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fatiando / verde

Processing and gridding spatial data, machine-learning style
https://www.fatiando.org/verde
BSD 3-Clause "New" or "Revised" License
600 stars 72 forks source link

Block reduction error when block size > coordinate variation #404

Closed mdtanker closed 1 year ago

mdtanker commented 1 year ago

Description of the problem:

I'm attempting to block-reduce some data along a single flight line. The flight line is oriented E-W, so there should only be a single block in the N-S direction, but several blocks in the E-W direction. The single N-S block is resulting in an error. I can fix this by using the shape parameter instead of size.

It looks like verde.line_coordinates needs at least 2 blocks to shift pixel registered values?

Full code that generated the error

df = rosetta[rosetta.Line.isin([200])]

reducer = vd.BlockReduce(np.mean, spacing=20e3,)

input_coords = (df.x, df.y)
input_data= df.Height

coords, data = reducer.filter(
        coordinates=input_coords,
        data=input_data,
    )

Full error message

ndexError                                Traceback (most recent call last)
Cell In[103], line 13
      9 input_coords = (df.x, df.y)
     10 input_data= df.Height
---> 13 coords, data = reducer.filter(
     14         coordinates=input_coords,
     15         data=input_data,
     16     )
     17 coords, data

File /home/tankerma/miniconda/envs/RIS_gravity_inversion/lib/python3.10/site-packages/verde/blockreduce.py:163, in BlockReduce.filter(self, coordinates, data, weights)
    118 """
    119 Apply the blocked aggregation to the given data.
    120 
   (...)
    158 
    159 """
    160 coordinates, data, weights = check_fit_input(
    161     coordinates, data, weights, unpack=False
    162 )
--> 163 blocks, labels = block_split(
    164     coordinates,
    165     spacing=self.spacing,
    166     shape=self.shape,
    167     adjust=self.adjust,
    168     region=self.region,
    169 )
    170 if any(w is None for w in weights):
    171     reduction = self.reduction

File /home/tankerma/miniconda/envs/RIS_gravity_inversion/lib/python3.10/site-packages/verde/coordinates.py:933, in block_split(coordinates, spacing, adjust, region, shape)
    931 if region is None:
    932     region = get_region(coordinates)
--> 933 block_coords = grid_coordinates(
    934     region, spacing=spacing, shape=shape, adjust=adjust, pixel_register=True
    935 )
    936 tree = kdtree(block_coords)
    937 labels = tree.query(np.transpose(n_1d_arrays(coordinates, 2)))[1]

File /home/tankerma/miniconda/envs/RIS_gravity_inversion/lib/python3.10/site-packages/verde/coordinates.py:574, in grid_coordinates(region, shape, spacing, adjust, pixel_register, extra_coords, meshgrid)
    564     spacing = (None, None)
    566 east = line_coordinates(
    567     region[0],
    568     region[1],
   (...)
    572     pixel_register=pixel_register,
    573 )
--> 574 north = line_coordinates(
    575     region[2],
    576     region[3],
    577     size=shape[0],
    578     spacing=spacing[0],
    579     adjust=adjust,
    580     pixel_register=pixel_register,
    581 )
    582 coordinates = [east, north]
    583 if meshgrid:

File /home/tankerma/miniconda/envs/RIS_gravity_inversion/lib/python3.10/site-packages/verde/coordinates.py:286, in line_coordinates(start, stop, size, spacing, adjust, pixel_register)
    284 values = np.linspace(start, stop, size)
    285 if pixel_register:
--> 286     values = values[:-1] + (values[1] - values[0]) / 2
    287 return values

