There seems to be some confusion about the nature of this repo. As you are aware, this repo only contains the Python front-end for WhiteboxTools and is not the WhiteboxTools project itself. Is it possible to make this distinction clearer on the homepage so that people don't continue to report issues here rather than at jblindsay/whitebox-tools? I would suggest 1) renaming of this repo to something like whitebox-python, 2) making the fact that this is a frontend only clearer (although I know that it is already there in the description), 3) adding a statement about issuing tool functioning specific errors to the appropriate repository.

• whitebox version: 2.3.4
• Python version: 3.11.9
• Operating System: ubuntu 20.04

Description

I have generated a tiff with wbt.fill_missing_data, however wbt itself can't parse result which it generated.

What I Did

dem='mosaic_hjlm_hgts.tif'
wbt = whitebox.WhiteboxTools()
work_dir = pathlib.Path(dem).parent.absolute()
wbt.set_working_dir(work_dir)
dem_fn = dem.split('.')[0]
wbt.fill_missing_data(i=dem, output=os.path.join(work_dir, f"{dem_fn}_fillmissingdata.tif"), filter=11, weight=2.0, no_edges=True)
wbt.fill_depressions_wang_and_liu(f"{dem_fn}_fillmissingdata.tif", f"{dem_fn}_filldepression.tif", fix_flats=True, flat_increment=None)

And this is log:

./whitebox_tools --run="FillMissingData" --wd="/home/username/interim/tests" --input='mosaic_hjlm_hgts.tif' --output='/home/username/interim/tests/mosaic_hjlm_hgts_fillmissingdata.tif' --filter=11 --weight=2.0 --no_edges -v --compress_rasters=False
******************************
* Welcome to FillMissingData *
* Powered by WhiteboxTools   *
* www.whiteboxgeo.com        *
******************************
Reading data...
Finding edge-connected NoData values...
Finding edge-connected NoData cells: 0%
Finding edge-connected NoData cells: 1%
……
Finding edge-connected NoData cells: 39%
Interpolating data holes...
Interpolating data holes: 0%
Interpolating data holes: 1%
……
Interpolating data holes: 99%
Interpolating data holes: 100%
Performing analysis: 0%
Performing analysis: 1%
……
Performing analysis: 99%
Performing analysis: 100%
Saving data...
Output file written
Elapsed Time (excluding I/O): 9min 44.703s

./whitebox_tools --run="FillDepressionsWangAndLiu" --wd="/home/username/interim/tests" --dem='mosaic_hjlm_hgts_fillmissingdata.tif' --output='mosaic_hjlm_hgts_filldepression.tif' --fix_flats -v --compress_rasters=False
****************************************
* Welcome to FillDepressionsWangAndLiu *
* Powered by WhiteboxTools             *
* www.whiteboxgeo.com                  *
****************************************
Reading data...
thread 'main' panicked at whitebox-raster/src/geotiff/ifd.rs:115:23:
**Error converting TAG(34737) to ASCII (value=[34, 195, 44, 7, 2, 0, 0, 0]) invalid utf-8 sequence of 1 bytes from index 1**
stack backtrace:
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.

So how to solve this problem?

whitebox version: whitebox-workflows 1.1.0
Python version: 3.11
Operating System: Windows

I am trying to generate contour curves from the following code:

import whitebox_workflows as wbw
wbe = wbw.WbEnvironment()

raster = wbe.read_raster('test.tif')

wbe.contours_from_raster(
raster,
'contours.shp',
contour_interval = 10,
base_contour = 57
)

However, the following error appears:
TypeError: WbEnvironment.contours_from_raster() got multiple values for argument 'contour_interval'

I tried using the default value, however the following error appears:
TypeError: argument 'contour_interval': must be real number, not str

• whitebox version: (latest, as of sept 2020)
• Python version: 3.7
• Operating System: Ubuntu 18.04

Description

I tried installing the latest version of Whitebox using:
pip install whitebox

It seems to install, but it won't run because I don't have glibc 2.29 ... (I can't even check the version)
error:
./whitebox_tools: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by ./whitebox_tools)

I'm running GLIBC 2.27... is upgrading to 2.29 really the only way to get whitebox working?

• whitebox version: 2.1.1
• Python version: 3.9.10
• Operating System: Ubuntu 20.04 under Windows WSL2

Description

Running the ConditionalEvaluation tool (also applies to RasterCalculator as per jblindsay/whitebox-tools#202) requires a manual permission change on the whitebox library folders and files. Without this, the tool crashes and throws a denied permissions exception.

When WBT executables are downloaded upon the first import whitebox, some permissions are rw-r--r-- (644), other are rwxr-xr-x (755). Changing all the whitebox/ folder, subfolders and files to rwxr-xr-x allowed the tool to run properly.

What I Did

import whitebox
wbt = whitebox.WhiteboxTools()

wbt.conditional_evaluation(
    i = "/path/to/raster/input.tif",
    output = "/path/to/raster/output.tif",
    statement = "'value >= 3'",
    true = 1,
    false = "nodata"
)

>>> ./whitebox_tools --run="ConditionalEvaluation" --input='/path/to/raster/input.tif' --statement='value >= 3' --true='1' --false='nodata' --output='/path/to/raster/output.tif'

>>> thread 'main' panicked at 'failed to execute process: Os { code: 13, kind: PermissionDenied, message: "Permission denied" }', whitebox-tools-app/src/tools/mod.rs:1264:26
>>> note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
>>> 0

Permissions change on the whitebox library folder and files, in your Python environment folder:

chmod -R 755 /path_to_conda_env/lib/python3.9/site-packages/whitebox/

wbt.conditional_evaluation(
    i = "/path/to/raster/input.tif",
    output = "/path/to/raster/output.tif",
    statement = "'value >= 3'",
    true = 1,
    false = "nodata"
)

>>> ./whitebox_tools --run="ConditionalEvaluation" --input='/path/to/raster/input.tif' --statement='value >= 3' --true='1' --false='nodata' --output='/path/to/raster/output.tif'
>>> (Tool runs normally).

