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Merge pull request #53 from sebhahn/fix_argsort
Avoid using argsort (speed issue)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 [email protected] | ||
| # 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. | ||
|
|
@@ -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: | ||
|
|
@@ -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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| 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 [email protected] | ||
| ''' | ||
| # * 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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| 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 [email protected] | ||
| ''' | ||
| # * 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 | ||
|
|
@@ -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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