IndexError: index 1 is out of bounds for axis 0 with size 1

System information

Output of conda list 
# packages in environment at /home/tankerma/miniconda/envs/RIS_gravity_inversion:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
affine                    2.4.0              pyhd8ed1ab_0    conda-forge
aiofiles                  22.1.0             pyhd8ed1ab_0    conda-forge
aiohttp                   3.8.4           py310h1fa729e_0    conda-forge
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
aiosqlite                 0.18.0             pyhd8ed1ab_0    conda-forge
alembic                   1.10.2             pyhd8ed1ab_0    conda-forge
alsa-lib                  1.2.8                h166bdaf_0    conda-forge
antarctic-plots           0.0.6                    pypi_0    pypi
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
aom                       3.5.0                h27087fc_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h5764c6d_3    conda-forge
arrow                     1.2.3                    pypi_0    pypi
arrow-cpp                 11.0.0          ha770c72_13_cpu    conda-forge
asciitree                 0.3.3                    pypi_0    pypi
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
async-timeout             4.0.2              pyhd8ed1ab_0    conda-forge
attr                      2.5.1                h166bdaf_1    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
aws-c-auth                0.6.26               hdca2abe_0    conda-forge
aws-c-cal                 0.5.21               h48707d8_2    conda-forge
aws-c-common              0.8.14               h0b41bf4_0    conda-forge
aws-c-compression         0.2.16               h03acc5a_5    conda-forge
aws-c-event-stream        0.2.20               h00877a2_4    conda-forge
aws-c-http                0.7.5                hf342b9f_5    conda-forge
aws-c-io                  0.13.19              hef0810e_1    conda-forge
aws-c-mqtt                0.8.6               h337b09f_11    conda-forge
aws-c-s3                  0.2.7                hde0a405_0    conda-forge
aws-c-sdkutils            0.1.8                h03acc5a_0    conda-forge
aws-checksums             0.1.14               h03acc5a_5    conda-forge
aws-crt-cpp               0.19.8              h85f3b07_11    conda-forge
aws-sdk-cpp               1.10.57              h17c43bd_8    conda-forge
babel                     2.12.1             pyhd8ed1ab_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.0             pyha770c72_0    conda-forge
black                     23.1.0                   pypi_0    pypi
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.3               hafa529b_0    conda-forge
bokeh                     2.4.3              pyhd8ed1ab_3    conda-forge
boost-cpp                 1.78.0               h75c5d50_1    conda-forge
branca                    0.6.0              pyhd8ed1ab_0    conda-forge
brotli                    1.0.9                h166bdaf_8    conda-forge
brotli-bin                1.0.9                h166bdaf_8    conda-forge
brotlipy                  0.7.0           py310h5764c6d_1005    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
cairo                     1.16.0            ha61ee94_1014    conda-forge
cartopy                   0.21.1          py310hcb7e713_0    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cf_xarray                 0.8.0              pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_3    conda-forge
cfgrib                    0.9.10.3                 pypi_0    pypi
cfitsio                   4.2.0                hd9d235c_0    conda-forge
cftime                    1.6.2           py310hde88566_1    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
click                     8.1.3           unix_pyhd8ed1ab_2    conda-forge
click-plugins             1.1.1                      py_0    conda-forge
cligj                     0.7.2              pyhd8ed1ab_1    conda-forge
cloudpickle               2.2.1              pyhd8ed1ab_0    conda-forge
cmaes                     0.9.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
colorcet                  3.0.1              pyhd8ed1ab_0    conda-forge
colorlog                  6.7.0           py310hff52083_1    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
conda                     23.1.0          py310hff52083_0    conda-forge
conda-package-handling    2.0.2              pyh38be061_0    conda-forge
conda-package-streaming   0.7.0              pyhd8ed1ab_1    conda-forge
contourpy                 1.0.7           py310hdf3cbec_0    conda-forge
coverage                  7.2.2           py310h1fa729e_0    conda-forge
cryptography              39.0.2          py310h34c0648_0    conda-forge
curl                      7.88.1               hdc1c0ab_1    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.0          py310h5764c6d_1    conda-forge
dask                      2023.3.1           pyhd8ed1ab_0    conda-forge
dask-core                 2023.3.1           pyhd8ed1ab_0    conda-forge
datashader                0.14.4             pyh1a96a4e_0    conda-forge
datashape                 0.5.4                      py_1    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
dcw-gmt                   2.1.1                ha770c72_0    conda-forge
debugpy                   1.6.6           py310heca2aa9_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
distributed               2023.3.1           pyhd8ed1ab_0    conda-forge
docrep                    0.3.2              pyh44b312d_0    conda-forge
double-conversion         3.2.0                h27087fc_1    conda-forge