• whitebox version:
• Python version: 2.3.3
• Operating System: Unix

This was first posted on the whitebox tracker (jblindsay/whitebox-tools#411)

Description

I noticed that since the recent release 2.3.3 on PyPi (https://pypi.org/project/whitebox/2.3.3/) a script of mine fails with the following whitebox debug logs

./whitebox_tools --run="ConditionalEvaluation" --wd="/celery" --input='a.tif' --statement=value == minvalue && value < -1000 - -true='b.tif' -v --compress_rasters=True
thread 'main' panicked at whitebox-tools-app/src/main.rs:72:21:
Unrecognized tool name ConditionalEvaluation.
run with `RUST_BACKTRACE=1` environment variable to display a backtrace

What I Did

The code has not changed and calls this function as follows:

wbt.conditional_evaluation(
                                "a.tif",
                                "b.tif",
                                statement="value == minvalue && value < -1000",
                                true="source.tif",
                                false="a.tif",
                            )

What could the issue be?

• whitebox version: 2.3.4
• Python version: 3.11.9
• Operating System: ubuntu 20.04

I want to extract d8 flow direction from my DEM file, and my file's path is:

/home/username/interim_dir/tests/merged_hjlm.tif

So I wrote this code:

dem = 'merged_hjlm.tif'
wbt = whitebox.WhiteboxTools()
# working_dir is /home/username/interim_dir/tests
wbt.set_working_dir(pathlib.Path(dem).parent.absolute())
wbt.fill_missing_data(i=dem, output="fillmissingdata.tif", filter=11, weight=2.0, no_edges=True)
wbt.fill_depressions_wang_and_liu("fillmissingdata.tif", "filldepression.tif", fix_flats=True, flat_increment=None,  # max_depth=None)
wbt.d8_pointer("filldepression.tif", "d8pointer.tif", esri_pntr=False)

However this process ended unnormally, and log is:

================== 1 passed, 3 warnings in 594.59s (0:09:54) ===================
./whitebox_tools --run="FillMissingData" --wd="/home/username/interim_dir/tests" --input='merged_hjlm.tif' --output='fillmissingdata.tif' --filter=11 --weight=2.0 --no_edges -v --compress_rasters=False

******************************
* Welcome to FillMissingData *
* Powered by WhiteboxTools   *
* www.whiteboxgeo.com        *
******************************
Reading data...
./whitebox_tools --run="FillDepressionsWangAndLiu" --wd="/home/username/interim_dir/tests" --dem='fillmissingdata.tif' --output='filldepression.tif' --fix_flats -v --compress_rasters=False

****************************************
* Welcome to FillDepressionsWangAndLiu *
* Powered by WhiteboxTools             *
* www.whiteboxgeo.com                  *
****************************************
Reading data...
thread 'main' panicked at whitebox-tools-app/src/main.rs:72:21:
No such file or directory (os error 2)
stack backtrace:
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
./whitebox_tools --run="D8Pointer" --wd="/home/username/interim_dir/tests" --dem='filldepression.tif' --output='d8pointer.tif' -v --compress_rasters=False

****************************
* Welcome to D8Pointer     *
* Powered by WhiteboxTools *
* www.whiteboxgeo.com      *
****************************
Reading data...
thread 'main' panicked at whitebox-tools-app/src/main.rs:72:21:
No such file or directory (os error 2)
stack backtrace:
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.

You can see fillmissingdata.tif isn't generated in my working dir so following steps can't run.
How to solve the problem? Hope for your reply.

• whitebox version: 2.0.3
• Python version: 3.9
• Operating System: RedHat Enterprise

Description

After using the whitebox tools clip function, the output lidar file seems to be corrupted. Attached is a zip folder with the lidar.laz tile. Also, here is an example error message I get when viewing the output file in lastools.
'chunk table and XXXXXXXXXX bytes are missing' is the common error message from the output file.

What I Did

wbt.clip_lidar_to_polygon(
    i="NEON_D01_HARV_DP1_732000_4713000_classified_point_cloud_colorized.laz", 
    polygons="towerPoly.shp", 
    output="lidarAOI.laz"
)

Thanks!

Any use of the python library attempts to download a tarball into a read only directly on my system. I already have whitebox_tools on my path, so I do not want to download it again.

1. The file should be downloaded into one of the XDG_* directories rather than into this read-only directory.
2. The file wouldn't work even if it was downloaded on my OS so I would prefer to have the option to skip this step.

