# Urban flood risk mitigation, soil group raster error? **URL:** \ **Category:** Software Support\ **Tags:** urban-flood\ **Created:** [February 10, 2023, 9:56am UTC](https://community.naturalcapitalalliance.org/t/urban-flood-risk-mitigation-soil-group-raster-error/3407 "2023-02-10T09:56:48Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![JosephFreimond](https://avatars.discourse-cdn.com/v4/letter/j/97f17d/32.png) [@JosephFreimond](https://community.naturalcapitalalliance.org/u/JosephFreimond)\ **Post date:** [February 10, 2023, 9:56am UTC](https://community.naturalcapitalalliance.org/t/urban-flood-risk-mitigation-soil-group-raster-error/3407/1 "2023-02-10T09:56:48Z")
Hello, I am trying to run the urban flood risk mitigation model for the study area of Johannesburg, South Africa. The software allows me to run the model using my data inputs, however I keep receiving errors, which I will paste below. I have tried several times to change the soil group raster, but I always run into the same error, despite the fact that my raster appears to only contain values within the permitted range (1,2,3,4). If anyone could help me with this I would be greatly appreciative. 02/10/2023 11:35:45 natcap.invest.utils Level 100 Writing log messages to [/Users/josephfreimond/Desktop/INVEST OUTPUTS/InVEST-natcap.invest.urban\_flood\_risk\_mitigation-log-2023-02-10–11\_35\_45.txt] 02/10/2023 11:35:45 **main** Level 100 Starting model with parameters: Arguments for InVEST natcap.invest.urban\_flood\_risk\_mitigation 3.12.1: aoi\_watersheds\_path /Volumes/JOE USB/inVest runoff Inputs/JHB\_Watersheds\_Study Area.shp built\_infrastructure\_vector\_path curve\_number\_table\_path /Users/josephfreimond/Desktop/DEA\_Biophysical\_Table\_INvest\_Test.csv infrastructure\_damage\_loss\_table\_path lulc\_path /Volumes/JOE USB/inVest runoff Inputs/dea\_land\_use\_raster.tif n\_workers -1 rainfall\_depth 12 results\_suffix soils\_hydrological\_group\_raster\_path /Volumes/JOE USB/inVest runoff Inputs/scs\_soil\_class\_test.tif workspace\_dir /Users/josephfreimond/Desktop/INVEST OUTPUTS 02/10/2023 11:35:45 natcap.invest.validation INFO Starting whole-model validation with ARGS\_SPEC 02/10/2023 11:35:45 pygeoprocessing.geoprocessing INFO starting stats\_worker 02/10/2023 11:35:45 pygeoprocessing.geoprocessing INFO started stats\_worker \ 02/10/2023 11:35:45 pygeoprocessing.geoprocessing ERROR exception encountered in raster\_calculator Traceback (most recent call last): File “natcap/invest/urban\_flood\_risk\_mitigation.py”, line 809, in \_lu\_to\_cn\_op File “\< **array\_function** internals\>”, line 180, in choose File “numpy/core/fromnumeric.py”, line 429, in choose File “numpy/core/fromnumeric.py”, line 57, in \_wrapfunc ValueError: invalid entry in choice array During handling of the above exception, another exception occurred: Traceback (most recent call last): File “pygeoprocessing/geoprocessing.py”, line 443, in raster\_calculator File “natcap/invest/urban\_flood\_risk\_mitigation.py”, line 816, in \_lu\_to\_cn\_op ValueError: invalid entry in choice array Check that the Soil Group raster does not contain values other than (1, 2, 3, 4) 02/10/2023 11:35:45 pygeoprocessing.geoprocessing INFO Waiting for raster stats worker result. 