eccodes                   1.5.1                    pypi_0    pypi
eigen                     3.4.0                h4bd325d_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
esmf                      8.4.1           nompi_he2e5181_0    conda-forge
esmpy                     8.4.1              pyhc1e730c_0    conda-forge
et-xmlfile                1.1.0                    pypi_0    pypi
exceptiongroup            1.1.1              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                h27087fc_0    conda-forge
fasteners                 0.18                     pypi_0    pypi
ffmpeg                    5.1.2           gpl_h8dda1f0_106    conda-forge
fftw                      3.3.10          nompi_hf0379b8_106    conda-forge
findlibs                  0.0.2                    pypi_0    pypi
fiona                     1.9.2           py310ha325b7b_0    conda-forge
flake8                    6.0.0                    pypi_0    pypi
flake8-pyproject          1.2.3                    pypi_0    pypi
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
fmt                       9.1.0                h924138e_0    conda-forge
folium                    0.14.0             pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.39.2          py310h1fa729e_0    conda-forge
fqdn                      1.5.1                    pypi_0    pypi
freetype                  2.12.1               hca18f0e_1    conda-forge
freexl                    1.0.6                h166bdaf_1    conda-forge
frozenlist                1.3.3           py310h5764c6d_0    conda-forge
fsspec                    2023.3.0           pyhd8ed1ab_1    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
gdal                      3.6.3           py310hc1b7723_0    conda-forge
geopandas                 0.12.2             pyhd8ed1ab_0    conda-forge
geopandas-base            0.12.2             pyha770c72_0    conda-forge
geos                      3.11.1               h27087fc_0    conda-forge
geotiff                   1.7.1                hb963b44_7    conda-forge
geoviews                  1.9.6              pyhd8ed1ab_0    conda-forge
geoviews-core             1.9.6              pyha770c72_0    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gflags                    2.2.2             he1b5a44_1004    conda-forge
ghostscript               9.54.0               h27087fc_2    conda-forge
giflib                    5.2.1                h0b41bf4_3    conda-forge
gl2ps                     1.4.2                h0708190_0    conda-forge
glew                      2.1.0                h9c3ff4c_2    conda-forge
glib                      2.74.1               h6239696_1    conda-forge
glib-tools                2.74.1               h6239696_1    conda-forge
glog                      0.6.0                h6f12383_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmt                       6.4.0                h3fec0b5_7    conda-forge
gnutls                    3.7.8                hf3e180e_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
greenlet                  2.0.2           py310heca2aa9_0    conda-forge
gshhg-gmt                 2.3.7             ha770c72_1003    conda-forge
gst-plugins-base          1.22.0               h4243ec0_2    conda-forge
gstatsim                  1.0.0                     dev_0    
gstreamer                 1.22.0               h25f0c4b_2    conda-forge
gstreamer-orc             0.4.33               h166bdaf_0    conda-forge
h5netcdf                  1.1.0                    pypi_0    pypi
h5py                      3.8.0                    pypi_0    pypi
harfbuzz                  6.0.0                h8e241bc_0    conda-forge
harmonica                 0.6.0              pyhd8ed1ab_0    conda-forge
hdf4                      4.2.15               h501b40f_6    conda-forge
hdf5                      1.12.2          nompi_h4df4325_101    conda-forge
heapdict                  1.0.1                      py_0    conda-forge
holoviews                 1.15.4             pyhd8ed1ab_0    conda-forge
hvplot                    0.8.3              pyhd8ed1ab_0    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imageio                   2.26.0             pyh24c5eb1_0    conda-forge
importlib-metadata        6.1.0              pyha770c72_0    conda-forge
importlib_metadata        6.1.0                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.22.0             pyh210e3f2_0    conda-forge
ipyleaflet                0.17.2                   pypi_0    pypi
ipython                   8.11.0             pyh41d4057_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.5              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0                  pypi_0    pypi
isort                     5.12.0             pyhd8ed1ab_1    conda-forge
jack                      1.9.22               h11f4161_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.2.0              pyhd8ed1ab_0    conda-forge
json-c                    0.16                 hc379101_0    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsoncpp                   1.9.5                h4bd325d_1    conda-forge
jsonpointer               2.3                      pypi_0    pypi
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter-server-proxy      3.2.2                    pypi_0    pypi
jupyter_bokeh             3.0.5              pyhd8ed1ab_0    conda-forge
jupyter_client            8.1.0              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.0           py310hff52083_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.5.0              pyhd8ed1ab_0    conda-forge