[nix-shell:~/whitebox-python]$ ./lidar.py 
Downloading WhiteboxTools pre-compiled binary for first time use ...
Unexpected error: <class 'OSError'>
Traceback (most recent call last):
  File "./lidar.py", line 5, in <module>
    from whitebox.whitebox_tools import WhiteboxTools
  File "/nix/store/cnzdmpl269k27j4j28l0xmi39yr278qw-python3-3.7.7-env/lib/python3.7/site-packages/whitebox/__init__.py", line 10, in <module>
    from .wb_runner import Runner
  File "/nix/store/cnzdmpl269k27j4j28l0xmi39yr278qw-python3-3.7.7-env/lib/python3.7/site-packages/whitebox/wb_runner.py", line 33, in <module>
    wbt = WhiteboxTools()
  File "/nix/store/cnzdmpl269k27j4j28l0xmi39yr278qw-python3-3.7.7-env/lib/python3.7/site-packages/whitebox/whitebox_tools.py", line 144, in __init__
    download_wbt()
  File "/nix/store/cnzdmpl269k27j4j28l0xmi39yr278qw-python3-3.7.7-env/lib/python3.7/site-packages/whitebox/whitebox_tools.py", line 55, in download_wbt
    urllib.request.urlretrieve(url, zip_name)   # Download WhiteboxTools
  File "/nix/store/syqcp8zb9c0vxj2sx6jbv5f9q7yki4jz-python3-3.7.7/lib/python3.7/urllib/request.py", line 257, in urlretrieve
    tfp = open(filename, 'wb')
OSError: [Errno 30] Read-only file system: '/nix/store/cnzdmpl269k27j4j28l0xmi39yr278qw-python3-3.7.7-env/lib/python3.7/site-packages/whitebox/WhiteboxTools_linux_amd64.tar.xz'

• whitebox version:2.0.0
• Python version:3.8
• Operating System: Scientific Linux 7.9, 'Nitrogen'

Description

I have developed a program that uses the python whitebox module on my own computer that uses Centos 8, but when I try to install on our scientific linux machines I get the following error:
./whitebox_tools: /lib64/libm.so.6: version GLIBC_2.27' not found (required by ./whitebox_tools) ./whitebox_tools: /lib64/libc.so.6: version GLIBC_2.18' not found (required by ./whitebox_tools)

What I Did

I've seen this thread, which seems to address the same issue:
(https://github.com/jblindsay/whitebox-tools/issues/112)
but the solution is for the whitebox tool and not the python module and I haven't been able to adapt it to my own situation. Is it possible, or am I barking up the wrong tree?

Thanks in advance

• whitebox version: v0.13.0
• Python version:
  • Python 3.6.7 (v3.6.7:6ec5cf24b7, Oct 20 2018, 03:02:14)
  • [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
• Operating System: MacOS Mojave 10.14.2

Description

Describe what you were trying to get done.

I have a small, 200 MB, colorized, indoor lidar point cloud of a conference room. I'm trying to extract a slice of it.

The lidar_info output is the following:

File Signature: LASF
File Source ID: 0
Global Encoding:
GPS time=GpsWeekTime,
Waveform data internal=false,
Waveform data external=false,
Return data synthetic=false,
CRS method=WellKnownText
Project ID (GUID): {0-0-0-00-000000}
System ID: EXTRACTION
Generating Software: WhiteboxTools 
Las Version: 1.3
File Creation Day/Year: 18/2019
Header Size: 235
Offset to Points: 440
Number of VLRs: 2
Point Format: 3
Point Record Length: 34
Num. of Points (32-bit): 5869712
Number of Points by Return: [11739424, 0, 0, 0, 0]
X Scale Factor: 0.0001
Y Scale Factor: 0.0001
Z Scale Factor: 0.0001
X Offset: -19.8205
Y Offset: -44.6813
Z Offset: 0.15910000000000002
Max X: 21.220100000000002
Min X: -19.8205
Max Y: 82.7065
Min Y: -44.6813
Max Z: 7.1942
Min Z: 0.15910000000000002
Waveform Data Start: 0
Min Intensity: 514
Max Intensity: 63737

Tell us what happened, what went wrong, and what you expected to happen.

When I try to use the lidar_elevation_slice command, it outputs a file the exact same size and no points have been removed as far as I can tell.

What I Did

Here is the command I'm running:

import whitebox
wbt = whitebox.WhiteboxTools()
wbt.set_working_dir(os.getcwd())
wbt.lidar_elevation_slice("test1.las", "test2.las", minz=3.0, maxz=5.0, cls=False)

The command-line output looks ok:

./whitebox_tools --run="LidarElevationSlice" --wd="<full path removed>/Data" --input='test1.las' --output='test2.las' --minz='3.0' --maxz='5.0' --inclassval=2 --outclassval=1 -v

***********************************
* Welcome to lidar_elevation_slice *
************************************
Reading input LAS file...
Performing analysis...
Saving data: 0%
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Writing output LAS file...
Complete!
0

But I get the entire file and not a slice.

What am I doing wrong?

Thanks in advance!

• whitebox version: 2.1.4
• Python version: 3.8
• Operating System: Scientific Linux (Rocky 8)

Description

This is probably not an issue with the tools, but am struggling to extract a continuous stream network from a DEM. I've been experimenting with it for some time but have been unable to improve on what I have now, which is 95% of a drainage network, but with intermittent gaps. The gaps occur where the downhill slope flattens off, even though there is still an obvious channel. I'm guessing that issue originates at the breach_depressions_least_cost stage, but I've experimented with the parameters and can't improve on what I have now, which is no good.

What I Did

dem.zip

My method is:

breach_depressions_least_cost: dist=10, max_cost=100, min_dist=True, fill=True,
d8_flow_accumulation: out_type="catchment area"
extract_streams: threshold=3000

Regarding the parameters. I've experimented with a wide range of values for breach depressions dist and max_cost. The values I've shown here work for most of the DEM, but still leave gaps in the stream network.

Any help would be appreciated.

