split hazard module (CLIMADA-project#871)

* Add geodataframe to centroids: first commit * Remove raster methods, obsolete methods, and fix some. * Remove test for removed methods * Fix from geodataframe method * Remove set meta to lat lon * Update all I/O methods * Remove area pixel * Add method to compute the area per pixel (not attribute) * Make get_area_pixel * Remove not often used dist_coast and elevation * Remove unused meta * Change Centroids call to new signature * Remove vector - raster hazard methods * Restore legacy excell reader * Remove clear method * Remove clear test * Update read/write centroids in hazard * Support empty on land or region id * Check for empty region id * Set region id correctly * Remove scheduler * Add docstring * Add legacy read hdf5 * Replace incorrect dot product * Remove meta in assign centroids * Remove matlab test file * Update set lat/lon * Update test with init * Add note on method * Add from_meta class method * Update centroids init * Update read raster intensity / fraction data * undo changelog duplications * Update test for points outside of raster within threshold * Docstring and cosmetics * Add to default crs method * Fix legacy from hdf5 for empty extra values * Update legacy from_hdf5 to exclude 'latitude'/'longitude' from extra * Update centroids.select to work properly with mask and indices * Fix forecast translate bug * Remove _set_centroids * Remove reproject raster * Remove test hazard raster * Update naming for plot fraction centroids * Replace HAZ_DEMO_MAT with HAZ_TEST_TC * Replace mat file with hdf5 test file * Rewrite write raster method for hazard * Add a default for sel_cen in mask * Correct indent typos * Change duplicate test function name * Replace mat file with hdf5 * Remove unused mat file import * Add legacy code to read old centroid hdf5 files. * Update access to centroids dist coast in gdf * test_trop_cyclone: get test centroids from data api * Add method to estimate meta raster from centroids * Remove unecessary conversion to ne_geom * Add good lat/lon values for unit test * centroids.centr.write_hdf5: eliminate side effect * centroids.centr.write_hdf5: elimination of side effect futile for pandas>=2.1 * centroids.test.TestCentroidsFuns.test_select_pass: adapt to downsized LAT/LON arrays * test_vec_ras: fix TestCentroids.test_centroids_check_pass * test_vec_ras: remove TestReader.test_write_read_points_h5 as it is redundant to and covered by test_centr.TestCentroidsWriter.test_read_write_hdf5 * fix typo in from_exposures method * centroids.centr.from_csv: write class method * centroids.centr.from_csv: correct order of xy * centroids.centr.from_excel: update method for gdf * centroids.centr. update csv and excel methods * Update tests in test_vec_ras * Update more tests and remove some with meta * centroids.centr.from_excel fix columnn indexing * Add possibility to NOT recenter crs for countires. This lead to a bug in the assign region id method because longitude of the countries geometry was shifted, but not the entry lat/lon points. * Add to_csre convenience method * Prepare the stage for setting other than admin0 region id * Remove uneeded import * cenctroids.centr: fix the obvious * gencenctroids.centr: change crs of the geodataframe instead of the geometry * white space cosmetics * PEP8 * Add solid region id and on land tests * Auto stash before merge of "feature/centroids_as_gdf" and "origin/feature/centroids_as_gdf" * Update distance and area tests * Update set crs in load vector shape file * centr.Centroids.from_excel: deal with region_id column * Fix write hazard raster with centroids.get_meta * Area pixel now correctly uses CEA * Add actual NE CRS test. * Make on_land and region_id always part of centroids * Update docstring * Update import path * Add overwrite argument to set region id and on land * Remove from base grid method * Fix some linting * Add some docstrings * Avoid costly computation in from geodataframe * Add comment * Fix typo * Fix set crs in from geodataframe * Make properties return arrays and not series * Remove not needed matlab vars * Revert return numpy arrays. * update from excel * update from_excel and from_csv * centroids.centr: from_excel fix column renaming and adapt to "new argument names" * Centroids.from_excel fix: switch key,val in test_storm_europe rather than in centr! * Return numpy arrays instead of series * Add some basic tests * Add tests for meta * Add tentative changelog. * Make keywords argument only : name lat/lon : remove set_* * Auto stash before revert of "Make keywords argument only : name lat/lon : remove set_*" * remove file * Fix exposures method test * Fix setting region id and on land at init. * Fix typo * Fix all close values for big numbers * Improve cosmetics. * update docstrings, doc cosmetics * update from_csv method, add test * remove DEF_VAR_CSV * Update from_excel method and test * remove unnecessary import * fix storm_europe tests * improve csv and excel tests * Apply suggestions from code review Co-authored-by: Lukas Riedel <[email protected]> * add excel, csv write methods and tests * Replace gdf with _gdf * Revert "Replace gdf with _gdf" This reverts commit c7e6ffd. * Update to_crs methods * Raise error if wrong exposures * Make from geodataframe more restrictive. * Use consistently to_crs method * Improve read centroids * Add literal to import * Update to crs with inplace argument * improve excel, csv method, test based on review * Update typing * Fix equal centroids for different gdf columns ordering * Make consistent gdf column ordering * Simplify from excel/csv * Add support for legacy hazard excell * Avoid single column loading error for df * fix path in write_excel, write_csv * fixing docstrings in centr.py * Update code cosmetics * Fix typo * Allo for kwargs in init and update from exposures * code linting * Centroids: test from_meta * Centroids: refined tests * Centroids: fix from_exposures * Centroids: implement get_pixel_shapes * Centroids: code linting and docstrings * hazard.test.test_base: remove undefined classes from main * hazard.base: remove unused imports * hazard.base: clean up imports * cosmetics * hazard.base.write_htdf5: add inline comment. * Centroids: fix _gdf_from_legacy_hdf signature * Centroids._gdf_from_legacy_hdf5: static, not classmethod * hazard.centroids.centr: pylint * centroids.centr : fix pydoc typos and pylint * climada.hazard.base: pylint * hazard.centroids.centr: pylint * climada.test.test_calicbration: use hzard test file with hdf5 format * Update climada/hazard/centroids/test/test_vec_ras.py Co-authored-by: Emanuel Schmid <[email protected]> * Hazard: fix write_raster, and some docstrings * test.test_calibration: fix test file name * test_api_client: added test for basic centroids plotting (just because it fails in PR CLIMADA-project#787) * centr.Centroids.plot: all changes reverted (with the exception of the obsolete `self.set_meta_to_lat_lon()`) * Hazard tutorial: use centroids.get_meta() instead of the attribute meta * Hazard tutorial: use Centroids() instead of from_lat_lon() * hazard tutorial: update Hazard from raster section * hazard tutorial: fix dist_coast access * climada.hazard.Hazard: remove broken vector file support * split hazard.base module into base, base_io and base_plot * test_base_xarray: logs format changed due to "sub-modules" * climada.hazard.HazardIO: remove broken vector file support * hazard.base_io: remove from_mat, move reproject_vector back to base * rename test_base_xarray * hazard.test: move TestReadExcel and TestReadHDF5 to test_base_io * climada.hazard.test.base/_io: fix imports * climada.hazard.centr: add deprecated methods section * fix from_tracks method, remove side effect * climada.hazard.trop_cyclone.TropCytlone.from_tracks: option for predefined dist_coast in centroids * TropicalCyclone.from_tracks pydoc * white space cosmetics * CHANGELOG: list deprecated and removed methods * Refactor and add to centroids testing * trop_cyclone.TropCyclone.from_tracks: fix dist_coast type * climada.hazard.Centroids: raise exception in deprecated methods that really _are_ failing now * redo lost commits on hazard.base * changelog: list added Centroids methods * hazard.centr: depreecated methods: pydoc string instaed of pass * fixing geodataframe issues * Revert "fixing geodataframe issues" This reverts commit d6d2859. * Changelog and module renaming * Changelog and module renaming * module renaming --------- Co-authored-by: Chahan Kropf <[email protected]> Co-authored-by: Sarah Hülsen <[email protected]> Co-authored-by: Igor Detring <[email protected]> Co-authored-by: Chahan M. Kropf <[email protected]> Co-authored-by: Lukas Riedel <[email protected]> Co-authored-by: Thomas Vogt <[email protected]> Co-authored-by: Thomas Vogt <[email protected]>
