diff --git a/.travis.yml b/.travis.yml index bf77561..d17b154 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,6 +4,8 @@ language: python python: - "2.7" +# - "3.5" +# - "3.6" addons: apt: @@ -16,11 +18,12 @@ install: # Make sure pip is up-to-date and has support for wheels - pip -q install -U pip # Install oq-engine dependencies - - pip -q install -r oq-engine/requirements-py27-linux64.txt - - pip -q install -e oq-engine/ - # Install HMTK extra dependencies - - pip -q install -r requirements-py27-linux64.txt - - pip -q install -e . + - if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then pip install -r oq-engine/requirements-py27-linux64.txt; + elif [[ $TRAVIS_PYTHON_VERSION == 3.5 ]]; then pip install -r oq-engine/requirements-py35-linux64.txt; + elif [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then pip install -r oq-engine/requirements-py36-linux64.txt; + else echo "Python not supported" && exit 1; fi + - pip install -e oq-engine/ + - pip install -e . script: - nosetests -vx tests diff --git a/README.md b/README.md index c84deff..6f7d76b 100755 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ gmpe-smtk ========= +[![Build Status](https://travis-ci.org/GEMScienceTools/gmpe-smtk.svg?branch=master)](https://travis-ci.org/GEMScienceTools/gmpe-smtk) Python and OpenQuake-based Toolkit for Analysis of Strong Motions and Interpretation of GMPEs @@ -16,7 +17,7 @@ License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Please take a minute of your time to read the disclaimer below. -Copyright (c) 2014-2017 GEM Foundation +Copyright (c) 2014-2018 GEM Foundation Disclaimer @@ -50,73 +51,31 @@ The GEM Foundation, and the authors of the software, assume no liability for use of the software. -dependencies +Installation ============ -The gmpe-smtk currently requires the following dependencies: +The gmpe-smtk is built on top of the [OpenQuake-engine](https://github.com/gem/oq-engine). +To install the toolkit, and ensure that it is aligned with the OpenQuake-engine +we recommend to install the OpenQuake-engine according to the instructions +given for your specific operating system. The full installation instructions for +OpenQuake can be found here: [https://github.com/gem/oq-engine](https://github.com/gem/oq-engine). -* OpenQuake Hazard Library ([oq-hazardlib](https://github.com/gem/oq-hazardlib)) -* Numpy (1.6.1 or later) (installed with oq-hazardlib) -* Scipy (0.11.0 or later) (installed with oq-hazardlib) -* Shapely (installed with oq-hazardlib) -* Matplotlib (1.3.x or later) -* h5py (2.2.0 or later) - -installation -============ - -* Windows - -Windows users should install the PythonXY software package (https://code.google.com/p/pythonxy/), which will install all of the dependencies except oq-hazardlib -To install oq-hazardlib it is recommended to install MinGW or Github for Windows. - -If using Github for Windows simply open a bash shell, clone the oq-hazardlib -repository using: - -```bash -git clone https://github.com/gem/oq-hazardlib.git -``` - -Then type - -```bash -cd oq-hazardlib -python setup.py install -``` - -To install the gmpe-smtk simply download the zipped code from the repository, -unzip it to a location of your choice then add the directory path to -the Environment Variables found in: - -My Computer -> Properties -> System Properties -> Advanced -> Environment Variables - -In the Environment Variables you will see a list of System Variables. Select -"Path" and then "Edit". Then simply add the directory of the gmpe-smtk to the -list of directories. - -* OSX/Linux - -To install oq-hazardlib simply clone the oq-hazardlib repository into a folder -of your choice. - +Once the OpenQuake-engine is installed, the gmpe-smtk repository is cloned by: ```bash -git clone https://github.com/gem/oq-hazardlib.git +git clone https://github.com/GEMScienceTools/gmpe-smtk ``` -Then run - +Then: ```bash -cd oq-hazardlib +cd gmpe-smtk python setup.py install ``` -Matplotlib and h5py can both be installed from the native package managers, -although it is recommended to use pip for this purpose. +For users interested in developing new features or contributing code to the +repository we strongly recommend to install the OpenQuake-engine according to +the instructions for [installing OpenQuake for development](https://github.com/gem/oq-engine/blob/master/doc/installing/development.md). -To install the gmpe-smtk, clone the code from the repository and then -add the following line to your bash or profile script: +The gmpe-smtk is currently written in Python 2.7 and work is now underway to +port this to Python 3.5. -```bash -export PYTHONPATH=/path/to/gmpe-smtk/:$PYTHONPATH -``` diff --git a/requirements-py27-linux64.txt b/requirements-py27-linux64.txt deleted file mode 100644 index 865f60e..0000000 --- a/requirements-py27-linux64.txt +++ /dev/null @@ -1,10 +0,0 @@ -# !! must update pip first! so wheels will be used !! - -# GEM Mirror -http://ftp.openquake.org/wheelhouse/linux/py27/PyYAML-3.12-cp27-cp27mu-manylinux1_x86_64.whl - -# Plotting stuff -http://ftp.openquake.org/wheelhouse/linux/py27/matplotlib-1.5.3-cp27-cp27mu-manylinux1_x86_64.whl -http://ftp.openquake.org/wheelhouse/linux/py/pyparsing-2.1.10-py2.py3-none-any.whl -http://ftp.openquake.org/wheelhouse/linux/py/cycler-0.10.0-py2.py3-none-any.whl -http://ftp.openquake.org/wheelhouse/linux/py/python_dateutil-2.6.0-py2.py3-none-any.whl diff --git a/requirements-py35-linux64.txt b/requirements-py35-linux64.txt deleted file mode 100644 index 73c9d36..0000000 --- a/requirements-py35-linux64.txt +++ /dev/null @@ -1,10 +0,0 @@ -# !! must update pip first! so wheels will be used !! - -# GEM Mirror -http://ftp.openquake.org/wheelhouse/linux/py35/PyYAML-3.12-cp35-cp35m-manylinux1_x86_64.whl - -# Plotting stuff -http://ftp.openquake.org/wheelhouse/linux/py35/matplotlib-1.5.3-cp35-cp35m-manylinux1_x86_64.whl -http://ftp.openquake.org/wheelhouse/linux/py/pyparsing-2.1.10-py2.py3-none-any.whl -http://ftp.openquake.org/wheelhouse/linux/py/cycler-0.10.0-py2.py3-none-any.whl -http://ftp.openquake.org/wheelhouse/linux/py/python_dateutil-2.6.0-py2.py3-none-any.whl diff --git a/smtk/hazard/conditional_simulation.py b/smtk/hazard/conditional_simulation.py index c03e838..82665a3 100755 --- a/smtk/hazard/conditional_simulation.py +++ b/smtk/hazard/conditional_simulation.py @@ -141,13 +141,13 @@ def conditional_simulation(known_sites, residuals, unknown_sites, imt, nsim, unknown_sites.depths = np.zeros_like(unknown_sites.depths) cov_kk = correlation_model._get_correlation_matrix(known_sites, imt).I cov_uu = correlation_model._get_correlation_matrix(unknown_sites, imt) - d_k_uk = np.zeros([known_sites.total_sites, unknown_sites.total_sites], + d_k_uk = np.zeros([len(known_sites), len(unknown_sites)], dtype=float) - for iloc in range(0, known_sites.total_sites): - d_k_uk[iloc, :] = geodetic_distance(known_sites.lons[iloc], - known_sites.lats[iloc], - unknown_sites.lons, - unknown_sites.lats) + for iloc in range(len(known_sites)): + d_k_uk[iloc, :] = geodetic_distance(known_sites.array["lons"][iloc], + known_sites.array["lats"][iloc], + unknown_sites.array["lons"], + unknown_sites.array["lats"]) cov_ku = correlation_model._get_correlation_model(d_k_uk, imt) mu = cov_ku.T * cov_kk * np.matrix(residuals).T stddev = cov_uu - (cov_ku.T * cov_kk * cov_ku) diff --git a/smtk/intensity_measures.py b/smtk/intensity_measures.py index 0c6ec31..9ded12c 100755 --- a/smtk/intensity_measures.py +++ b/smtk/intensity_measures.py @@ -186,7 +186,7 @@ def get_response_spectrum(acceleration, time_step, periods, damping=0.05, periods, damping, units) - spectrum, time_series, accel, vel, disp = response_spec.evaluate() + spectrum, time_series, accel, vel, disp = response_spec() spectrum["PGA"] = time_series["PGA"] spectrum["PGV"] = time_series["PGV"] spectrum["PGD"] = time_series["PGD"] @@ -231,7 +231,7 @@ def geometric_mean_spectrum(sax, say): Dictionary of response spectrum outputs from y-component """ sa_gm = {} - for key in sax.keys(): + for key in sax: if key == "Period": sa_gm[key] = sax[key] else: @@ -243,7 +243,7 @@ def