Thanks,
Rick

• whitebox version: 1.2.0
• Python version: 3.5
• Operating System: ubuntu 16.04

Description

Describe what you were trying to get done.
.Traceback (most recent call last):
File "", line 1, in
File "/home/Documents/venvs/base_all/lib/python3.5/site-packages/whitebox/wb_runner.py", line 1316, in Runner
wbr = WbRunner(tool_name)
File "/home/Documents/venvs/base_all/lib/python3.5/site-packages/whitebox/wb_runner.py", line 767, in init
self.create_widgets()
File "/home/Documents/venvs/base_all/lib/python3.5/site-packages/whitebox/wb_runner.py", line 789, in create_widgets
self.get_tools_list()
File "/home/Documents/venvs/base_all/lib/python3.5/site-packages/whitebox/wb_runner.py", line 1022, in get_tools_list
self.tool_name = self.tools_list[0]
IndexError: list index out of range

What I Did

whitebox.Runner()

Paste the command(s) you ran and the output.
If there was a crash, please include the traceback here.

• whitebox version: 2.3.1
• Python version: 3.11.0
• Operating System: Windows 10 Enterprise

Description

Hi,
I installed whitebox from conda.

When I run any command (e.g., wbt.d8_pointer, wbt.d8_flow_accumulation, or any other) from a python script I get the following error:
AttributeError: module 'whitebox' has no attribute 'flow_accumulation_full_workflow'

This happen with any command I use.

When I run instead the GUI wbt.Runner() everything works fine and I can correctly do all the operations I need from the GUI.

I tried to uninstall and reinstall the package, to install it in a separate environment, but still no changes.

What is it happening? How could I solve the issue? (I would like to write a sequence of operations that I can run every time I need, without having to repeat it "by hand" every time using the GUI.

Thanks a lot for your help!
Stefano

Description

Hello! Mr.WU. When I turn a single pixel wide raster into a line vector, the previously continuous closed shape becomes a broken line segment. How to avoid this problem?

code

from WBT.whitebox_tools import WhiteboxTools

if __name__ == "__main__":
    rasterPath = "/home/BE/results/cq_test_edge.tif"
    outputPath = "/home/BE/results/cq_test_edge4.shp"
    wbt = WhiteboxTools()

    wbt.raster_to_vector_lines(rasterPath, outputPath)

• whitebox version: 2.0.1
• Python version: 3.7.10
• Operating System: Windows 10 Education 64-bit

Description

Unexpected error when I ran whitebox.WhiteboxTools()

What I Did

import whitebox
print(whitebox.__version__)
wbt = whitebox.WhiteboxTools()

2.0.1
Unexpected error: <class 'urllib.error.URLError'>
URLError: <urlopen error unknown url type: hhttps>

Conda info

     active environment : tiruan
    active env location : F:\Anaconda3\envs\tiruan
            shell level : 1
       user config file : C:\Users\Muhammad Ichsan\.condarc
 populated config files : C:\Users\Muhammad Ichsan\.condarc
          conda version : 4.10.3
    conda-build version : 3.21.4
         python version : 3.7.10.final.0
       virtual packages : __cuda=10.2=0
                          __win=0=0
                          __archspec=1=x86_64
       base environment : F:\Anaconda3  (writable)
      conda av data dir : F:\Anaconda3\etc\conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/win-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/win-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
          package cache : F:\Anaconda3\pkgs
                          C:\Users\Muhammad Ichsan\.conda\pkgs
                          C:\Users\Muhammad Ichsan\AppData\Local\conda\conda\pkgs
       envs directories : F:\Anaconda3\envs
                          C:\Users\Muhammad Ichsan\.conda\envs
                          C:\Users\Muhammad Ichsan\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.7.10 Windows/10 Windows/10.0.16299
          administrator : False
             netrc file : None
           offline mode : False

Additional note : I installed whitebox (with pip) to another conda environment. It gave same error.

• whitebox version: 0.9.0
• Python version: 3.7.3
• Operating System: Windows 10

Description

The whitebox tool "VectorPolygonsToRaster" return a different result compare to the Whitebox GAT -win tool "Vector polygons to raster" . The output .tif has gaps!!!

What I Did

from whitebox import WhiteboxTools

# Set up the environment
wbt = WhiteboxTools()
data_dir = "/../whitebox_issue"
wbt.work_dir = (data_dir) 

i_vector = "poly.shp"
fieldZ = "Value"
out_raster = "poly2raster_PYTHON.tif"

wbt.vector_polygons_to_raster(
    i=i_vector,
    output=out_raster,
    field=fieldZ,
    nodata=True,
    cell_size=1,
   # base=None,
   # callback=default_callback
)

• whitebox version: 2.0.3
• Python version: 3.8
• Operating System: "Rocky Linux 8.5

Description

I am creating drainage lines from an input DEM. I am running the following tools in succession so that the output of a tool becomes the input of the next:

• breach_depressions_least_cost
• d8_pointer
• d8_flow_accumulation
• extract_streams

It all works and I'm happy with the output, but I get a lot of warning messages about resource warnings like the following:

/usr/lib64/python3.8/subprocess.py:946: ResourceWarning: subprocess 2454694 is still running
_warn("subprocess %s is still running" % self.pid,
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/mydata/drainage_lines.py:558: ResourceWarning: unclosed file <_io.TextIOWrapper name=7 encoding='UTF-8'>
wbt.set_verbose_mode(False)

This fills the error log with messages, despite the fact that tool appears to function fine. I've searched for the process ids but they seem to have been closed, despite the message.

Is there a step I need to take after running one tool and before running the next?

