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Merge pull request #53 from sebhahn/fix_argsort
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Avoid using argsort (speed issue)
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sebhahn authored Jan 17, 2018
2 parents 5a09264 + 768e640 commit d1547fc
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6 changes: 6 additions & 0 deletions CHANGES.rst
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Changelog
=========

v0.2.5
======

- Fix speed bug of gpi2cell
- Update copyright header

v0.2.4
======

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26 changes: 14 additions & 12 deletions LICENSE.txt
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@@ -1,4 +1,4 @@
Copyright (c) 2015, Vienna University of Technology
Copyright (c) 2018, TU Wien, Department of Geodesy and Geoinformation
All rights reserved.

Redistribution and use in source and binary forms, with or without
Expand All @@ -11,17 +11,19 @@ modification, are permitted provided that the following conditions are met:
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.

* Neither the name of pygeogrids nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
* Neither the name of TU Wien, Department of Geodesy and Geoinformation
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL TU WIEN, DEPARTMENT OF GEODESY AND
GEOINFORMATION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
40 changes: 20 additions & 20 deletions pygeogrids/geodetic_datum.py
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@@ -1,29 +1,29 @@
# Copyright (c) 2016
# Vienna University of Technology, Department of Geodesy and Geoinformation
# Copyright (c) 2018, TU Wien, Department of Geodesy and Geoinformation
# All rights reserved.

# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the <organization> nor the
# names of its contributors may be used to endorse or promote products
# derived from this software without specific prior written permission.
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of TU Wien, Department of Geodesy and Geoinformation
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written
# permission.

# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
# OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
# STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL TU WIEN, DEPARTMENT OF GEODESY AND
# GEOINFORMATION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


import numpy as np
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46 changes: 21 additions & 25 deletions pygeogrids/grids.py
100755 → 100644
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@@ -1,33 +1,29 @@
# Copyright (c) 2015, Vienna University of Technology,
# Department of Geodesy and Geoinformation
# Copyright (c) 2018, TU Wien, Department of Geodesy and Geoinformation
# All rights reserved.

# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the Vienna University of Technology, Department
# of Geodesy and Geoinformation nor the names of its contributors may
# be used to endorse or promote products derived from this software
# without specific prior written permission.
# * Neither the name of TU Wien, Department of Geodesy and Geoinformation
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written
# permission.

# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL VIENNA UNIVERSITY OF TECHNOLOGY,
# DEPARTMENT OF GEODESY AND GEOINFORMATION BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

# created on Aug 26, 2013
# author: Christoph Paulik Christoph.Paulik@geo.tuwien.ac.at
# ARE DISCLAIMED. IN NO EVENT SHALL TU WIEN, DEPARTMENT OF GEODESY AND
# GEOINFORMATION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

"""
The grids module defines the grid classes.
Expand Down Expand Up @@ -762,6 +758,7 @@ def __init__(self, lon, lat, cells, gpis=None, geodatum='WGS84',
geodatum=geodatum, subset=subset,
setup_kdTree=setup_kdTree, **kwargs)

self.gpi_lut = None
cells = np.asanyarray(cells)

if self.arrlon.shape != cells.shape:
Expand Down Expand Up @@ -795,12 +792,11 @@ def gpi2cell(self, gpi):
if self.gpidirect:
cell = self.arrcell[gpi]
else:
# get the indices that would sort the gpis
gpisorted = np.argsort(self.gpis)
# find the position where the gpis fit in the sorted array
pos = np.searchsorted(self.gpis[gpisorted], gpi)
index = gpisorted[pos]
cell = self.arrcell[index]
if self.gpi_lut is None:
self.gpi_lut = np.zeros(self.gpis.max() + 1, dtype=np.int32)
self.gpi_lut[self.gpis] = np.arange(self.gpis.size)

cell = self.arrcell[self.gpi_lut[gpi]]

if not iterable:
cell = cell[0]
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43 changes: 19 additions & 24 deletions pygeogrids/nearest_neighbor.py
Original file line number Diff line number Diff line change
@@ -1,34 +1,29 @@
# Copyright (c) 2013,Vienna University of Technology, Department of Geodesy and Geoinformation
# Copyright (c) 2018, TU Wien, Department of Geodesy and Geoinformation
# All rights reserved.

# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the <organization> nor the
# names of its contributors may be used to endorse or promote products
# derived from this software without specific prior written permission.

# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


'''
Created on Jul 30, 2013
@author: Christoph Paulik christoph.paulik@geo.tuwien.ac.at
'''
# * Neither the name of TU Wien, Department of Geodesy and Geoinformation
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written
# permission.

# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL TU WIEN, DEPARTMENT OF GEODESY AND
# GEOINFORMATION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

import numpy as np

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65 changes: 30 additions & 35 deletions pygeogrids/netcdf.py
100755 → 100644
Original file line number Diff line number Diff line change
@@ -1,36 +1,34 @@
# Copyright (c) 2013,Vienna University of Technology, Department of Geodesy and Geoinformation
# Copyright (c) 2018, TU Wien, Department of Geodesy and Geoinformation
# All rights reserved.

# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the Vienna University of Technology, Department of Geodesy and Geoinformation nor the
# names of its contributors may be used to endorse or promote products
# derived from this software without specific prior written permission.

# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL VIENNA UNIVERSITY OF TECHNOLOGY,
# DEPARTMENT OF GEODESY AND GEOINFORMATION BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

'''
Created on Jan 21, 2014
Module for saving grid to netCDF
@author: Christoph Paulik christoph.paulik@geo.tuwien.ac.at
'''
# * Neither the name of TU Wien, Department of Geodesy and Geoinformation
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written
# permission.

# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL TU WIEN, DEPARTMENT OF GEODESY AND
# GEOINFORMATION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

"""
Module for saving grid to netCDF.
"""

from netCDF4 import Dataset
import numpy as np
import os
Expand Down Expand Up @@ -268,15 +266,12 @@ def sort_for_netcdf(lons, lats, values):
reshape(lons.shape)
[idxlat, np.arange(lons.shape[1])], axis=1)

values = arrval[idxlatsrt].reshape(*lons.shape)\
[idxlat, np.arange(lons.shape[1])]\
[np.arange(lons.shape[0])[:, None], idxlon]
lons = arrlon[idxlatsrt].reshape(*lons.shape)\
[idxlat, np.arange(lons.shape[1])]\
[np.arange(lons.shape[0])[:, None], idxlon]
lats = arrlat[idxlatsrt].reshape(*lons.shape)\
[idxlat, np.arange(lons.shape[1])]\
[np.arange(lons.shape[0])[:, None], idxlon]
values = arrval[idxlatsrt].reshape(
*lons.shape)[idxlat, np.arange(lons.shape[1])][np.arange(lons.shape[0])[:, None], idxlon]
lons = arrlon[idxlatsrt].reshape(
*lons.shape)[idxlat, np.arange(lons.shape[1])][np.arange(lons.shape[0])[:, None], idxlon]
lats = arrlat[idxlatsrt].reshape(
*lons.shape)[idxlat, np.arange(lons.shape[1])][np.arange(lons.shape[0])[:, None], idxlon]
return lons, lats, values


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31 changes: 15 additions & 16 deletions pygeogrids/plotting.py
Original file line number Diff line number Diff line change
@@ -1,30 +1,29 @@
# Copyright (c) 2016, Vienna University of Technology,
# Department of Geodesy and Geoinformation
# Copyright (c) 2018, TU Wien, Department of Geodesy and Geoinformation
# All rights reserved.

# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the Vienna University of Technology, Department
# of Geodesy and Geoinformation nor the names of its contributors may
# be used to endorse or promote products derived from this software
# without specific prior written permission.
# * Neither the name of TU Wien, Department of Geodesy and Geoinformation
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written
# permission.

# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL VIENNA UNIVERSITY OF TECHNOLOGY,
# DEPARTMENT OF GEODESY AND GEOINFORMATION BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ARE DISCLAIMED. IN NO EVENT SHALL TU WIEN, DEPARTMENT OF GEODESY AND
# GEOINFORMATION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

import warnings
try:
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