jupyter_server_fileid     0.8.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyter_server_ydoc       0.8.0              pyhd8ed1ab_0    conda-forge
jupyter_ydoc              0.2.3              pyhd8ed1ab_0    conda-forge
jupyterlab                3.6.2              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.20.0             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.6              pyhd8ed1ab_0    conda-forge
kealib                    1.5.0                ha7026e8_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4           py310hbf28c38_1    conda-forge
krb5                      1.20.1               h81ceb04_0    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
lcms2                     2.15                 haa2dc70_1    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libabseil                 20230125.0      cxx17_hcb278e6_1    conda-forge
libaec                    1.0.6                hcb278e6_1    conda-forge
libarchive                3.6.2                h3d51595_0    conda-forge
libarrow                  11.0.0          h93537a5_13_cpu    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_8    conda-forge
libbrotlidec              1.0.9                h166bdaf_8    conda-forge
libbrotlienc              1.0.9                h166bdaf_8    conda-forge
libcap                    2.66                 ha37c62d_0    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libclang                  15.0.7          default_had23c3d_1    conda-forge
libclang13                15.0.7          default_h3e3d535_1    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcups                   2.3.3                h36d4200_3    conda-forge
libcurl                   7.88.1               hdc1c0ab_1    conda-forge
libdb                     6.2.32               h9c3ff4c_0    conda-forge
libdeflate                1.17                 h0b41bf4_0    conda-forge
libdrm                    2.4.114              h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h28343ad_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.4.2                h27087fc_0    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgcrypt                 1.10.1               h166bdaf_0    conda-forge
libgdal                   3.6.3                hb7af45b_0    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libglib                   2.74.1               h606061b_1    conda-forge
libglu                    9.0.0             he1b5a44_1001    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libgoogle-cloud           2.8.0                h0bc5f78_1    conda-forge
libgpg-error              1.46                 h620e276_0    conda-forge
libgrpc                   1.52.1               hcf146ea_1    conda-forge
libhwloc                  2.9.0                hd6dc26d_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libidn2                   2.3.4                h166bdaf_0    conda-forge
libjpeg-turbo             2.1.5.1              h0b41bf4_0    conda-forge
libkml                    1.3.0             h37653c0_1015    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libllvm11                 11.1.0               he0ac6c6_5    conda-forge
libllvm15                 15.0.7               hadd5161_1    conda-forge
libmamba                  1.3.1                hcea66bb_2    conda-forge
libmambapy                1.3.1           py310h1428755_2    conda-forge
libnetcdf                 4.9.1           nompi_hd2e9713_102    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libnuma                   2.0.16               h0b41bf4_1    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpciaccess              0.17                 h166bdaf_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libpq                     15.2                 hb675445_0    conda-forge
libprotobuf               3.21.12              h3eb15da_0    conda-forge
librttopo                 1.1.0               ha49c73b_12    conda-forge
libsndfile                1.2.0                hb75c966_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsolv                   0.7.23               h3eb15da_0    conda-forge
libspatialindex           1.9.3                h9c3ff4c_4    conda-forge
libspatialite             5.0.1               h221c8f1_23    conda-forge
libsqlite                 3.40.0               h753d276_0    conda-forge
libssh2                   1.10.0               hf14f497_3    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libsystemd0               252                  h2a991cd_0    conda-forge
libtasn1                  4.19.0               h166bdaf_0    conda-forge
libtheora                 1.1.1             h7f98852_1005    conda-forge
libthrift                 0.18.1               h5e4af38_0    conda-forge
libtiff                   4.5.0                hddfeb54_5    conda-forge
libtool                   2.4.7                h27087fc_0    conda-forge
libudev1                  253                  h0b41bf4_0    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libutf8proc               2.8.0                h166bdaf_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libva                     2.18.0               h0b41bf4_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libvpx                    1.11.0               h9c3ff4c_3    conda-forge
libwebp-base              1.3.0                h0b41bf4_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxkbcommon              1.5.0                h79f4944_1    conda-forge
libxml2                   2.10.3               hca2bb57_4    conda-forge