• whitebox version: 1.4.0
• Python version: 3.6
• Operating System: Linux 18.04 LTS

Description

Hey, I'm getting error in the Docker geemap container when import whitebox for the first time.

It is not a problem if I type again an import. I couldn't understand why this throws an error. Here is a related issue:
https://stackoverflow.com/questions/42441211/python-urllib-error-httperror-http-error-404-not-found

I guess this is not an important error and related to network issues. I wanted to add in case someone sees the error message.

What I Did

docker run -it --name geemap_latest -p 8888:8888 -p 6006:6006 -v C:/Users/batuh/Desktop:/geemap/data bkavlak/geemap:latest bash
import whitebox

• whitebox version: 1.5.1
• Python version: 3.6
• Operating System: CentOS 8

Description

It seems to install, but it won't run any functionality.
error:
./whitebox_tools: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by ./whitebox_tools)

What I Did

print(wbt.license())
./whitebox_tools: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by ./whitebox_tools)

• whitebox version: 2.2.0
• Python version: 3.8.10
• Operating System: Ubuntu 20.04

Description

I'm trying to download the WBT binaries for use in a docker container. I would like to be able to have them set up in the docker image so that each container will not have to download them individually.

What I Did

Here's what I'm running inside my terminal to try to download the binaries and the error it produces:

# python /usr/local/lib/python3.8/dist-packages/whitebox/download_wbt.py
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/pkg_resources/__init__.py", line 388, in get_provider
    module = sys.modules[moduleOrReq]
KeyError: 'whitebox'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/whitebox/download_wbt.py", line 182, in <module>
    download_wbt()
  File "/usr/local/lib/python3.8/dist-packages/whitebox/download_wbt.py", line 20, in download_wbt
    pkg_resources.resource_filename(package_name, "whitebox_tools.py")
  File "/usr/local/lib/python3.8/dist-packages/pkg_resources/__init__.py", line 1201, in resource_filename
    return get_provider(package_or_requirement).get_resource_filename(
  File "/usr/local/lib/python3.8/dist-packages/pkg_resources/__init__.py", line 390, in get_provider
    __import__(moduleOrReq)
  File "/usr/local/lib/python3.8/dist-packages/whitebox/whitebox.py", line 5, in <module>
    from .whitebox_tools import WhiteboxTools
ImportError: attempted relative import with no known parent package

However, opening a python interpreter and running from whitebox import WhiteboxTools; WhiteboxTools() will successfully download the binaries.

• whitebox version:
• Python version:
• Operating System:

Description

When running the LidarIdwInterpolation function using the Python front end for whitebox, the coordinate reference system (CRS) is not saved to the output .tif file.

What I Did

Basic command of function was used.

    wbt.lidar_idw_interpolation(
        i=f, 
        output=outdir+fname_dem, 
        parameter="elevation", 
        returns="all", 
        resolution=1.0, 
        weight=1.0, 
        radius=5, 
        exclude_cls='3,4,5,6,7,18', 
        minz=None, 
        maxz=None
    )

Thanks in advance.

I was able to install whiteboxtools in AWS Sagemaker notebook instance.
When I tried to execute commands:

import whitebox
wbt = whitebox.WhiteboxTools()
print(wbt.tool_help("ElevPercentile")) and
print(wbt.help())

There is no output printed.
Can anyone help me with how to use whiteboxtools and get results in AWS cloud. Thank you in advance.

• whitebox version: latest
• Python version: 3.4
• Operating System: windows 10

Description

D:\Python34\python3.exe F:/demospace/whitebox/run.py
Traceback (most recent call last):
File "F:/demospace/whitebox/run.py", line 7, in
whitebox.Runner()
File "D:\Python34\lib\site-packages\whitebox\wb_runner.py", line 1129, in Runner
wbr = WbRunner(tool_name)
File "D:\Python34\lib\site-packages\whitebox\wb_runner.py", line 729, in init
for filename in glob.iglob('**/*', recursive=True):
TypeError: iglob() got an unexpected keyword argument 'recursive'

What I Did

import whitebox
whitebox.Runner()

Starting from yesterday I am unable to create instances of WhiteBoxTools in Python 3. I get this error:

FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.8/dist-packages/whitebox/WBT/img'

It looks like something related to this package:

WhiteboxTools_linux_amd64.zip

root@bdfd55668517:/src# python3
Python 3.8.10 (default, Mar 13 2023, 10:26:41) 
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

>>> from whitebox import WhiteboxTools
>>> wbt = WhiteboxTools()

Downloading WhiteboxTools pre-compiled binary for first time use ...
Decompressing WhiteboxTools_linux_amd64.zip ...
WhiteboxTools package directory: /usr/local/lib/python3.8/dist-packages/whitebox
Unexpected error: <class 'FileNotFoundError'>
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.8/dist-packages/whitebox/whitebox_tools.py", line 278, in __init__
    download_wbt()
  File "/usr/local/lib/python3.8/dist-packages/whitebox/whitebox_tools.py", line 157, in download_wbt
    shutil.copytree(init_img_dir, new_img_dir)
  File "/usr/lib/python3.8/shutil.py", line 555, in copytree
    with os.scandir(src) as itr:
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.8/dist-packages/whitebox/WBT/img'

Thanks!