02/10/2023 11:35:45 pygeoprocessing.geoprocessing\_core WARNING No valid pixels were received, sending None. 02/10/2023 11:35:45 taskgraph.Task ERROR Something went wrong when adding task create Curve Number raster (1), terminating taskgraph. Traceback (most recent call last): File “natcap/invest/urban\_flood\_risk\_mitigation.py”, line 809, in \_lu\_to\_cn\_op File “\< **array\_function** internals\>”, line 180, in choose File “numpy/core/fromnumeric.py”, line 429, in choose File “numpy/core/fromnumeric.py”, line 57, in \_wrapfunc ValueError: invalid entry in choice array During handling of the above exception, another exception occurred: Traceback (most recent call last): File “taskgraph/Task.py”, line 674, in add\_task File “taskgraph/Task.py”, line 1093, in \_call File “pygeoprocessing/geoprocessing.py”, line 443, in raster\_calculator File “natcap/invest/urban\_flood\_risk\_mitigation.py”, line 816, in \_lu\_to\_cn\_op ValueError: invalid entry in choice array Check that the Soil Group raster does not contain values other than (1, 2, 3, 4) 02/10/2023 11:35:45 natcap.invest.utils ERROR Exception while executing natcap.invest.urban\_flood\_risk\_mitigation Traceback (most recent call last): File “natcap/invest/urban\_flood\_risk\_mitigation.py”, line 809, in \_lu\_to\_cn\_op File “\< **array\_function** internals\>”, line 180, in choose File “numpy/core/fromnumeric.py”, line 429, in choose File “numpy/core/fromnumeric.py”, line 57, in \_wrapfunc ValueError: invalid entry in choice array During handling of the above exception, another exception occurred: Traceback (most recent call last): File “natcap/invest/utils.py”, line 164, in prepare\_workspace File “invest/cli.py”, line 486, in main File “natcap/invest/urban\_flood\_risk\_mitigation.py”, line 232, in execute File “taskgraph/Task.py”, line 674, in add\_task File “taskgraph/Task.py”, line 1093, in \_call File “pygeoprocessing/geoprocessing.py”, line 443, in raster\_calculator File “natcap/invest/urban\_flood\_risk\_mitigation.py”, line 816, in \_lu\_to\_cn\_op ValueError: invalid entry in choice array Check that the Soil Group raster does not contain values other than (1, 2, 3, 4) 02/10/2023 11:35:45 natcap.invest.utils INFO Elapsed time: 0.41s 02/10/2023 11:35:45 natcap.invest.utils INFO Execution finished Here I will attach the data inputs I am using: Land use raster: [dea-export\_raster.tif](https://community.naturalcapitalalliance.org/uploads/short-url/1vQP6LVD1sJ2sTzKYxewnwbXNp0.tif) (18.8 KB) Soil raster (I have tried multiple versions of this, but this is the one I am currently trying to use): [scs\_soil\_class\_test.tif](https://community.naturalcapitalalliance.org/uploads/short-url/iErkAaD11rJxdr6FTY9wCOyAUtD.tif) (146.6 KB) Rainfall depth: 12mm The area of interest is a shapefile of sub-watersheds in Johannesburg. Thank you so much. ---
**Author:** ![swolny](https://yyz1.discourse-cdn.com/flex031/user_avatar/community.naturalcapitalalliance.org/swolny/32/181_2.png) [@swolny](https://community.naturalcapitalalliance.org/u/swolny)\ **Post date:** [February 13, 2023, 4:54pm UTC](https://community.naturalcapitalalliance.org/t/urban-flood-risk-mitigation-soil-group-raster-error/3407/2 "2023-02-13T16:54:49Z")
Welcome to the forum @JosephFreimond, and thanks for posting your logfile and data. Looking at _scs\_soil\_class\_test.tif_ in a GIS, it contains values of 0, 2, 3 and 4. It looks like 0 might be a background value, not intended to be valid soil group data. So you might try setting your NoData value to 0 and see if that helps. ~ Stacie ---
**Author:** ![JosephFreimond](https://avatars.discourse-cdn.com/v4/letter/j/97f17d/32.png) [@JosephFreimond](https://community.naturalcapitalalliance.org/u/JosephFreimond)\ **Post date:** [February 15, 2023, 7:47am UTC](https://community.naturalcapitalalliance.org/t/urban-flood-risk-mitigation-soil-group-raster-error/3407/3 "2023-02-15T07:47:07Z")
Hello Stacie, thank you so much for your help. I managed to get it to work. ---