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line-profiler             4.0.3                    pypi_0    pypi
llvmlite                  0.39.1          py310h58363a5_1    conda-forge
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lz4                       4.3.2           py310h0cfdcf0_0    conda-forge
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lzo                       2.10              h516909a_1000    conda-forge
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mapclassify               2.5.0              pyhd8ed1ab_1    conda-forge
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matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
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mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
mpg123                    1.31.3               hcb278e6_0    conda-forge
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mysql-common              8.0.32               ha901b37_0    conda-forge
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numpy                     1.23.5          py310h53a5b5f_0    conda-forge
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patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
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ply                       3.11                       py_1    conda-forge
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poppler-data              0.4.12               hd8ed1ab_0    conda-forge
postgresql                15.2                 h3248436_0    conda-forge
proj                      9.1.1                h8ffa02c_2    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
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prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
psutil                    5.9.4           py310h5764c6d_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pugixml                   1.11.4               h9c3ff4c_0    conda-forge
pulseaudio                16.1                 ha8d29e2_1    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pyarrow                   11.0.0          py310h633f555_13_cpu    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycodestyle               2.10.0                   pypi_0    pypi
pycosat                   0.6.4           py310h5764c6d_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyct                      0.4.6                      py_0    conda-forge
pyct-core                 0.4.6                      py_0    conda-forge
pyflakes                  3.0.1                    pypi_0    pypi
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pygmt                     0.8.0              pyhd8ed1ab_0    conda-forge
pyinterp                  2023.2.1        openblas_py310hb50a16d_100    conda-forge
pykdtree                  1.3.7.post0     py310h0a54255_0    conda-forge
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pyopenssl                 23.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyproj                    3.4.1           py310h15e2413_1    conda-forge
pyqt                      5.15.7          py310hab646b1_3    conda-forge
pyqt5-sip                 12.11.0         py310heca2aa9_3    conda-forge
pyrsistent                0.19.3          py310h1fa729e_0    conda-forge
pyshp                     2.3.1              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytest                    7.2.2              pyhd8ed1ab_0    conda-forge
pytest-cov                4.0.0              pyhd8ed1ab_0    conda-forge
python                    3.10.9          he550d4f_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-dotenv             1.0.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pytz                      2022.7.1           pyhd8ed1ab_0    conda-forge
pyvista                   0.38.5             pyhd8ed1ab_0    conda-forge
pyvista-xarray            0.1.3              pyhd8ed1ab_0    conda-forge
pyviz_comms               2.2.1              pyhd8ed1ab_1    conda-forge
pyyaml                    6.0             py310h5764c6d_5    conda-forge
pyzmq                     25.0.2          py310h059b190_0    conda-forge
qt-main                   5.15.8               h67dfc38_7    conda-forge
rasterio                  1.3.6           py310h3e853a9_0    conda-forge
re2                       2023.02.02           hcb278e6_0    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
reproc                    14.2.4               h0b41bf4_0    conda-forge
reproc-cpp                14.2.4               hcb278e6_0    conda-forge
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rioxarray                 0.14.0             pyhd8ed1ab_0    conda-forge
ris-gravity-inversion     0.0.1                    pypi_0    pypi
rtree                     1.0.1           py310hbdcdc62_1    conda-forge
ruamel.yaml               0.17.21         py310h1fa729e_3    conda-forge
ruamel.yaml.clib          0.2.7           py310h1fa729e_1    conda-forge
s2n                       1.3.39               h3358134_0    conda-forge
scikit-gstat              1.0.9           py310hff52083_0    conda-forge
scikit-learn              1.2.2           py310h209a8ca_0    conda-forge
scipy                     1.10.1          py310h8deb116_0    conda-forge
scooby                    0.7.1              pyhd8ed1ab_0    conda-forge
seaborn                   0.12.2               hd8ed1ab_0    conda-forge
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simpervisor               0.4                      pypi_0    pypi