• whitebox version: newest
• Python version: python 3.8
• Operating System: Mac

Description

Describe what you were trying to get done.
replace the rasterline values with DEM values

What I Did

wbt.conditional_evaluation(
i='/home/jovyan/data/mynotebook/data/rasterline.tif',
output='/home/jovyan/data/mynotebook/data/boundry.tif',
statement='value >= 0.0',
true='/home/jovyan/data/mynotebook/data/Elevation1.tif',
false='#')

Paste the command(s) you ran and the output.
return 0

• whitebox version: 2.0.0
• Python version: 3.6
• Operating System: Windows 10

Description

The documentation for the raster_calculator function on the Python frontend does not seem to be correct. It currently reads: "This tool performs a conditional evaluaton (if-then-else) operation on a raster", which is the documentation for the conditional_evaluation tool. This is a very small issue but I thought I would raise it because it has an easy fix.

Thanks,
Marc

• whitebox version: 2.1.2
• Python version: 3.10
• Operating System: Windows 64-bit

Description

When running the LidarIdwInterpolation function using the Python front end for whitebox, the coordinate reference system (CRS) is not saved to the output .tif file.

What I Did

Basic command of function was used.

    wbt.lidar_idw_interpolation(
        i=f, 
        output=outdir+fname_dem, 
        parameter="elevation", 
        returns="all", 
        resolution=1.0, 
        weight=1.0, 
        radius=5, 
        exclude_cls='3,4,5,6,7,18', 
        minz=None, 
        maxz=None
    )

Thanks in advance.

• whitebox version: v 2.2.0
• Python version:3.9
• Operating System: windows 11

Hello Prof. Wu,

I tried to use the mosaic function according to the tutorial https://jblindsay.github.io/wbt_book/tutorials/mosaic.html, and it does not work.

here is the error report:

--output='M:\test\output\NAME_OF_FILE.tif' --method=nn -v --compress_rasters=False

• Welcome to Mosaic *
• Powered by WhiteboxTools *
• www.whiteboxgeo.com *

Number of tiles: 2
Reading data...
thread 'main' panicked at 'index out of bounds: the len is 2 but the index is 2', whitebox-raster\src\geotiff\mod.rs:797:44
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

I do not know how to solve this problem, can you help me?

Best regards

• whitebox version: 2.0.3
• Python version: 3.9
• Operating System: RedHat Enterprise

Description

When using any whitebox functions for python, the current working directory is reset to the whitebox directory in my anaconda environment (e.g. /home/user_name/minconda3/envs/osgeo-env-v1/lib/python3.8/site-packages/whitebox). This causes many problems, since I am using whitebox functions across multiple scripts for my automated workflow.

To clarify, after importing whitebox, the current working directory is set to my project directory where my python file is calling whitebox, which is what I want. But after using a function it is reset to the whitebox directory, so the functions do not end up running.

I am attempting this in jupyter notebook.

What I Did

from whitebox import whitebox_tools
wbt = whitebox_tools.WhiteboxTools()
CWD = "/home/user_name/project/data"
wbt.set_working_dir(CWD)
wbt.clip_lidar_to_polygon("./filename.las", polygons="./poly_shapefile.shp", output="./lidarClip.las")

Below is the error messages I receive.

Thank you for your time in reading this.

This is a follow up of #67.

We think that the release cycle as currently implemented between the Python bindings and the back-end of WhiteboxTools is somewhat misleading to the user, and could lead to tricky situations.

Indeed, as a consuming developer, we expect the version of the Python bindings available on PyPI to be in sync with the WhiteboxTools back-end. When using v2.3.0 of the Python bindings, we should be using v2.3.0 of the WhiteboxTools back-end. This is a strong expectation made by any developer using virtually any third-party library. It notably allows rolling back to an earlier version when a newly released version breaks (which was the case between v2.3.0 and 2.4.0). However, we discovered, while dealing with #67, that this was actually not the case when using the Python bindings of Whitebox, because the Python bindings dynamically download the latest version of the WhiteboxTools back-end binaries from the Whitebox server. This means that it was basically impossible for us to rollback to v2.3.0, because v2.3.0 of the Python bindings was downloading v2.4.0 of the WhiteboxTools back-end anyway.

We think that more proper designs could be implemented easily. Here are a couple options that we can think of:

1. Package the WhiteboxTools back-end binaries directly in the package uploaded to PyPI. This allows the maintainer of the Python bindings to freeze/package the version of the back-end that's going to be used by the Python bindings, ensuring that they remain in sync.
2. Compile the WhiteboxTools back-end binaries as part of the build process of the Python bindings, before uploading to PyPI. This is a slight variation of option 1 that starts from the sources of the back-end instead of the pre-built binaries.
3. Ask the maintainer of the WhiteboxTools back-end (@jblindsay) to host versioned binaries on the Whitebox server, instead of only the latest version. This would allow the Python bindings to still download the binaries from the server, but at least use the version of the back-end that is in sync with that of the Python bindings.

We think that options 1 and 2 would be best, 3 being a bit more hacky and error-prone, in case there's an issue with the Whitebox server.

Let us know if we can help in any way. We think that this would be a major improvement of this (already) great toolbox, and a step that would take it closer to being production-ready in a lot of cases.