arithmetic_mean_spectrum(sax, say): Returns the arithmetic mean of the response spectrum """ sa_am = {} - for key in sax.keys(): + for key in sax: if key == "Period": sa_am[key] = sax[key] else: @@ -255,7 +255,7 @@ def envelope_spectrum(sax, say): Returns the envelope of the response spectrum """ sa_env = {} - for key in sax.keys(): + for key in sax: if key == "Period": sa_env[key] = sax[key] else: diff --git a/smtk/parsers/simple_flatfile_parser_sara.py b/smtk/parsers/simple_flatfile_parser_sara.py index 788e29b..6c9f3f2 100755 --- a/smtk/parsers/simple_flatfile_parser_sara.py +++ b/smtk/parsers/simple_flatfile_parser_sara.py @@ -1,736 +1,737 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -# vim: tabstop=4 shiftwidth=4 softtabstop=4 -# -# Copyright (C) 2014-2017 GEM Foundation and G. Weatherill -# -# OpenQuake is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License as published -# by the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# OpenQuake 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 Affero General Public License for more details. -# -# You should have received a copy of the GNU Affero General Public License -# along with OpenQuake. If not, see . - -""" -Parser from a "Simple Flatfile + ascii format" to SMTK -""" -import os -import csv -import numpy as np -import copy -import h5py -from sets import Set -from linecache import getline -from collections import OrderedDict -from datetime import datetime -# In order to define default fault dimension import scaling relationships -from openquake.hazardlib.scalerel.strasser2010 import (StrasserInterface, - StrasserIntraslab) -from openquake.hazardlib.scalerel.wc1994 import WC1994 -from openquake.hazardlib.geo.mesh import Mesh, RectangularMesh -from openquake.hazardlib.geo.point import Point -from openquake.hazardlib.geo.line import Line -from openquake.hazardlib.geo.surface.simple_fault import SimpleFaultSurface -import smtk.trellis.configure as rcfg -from smtk.sm_database import * -from smtk.sm_utils import convert_accel_units -from smtk.parsers.base_database_parser import (get_float, get_int, - get_positive_float, - get_positive_int, - SMDatabaseReader, - SMTimeSeriesReader, - SMSpectraReader) - -HEADER_LIST = Set([ - 'Record Sequence Number', 'EQID', 'Earthquake Name', 'Country', 'Year', - 'Month', 'Day', 'Hour', 'Minute', 'Second', - 'Epicenter Latitude (deg; positive N)', - 'Epicenter Longitude (deg; positive E)', 'Hypocenter Depth (km)', - 'Magnitude', 'Magnitude type', 'Magnitude uncertainty', 'Mo (dyne.cm)', - 'Tectonic environment (Crustal; Inslab; Interface; Stable; Geothermal; Volcanic; Oceanic_crust)', - 'Earthquake in Extensional Regime: 1=Yes; 0=No', - 'Nodal Plane 1 Strike (deg)', - 'Nodal Plane 1 Dip (deg)', 'Nodal Plane 1 Rake Angle (deg)', - 'Nodal Plane 2 Strike (deg)', 'Nodal Plane 2 Dip (deg)', - 'Nodal Plane 2 Rake Angle (deg)', 'Fault Plane (1; 2; X)', - 'Style-of-Faulting (S; R; N; U)', 'Fault Name', - 'Depth to Top Of Fault Rupture Model', - 'Fault Rupture Length (km)', 'Fault Rupture Width (km)', - 'Along-strike Hypocenter location on the fault (fraction between 0 and 1)', - 'Along-width Hypocenter location on the fault (fraction between 0 and 1)', - 'Static Stress Drop (bars)', 'Type Static Stress Drop', - 'Directivity flag (Y; N; U)', 'Station ID', 'Station Code', - 'Station Latitude (deg positive N)', 'Station Longitude (deg positive E)', - 'Station Elevation (m)', - 'Site Class (Hard Rock; Rock; Stiff Soil; Soft Soil)', - 'Preferred NEHRP Based on Vs30', 'Preferred Vs30 (m/s)', - 'Measured(1)/Inferred(2) Class', 'Sigma of Vs30 (in natural log Units)', - 'Depth to Basement Rock', 'Z1 (m)','Z2.5 (m)', 'Epicentral Distance (km)', - 'Hypocentral Distance (km)', 'Joyner-Boore Distance (km)', - 'Rupture Distance (km)', 'Source to Site Azimuth (deg)', 'FW/HW Indicator', - 'Forearc/Backarc for subduction events', 'File Name (Horizontal 1)', - 'File Name (Horizontal 2)','File Name (Vertical)', - 'Digital (D)/Analog (A) Recording', 'Acceleration (A)/Velocity (V)', - 'Unit (cm/s/s; m/s/s; g)', 'File format', 'Processing flag', - 'Type of Filter','npass','nroll','HP-H1 (Hz)','HP-H2 (Hz)', - 'LP-H1 (Hz)', 'LP-H2 (Hz)', 'Factor', 'Lowest Usable Freq - H1 (Hz)', - 'Lowest Usable Freq - H2 (Hz)', 'Lowest Usable Freq - Ave. Component (Hz)', - 'Maximum Usable Freq - Ave. Component (Hz)', 'HP-V (Hz)', 'LP-V (Hz)', - 'Lowest Usable Freq - V (Hz)','Comments']) - -FILTER_TYPE = {"BW": "Butterworth", - "OR": "Ormsby", - "Ormsby": "Ormsby", - "Acausal Butterworth": "Acausal Butterworth", - "Causal Butterworth": "Causal Butterworth"} - -NEW_MECHANISM_TYPE = {"N": "Normal", - "S": "Strike-Slip", - "R": "Reverse", - "U": "Unknown", - "RO": "Reverse-Oblique", - "NO": "Normal-Oblique"} - -class SimpleFlatfileParserV9(SMDatabaseReader): - """ - Parser for strong motio database stored in a "Simple" flatfile format. - Typically this format is an Excel spreadsheet, though for the current - purposes it is assumed the spreadsheet is formatted as csv - """ - def parse(self): - """ - Parses the database - """ - HEADER_LIST1 = copy.deepcopy(HEADER_LIST) - self._header_check(HEADER_LIST1) - # Read in csv - reader = csv.DictReader(open(self.filename, "r")) - metadata = [] - self.database = GroundMotionDatabase(self.id, self.name) - self._get_site_id = self.database._get_site_id - for row in reader: - self.database.records.append(self._parse_record(row)) - return self.database - - def _header_check(self, headerslist): - """ - Checks to see if any of the headers are missing, raises error if so. - Also informs the user of redundent headers in the input file. - """ - # Check which of the pre-defined headers are missing - headers = Set((getline(self.filename, 1).rstrip("\n")).split(",")) - missing_headers = headerslist.difference(headers) - if len(missing_headers) > 0: - output_string = ", ".join([value for value in missing_headers]) - raise IOError("The following headers are missing from the input " - "file: %s" % output_string) - - additional_headers = headers.difference(headerslist) - if len(additional_headers) > 0: - for header in additional_headers: - print "Header %s not recognised - ignoring this data!" % header - return - - def _parse_record(self, metadata): - """ - Parses the record information and returns an instance of the - :class: smtk.sm_database.GroundMotionRecord - """ - # Waveform ID - wfid = metadata["Record Sequence Number"] - # Event information - event = self._parse_event_data(metadata) - # Site information - site = self._parse_site_data(metadata) - # Distance Information - distances = self._parse_distance_data(event, site, metadata) - # Components - x_comp, y_comp, vertical = self._parse_processing_data(wfid, metadata) - # Return record metadata - lup = get_float(metadata["Lowest Usable Freq - Ave. Component (Hz)"]) - if lup: - lup = 1. / lup - sup = get_float(metadata["Maximum Usable Freq - Ave. Component (Hz)"]) - if sup: - sup = 1. / sup - return GroundMotionRecord(wfid, - [metadata["File Name (Horizontal 1)"], - metadata["File Name (Horizontal 2)"], - metadata["File Name (Vertical)"]], - event, - distances, - site, - x_comp, - y_comp, - longest_period=lup, - shortest_period=sup) - - def _parse_event_data(self, metadata): - """ - Read in the distance related metadata and return an instance of the - :class: smtk.sm_database.Earthquake - - """ - data_fields = ['Month', 'Day', 'Hour', 'Minute', 'Second'] - for f in data_fields: - metadata[f] = metadata[f].zfill(2) - - # Date and Time - year, month, day, hour, minute, second = self._validate_datetime( - metadata) - #year = get_int(metadata["Year"]) - #month = get_int(metadata["Month"]) - #day = get_int(metadata["Day"]) - #hour = get_int(metadata["Hour"]) - #minute = get_int(metadata["Minute"]) - #second = get_int(metadata["Second"]) - eq_datetime = datetime(year, month, day, hour, minute, second) - # Event ID and Name - eq_id = metadata["EQID"] - eq_name = metadata["Earthquake Name"] - # Focal Mechanism - focal_mechanism = self._get_focal_mechanism(eq_id, eq_name, metadata) - - focal_mechanism.scalar_moment = get_float(metadata["Mo (dyne.cm)"]) *\ - 1E-7 - # Read magnitude - pref_mag = Magnitude(get_float(metadata["Magnitude"]), - metadata["Magnitude type"], - sigma=get_float(metadata["Magnitude uncertainty"])) - # Create Earthquake Class - eqk = Earthquake(eq_id, eq_name, eq_datetime, - get_float(metadata["Epicenter Longitude (deg; positive E)"]), - get_float(metadata["Epicenter Latitude (deg; positive N)"]), - get_float(metadata["Hypocenter Depth (km)"]), - pref_mag, - focal_mechanism, - metadata["Country"]) - - # hypocenter location - f1 = get_float(metadata[ - "Along-strike Hypocenter location " + - "on the fault (fraction between 0 and 1)"]) - f2 = get_float(metadata[ - "Along-width Hypocenter location " + - "on the fault (fraction between 0 and 1)"]) - if f1 is None or f2 is None: - hypo_loc = (0.5, 0.7) - else: - hypo_loc = (f1, f2) - - eqk.tectonic_region = metadata["Tectonic environment (Crustal; Inslab; Interface; Stable; Geothermal; Volcanic; Oceanic_crust)"] - if (eqk.tectonic_region == "Stable" or - eqk.tectonic_region == "Crustal" or - eqk.tectonic_region == "Oceanic_crust"): - msr=WC1994() - elif eqk.tectonic_region == "Inslab": - msr=StrasserIntraslab() - elif eqk.tectonic_region == "Interface": - msr=StrasserInterface() - - # Warning rake set to 0.0 in scaling relationship - applies only - # to WC1994 - area = msr.get_median_area(pref_mag.value, 0.0) - aspect_ratio = 1.5 - width_model = np.sqrt(area / aspect_ratio) - length_model = aspect_ratio * width_model - ztor_model = eqk.depth - width_model / 2. - if ztor_model < 0: - ztor_model = 0.0 - - length = get_positive_float(metadata["Fault Rupture Length (km)"]) - if length is None: - length = length_model - width = get_positive_float(metadata["Fault Rupture Width (km)"]) - if width is None: - width = width_model - ztor = get_float(metadata["Depth to Top Of Fault Rupture Model"]) - if ztor is None: - ztor=ztor_model - - # Rupture - eqk.rupture = Rupture(eq_id, - eq_name, - pref_mag, - length, - width, - ztor, - hypo_loc=hypo_loc) -# get_float(metadata["Fault Rupture Length (km)"]), -# get_float(metadata["Fault Rupture Width (km)"]), -# get_float(metadata["Depth to Top Of Fault Rupture Model"]), -# hypo_loc=hypo_loc) - eqk.rupture.get_area() - return eqk - - @staticmethod - def _validate_datetime(metadata): - """ - SARA flatfile should be formatted correctly but other flatfiles - are prone to bad datetime values - these will be overwritten - """ - return (get_int(metadata["Year"]), get_int(metadata["Month"]), - get_int(metadata["Day"]), get_int(metadata["Hour"]), - get_int(metadata["Minute"]), get_int(metadata["Second"])) - - def _get_focal_mechanism(self, eq_id, eq_name, metadata): - """ - Returns the focal mechanism information as an instance of the - :class: smtk.sigma_database.FocalMechanism - """ - nodal_planes = GCMTNodalPlanes() - # By default nodal plane 1 is assumed to be the fault plane in smtk. - # Depending on parameter fault_plane import correct angles in nodal - # planes 1 and 2 (1 being the fault plane) - if metadata['Fault Plane (1; 2; X)'] == '1': - nodal_planes.nodal_plane_1 = { - "strike": get_float(metadata['Nodal Plane 1 Strike (deg)']), - "dip": get_float(metadata['Nodal Plane 1 Dip (deg)']), - "rake": get_float(metadata['Nodal Plane 1 Rake Angle (deg)'])} - - nodal_planes.nodal_plane_2 = { - "strike": get_float(metadata['Nodal Plane 2 Strike (deg)']), - "dip": get_float(metadata['Nodal Plane 2 Dip (deg)']), - "rake": get_float(metadata['Nodal Plane 2 Rake Angle (deg)'])} - elif metadata['Fault Plane (1; 2; X)'] == '2': - nodal_planes.nodal_plane_1 = { - "strike": get_float(metadata['Nodal Plane 2 Strike (deg)']), - "dip": get_float(metadata['Nodal Plane 2 Dip (deg)']), - "rake": get_float(metadata['Nodal Plane 2 Rake Angle (deg)'])} - - nodal_planes.nodal_plane_2 = { - "strike": get_float(metadata['Nodal Plane 1 Strike (deg)']), - "dip": get_float(metadata['Nodal Plane 1 Dip (deg)']), - "rake": get_float(metadata['Nodal Plane 1 Rake Angle (deg)'])} - elif metadata['Fault Plane (1; 2; X)'] == 'X': - # Check if values for strike or dip are given otherwise set - # strike=0 and dip=90 and fill strike and dip for fault plane 1 - # What can we do for rake? - strike = get_float(metadata['Nodal Plane 1 Strike (deg)']) - if strike is None: - strike = get_float(metadata['Nodal Plane 2 Strike (deg)']) - if strike is None: - strike = 0.0 - dip = get_float(metadata['Nodal Plane 1 Dip (deg)']) - if dip is None: - dip = get_float(metadata['Nodal Plane 2 Dip (deg)']) - if dip is None: - dip = 90.0 - nodal_planes.nodal_plane_1 = {"strike": strike, - "dip": dip, - "rake": None} - nodal_planes.nodal_plane_2 = {"strike": None, - "dip": None, - "rake": None} - - nodal_planes = self._check_mechanism(nodal_planes) - principal_axes = GCMTPrincipalAxes() - mech_type =\ - NEW_MECHANISM_TYPE[metadata["Style-of-Faulting (S; R; N; U)"]] - return FocalMechanism(eq_id, eq_name, nodal_planes, principal_axes, - mechanism_type=mech_type) - - def _check_mechanism(self, nodal_planes): - """ - Verify that the nodal planes are valid, and default nodal plane 1 - to a "null" plane if not - """ - if nodal_planes.nodal_plane_1["strike"]: - nodal_planes.nodal_plane_1["strike"] = \ - nodal_planes.nodal_plane_1["strike"] % 360.0 - if nodal_planes.nodal_plane_2["strike"]: - nodal_planes.nodal_plane_2["strike"] = \ - nodal_planes.nodal_plane_2["strike"] % 360.0 - - valid_plane_1 = nodal_planes.nodal_plane_1["strike"] >= 0.0 and\ - nodal_planes.nodal_plane_1["strike"] < 360.0 and\ - nodal_planes.nodal_plane_1["dip"] > 0.0 and\ - nodal_planes.nodal_plane_1["dip"] <= 90.0 and\ - nodal_planes.nodal_plane_1["rake"] >= -180.0 and\ - nodal_planes.nodal_plane_1["rake"] <= 180.0 - valid_plane_2 = nodal_planes.nodal_plane_2["strike"] >= 0.0 and\ - nodal_planes.nodal_plane_2["strike"] <= 360.0 and\ - nodal_planes.nodal_plane_2["dip"] > 0.0 and\ - nodal_planes.nodal_plane_2["dip"] <= 90.0 and\ - nodal_planes.nodal_plane_2["rake"] >= -180.0 and\ - nodal_planes.nodal_plane_2["rake"] <= 180.0 - if valid_plane_1: - return nodal_planes - - # If nodal plane 2 is valid then swap over - if valid_plane_2: - np1 = copy.deepcopy(nodal_planes.nodal_plane_1) - np2 = copy.deepcopy(nodal_planes.nodal_plane_2) - nodal_planes.nodal_plane_1 = np2 - nodal_planes.nodal_plane_2 = np1 - else: - nodal_planes.nodal_plane_1 = {"strike": 0.0, - "dip": 90.0, - "rake": 0.0} - return nodal_planes - - - - - def _parse_distance_data(self, event, site, metadata): - """ - Read in the distance related metadata and return an instance of the - :class: smtk.sm_database.RecordDistance - """ - # Compute various distance metrics - # Add calculation of Repi, Rhypo from event and station localizations - # (latitudes, longitudes, depth, elevation)? - target_site = Mesh(np.array([site.longitude]), - np.array([site.latitude]), - np.array([-site.altitude / 1000.0])) - # Warning ratio fixed to 1.5 - ratio=1.5 - surface_modeled = rcfg.create_planar_surface( - Point(event.longitude, event.latitude, event.depth), - event.mechanism.nodal_planes.nodal_plane_1['strike'], - event.mechanism.nodal_planes.nodal_plane_1['dip'], - event.rupture.area, - ratio) - hypocenter = rcfg.get_hypocentre_on_planar_surface( - surface_modeled, - event.rupture.hypo_loc) - try: - surface_modeled._create_mesh() - except: - dip = surface_modeled.get_dip() - dip_dir = (surface_modeled.get_strike() - 90.) % 360. - ztor = surface_modeled.top_left.depth - d_x = ztor * np.tan(np.radians(90.0 - dip)) - top_left_surface = surface_modeled.top_left.point_at(d_x, - -ztor, - dip_dir) - top_left_surface.depth = 0. - top_right_surface = surface_modeled.top_right.point_at(d_x, - -ztor, - dip_dir) - top_right_surface.depth = 0. - surface_modeled = SimpleFaultSurface.from_fault_data( - Line([top_left_surface, top_right_surface]), - surface_modeled.top_left.depth, - surface_modeled.bottom_left.depth, - surface_modeled.get_dip(), - 1.0) - - # Rhypo - Rhypo = get_float(metadata["Hypocentral Distance (km)"]) - if Rhypo is None: - Rhypo = hypocenter.distance_to_mesh(target_site) - # Repi - Repi = get_float(metadata["Epicentral Distance (km)"]) - if Repi