Writing maps to disk #181
Comments
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Can you paste the contents of the INI file here please? |
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Hi @ranjanan, thanks for getting back to me. The contents of the INI file are the same as in I have flagged 'write_volts_maps' to [Options for advanced mode]
ground_file_is_resistances = False
source_file = (Browse for a current source file)
remove_src_or_gnd = keepall
ground_file = (Browse for a ground point file)
use_unit_currents = False
use_direct_grounds = False
[Calculation options]
low_memory_mode = False
solver = cg+amg
print_timings = False
[Options for pairwise and one-to-all and all-to-one modes]
included_pairs_file = None
use_included_pairs = False
point_file = C:/Users/simon.tarr/Documents/Circuitscape.jl/test/input/raster/one_to_all/2/points.asc
[Output options]
write_cum_cur_map_only = False
log_transform_maps = False
output_file = C:/Users/simon.tarr/Documents/Circuitscape.jl/test/output/allToOneVerify2.asc
write_max_cur_maps = False
write_volt_maps = True
set_null_currents_to_nodata = False
set_null_voltages_to_nodata = False
compress_grids = False
write_cur_maps = False
[Short circuit regions (aka polygons)]
use_polygons = True
polygon_file = C:/Users/simon.tarr/Documents/Circuitscape.jl/test/input/raster/one_to_all/2/polygons.asc
[Connection scheme for raster habitat data]
connect_four_neighbors_only = True
connect_using_avg_resistances = True
[Habitat raster or graph]
habitat_file = C:/Users/simon.tarr/Documents/Circuitscape.jl/test/input/raster/one_to_all/2/cellmap.asc
habitat_map_is_resistances = False
[Options for one-to-all and all-to-one modes]
use_variable_source_strengths = False
variable_source_file = None
[Version]
version = unknown
[Mask file]
use_mask = False
mask_file = None
[Circuitscape mode]
data_type = raster
scenario = all-to-oneI've noticed that the file paths |
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No the scenario is totally fine. Could you the paste the full stack trace of the error you get when you run |
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As requested: |
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Here is some extra information which may help with troubleshooting. Using Circuitscape v4.0 (GUI) and the toy raster files which you can download from this gist, I can generate a sensible looking current flow output between two nodes. Here's a screen grab of the v4.0 settings I'm using:
I get the following output when plotting the current output in R:
If I run the same analysis using Circuitscape v5.5.0 GUI (as downloaded here) I get a ton of error messages within the Julia shell. Here's a screen grab of the v5.5.0 GUI with the settings I'm using:
I do not get any current output files in the output folder that I have specified. I do get a file (which I have named output.out) which seems to show the input settings for me (I guess this is just a general log of the initial settings): This is the mess from the Julia shell which runs in the background: If I run the same analysis using the Julia command line My biggest concern in that output is the program's insistence in reading and writing to C:/Users/ as it generates this error: |
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Thank you for the detailed bug report! |
Merged
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Yeah, I found the bug. It's messing up with the |
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@simon-tarr I've fixed this via the PR and tagged a new release. I'll ping you here once the release is registered, and then you'll be able to use it. |
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@ranjanan that's great thank you very much for the speedy fix. |
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@simon-tarr the new version just got registered. Could you do |
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Hi @ranjanan I've updated to v.5.5.2 and restarted Julia, as requested. I've hit a new |
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Hello @ranjanan I was wondering if there was any update to this? I appreciate your assistance thus far and many thanks in advance. |
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Hi @simon-tarr, sorry about the new error you're facing. I didn't fix all instances of that bug in the code. I have a couple of urgent thiings to do right now, and will get to this in the weekend. Thank you for your patience thus far! |
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Hi @ranjanan no worries. As this issue is set as closed, I was just making sure that it hadn't been forgotten about. Looking forward to the fix so that I can explore the model. |
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Hi @ranjanan I'm getting a couple of new errors now, I'm afraid. The first error occurred reasonably quickly after submitting the job: The second error occurred much later in the analysis (after I re-ran it with the same .ini file and rasters) and the stack track is much shorter: This second error appears to be occurring immediately after solving the final pair in my example. Any ideas what may be causing this? I'm running a pairwise raster analysis which worked using Circuitscape v4.0 (with the same resistance and focal point files). Many thanks |
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Hi @simon-tarr I tagged another release v5.5.3 recently. Can you update Circuitscape and check if this particular issue is resolved? |
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For the new errors, could you please open a new issue? My semester is over at the end of this week and I'll make sure you have a Circuitscape that works properly. |
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Hello,
Very new to Julia and Circuitscape.jl, so please forgive a very basic question. I'm wondering how I can write raster images of the outputs? I've opened one of the example .ini files in
input/raster/all_to_one/2/allToOneVerify2.iniand there are various flags within the output section which are all set to 'false'. I've tried to set some of these flags to 'true' and I either get no outputs from running the .ini file or I get an error of:ERROR: SystemError: opening file "C:/Users/simon_curmap_1.asc": Permission deniedI'm not sure where the
simon_curmap_1.ascbit comes from as nowhere in the .ini file have I specified the pathC:/users/or a file name ofsimon_curmap_1.asc(In fact, the .ini file is exactly as cloned from Github, except I've toggled a few flags i.e. none of the file paths have been changed).Is there a full tutorial online using circuitscape.jl that I could perhaps follow? I am aware of the rather comprehensive documentation at https://circuitscape.org/docs/ for the GUI version 4.0 (and some help regarding Python) but there doesn't appear to be any documentation on using Circuitscape in Julia.
Thanks in advance for your help.
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