• whitebox version: 0.8.0.dev0
• Python version: 3.9.16
• Operating System: Windows

Description

I am trying to run the flightline overlap tool within a function in a larger python script. I have run it fine on my computer that I installed whitebox tools on more than a year ago (it is using whitebox version 2.1.2), but I had to get it setup for someone else and had to have them install whitebox tools. We used the conda install line from the anaconda website (https://anaconda.org/conda-forge/whitebox_tools): "conda install -c conda-forge whitebox_tools". After successfully installing, I checked the version and was surprised that it was 0.8.0.dev0. The first thing that was different when using it was just importing the module. In my scripts I could use "import whitebox" and on the computer with the new install of whitebox it has to be imported with "import whitebox_tools". When I run FlightlineOverlap on my computer I get the expected/correct outputs. On the new install I get this error:

[WinError 2] The system cannot find the file specified

What I Did

import os
try:
    import whitebox
except:
    import whitebox_tools as whitebox
wbt = whitebox.WhiteboxTools()

lidar_dir = r"path\to\lidar"
raster_dir = r"path\to\raster"
pre_name="Test"

# Create overlap raster for lidar swaths.
def create_overlap(lidar_dir, pre_name, raster_dir):
    print("Creating overlap raster...")
    overlap_raster = os.path.join(raster_dir, pre_name+"_Overlap.tif")

    wbt.set_working_dir(lidar_dir)
    wbt.flightline_overlap(i=None, output=overlap_raster, resolution=1)

    print("Overlap raster created.")
    return overlap_raster

create_overlap(lidar_dir, pre_name, raster_dir)

Again, I get this error when running:
[WinError 2] The system cannot find the file specified

Thanks in advance!

• whitebox version: 2.2.0
• Python version: 3.10.8
• Operating System: Docker Image, python:3.10-slim-bullseye

Description

Hi, I’m trying to compute the flow length using downslope_flowpath_length function. The tool seems to work, but I have negative lengths as results. Am I doing something wrong? Could you explain what the output represents?
Thank you!

What I Did

wbt.downslope_flowpath_length(flow_dir_catch, flowlength_catch, esri_pntr=True)

(I opened the raster in QGIS for convenience)
Python result:

Expected result:

• whitebox version: v2.2.0
• Python version: Python 3.9.13
• Operating System: macOsX 13.2, Ubuntu 20.04, Ubuntu 22.04

Description

I am trying to convert lidar files to DSM raster, using method lidar_digital_surface_model.
For certain lidars, the method is getting stuck at filtering.
Example input lidar files can be obtained from USGS links:

1. https://rockyweb.usgs.gov/vdelivery/Datasets/Staged/Elevation/LPC/Projects/FEMA_R6_AR_Dardanelle_Reservoir_QL2_Lidar/AR_DardanelleReservoir_2015/LAZ/USGS_LPC_FEMA_R6_AR_Dardanelle_Reservoir_QL2_Lidar_15svv560345.laz

2. https://rockyweb.usgs.gov/vdelivery/Datasets/Staged/Elevation/LPC/Projects/FEMA_R6_AR_Dardanelle_Reservoir_QL2_Lidar/AR_DardanelleReservoir_2015/LAZ/USGS_LPC_FEMA_R6_AR_Dardanelle_Reservoir_QL2_Lidar_15svv560270.laz

Logs:

./whitebox_tools --run="LidarDigitalSurfaceModel" --wd="/tmp" --input='647910b9d34eac007b50fc55_USGS_LPC_FEMA_R6_AR_Dardanelle_Reservoir_QL2_Lidar_15svv560345.laz' --output='dsm_from_laz_1.tif' --resolution=0.5 --radius=0.5

***************************************
* Welcome to LidarDigitalSurfaceModel *
* Powered by WhiteboxTools            *
* www.whiteboxgeo.com                 *
***************************************
Performing interpolation...
Reading input LiDAR file...
Reading points: 0%
Reading points: 1%
Reading points: 2%
Reading points: 3%
.....
.....

Reading points: 99%
Reading points: 100%
Filtering points: 0%
Filtering points: 1%
Filtering points: 2%
Filtering points: 3%
....
....
Filtering points: 30%
Filtering points: 31%
Filtering points: 32%

Process got stuck at 32% for one on the Lidar file. This percentage varies from Lidar to Lidar.

Expected result:

• Should convert Lidar to DSM raster
• Or should fail gracefully

What I Did

Code used:

import whitebox

def convert_to_dsm(laz_file_name, output_file_name):
    wbt_digital_surface_model_lidar(laz_file_name, output_file_name)

def __handle_whitebox_errors__(output):
    if 'panicked' in output or 'Error reading LAZ' in output or 'Warning: No points found' in output:
       
        print(f"whitebox processing of lidar throw error: {output}")
        raise Exception(message = f"whitebox processing of lidar throw error: {output}")       
    else:
        print(f"{output}")

def wbt_digital_surface_model_lidar(lidar_file, converted_file_name) -> str:
    print("#initialize whitebox tool")
    wbt = whitebox.WhiteboxTools()
    print(f"Whitebox tool version: {wbt.version()}")
    wbt.work_dir = "/tmp"
    dsm_output_tif = converted_file_name 
    callback_function = lambda output: __handle_whitebox_errors__(output)
    
    wbt.lidar_digital_surface_model(
        i=lidar_file,
        output=dsm_output_tif,
        resolution=0.5,
        radius=0.5, 
        minz=None, 
        maxz=None, 
        max_triangle_edge_length=None,
        callback=callback_function
    )               
         
    print(f"dsm_output_tif: {dsm_output_tif}")
    return dsm_output_tif

if __name__ == "__main__":
    laz_file = "647910b9d34eac007b50fc55_USGS_LPC_FEMA_R6_AR_Dardanelle_Reservoir_QL2_Lidar_15svv560345.laz"
    tif_file_name = "dsm_from_laz_1.tif"
    convert_to_dsm(laz_file, tif_file_name)

    

• whitebox version: 2.1.4
• Python version: 3.8
• Operating System: Win11/WSL2

Description

Hi. I used LidarPointStats tool through whitebox-python to create a grid with each raster cell representing the number of points. The tool worked fine. However, it looks like the output is either incorrect or shifted (see a screenshot below). Is this the expected behaviour or am I doing something wrong?