gdeskos · Jun 30, 2024 · b2b0872 · b2b0872
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ Code freeze date: YYYY-MM-DD
 CLIMADA tutorials. [#872](https://github.com/CLIMADA-project/climada_python/pull/872)
 - Centroids complete overhaul. Most function should be backward compatible. Internal data is stored in a geodataframe attribute. Raster are now stored as points, and the meta attribute is removed. Several methds were deprecated or removed. [#787](https://github.com/CLIMADA-project/climada_python/pull/787)
 - Improved error messages produced by `ImpactCalc.impact()` in case impact function in the exposures is not found in impf_set [#863](https://github.com/CLIMADA-project/climada_python/pull/863)
+- Changed module structure: `climada.hazard.Hazard` has been split into the modules `base`, `io` and `plot` [#871](https://github.com/CLIMADA-project/climada_python/pull/871)
 
 ### Fixed
 

diff --git a/climada/entity/exposures/base.py b/climada/entity/exposures/base.py
@@ -486,7 +486,7 @@ def from_raster(cls, file_name, band=1, src_crs=None, window=None,
             reproject to given crs
         transform : rasterio.Affine
             affine transformation to apply
-        wdith : float
+        width : float
             number of lons for transform
         height : float
             number of lats for transform

diff --git a/climada/hazard/base.py b/climada/hazard/base.py
diff --git a/climada/hazard/io.py b/climada/hazard/io.py
diff --git a/climada/hazard/plot.py b/climada/hazard/plot.py
@@ -0,0 +1,283 @@
+"""
+This file is part of CLIMADA.
+
+Copyright (C) 2017 ETH Zurich, CLIMADA contributors listed in AUTHORS.
+
+CLIMADA is free software: you can redistribute it and/or modify it under the
+terms of the GNU General Public License as published by the Free
+Software Foundation, version 3.
+
+CLIMADA is distributed in the hope that it will be useful, but WITHOUT ANY
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with CLIMADA. If not, see <https://www.gnu.org/licenses/>.
+
+---
+
+Define Hazard Plotting Methods.
+"""
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+import climada.util.plot as u_plot
+
+
+# pylint: disable=no-member
+
+class HazardPlot():
+    """
+    Contains all plotting methods of the Hazard class
+    """
+
+    def plot_rp_intensity(self, return_periods=(25, 50, 100, 250),
+                          smooth=True, axis=None, figsize=(9, 13), adapt_fontsize=True,
+                          **kwargs):
+        """Compute and plot hazard exceedance intensity maps for different
+        return periods. Calls local_exceedance_inten.
+
+        Parameters
+        ----------
+        return_periods: tuple(int), optional
+            return periods to consider
+        smooth: bool, optional
+            smooth plot to plot.RESOLUTIONxplot.RESOLUTION
+        axis: matplotlib.axes._subplots.AxesSubplot, optional
+            axis to use
+        figsize: tuple, optional
+            figure size for plt.subplots
+        kwargs: optional
+            arguments for pcolormesh matplotlib function used in event plots
+
+        Returns
+        -------
+        axis, inten_stats:  matplotlib.axes._subplots.AxesSubplot, np.ndarray
+            intenstats is return_periods.size x num_centroids
+        """
+        inten_stats = self.local_exceedance_inten(np.array(return_periods))
+        colbar_name = 'Intensity (' + self.units + ')'
+        title = list()
+        for ret in return_periods:
+            title.append('Return period: ' + str(ret) + ' years')
+        axis = u_plot.geo_im_from_array(inten_stats, self.centroids.coord,
+                                        colbar_name, title, smooth=smooth, axes=axis,
+                                        figsize=figsize, adapt_fontsize=adapt_fontsize, **kwargs)
+        return axis, inten_stats
+
+    def plot_intensity(self, event=None, centr=None, smooth=True, axis=None, adapt_fontsize=True,
+                       **kwargs):
+        """Plot intensity values for a selected event or centroid.
+
+        Parameters
+        ----------
+        event: int or str, optional
+            If event > 0, plot intensities of
+            event with id = event. If event = 0, plot maximum intensity in
+            each centroid. If event < 0, plot abs(event)-largest event. If
+            event is string, plot events with that name.
