> Subject: Re: [Circuitscape/Circuitscape.jl] memory error (#292) I have rechecked it is regarded as resistance file only. On Wed, 30 Jun 2021, 2:09 am Ranjan Anantharaman, ***@***.*** <mailto:***@***.***> > wrote: > Could you check whether your resistance file is regarded as resistances or > conductances? > > > > In your INI file, there should be an option like the following: > https://github.com/Circuitscape/Circuitscape.jl/blob/master/test/input/raster/pairwise/1/sgVerify1.ini#L40 > > > > Basically, if the resistance file you’re feeding Circuitscape contains > resistances, that flag should be true. And false if it’s conductances. > > > > From: ModiShrushti ***@***.*** <mailto:***@***.***> > > Sent: Tuesday, June 29, 2021 1:44 PM > To: Circuitscape/Circuitscape.jl ***@***.*** <mailto:***@***.***> > > Cc: Ranjan Anantharaman ***@***.*** <mailto:***@***.***> >; Comment ***@***.*** <mailto:***@***.***> > > Subject: Re: [Circuitscape/Circuitscape.jl] memory error (#292) > > > > Hi, > I was able to successfully run Circuitscape julia and I was using the same > resistance file for optimisation in ResistanceGA. After fixing everything I > realised that I am getting the opposite results from what has been > expected. I am getting higher resistance for favourable habitat and > vice-versa based on the ecology of my species. After some reading I > realised the issue can be with the resistance surface . This is the > sequence which I used for generation of input resistance surface for > Circuitscape. Please correct me if I am wrong. > > 1. Convert all the files into raster format > 2. Reclassify the categories using *reclassify tool in ArcGIS* > 3. Make all the resistance surface with similar resolution and convert into > .asc format using "*export to circuitscape"* tool in ArcGIS > 4. Use *Gnarly toolbox* for final input and adding the resistance and > habitat quality value for each category > > > > Thanks > Shrushti > > Shrushti Modi > Ph.D. Scholar, > Dept. of Animal Ecology and Conservation Biology, > Wildlife Institute of India, > Dehradun > Ph: +917088383245 > Email Address: ***@***.*** <mailto:***@***.***> <mailto:***@***.***> , ***@***.*** <mailto:***@***.***> <mailto:***@***.***> > > > > On Thu, May 27, 2021 at 8:17 PM Ranjan Anantharaman < > ***@***.*** <mailto:***@***.***> <mailto:***@***.***> > wrote: > > > Feel free to post questions here. I'm happy to guide you through the > > process. Once we figure it out, I'm happy to add any documentation you > > think is useful for this use case. > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > < > #292 (comment) > >, > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AUFH5JSYT6S5KX6GMGCK4SDTPZLP5ANCNFSM45JAA7ZQ > > > > . > > > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub < > #292 (comment) > > , or unsubscribe < > https://github.com/notifications/unsubscribe-auth/ACFOAQN25EPM6NQGDJVW3Q3TVIA5TANCNFSM45JAA7ZQ > > . < > https://github.com/notifications/beacon/ACFOAQIUVGCBHIW5EXENVO3TVIA5TA5CNFSM45JAA7Z2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOGPTTVUA.gif > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > < #292 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AUFH5JXOHALCJMUWT4XCPF3TVIVQLANCNFSM45JAA7ZQ > > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub < #292 (comment)> , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ACFOAQISC4JEXX74TUHTSZTTVKCMPANCNFSM45JAA7ZQ> . < https://github.com/notifications/beacon/ACFOAQP3TL2TSEPCLWGK5WTTVKCMPA5CNFSM45JAA7Z2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOGPVVDRI.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#292 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUFH5JUJ344W4BQ7ACD6ZY3TVMRCRANCNFSM45JAA7ZQ> .

[ranjanan]

Hey Shrushti,

I can't see the attachments. You're going to have to either attach them on Github or send a google drive link. Please be sure to include all your INI, focal points files, reclass table, and other things. If you did the reclassification in Circuitscape itself, you may be running into #231

[ModiShrushti]

I have gnarly tool for final file. I am attaching all of them here. inputvariable_r_sum.asc <https://drive.google.com/file/d/1q-crCniyt-7ToOJVGudWNZaWWm3XgDUT/view?usp=drive_web> poptignode2.asc <https://drive.google.com/file/d/1Jh752P9nfEh7SKSZ8gRNLo6s2atFIYQE/view?usp=drive_web> sumtest <https://drive.google.com/file/d/1tdODxfi90L7ATfzjyEy2YNbCzoDgQ0PM/view?usp=drive_web> Shrushti Modi Ph.D. Scholar, Dept. of Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun Ph: +917088383245 Email Address: ***@***.***, ***@***.***

…

On Wed, Jun 30, 2021 at 9:39 PM Ranjan Anantharaman < ***@***.***> wrote: Hey Shrushti, I can't see the attachments. You're going to have to either attach them on Github or send a google drive link. Please be sure to include all your INI, focal points files, reclass table, and other things. If you did the reclassification in Circuitscape itself, you may be running into #231 <#231> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#292 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUFH5JR7XFTMUIEGTQRVFSLTVM6TFANCNFSM45JAA7ZQ> .

[ranjanan]

@ModiShrushti I get "AccessDenied" on your files. Could you enable access to them?

[ranjanan]

@ModiShrushti another follow up.

[ranjanan]

Closing this for now. Please reopen if there's an issue