What I Did

wbt.lidar_point_stats(
    i=lidar.las, 
    resolution=1.0,
    num_points=True,
    num_pulses=False,
    avg_points_per_pulse=False,
    z_range=False,
    intensity_range=False,
    predom_class=False
)

• whitebox version:1.5.1
• Python version: 3.7.0 (v3.7.0:1bf9cc5093, Jun 27 2018, 04:59:51) [MSC v.1914 64 bit (AMD64)]
• Operating System: Windows 10 64bit

Description

I'm running the OSGeo pyqgis distribution

pip install whitebox

works fine. However, my distribution seems to be missing Tkinter. I believe there is something with QGIS that doesn't let Tkinter run/install.

Is there way to change the backend of whitebox? Or another workaround that will let me run the pyqgis AND whitebox API?

import whitebox
ModuleNotFoundError: No module named '_tkinter'

• whitebox version: 2.3.4
• Python version: 3.10
• Operating System: Ubuntu

Description

We have a need to create a docker image that no longer calls out to the outside world for any calls at run-time. When we get to our python code that calls whitebox, it always calls externally to Downloading WhiteboxTools pre-compiled binary for first time use.

What I Did

I have tried dozens and dozens of ways to see if I can get my /usr/local/lib/python3.10/dist-packages/whitebox populated with the right files and permissions that were placed after the run-time "Downloading...." code. I did notice the download_wbt function in the init for that the whitebox_tools.py.

And yes, I do have whitebox 2.3.4 being loading via the pipfile.

From what I can tell, there is no way around this. Is that true? Is there a way I can download the binaries (or the zip) and setup the correct files during my dockerbuild, then block the call to the download_wbt?

Thoughts / suggestions / Fix request?

Rob

Paste the command(s) you ran and the output.
If there was a crash, please include the traceback here.

• whitebox version: 1.5.0
• Python version: 3.6.10
• Operating System: Ubuntu 20.04

Description

I would like to use WhiteboxTools v1.5.0 in order to use

https://github.com/NCAR/wrf_hydro_gis_preprocessor

but unforuntately, I can't pin WhiteboxTools to v1.5.0, despite
being aware of issues like this:

https://stackoverflow.com/questions/67495221/conda-environment-has-access-to-system-modules-how-to-prevent

What I Did

My steps to reproduce on Ubuntu 20.04 are:

rm -rf ~/miniconda3 ~/.condarc ~/.conda ~/.continuum
bash Miniconda3-py38_4.12.0-Linux-x86_64.sh
conda init
conda config --add channels conda-forge
conda create -n wrfh_gis_env -c conda-forge python=3.6 gdal netCDF4 numpy pyproj whitebox=1.5.0
conda activate wrfh_gis_env
(wrfh_gis_env) > python

from whitebox.whitebox_tools import WhiteboxTools
print(' Using {0}'.format(WhiteboxTools().version().split('\n')[0]))
Using WhiteboxTools v2.1.0 by Dr. John B. Lindsay (c) 2017-2021

Please note that outside of wrfh_gis_env, I do not have access
to WhiteboxTools v2.1.0:

python3.8

from whitebox.whitebox_tools import WhiteboxTools
Traceback (most recent call last):
File "", line 1, in
ModuleNotFoundError: No module named 'whitebox'

Does anyone know how I might pin WhiteboxTools to v1.5.0?

PS - Even from inside wrfh_gis_env, it's still not clear where v2.1.0 comes from:

conda activate wrfh_gis_env
(wrfh_gis_env) > python

import whitebox as ; print(.path)
['/home/soft/miniconda3/envs/wrfh_gis_env/lib/python3.6/site-packages/whitebox']

conda deactivate
cd /home/soft/miniconda3/envs/wrfh_gis_env/lib/python3.6/site-packages/whitebox
ls -al

drwxrwxr-x 4 4096 Jun 28 15:54 WBT
-rw-rw-r-- 1 25866248 Jun 28 15:54 WhiteboxTools_linux_amd64.zip
-rw-rw-r-- 2 221 Jun 6 2021 init.py
drwxrwxr-x 2 4096 Jun 28 15:58 pycache
-rw-rw-r-- 2 3904 Jun 6 2021 automation.py
-rw-rw-r-- 2 416 Jun 6 2021 cli.py
-rw-rw-r-- 2 3831 Jun 6 2021 download_wbt.py
-rw-rw-r-- 2 2469 Jun 6 2021 example.py
drwxrwxr-x 2 4096 Jun 28 15:54 img
drwxrwxr-x 2 4096 Jun 28 15:54 plugins
drwxrwxr-x 2 4096 Jun 28 15:54 testdata
-rw-rw-r-- 2 58608 Jun 6 2021 wb_runner.py
-rw-rw-r-- 2 44 Jun 6 2021 whitebox.py
-rw-rw-r-- 2 6146 Jun 6 2021 whitebox_example.py
-rwxr-xr-x 1 29133144 Jun 28 15:54 whitebox_tools
-rw-rw-r-- 2 401432 Jun 6 2021 whitebox_tools.py

grep 2.1.0 *
Binary file WhiteboxTools_linux_amd64.zip matches
Binary file whitebox_tools matches

cat init.py

-- coding: utf-8 --

"""Top-level package for whitebox."""

author = """Qiusheng Wu"""
email = '[email protected]'
version = '1.5.0'

from .whitebox_tools import WhiteboxTools
from .wb_runner import Runner