sip                       6.7.7           py310heca2aa9_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snakeviz                  2.1.1              pyhd8ed1ab_0    conda-forge
snappy                    1.1.10               h9fff704_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
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sqlite                    3.40.0               h4ff8645_0    conda-forge
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statsmodels               0.13.5          py310hde88566_2    conda-forge
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tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
tenacity                  8.2.2              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tiledb                    2.13.2               hd532e3d_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tokenize-rt               5.0.0                    pypi_0    pypi
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.2             py310h5764c6d_1    conda-forge
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
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traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
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trame                     2.3.2                    pypi_0    pypi
trame-client              2.7.4                    pypi_0    pypi
trame-components          2.1.0                    pypi_0    pypi
trame-deckgl              2.0.1                    pypi_0    pypi
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trame-rca                 0.3.0                    pypi_0    pypi
trame-router              2.0.1                    pypi_0    pypi
trame-server              2.9.1                    pypi_0    pypi
trame-simput              2.3.1                    pypi_0    pypi
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trame-vuetify             2.2.4                    pypi_0    pypi
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
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tzdata                    2022g                h191b570_0    conda-forge
ucx                       1.14.0               ha0ee010_0    conda-forge
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utfcpp                    3.2.3                ha770c72_0    conda-forge
verde                     1.7.0.post25+g0a4478a          pypi_0    pypi
vtk                       9.2.6           qt_py310h2e23b3e_201    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webcolors                 1.12                     pypi_0    pypi
webencodings              0.5.1                      py_1    conda-forge
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widgetsnbextension        4.0.6              pyhd8ed1ab_0    conda-forge
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x264                      1!164.3095           h166bdaf_2    conda-forge
x265                      3.5                  h924138e_3    conda-forge
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xarray-extras             0.5.0           py310h6acc77f_1    conda-forge
xcb-util                  0.4.0                h516909a_0    conda-forge
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xcb-util-keysyms          0.4.0                h516909a_0    conda-forge
xcb-util-renderutil       0.3.9                h166bdaf_0    conda-forge
xcb-util-wm               0.4.1                h516909a_0    conda-forge
xerces-c                  3.2.4                h55805fa_1    conda-forge
xesmf                     0.7.0              pyhd8ed1ab_0    conda-forge
xkeyboard-config          2.38                 h0b41bf4_0    conda-forge
xorg-fixesproto           5.0               h7f98852_1002    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.8.4                h0b41bf4_0    conda-forge
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xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
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xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xf86vidmodeproto     2.3.1             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xrft                      1.0.1                    pypi_0    pypi
xyzservices               2023.2.0           pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
y-py                      0.5.9           py310h4426083_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.7.0                h27087fc_2    conda-forge
yarl                      1.8.2           py310h5764c6d_0    conda-forge
ypy-websocket             0.8.2              pyhd8ed1ab_0    conda-forge
zarr                      2.14.2                   pypi_0    pypi
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zict                      2.2.0              pyhd8ed1ab_0    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstandard                 0.19.0          py310hdeb6495_1    conda-forge
zstd                      1.5.2                h3eb15da_6    conda-forge
leouieda commented 1 year ago

@mdtanker thanks for reporting! The problem was that we should be adjusting the spacing or the region to make sure there are always two nodes in the coordinates generated but this wasn't working for spacing >= 2 * (stop - start). I tracked it down to our adjustment code in spacing_to_size and implemented a fix in #406.

Could you check that the code in the main branch fixes your issue? If it doesn't, please feel free to re-open this issue.

mdtanker commented 1 year ago

@leouieda Sorry for the slow response on this. I just checked and your fix seems to have worked. Thanks for solving this!

leouieda commented 1 year ago

No worries! Thanks for checking and I'm glad it worked out 😁