+        centr: int or tuple, optional
+            If centr > 0, plot intensity
+            of all events at centroid with id = centr. If centr = 0,
+            plot maximum intensity of each event. If centr < 0,
+            plot abs(centr)-largest centroid where higher intensities
+            are reached. If tuple with (lat, lon) plot intensity of nearest
+            centroid.
+        smooth: bool, optional
+            Rescale data to RESOLUTIONxRESOLUTION pixels (see constant
+            in module `climada.util.plot`)
+        axis: matplotlib.axes._subplots.AxesSubplot, optional
+            axis to use
+        kwargs: optional
+            arguments for pcolormesh matplotlib function
+            used in event plots or for plot function used in centroids plots
+
+        Returns
+        -------
+            matplotlib.axes._subplots.AxesSubplot
+
+        Raises
+        ------
+            ValueError
+        """
+        col_label = f'Intensity ({self.units})'
+        crs_epsg, _ = u_plot.get_transformation(self.centroids.geometry.crs)
+        if event is not None:
+            if isinstance(event, str):
+                event = self.get_event_id(event)
+            return self._event_plot(event, self.intensity, col_label,
+                                    smooth, crs_epsg, axis, adapt_fontsize=adapt_fontsize, **kwargs)
+        if centr is not None:
+            if isinstance(centr, tuple):
+                _, _, centr = self.centroids.get_closest_point(centr[0], centr[1])
+            return self._centr_plot(centr, self.intensity, col_label, axis, **kwargs)
+
+        raise ValueError("Provide one event id or one centroid id.")
+
+    def plot_fraction(self, event=None, centr=None, smooth=True, axis=None,
+                      **kwargs):
+        """Plot fraction values for a selected event or centroid.
+
+        Parameters
+        ----------
+        event: int or str, optional
+            If event > 0, plot fraction of event
+            with id = event. If event = 0, plot maximum fraction in each
+            centroid. If event < 0, plot abs(event)-largest event. If event
+            is string, plot events with that name.
+        centr: int or tuple, optional
+            If centr > 0, plot fraction
+            of all events at centroid with id = centr. If centr = 0,
+            plot maximum fraction of each event. If centr < 0,
+            plot abs(centr)-largest centroid where highest fractions
+            are reached. If tuple with (lat, lon) plot fraction of nearest
+            centroid.
+        smooth: bool, optional
+            Rescale data to RESOLUTIONxRESOLUTION pixels (see constant
+            in module `climada.util.plot`)
+        axis: matplotlib.axes._subplots.AxesSubplot, optional
+            axis to use
+        kwargs: optional
+            arguments for pcolormesh matplotlib function
+            used in event plots or for plot function used in centroids plots
+
+        Returns
+        -------
+            matplotlib.axes._subplots.AxesSubplot
+
+        Raises
+        ------
+            ValueError
+        """
+        col_label = 'Fraction'
+        if event is not None:
+            if isinstance(event, str):
+                event = self.get_event_id(event)
+            return self._event_plot(event, self.fraction, col_label, smooth, axis,
+                                    **kwargs)
+        if centr is not None:
+            if isinstance(centr, tuple):
+                _, _, centr = self.centroids.get_closest_point(centr[0], centr[1])
+            return self._centr_plot(centr, self.fraction, col_label, axis, **kwargs)
+
+        raise ValueError("Provide one event id or one centroid id.")
+
+    def _event_plot(self, event_id, mat_var, col_name, smooth, crs_espg, axis=None,
+                    figsize=(9, 13), adapt_fontsize=True, **kwargs):
+        """Plot an event of the input matrix.
+
+        Parameters
+        ----------
+        event_id: int or np.array(int)
+            If event_id > 0, plot mat_var of
+            event with id = event_id. If event_id = 0, plot maximum
+            mat_var in each centroid. If event_id < 0, plot
+            abs(event_id)-largest event.