**Author:** ![Maurizia](https://avatars.discourse-cdn.com/v4/letter/m/7ab992/32.png) [@Maurizia](https://community.naturalcapitalalliance.org/u/Maurizia)\ **Post date:** [May 1, 2023, 10:51am UTC](https://community.naturalcapitalalliance.org/t/urban-flood-risk-mitigation-soil-group-raster-error/3407/4 "2023-05-01T10:51:00Z")
Hi everyone, I am running into the same problem plus a different one. My model is for the subwatersheds of Stockholm, Sweden. When trying to run the model I am getting the following log: 05/01/2023 11:54:16 osgeo WARNING [errno 1] The definition of projected CRS EPSG:3006 got from GeoTIFF keys is not the same as the one from the EPSG registry, which may cause issues during reprojection operations. Set GTIFF\_SRS\_SOURCE configuration option to EPSG to use official parameters (overriding the ones from GeoTIFF keys), or to GEOKEYS to use custom values from GeoTIFF keys and drop the EPSG code. This message is repeated 9 times and then the log goes on as follows: 05/01/2023 11:54:20 pygeoprocessing.geoprocessing INFO 2 of 2 aligned: aligned\_soils\_hydrological\_group\_UFRM\_noEcon\_1.tif 05/01/2023 11:54:20 pygeoprocessing.geoprocessing INFO aligned all 2 rasters. 05/01/2023 11:54:20 pygeoprocessing.geoprocessing INFO starting stats\_worker 05/01/2023 11:54:20 pygeoprocessing.geoprocessing INFO started stats\_worker \ 05/01/2023 11:54:20 pygeoprocessing.geoprocessing ERROR exception encountered in raster\_calculator Traceback (most recent call last): File “natcap\invest\urban\_flood\_risk\_mitigation.py”, line 910, in \_lu\_to\_cn\_op File “\< **array\_function** internals\>”, line 200, in choose File “numpy\core\fromnumeric.py”, line 429, in choose File “numpy\core\fromnumeric.py”, line 57, in \_wrapfunc ValueError: invalid entry in choice array During handling of the above exception, another exception occurred: Traceback (most recent call last): File “pygeoprocessing\geoprocessing.py”, line 517, in raster\_calculator File “natcap\invest\urban\_flood\_risk\_mitigation.py”, line 917, in \_lu\_to\_cn\_op ValueError: invalid entry in choice array Check that the Soil Group raster does not contain values other than (1, 2, 3, 4) 05/01/2023 11:54:20 pygeoprocessing.geoprocessing INFO Waiting for raster stats worker result. 05/01/2023 11:54:20 pygeoprocessing.geoprocessing\_core WARNING No valid pixels were received, sending None. 05/01/2023 11:54:20 taskgraph.Task ERROR Something went wrong when adding task create Curve Number raster (1), terminating taskgraph. Traceback (most recent call last): File “natcap\invest\urban\_flood\_risk\_mitigation.py”, line 910, in \_lu\_to\_cn\_op File “\< **array\_function** internals\>”, line 200, in choose File “numpy\core\fromnumeric.py”, line 429, in choose File “numpy\core\fromnumeric.py”, line 57, in \_wrapfunc ValueError: invalid entry in choice array During handling of the above exception, another exception occurred: Traceback (most recent call last): File “taskgraph\Task.py”, line 674, in add\_task File “taskgraph\Task.py”, line 1093, in \_call File “pygeoprocessing\geoprocessing.py”, line 517, in raster\_calculator File “natcap\invest\urban\_flood\_risk\_mitigation.py”, line 917, in \_lu\_to\_cn\_op ValueError: invalid entry in choice array Check that the Soil Group raster does not contain values other than (1, 2, 3, 4) 05/01/2023 11:54:20 