is None: - Repi= hypocenter.distance_to_mesh(target_site, with_depths=False) - # Rrup - Rrup = get_float(metadata["Rupture Distance (km)"]) - if Rrup is None: - Rrup = surface_modeled.get_min_distance(target_site) - # Rjb - Rjb = get_float(metadata["Joyner-Boore Distance (km)"]) - if Rjb is None: - Rjb = surface_modeled.get_joyner_boore_distance(target_site) - # Need to check if Rx and Ry0 are consistant with the other metrics - # when those are coming from the flatfile? - # Rx - Rx = surface_modeled.get_rx_distance(target_site) - # Ry0 - Ry0 = surface_modeled.get_ry0_distance(target_site) - - distance = RecordDistance( - repi = float(Repi), - rhypo = float(Rhypo), - rjb = float(Rjb), - rrup = float(Rrup), - r_x = float(Rx), - ry0 = float(Ry0)) - distance.azimuth = get_float(metadata["Source to Site Azimuth (deg)"]) - #distance.hanging_wall = get_float(metadata["FW/HW Indicator"]) - if metadata["FW/HW Indicator"] == "HW": - distance.hanging_wall = True - elif metadata["FW/HW Indicator"] == "FW": - distance.hanging_wall = False - else: - pass - - return distance - - def _parse_site_data(self, metadata): - """ - Returns the site data as an instance of the :class: - smtk.sm_database.RecordSite - """ - site = RecordSite( - self._get_site_id(metadata["Station ID"]), - metadata["Station ID"], - metadata["Station Code"], - get_float(metadata["Station Longitude (deg positive E)"]), - get_float(metadata["Station Latitude (deg positive N)"]), - get_float(metadata["Station Elevation (m)"]), - get_float(metadata["Preferred Vs30 (m/s)"]), - site_class=metadata['Site Class (Hard Rock; Rock; Stiff Soil; Soft Soil)'], - network_code=None, # not provided - ) - # network_code=metadata["Owner"]) - site.nehrp = metadata["Preferred NEHRP Based on Vs30"] - site.vs30_measured_type = metadata["Measured(1)/Inferred(2) Class"] - if metadata["Measured(1)/Inferred(2) Class"] == "1": - site.vs30_measured = True - else: - site.vs30_measured = False - site.vs30_uncertainty = get_float( - metadata["Sigma of Vs30 (in natural log Units)"]) - site.z1pt0 = get_float(metadata["Z1 (m)"]) - site.z1pt5 = None - # site.z1pt5 = get_float(metadata["Z1.5 (m)"]) - site.z2pt5 = get_float(metadata["Z2.5 (m)"]) - # Implement default values for z1pt0 and z2pt5 - if site.z1pt0 is None: - site.z1pt0 = rcfg.vs30_to_z1pt0_as08(site.vs30) - if site.z2pt5 is None: - site.z2pt5 = rcfg.z1pt0_to_z2pt5(site.z1pt0) - else: - # Need to convert z2pt5 from m to km - site.z2pt5 = site.z2pt5/1000.0 - if "Backarc" in metadata["Forearc/Backarc for subduction events"]: - site.backarc = True - site.instrument_type = metadata["Digital (D)/Analog (A) Recording"] - return site - - def _parse_processing_data(self, wfid, metadata): - """ - Parses the information for each component - """ - if metadata["Type of Filter"]: - filter_params1 = { - 'Type': FILTER_TYPE[metadata["Type of Filter"]], - 'Order': None, - 'Passes': get_positive_int(metadata['npass']), - 'NRoll': get_positive_int(metadata['nroll']), - 'High-Cut': get_positive_float(metadata["LP-H1 (Hz)"]), - 'Low-Cut': get_positive_float(metadata["HP-H1 (Hz)"])} - - filter_params2 = { - 'Type': FILTER_TYPE[metadata["Type of Filter"]], - 'Order': None, - 'Passes': get_positive_int(metadata['npass']), - 'NRoll': get_positive_int(metadata['nroll']), - 'High-Cut': get_positive_float(metadata["LP-H2 (Hz)"]), - 'Low-Cut': get_positive_float(metadata["HP-H2 (Hz)"])} - else: - filter_params1, filter_params2 = None, None - - intensity_measures = { - # All m - convert to cm - 'PGA': None, - 'PGV': None, - 'PGD': None - } - luf1 = get_float(metadata["Lowest Usable Freq - H1 (Hz)"]) - if luf1 and luf1 > 0.0: - lup1 = 1. / luf1 - else: - lup1 = None - luf2 = get_float(metadata["Lowest Usable Freq - H2 (Hz)"]) - if luf2 and luf2 > 0.0: - lup2 = 1. / luf2 - else: - lup2 = None - xcomp = Component(wfid, "1", - ims=intensity_measures, - longest_period=lup1, - waveform_filter=filter_params1, - units=metadata["Unit (cm/s/s; m/s/s; g)"]) - - ycomp = Component(wfid, "2", - ims=intensity_measures, - longest_period=lup2, - waveform_filter=filter_params2, - units=metadata["Unit (cm/s/s; m/s/s; g)"]) - - luf3 = get_float(metadata["Lowest Usable Freq - V (Hz)"]) - if luf3 and luf3 > 0.0: - filter_params3 = { - 'Type': FILTER_TYPE[metadata["Type of Filter"]], - 'Order': None, - 'Passes': get_int(metadata['npass']), - 'NRoll': get_int(metadata['nroll']), - 'High-Cut': get_float(metadata["LP-V (Hz)"]), - 'Low-Cut': get_float(metadata["HP-V (Hz)"])} - lup3 = 1. / luf3 - zcomp = Component(wfid, "V", - ims=intensity_measures, - longest_period=lup3, - waveform_filter=filter_params3, - units=metadata["Unit (cm/s/s; m/s/s; g)"]) - return xcomp, ycomp, zcomp - else: - return xcomp, ycomp, None - - - - -class NearFaultFlatFileParser(SimpleFlatfileParserV9): - - def parse(self): - """ - Parses the database - """ - HEADER_LIST1 = copy.deepcopy(HEADER_LIST) - HEADER_LIST1.add("Rcdpp") - self._header_check(HEADER_LIST1) - # Read in csv - reader = csv.DictReader(open(self.filename, "r")) - metadata = [] - self.database = GroundMotionDatabase(self.id, self.name) - self._get_site_id = self.database._get_site_id - for row in reader: - self.database.records.append(self._parse_record(row)) - return self.database - - def _parse_distance_data(self, event, site, metadata): - """ - Read in the distance related metadata and return an instance of the - :class: smtk.sm_database.RecordDistance - """ - # Compute various distance metrics - # Add calculation of Repi, Rhypo from event and station localizations - # (latitudes, longitudes, depth, elevation)? - target_site = Mesh(np.array([site.longitude]), - np.array([site.latitude]), - np.array([-site.altitude / 1000.0])) - # Warning ratio fixed to 1.5 - ratio=1.5 - surface_modeled = rcfg.create_planar_surface( - Point(event.longitude, event.latitude, event.depth), - event.mechanism.nodal_planes.nodal_plane_1['strike'], - event.mechanism.nodal_planes.nodal_plane_1['dip'], - event.rupture.area, - ratio) - hypocenter = rcfg.get_hypocentre_on_planar_surface( - surface_modeled, - event.rupture.hypo_loc) - try: - surface_modeled._create_mesh() - except: - dip = surface_modeled.get_dip() - dip_dir = (surface_modeled.get_strike() - 90.) % 360. - ztor = surface_modeled.top_left.depth - d_x = ztor * np.tan(np.radians(90.0 - dip)) - top_left_surface = surface_modeled.top_left.point_at(d_x, - -ztor, - dip_dir) - top_left_surface.depth = 0. - top_right_surface = surface_modeled.top_right.point_at(d_x, - -ztor, - dip_dir) - top_right_surface.depth = 0. - surface_modeled = SimpleFaultSurface.from_fault_data( - Line([top_left_surface, top_right_surface]), - surface_modeled.top_left.depth, - surface_modeled.bottom_left.depth, - surface_modeled.get_dip(), - 1.0) - - # Rhypo - Rhypo = get_float(metadata["Hypocentral Distance (km)"]) - if Rhypo is None: - Rhypo = hypocenter.distance_to_mesh(target_site) - # Repi - Repi = get_float(metadata["Epicentral Distance (km)"]) - if Repi is None: - Repi= hypocenter.distance_to_mesh(target_site, with_depths=False) - # Rrup - Rrup = get_float(metadata["Rupture Distance (km)"]) - if Rrup is None: - Rrup = surface_modeled.get_min_distance(target_site) - # Rjb - Rjb = get_float(metadata["Joyner-Boore Distance (km)"]) - if Rjb is None: - Rjb = surface_modeled.get_joyner_boore_distance(target_site) - # Rcdpp - Rcdpp = get_float(metadata["Rcdpp"]) - if Rcdpp is None: - Rcdpp = surface_modeled.get_cdppvalue(target_site) - # Need to check if Rx and Ry0 are consistant with the other metrics - # when those are coming from the flatfile? - # Rx - Rx = surface_modeled.get_rx_distance(target_site) - # Ry0 - Ry0 = surface_modeled.get_ry0_distance(target_site) - - distance = RecordDistance( - repi = float(Repi), - rhypo = float(Rhypo), - rjb = float(Rjb), - rrup = float(Rrup), - r_x = float(Rx), - ry0 = float(Ry0), - rcdpp = float(Rcdpp) ) - distance.azimuth = get_float(metadata["Source to Site Azimuth (deg)"]) - #distance.hanging_wall = get_float(metadata["FW/HW Indicator"]) - if metadata["FW/HW Indicator"] == "HW": - distance.hanging_wall = True - elif metadata["FW/HW