+        mat_var: sparse matrix
+            Sparse matrix where each row is an event
+        col_name: sparse matrix
+            Colorbar label
+        smooth: bool, optional
+            smooth plot to plot.RESOLUTIONxplot.RESOLUTION
+        axis: matplotlib.axes._subplots.AxesSubplot, optional
+            axis to use
+        figsize: tuple, optional
+            figure size for plt.subplots
+        kwargs: optional
+            arguments for pcolormesh matplotlib function
+
+        Returns
+        -------
+            matplotlib.figure.Figure, matplotlib.axes._subplots.AxesSubplot
+        """
+        if not isinstance(event_id, np.ndarray):
+            event_id = np.array([event_id])
+        array_val = list()
+        l_title = list()
+        for ev_id in event_id:
+            if ev_id > 0:
+                try:
+                    event_pos = np.where(self.event_id == ev_id)[0][0]
+                except IndexError as err:
+                    raise ValueError(f'Wrong event id: {ev_id}.') from err
+                im_val = mat_var[event_pos, :].toarray().transpose()
+                title = f'Event ID {self.event_id[event_pos]}: {self.event_name[event_pos]}'
+            elif ev_id < 0:
+                max_inten = np.asarray(np.sum(mat_var, axis=1)).reshape(-1)
+                event_pos = np.argpartition(max_inten, ev_id)[ev_id:]
+                event_pos = event_pos[np.argsort(max_inten[event_pos])][0]
+                im_val = mat_var[event_pos, :].toarray().transpose()
+                title = (f'{np.abs(ev_id)}-largest Event. ID {self.event_id[event_pos]}:'
+                         f' {self.event_name[event_pos]}')
+            else:
+                im_val = np.max(mat_var, axis=0).toarray().transpose()
+                title = f'{self.haz_type} max intensity at each point'
+
+            array_val.append(im_val)
+            l_title.append(title)
+
+        return u_plot.geo_im_from_array(array_val, self.centroids.coord, col_name,
+                                        l_title, smooth=smooth, axes=axis, figsize=figsize,
+                                        proj=crs_espg, adapt_fontsize=adapt_fontsize, **kwargs)
+
+    def _centr_plot(self, centr_idx, mat_var, col_name, axis=None, **kwargs):
+        """Plot a centroid of the input matrix.
+
+        Parameters
+        ----------
+        centr_id: int
+            If centr_id > 0, plot mat_var
+            of all events at centroid with id = centr_id. If centr_id = 0,
+            plot maximum mat_var of each event. If centr_id < 0,
+            plot abs(centr_id)-largest centroid where highest mat_var
+            are reached.
+        mat_var: sparse matrix
+            Sparse matrix where each column represents
+            a centroid
+        col_name: sparse matrix
+            Colorbar label
+        axis: matplotlib.axes._subplots.AxesSubplot, optional
+            axis to use
+        kwargs: optional
+            arguments for plot matplotlib function
+
+        Returns
+        -------
+            matplotlib.figure.Figure, matplotlib.axes._subplots.AxesSubplot
+        """
+        coord = self.centroids.coord
+        if centr_idx > 0:
+            try:
+                centr_pos = centr_idx
+            except IndexError as err:
+                raise ValueError(f'Wrong centroid id: {centr_idx}.') from err
+            array_val = mat_var[:, centr_pos].toarray()
+            title = (
+                f'Centroid {centr_idx}:'
+                f' ({np.around(coord[centr_pos, 0], 3)}, {np.around(coord[centr_pos, 1],3)})'
+            )
+        elif centr_idx < 0:
+            max_inten = np.asarray(np.sum(mat_var, axis=0)).reshape(-1)
+            centr_pos = np.argpartition(max_inten, centr_idx)[centr_idx:]
+            centr_pos = centr_pos[np.argsort(max_inten[centr_pos])][0]
+            array_val = mat_var[:, centr_pos].toarray()
+
+            title = (
+                f'{np.abs(centr_idx)}-largest Centroid. {centr_pos}:'
+                f' ({np.around(coord[centr_pos, 0], 3)}, {np.around(coord[centr_pos, 1], 3)})'
+            )
+        else:
+            array_val = np.max(mat_var, axis=1).toarray()
+            title = f'{self.haz_type} max intensity at each event'
+
+        if not axis:
+            _, axis = plt.subplots(1)
+        if 'color' not in kwargs:
+            kwargs['color'] = 'b'
+        axis.set_title(title)
+        axis.set_xlabel('Event number')
+        axis.set_ylabel(str(col_name))
+        axis.plot(range(len(array_val)), array_val, **kwargs)
+        axis.set_xlim([0, len(array_val)])
+        return axis