natcap.invest.utils ERROR Exception while executing natcap.invest.urban\_flood\_risk\_mitigation Traceback (most recent call last): File “natcap\invest\urban\_flood\_risk\_mitigation.py”, line 910, in \_lu\_to\_cn\_op File “\< **array\_function** internals\>”, line 200, in choose File “numpy\core\fromnumeric.py”, line 429, in choose File “numpy\core\fromnumeric.py”, line 57, in \_wrapfunc ValueError: invalid entry in choice array During handling of the above exception, another exception occurred: Traceback (most recent call last): File “natcap\invest\utils.py”, line 164, in prepare\_workspace File “invest\cli.py”, line 469, in main File “natcap\invest\urban\_flood\_risk\_mitigation.py”, line 333, in execute File “taskgraph\Task.py”, line 674, in add\_task File “taskgraph\Task.py”, line 1093, in \_call File “pygeoprocessing\geoprocessing.py”, line 517, in raster\_calculator File “natcap\invest\urban\_flood\_risk\_mitigation.py”, line 917, in \_lu\_to\_cn\_op ValueError: invalid entry in choice array Check that the Soil Group raster does not contain values other than (1, 2, 3, 4) 05/01/2023 11:54:20 natcap.invest.utils INFO Elapsed time: 5.17s 05/01/2023 11:54:20 natcap.invest.utils INFO Execution finished If I understand correctly, something is off with the coordinate system of my .tif files, and there is a problem with my soil hydrologic raster, that the grouping is not correct. Here already a screenshot of the attribute table of my soil hydrologic raster, as you can see there are two different OIDs for group 4, due to reclassification from B/D and C/D group to D. Is that the potential source of the problem? ![image](https://canada1.discourse-cdn.com/flex031/uploads/naturalcapitalproject/original/2X/e/e03ae32051cd1b928ba96a095d64f37dc5a1ca81.png) Apart from that, here is my other input data: [AoI\_Stockholm\_subwatersheds.zip](https://community.naturalcapitalalliance.org/uploads/short-url/uXrAZaEdDvx4o8dzNGtPORS7sxP.zip) (250.4 KB) Rainfall depth: 105.7 [LC\_Stockholm\_subwatersheds.zip](https://community.naturalcapitalalliance.org/uploads/short-url/cF9HtwMnPL1GFR1R4eTbH8vmdfv.zip) (1.8 MB) [BiophysicalTable\_UFRM\_Stockholm.csv](https://community.naturalcapitalalliance.org/uploads/short-url/tSOAA05TrJeFzqiMT686X3ZJe5Z.csv) (2.7 KB) [SoilGroups\_Stockholm.zip](https://community.naturalcapitalalliance.org/uploads/short-url/2MdO6KBFpsiYUD7l5bi6DEKMH2e.zip) (11.3 KB) I hope this is all the necessary information. Any help with this would be much appreciated, thanks in advance! Maurizia ---
**Author:** ![Maurizia](https://avatars.discourse-cdn.com/v4/letter/m/7ab992/32.png) [@Maurizia](https://community.naturalcapitalalliance.org/u/Maurizia)\ **Post date:** [May 5, 2023, 11:41am UTC](https://community.naturalcapitalalliance.org/t/urban-flood-risk-mitigation-soil-group-raster-error/3407/5 "2023-05-05T11:41:23Z")
Solved! I had overlooked that InVEST is working with numbers from the “Value” column, not with the “HySoilTyp\_”. So after reclassifying the numbers in the “Value” column the model now runs smoothly! ---
**Author:** ![system](https://canada1.discourse-cdn.com/flex031/uploads/naturalcapitalproject/original/2X/8/8d95591aa074da87ea0fdd61ca47c1c3c0588aa7.png) [@system](https://community.naturalcapitalalliance.org/u/system)\ **Post date:** [May 12, 2023, 11:41am UTC](https://community.naturalcapitalalliance.org/t/urban-flood-risk-mitigation-soil-group-raster-error/3407/6 "2023-05-12T11:41:33Z")
Closed on May 12, 2023, 11:41am UTC This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.