Indicator"] == "FW": - distance.hanging_wall = False - else: - pass - - return distance - -class SimpleAsciiTimeseriesReader(SMTimeSeriesReader): - """ - Parses a simple ascii representation of a record in which the first line - contains the number of values and the time-step. Whilst the rest of the - file contains the acceleration record - """ - def parse_records(self, record): - """ - Parses the record set - """ - time_series = OrderedDict([ - ("X", {"Original": {}, "SDOF": {}}), - ("Y", {"Original": {}, "SDOF": {}}), - ("V", {"Original": {}, "SDOF": {}})]) - - target_names = time_series.keys() - for iloc, ifile in enumerate(self.input_files): - if not os.path.exists(ifile): - if iloc < 2: - # Expected horizontal component is missing - raise error - raise ValueError("Horizontal record %s is expected but " - "not found!" % ifile) - else: - print "Vertical record file %s not found" % ifile - del time_series["V"] - continue - else: - time_series[target_names[iloc]]["Original"] = \ - self._parse_time_history(ifile, record.xrecord.units) - if iloc < 2: - del time_series["V"] - - return time_series - - def _parse_time_history(self, ifile, units="cm/s/s"): - """ - Parses the time history from the file and returns a dictionary of - time-series properties - """ - output = {} - accel = np.genfromtxt(ifile, skip_header=1) - output["Acceleration"] = convert_accel_units(accel, self.units) - nvals, time_step = (getline(ifile, 1).rstrip("\n")).split() - output["Time-step"] = float(time_step) - output["Number Steps"] = int(nvals) - output["Units"] = units - output["PGA"] = np.max(np.fabs(output["Acceleration"])) - return output +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# vim: tabstop=4 shiftwidth=4 softtabstop=4 +# +# Copyright (C) 2014-2017 GEM Foundation and G. Weatherill +# +# OpenQuake is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License as published +# by the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# OpenQuake 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 Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with OpenQuake. If not, see . + +""" +Parser from a "Simple Flatfile + ascii format" to SMTK +""" +import os +import csv +import numpy as np +import copy +import h5py +from sets import Set +from linecache import getline +from collections import OrderedDict +from datetime import datetime +# In order to define default fault dimension import scaling relationships +from openquake.hazardlib.scalerel.strasser2010 import (StrasserInterface, + StrasserIntraslab) +from openquake.hazardlib.scalerel.wc1994 import WC1994 +from openquake.hazardlib.geo.mesh import Mesh, RectangularMesh +from openquake.hazardlib.geo.point import Point +from openquake.hazardlib.geo.line import Line +from openquake.hazardlib.geo.surface.simple_fault import SimpleFaultSurface +import smtk.trellis.configure as rcfg +from smtk.sm_database import * +from smtk.sm_utils import convert_accel_units +from smtk.parsers.base_database_parser import (get_float, get_int, + get_positive_float, + get_positive_int, + SMDatabaseReader, + SMTimeSeriesReader, + SMSpectraReader) + +HEADER_LIST = Set([ + 'Record Sequence Number', 'EQID', 'Earthquake Name', 'Country', 'Year', + 'Month', 'Day', 'Hour', 'Minute', 'Second', + 'Epicenter Latitude (deg; positive N)', + 'Epicenter Longitude (deg; positive E)', 'Hypocenter Depth (km)', + 'Magnitude', 'Magnitude type', 'Magnitude uncertainty', 'Mo (dyne.cm)', + 'Tectonic environment (Crustal; Inslab; Interface; Stable; Geothermal; Volcanic; Oceanic_crust)', + 'Earthquake in Extensional Regime: 1=Yes; 0=No', + 'Nodal Plane 1 Strike (deg)', + 'Nodal Plane 1 Dip (deg)', 'Nodal Plane 1 Rake Angle (deg)', + 'Nodal Plane 2 Strike (deg)', 'Nodal Plane 2 Dip (deg)', + 'Nodal Plane 2 Rake Angle (deg)', 'Fault Plane (1; 2; X)', + 'Style-of-Faulting (S; R; N; U)', 'Fault Name', + 'Depth to Top Of Fault Rupture Model', + 'Fault Rupture Length (km)', 'Fault Rupture Width (km)', + 'Along-strike Hypocenter location on the fault (fraction between 0 and 1)', + 'Along-width Hypocenter location on the fault (fraction between 0 and 1)', + 'Static Stress Drop (bars)', 'Type Static Stress Drop', + 'Directivity flag (Y; N; U)', 'Station ID', 'Station Code', + 'Station Latitude (deg positive N)', 'Station Longitude (deg positive E)', + 'Station Elevation (m)', + 'Site Class (Hard Rock; Rock; Stiff Soil; Soft Soil)', + 'Preferred NEHRP Based on Vs30', 'Preferred Vs30 (m/s)', + 'Measured(1)/Inferred(2) Class', 'Sigma of Vs30 (in natural log Units)', + 'Depth to Basement Rock', 'Z1 (m)','Z2.5 (m)', 'Epicentral Distance (km)', + 'Hypocentral Distance (km)', 'Joyner-Boore Distance (km)', + 'Rupture Distance (km)', 'Source to Site Azimuth (deg)', 'FW/HW Indicator', + 'Forearc/Backarc for subduction events', 'File Name (Horizontal 1)', + 'File Name (Horizontal 2)','File Name (Vertical)', + 'Digital (D)/Analog (A) Recording', 'Acceleration (A)/Velocity (V)', + 'Unit (cm/s/s; m/s/s; g)', 'File format', 'Processing flag', + 'Type of Filter','npass','nroll','HP-H1 (Hz)','HP-H2 (Hz)', + 'LP-H1 (Hz)', 'LP-H2 (Hz)', 'Factor', 'Lowest Usable Freq - H1 (Hz)', + 'Lowest Usable Freq - H2 (Hz)', 'Lowest Usable Freq - Ave. Component (Hz)', + 'Maximum Usable Freq - Ave. Component (Hz)', 'HP-V (Hz)', 'LP-V (Hz)', + 'Lowest Usable Freq - V (Hz)','Comments']) + +FILTER_TYPE = {"BW": "Butterworth", + "OR": "Ormsby", + "Ormsby": "Ormsby", + "Acausal Butterworth": "Acausal Butterworth", + "Causal Butterworth": "Causal Butterworth"} + +NEW_MECHANISM_TYPE = {"N": "Normal", + "S": "Strike-Slip", + "R": "Reverse", + "U": "Unknown", + "RO": "Reverse-Oblique", + "NO": "Normal-Oblique"} + +class SimpleFlatfileParserV9(SMDatabaseReader): + """ + Parser for strong motio database stored in a "Simple" flatfile format. + Typically this format is an Excel spreadsheet, though for the current + purposes it is assumed the spreadsheet is formatted as csv + """ + def parse(self): + """ + Parses the database + """ + HEADER_LIST1 = copy.deepcopy(HEADER_LIST) + self._header_check(HEADER_LIST1) + # Read in csv + reader = csv.DictReader(open(self.filename, "r")) + metadata = [] + self.database = GroundMotionDatabase(self.id, self.name) + self._get_site_id = self.database._get_site_id + for row in reader: + self.database.records.append(self._parse_record(row)) + return self.database + + def _header_check(self, headerslist): + """ + Checks to see if any of the headers are missing, raises error if so. + Also informs the user of redundent headers in the input file. + """ + # Check which of the pre-defined headers are missing + headers = Set((getline(self.filename, 1).rstrip("\n")).split(",")) + missing_headers = headerslist.difference(headers) + if len(missing_headers) > 0: + output_string = ", ".join([value for value in missing_headers]) + raise IOError("The following headers are missing from the input " + "file: %s" % output_string) + + additional_headers = headers.difference(headerslist) + if len(additional_headers) > 0: + for header in additional_headers: + print "Header %s not recognised - ignoring this data!" % header + return + + def _parse_record(self, metadata): + """ + Parses the record information and returns an instance of the + :class: smtk.sm_database.GroundMotionRecord + """ + # Waveform ID + wfid = metadata["Record Sequence Number"] + # Event information + event = self._parse_event_data(metadata) + # Site information + site = self._parse_site_data(metadata) + # Distance Information + distances, surface = self._parse_distance_data(event, site, metadata) + event.rupture.surface = surface + # Components + x_comp, y_comp, vertical = self._parse_processing_data(wfid, metadata) + # Return record metadata + lup = get_float(metadata["Lowest Usable Freq - Ave. Component (Hz)"]) + if lup: + lup = 1. / lup + sup = get_float(metadata["Maximum Usable Freq - Ave. Component (Hz)"]) + if sup: + sup = 1. / sup + return GroundMotionRecord(wfid, + [metadata["File Name (Horizontal 1)"], + metadata["File Name (Horizontal 2)"], + metadata["File Name (Vertical)"]], + event, + distances, + site, + x_comp, + y_comp, + longest_period=lup, + shortest_period=sup) + + def _parse_event_data(self, metadata): + """ + Read in the distance related metadata and return an instance of the + :class: smtk.sm_database.Earthquake + + """ + data_fields = ['Month', 'Day', 'Hour', 'Minute', 'Second'] + for f in data_fields: + metadata[f] = metadata[f].zfill(2) + + # Date and Time + year, month, day, hour, minute, second = self._validate_datetime( + metadata) + #year = get_int(metadata["Year"]) + #month = get_int(metadata["Month"]) + #day = get_int(metadata["Day"]) + #hour = get_int(metadata["Hour"]) + #minute = get_int(metadata["Minute"]) + #second = get_int(metadata["Second"]) + eq_datetime = datetime(year, month, day, hour, minute, second) + # Event ID and Name + eq_id = metadata["EQID"] + eq_name = metadata["Earthquake Name"] + # Focal Mechanism + focal_mechanism = self._get_focal_mechanism(eq_id, eq_name, metadata) + + focal_mechanism.scalar_moment = get_float(metadata["Mo (dyne.cm)"]) *\ + 1E-7 + # Read magnitude + pref_mag = Magnitude(get_float(metadata["Magnitude"]), + metadata["Magnitude type"], + sigma=get_float(metadata["Magnitude uncertainty"])) + # Create Earthquake Class + eqk = Earthquake(eq_id, eq_name, eq_datetime, + get_float(metadata["Epicenter Longitude (deg; positive E)"]), + get_float(metadata["Epicenter Latitude (deg; positive N)"]), + get_float(metadata["Hypocenter Depth (km)"]), + pref_mag, + focal_mechanism, + metadata["Country"]) + + # hypocenter location + f1 = get_float(metadata[ + "Along-strike Hypocenter location " + + "on the fault (fraction between 0 and 1)"]) + f2 = get_float(metadata[ + "Along-width Hypocenter location " + + "on the fault (fraction between 0 and 1)"]) + if f1 is None or f2 is None: + hypo_loc = (0.5, 0.7) + else: + hypo_loc = (f1, f2) + + eqk.tectonic_region = metadata["Tectonic environment (Crustal; Inslab; Interface; Stable; Geothermal; Volcanic; Oceanic_crust)"] + if (eqk.tectonic_region == "Stable" or + eqk.tectonic_region == "Crustal" or + eqk.tectonic_region == "Oceanic_crust"): + msr=WC1994() + elif eqk.tectonic_region == "Inslab": + msr=StrasserIntraslab() + elif eqk.tectonic_region == "Interface": + msr=StrasserInterface() + + # Warning rake set to 0.0 in scaling relationship - applies only + # to WC1994 + area = msr.get_median_area(pref_mag.value, 0.0) + aspect_ratio = 1.5 + width_model = np.sqrt(area / aspect_ratio) + length_model = aspect_ratio * width_model + ztor_model = eqk.depth - width_model / 2. + if ztor_model < 0: + ztor_model = 0.0 + + length = get_positive_float(metadata["Fault Rupture Length (km)"]) + if length is None: + length = length_model + width = get_positive_float(metadata["Fault Rupture Width (km)"]) + if width is None: + width = width_model + ztor = get_float(metadata["Depth to Top Of Fault Rupture Model"]) + if ztor is None: + ztor=ztor_model + + # Rupture + eqk.rupture = Rupture(eq_id, + eq_name, + pref_mag, + length, + width, + ztor, + hypo_loc=hypo_loc) +# get_float(metadata["Fault Rupture Length (km)"]), +# get_float(metadata["Fault Rupture Width (km)"]), +# get_float(metadata["Depth to Top Of Fault Rupture Model"]), +# hypo_loc=hypo_loc) + eqk.rupture.get_area() + return eqk + + @staticmethod + def _validate_datetime(metadata): + """ + SARA flatfile should be formatted correctly but other flatfiles + are prone to bad datetime values - these will be overwritten + """ + return (get_int(metadata["Year"]), get_int(metadata["Month"]), + get_int(metadata["Day"]), get_int(metadata["Hour"]), + get_int(metadata["Minute"]), get_int(metadata["Second"])) + + def _get_focal_mechanism(self, eq_id, eq_name, metadata): + """ + Returns the focal mechanism information as an instance of the + :class: smtk.sigma_database.FocalMechanism + """ + nodal_planes = GCMTNodalPlanes() + # By default nodal plane 1 is assumed to be the fault plane in smtk. + # Depending on parameter fault_plane import correct angles in nodal + # planes 1 and 2 (1 being the fault plane) + if metadata['Fault Plane (1; 2; X)'] == '1': + nodal_planes.nodal_plane_1 = { + "strike": get_float(metadata['Nodal Plane 1 Strike (deg)']), + "dip": get_float(metadata['Nodal Plane 1 Dip (deg)']), + "rake": get_float(metadata['Nodal Plane 1 Rake Angle (deg)'])} + + nodal_planes.nodal_plane_2 = { + "strike": get_float(metadata['Nodal Plane 2 Strike (deg)']), + "dip": get_float(metadata['Nodal Plane 2 Dip (deg)']), + "rake": get_float(metadata['Nodal Plane 2 Rake Angle (deg)'])} + elif metadata['Fault Plane (1; 2; X)'] == '2': + nodal_planes.nodal_plane_1 = { + "strike": get_float(metadata['Nodal Plane 2 Strike (deg)']), + "dip": get_float(metadata['Nodal Plane 2 Dip (deg)']), + "rake": get_float(metadata['Nodal Plane 2 Rake Angle (deg)'])} + + nodal_planes.nodal_plane_2 = { + "strike": get_float(metadata['Nodal Plane 1 Strike (deg)']), + "dip": get_float(metadata['Nodal Plane 1 Dip (deg)']), + "rake": get_float(metadata['Nodal Plane 1 Rake Angle (deg)'])} + elif metadata['Fault Plane (1; 2; X)'] == 'X': + # Check if values for strike or dip are given otherwise set + # strike=0 and dip=90 and fill strike and dip for fault plane 1 + # What can we do for rake? + strike = get_float(metadata['Nodal Plane 1 Strike (deg)']) + if strike is None: + strike = get_float(metadata['Nodal Plane 2 Strike (deg)']) + if strike is None: + strike = 0.0 + dip = get_float(metadata['Nodal Plane 1 Dip (deg)']) + if dip is None: + dip = get_float(metadata['Nodal Plane 2 Dip (deg)']) + if dip is None: + dip = 90.0 + nodal_planes.nodal_plane_1 = {"strike": strike, + "dip": dip, + "rake": None} + nodal_planes.nodal_plane_2 = {"strike": None, + "dip": None, + "rake": None} + + nodal_planes = self._check_mechanism(nodal_planes) + principal_axes = GCMTPrincipalAxes() + mech_type =\ + NEW_MECHANISM_TYPE[metadata["Style-of-Faulting (S; R; N; U)"]] + return FocalMechanism(eq_id, eq_name, nodal_planes, principal_axes, + mechanism_type=mech_type) + + def _check_mechanism(self, nodal_planes): + """ + Verify that the nodal planes are valid, and default nodal plane 1 + to a "null" plane if not + """ + if nodal_planes.nodal_plane_1["strike"]: + nodal_planes.nodal_plane_1["strike"] = \ + nodal_planes.nodal_plane_1["strike"] % 360.0 + if nodal_planes.nodal_plane_2["strike"]: + nodal_planes.nodal_plane_2["strike"] = \ + nodal_planes.nodal_plane_2["strike"] % 360.0 + + valid_plane_1 = nodal_planes.nodal_plane_1["strike"] >= 0.0 and\ + nodal_planes.nodal_plane_1["strike"] < 360.0 and\ + nodal_planes.nodal_plane_1["dip"] > 0.0 and\ + nodal_planes.nodal_plane_1["dip"] <= 90.0 and\ + nodal_planes.nodal_plane_1["rake"] >= -180.0 and\ + nodal_planes.nodal_plane_1["rake"] <= 180.0 + valid_plane_2 = nodal_planes.nodal_plane_2["strike"] >= 0.0 and\ + nodal_planes.nodal_plane_2["strike"] <= 360.0 and\ + nodal_planes.nodal_plane_2["dip"] > 0.0 and\ + nodal_planes.nodal_plane_2["dip"] <= 90.0 and\ + nodal_planes.nodal_plane_2["rake"] >= -180.0 and\ + nodal_planes.nodal_plane_2["rake"] <= 180.0 + if valid_plane_1: + return nodal_planes + + # If nodal plane 2 is valid then swap over + if valid_plane_2: + np1 = copy.deepcopy(nodal_planes.nodal_plane_1) + np2 = copy.deepcopy(nodal_planes.nodal_plane_2) + nodal_planes.nodal_plane_1 = np2 + nodal_planes.nodal_plane_2 = np1 + else: + nodal_planes.nodal_plane_1 = {"strike": 0.0, + "dip": 90.0, + "rake": 0.0} + return nodal_planes + + + + + def _parse_distance_data(self, event, site, metadata): + """ + Read in the distance related metadata and return an instance of the + :class: smtk.sm_database.RecordDistance + """ + # Compute various distance metrics + # Add calculation of Repi, Rhypo from event and station localizations + # (latitudes, longitudes, depth, elevation)? + target_site = Mesh(np.array([site.longitude]), + np.array([site.latitude]), + np.array([-site.altitude / 1000.0])) + # Warning ratio fixed to 1.5 + ratio=1.5 + surface_modeled = rcfg.create_planar_surface( + Point(event.longitude, event.latitude, event.depth), + event.mechanism.nodal_planes.nodal_plane_1['strike'], + event.mechanism.nodal_planes.nodal_plane_1['dip'], + event.rupture.area, + ratio) + hypocenter = rcfg.get_hypocentre_on_planar_surface( + surface_modeled, + event.rupture.hypo_loc) + try: + surface_modeled._create_mesh() + except: + dip = surface_modeled.get_dip() + dip_dir = (surface_modeled.get_strike() - 90.) % 360. + ztor = surface_modeled.top_left.depth + d_x = ztor * np.tan(np.radians(90.0 - dip)) + top_left_surface = surface_modeled.top_left.point_at(d_x, + -ztor, + dip_dir) + top_left_surface.depth = 0. + top_right_surface = surface_modeled.top_right.point_at(d_x, + -ztor, + dip_dir) + top_right_surface.depth = 0. + surface_modeled = SimpleFaultSurface.from_fault_data( + Line([top_left_surface, top_right_surface]), + surface_modeled.top_left.depth, + surface_modeled.bottom_left.depth, + surface_modeled.get_dip(), + 1.0) + + # Rhypo + Rhypo = get_float(metadata["Hypocentral Distance (km)"]) + if Rhypo is None: + Rhypo = hypocenter.distance_to_mesh(target_site) + # Repi + Repi = get_float(metadata["Epicentral Distance (km)"]) + if Repi is None: + Repi= hypocenter.distance_to_mesh(target_site, with_depths=False) + # Rrup + Rrup = get_float(metadata["Rupture Distance (km)"]) + if Rrup is None: + Rrup = surface_modeled.get_min_distance(target_site) + # Rjb + Rjb = get_float(metadata["Joyner-Boore Distance (km)"]) + if Rjb is None: + Rjb = surface_modeled.get_joyner_boore_distance(target_site) + # Need to check if Rx and Ry0 are consistant with the other metrics + # when those are coming from the flatfile? + # Rx + Rx = surface_modeled.get_rx_distance(target_site) + # Ry0 + Ry0 = surface_modeled.get_ry0_distance(target_site) + + distance = RecordDistance( + repi = float(Repi), + rhypo = float(Rhypo), + rjb = float(Rjb), + rrup = float(Rrup), + r_x = float(Rx), + ry0 = float(Ry0)) + distance.azimuth = get_float(metadata["Source to Site Azimuth (deg)"]) + #distance.hanging_wall = get_float(metadata["FW/HW Indicator"]) + if metadata["FW/HW Indicator"] == "HW": + distance.hanging_wall = True + elif metadata["FW/HW Indicator"] == "FW": + distance.hanging_wall = False + else: + pass + + return distance, surface_modeled + + def _parse_site_data(self, metadata): + """ + Returns the site data as an instance of the :class: + smtk.sm_database.RecordSite + """ + site = RecordSite( + self._get_site_id(metadata["Station ID"]), + metadata["Station ID"], + metadata["Station Code"], + get_float(metadata["Station Longitude (deg positive E)"]), + get_float(metadata["Station Latitude (deg positive N)"]), + get_float(metadata["Station Elevation (m)"]), + get_float(metadata["Preferred Vs30 (m/s)"]), + site_class=metadata['Site Class (Hard Rock; Rock; Stiff Soil; Soft Soil)'], + network_code=None, # not provided + ) + # network_code=metadata["Owner"]) + site.nehrp = metadata["Preferred NEHRP Based on Vs30"] + site.vs30_measured_type = metadata["Measured(1)/Inferred(2) Class"] + if metadata["Measured(1)/Inferred(2) Class"] == "1": + site.vs30_measured = True + else: + site.vs30_measured = False + site.vs30_uncertainty = get_float( + metadata["Sigma of Vs30 (in natural log Units)"]) + site.z1pt0 = get_float(metadata["Z1 (m)"]) + site.z1pt5 = None + # site.z1pt5 = get_float(metadata["Z1.5 (m)"]) + site.z2pt5 = get_float(metadata["Z2.5 (m)"]) + # Implement default values for z1pt0 and z2pt5 + if site.z1pt0 is None: + site.z1pt0 = rcfg.vs30_to_z1pt0_as08(site.vs30) + if site.z2pt5 is None: + site.z2pt5 = rcfg.z1pt0_to_z2pt5(site.z1pt0) + else: + # Need to convert z2pt5 from m to km + site.z2pt5 = site.z2pt5/1000.0 + if "Backarc" in metadata["Forearc/Backarc for subduction events"]: + site.backarc = True + site.instrument_type = metadata["Digital (D)/Analog (A) Recording"] + return site + + def _parse_processing_data(self, wfid, metadata): + """ + Parses the information for each component + """ + if metadata["Type of Filter"]: + filter_params1 = { + 'Type': FILTER_TYPE[metadata["Type of Filter"]], + 'Order': None, + 'Passes': get_positive_int(metadata['npass']), + 'NRoll': get_positive_int(metadata['nroll']), + 'High-Cut': get_positive_float(metadata["LP-H1 (Hz)"]), + 'Low-Cut': get_positive_float(metadata["HP-H1 (Hz)"])} + + filter_params2 = { + 'Type': FILTER_TYPE[metadata["Type of Filter"]], + 'Order': None, + 'Passes': get_positive_int(metadata['npass']), + 'NRoll': get_positive_int(metadata['nroll']), + 'High-Cut': get_positive_float(metadata["LP-H2 (Hz)"]), + 'Low-Cut': get_positive_float(metadata["HP-H2 (Hz)"])} + else: + filter_params1, filter_params2 = None, None + + intensity_measures = { + # All m - convert to cm + 'PGA': None, + 'PGV': None, + 'PGD': None + } + luf1 = get_float(metadata["Lowest Usable Freq - H1 (Hz)"]) + if luf1 and luf1 > 0.0: + lup1 = 1. / luf1 + else: + lup1 = None + luf2 = get_float(metadata["Lowest Usable Freq - H2 (Hz)"]) + if luf2 and luf2 > 0.0: + lup2 = 1. / luf2 + else: + lup2 = None + xcomp = Component(wfid, "1", + ims=intensity_measures, + longest_period=lup1, + waveform_filter=filter_params1, + units=metadata["Unit (cm/s/s; m/s/s; g)"]) + + ycomp = Component(wfid, "2", + ims=intensity_measures, + longest_period=lup2, + waveform_filter=filter_params2, + units=metadata["Unit (cm/s/s; m/s/s; g)"]) + + luf3 = get_float(metadata["Lowest Usable Freq - V (Hz)"]) + if luf3 and luf3 > 0.0: + filter_params3 = { + 'Type': FILTER_TYPE[metadata["Type of Filter"]], + 'Order': None, + 'Passes': get_int(metadata['npass']), + 'NRoll': get_int(metadata['nroll']), + 'High-Cut': get_float(metadata["LP-V (Hz)"]), + 'Low-Cut': get_float(metadata["HP-V (Hz)"])} + lup3 = 1. / luf3 + zcomp = Component(wfid, "V", + ims=intensity_measures, + longest_period=lup3, + waveform_filter=filter_params3, + units=metadata["Unit (cm/s/s; m/s/s; g)"]) + return xcomp, ycomp, zcomp + else: + return xcomp, ycomp, None + + + + +class NearFaultFlatFileParser(SimpleFlatfileParserV9): + + def parse(self): + """ + Parses the database + """ + HEADER_LIST1 = copy.deepcopy(HEADER_LIST) + HEADER_LIST1.add("Rcdpp") + self._header_check(HEADER_LIST1) + # Read in csv + reader = csv.DictReader(open(self.filename, "r")) + metadata = [] + self.database = GroundMotionDatabase(self.id, self.name) + self._get_site_id = self.database._get_site_id + for row in reader: + self.database.records.append(self._parse_record(row)) + return self.database + + def _parse_distance_data(self, event, site, metadata): + """ + Read in the distance related metadata and return an instance of the + :class: smtk.sm_database.RecordDistance + """ + # Compute various distance metrics + # Add calculation of Repi, Rhypo from event and station localizations + # (latitudes, longitudes, depth, elevation)? + target_site = Mesh(np.array([site.longitude]), + np.array([site.latitude]), + np.array([-site.altitude / 1000.0])) + # Warning ratio fixed to 1.5 + ratio=1.5 + surface_modeled = rcfg.create_planar_surface( + Point(event.longitude, event.latitude, event.depth), + event.mechanism.nodal_planes.nodal_plane_1['strike'], + event.mechanism.nodal_planes.nodal_plane_1['dip'], + event.rupture.area, + ratio) + hypocenter = rcfg.get_hypocentre_on_planar_surface( + surface_modeled, + event.rupture.hypo_loc) + try: + surface_modeled._create_mesh() + except: + dip = surface_modeled.get_dip() + dip_dir = (surface_modeled.get_strike() - 90.) % 360. + ztor = surface_modeled.top_left.depth + d_x = ztor * np.tan(np.radians(90.0 - dip)) + top_left_surface = surface_modeled.top_left.point_at(d_x, + -ztor, + dip_dir) + top_left_surface.depth = 0. + top_right_surface = surface_modeled.top_right.point_at(d_x, + -ztor, + dip_dir) + top_right_surface.depth = 0. + surface_modeled = SimpleFaultSurface.from_fault_data( + Line([top_left_surface, top_right_surface]), + surface_modeled.top_left.depth, + surface_modeled.bottom_left.depth, + surface_modeled.get_dip(), + 1.0) + + # Rhypo + Rhypo = get_float(metadata["Hypocentral Distance (km)"]) + if Rhypo is None: + Rhypo = hypocenter.distance_to_mesh(target_site) + # Repi + Repi = get_float(metadata["Epicentral Distance (km)"]) + if Repi is None: + Repi= hypocenter.distance_to_mesh(target_site, with_depths=False) + # Rrup + Rrup = get_float(metadata["Rupture Distance (km)"]) + if Rrup is None: + Rrup = surface_modeled.get_min_distance(target_site) + # Rjb + Rjb = get_float(metadata["Joyner-Boore Distance (km)"]) + if Rjb is None: + Rjb = surface_modeled.get_joyner_boore_distance(target_site) + # Rcdpp + Rcdpp = get_float(metadata["Rcdpp"]) + if Rcdpp is None: + Rcdpp = surface_modeled.get_cdppvalue(target_site) + # Need to check if Rx and Ry0 are consistant with the other metrics + # when those are coming from the flatfile? + # Rx + Rx = surface_modeled.get_rx_distance(target_site) + # Ry0 + Ry0 = surface_modeled.get_ry0_distance(target_site) + + distance = RecordDistance( + repi = float(Repi), + rhypo = float(Rhypo), + rjb = float(Rjb), + rrup = float(Rrup), + r_x = float(Rx), + ry0 = float(Ry0), + rcdpp = float(Rcdpp) ) + distance.azimuth = get_float(metadata["Source to Site Azimuth (deg)"]) + #distance.hanging_wall = get_float(metadata["FW/HW Indicator"]) + if metadata["FW/HW Indicator"] == "HW": + distance.hanging_wall = True + elif metadata["FW/HW Indicator"] == "FW": + distance.hanging_wall = False + else: + pass + + return distance + +class SimpleAsciiTimeseriesReader(SMTimeSeriesReader): + """ + Parses a simple ascii representation of a record in which the first line + contains the number of values and the time-step. Whilst the rest of the + file contains the acceleration record + """ + def parse_records(self, record): + """ + Parses the record set + """ + time_series = OrderedDict([ + ("X", {"Original": {}, "SDOF": {}}), + ("Y", {"Original": {}, "SDOF": {}}), + ("V", {"Original": {}, "SDOF": {}})]) + + target_names = time_series.keys() + for iloc, ifile in enumerate(self.input_files): + if not os.path.exists(ifile): + if iloc < 2: + # Expected horizontal component is missing - raise error + raise ValueError("Horizontal record %s is expected but " + "not found!" % ifile) + else: + print "Vertical record file %s not found" % ifile + del time_series["V"] + continue + else: + time_series[target_names[iloc]]["Original"] = \ + self._parse_time_history(ifile, record.xrecord.units) + if iloc < 2: + del time_series["V"] + + return time_series + + def _parse_time_history(self, ifile, units="cm/s/s"): + """ + Parses the time history from the file and returns a dictionary of + time-series properties + """ + output = {} + accel = np.genfromtxt(ifile, skip_header=1) + output["Acceleration"] = convert_accel_units(accel, self.units) + nvals, time_step = (getline(ifile, 1).rstrip("\n")).split() + output["Time-step"] = float(time_step) + output["Number Steps"] = int(nvals) + output["Units"] = units + output["PGA"] = np.max(np.fabs(output["Acceleration"])) + return output diff --git a/smtk/residuals/gmpe_residuals.py b/smtk/residuals/gmpe_residuals.py index 81b677d..df22dd0 100755 --- a/smtk/residuals/gmpe_residuals.py +++ b/smtk/residuals/gmpe_residuals.py @@ -288,18 +288,20 @@ def __init__(self, gmpe_list, imts): self.gmpe_sa_limits = {} self.gmpe_scalars = {} for gmpe in self.gmpe_list: - gmpe_dict_1 = {} - gmpe_dict_2 = {} + gmpe_dict_1 = OrderedDict([]) + gmpe_dict_2 = OrderedDict([]) self.unique_indices[gmpe] = {} # Get the period range and the coefficient types gmpe_i = GSIM_LIST[gmpe]() for c in dir(gmpe_i): - if 'COEFFS' in c: + #if 'COEFFS' in c: + if c == 'COEFFS': pers = [sa.period for sa in getattr(gmpe_i,c).sa_coeffs] min_per, max_per = (min(pers), max(pers)) self.gmpe_sa_limits[gmpe] = (min_per, max_per) for c in dir(gmpe_i): - if 'COEFFS' in c: + #if 'COEFFS' in c: + if c == 'COEFFS': self.gmpe_scalars[gmpe] = getattr(gmpe_i,c).non_sa_coeffs.keys() for imtx in self.imts: if "SA(" in imtx: @@ -352,15 +354,21 @@ def get_residuals(self, database, nodal_plane_index=1, if res_type == "Inter event": inter_ev = \ context["Residual"][gmpe][imtx][res_type] - inter_ev, inter_idx = np.unique( - inter_ev, - return_index=True) - self.residuals[gmpe][imtx][res_type].extend( - inter_ev.tolist()) - #inter_mags = (context["Rupture"].mag * - # np.ones(len(inter_ev))).tolist() - self.unique_indices[gmpe][imtx].append( - inter_idx) + if np.all( + np.fabs(inter_ev - inter_ev[0]) < 1.0E-12): + # Single inter-event residual + self.residuals[gmpe][imtx][res_type].append( + inter_ev[0]) + # Append indices + self.unique_indices[gmpe][imtx].append( + np.array([0])) + else: + # Inter event residuals per-site e.g. Chiou + # & Youngs (2008; 2014) case + self.residuals[gmpe][imtx][res_type].extend( + inter_ev.tolist()) + self.unique_indices[gmpe][imtx].append( + np.arange(len(inter_ev))) else: self.residuals[gmpe][imtx][res_type].extend( context["Residual"][gmpe][imtx][res_type].tolist()) @@ -383,8 +391,6 @@ def get_residuals(self, database, nodal_plane_index=1, self.modelled[gmpe][imtx][res_type]) self.modelled[gmpe][imtx]["Mean"] = np.array( self.modelled[gmpe][imtx]["Mean"]) - #self.unique_magnitudes[gmpe][imtx] = np.array( - # self.unique_magnitudes[gmpe][imtx]) def get_observations(self, context, component="Geometric"): """ @@ -459,7 +465,7 @@ def calculate_residuals(self, context, normalise=True): # Calculate residual residual = {} for gmpe in self.gmpe_list: - residual[gmpe] = {} + residual[gmpe] = OrderedDict([]) for imtx in self.imts: residual[gmpe][imtx] = {} obs = np.log(context["Observations"][imtx]) @@ -500,29 +506,14 @@ def get_residual_statistics(self): """ Retreives the mean and standard deviation values of the residuals """ - statistics = OrderedDict([(gmpe, {}) for gmpe in self.gmpe_list]) + statistics = OrderedDict([(gmpe, OrderedDict([])) + for gmpe in self.gmpe_list]) for gmpe in self.gmpe_list: for imtx in self.imts: if not self.residuals[gmpe][imtx]: continue statistics[gmpe][imtx] = {} for res_type in self.types[gmpe][imtx]: -# if res_type == "Inter event": -# # As the inter-event term may be vectorial with -# # repeated columns, get take only one value of inter- -# # event residual if unique -# delta_e = np.array([], dtype="float") -# for ctxt in self.contexts: -# iev_res = np.unique( -# ctxt["Residual"][gmpe][imtx]["Inter event"]) -# delta_e = np.hstack([delta_e, iev_res]) -# #print delta_e -# data = { -# "Mean": np.mean(delta_e), -# #self.residuals[gmpe][imtx][res_type]), -# "Std Dev": np.std(delta_e)} -# #self.residuals[gmpe][imtx][res_type])} -# else: data = { "Mean": np.mean( self.residuals[gmpe][imtx][res_type]), @@ -540,7 +531,7 @@ def pretty_print(self, filename=None, sep=","): else: fid = sys.stdout fid.write("Ground Motion Residuals\n") - # Prin headers + # Print headers event = self.contexts[0] header_set = [] header_set.extend([key for key in event["Distances"].__dict__]) @@ -647,7 +638,8 @@ def get_likelihood_values(self): residuals according to Equation 9 of Scherbaum et al (2004) """ statistics = self.get_residual_statistics() - lh_values = OrderedDict([(gmpe, {}) for gmpe in self.gmpe_list]) + lh_values = OrderedDict([(gmpe, OrderedDict([])) + for gmpe in self.gmpe_list]) for gmpe in self.gmpe_list: for imtx in self.imts: if not self.residuals[gmpe][imtx]: @@ -775,7 +767,6 @@ def bootstrap_llh(ij, contexts, gmpes, imts): """ # Sample contexts timer_on = datetime.now() - print(ij) neqs = len(contexts) isamp = np.random.randint(0, neqs, neqs) new_contexts = [contexts[i] for i in isamp] diff --git a/smtk/response_spectrum.py b/smtk/response_spectrum.py index a72c70d..8cc626b 100755 --- a/smtk/response_spectrum.py +++ b/smtk/response_spectrum.py @@ -26,7 +26,7 @@ from math import sqrt from scipy.integrate import cumtrapz import matplotlib.pyplot as plt -from sm_utils import (_save_image, +from smtk.sm_utils import (_save_image, get_time_vector, convert_accel_units, get_velocity_displacement) @@ -62,7 +62,7 @@ def __init__(self, acceleration, time_step, periods, damping=0.05, self.response_spectrum = None - def evaluate(self): + def __call__(self): ''' Evaluates the response spectrum :returns: @@ -88,9 +88,8 @@ def evaluate(self): accel - Acceleration response of Single Degree of Freedom Oscillator vel - Velocity response of Single Degree of Freedom Oscillator disp - Displacement response of Single Degree of Freedom Oscillator - ''' - + raise NotImplementedError("Cannot call Base Response Spectrum") class NewmarkBeta(ResponseSpectrum): @@ -98,7 +97,7 @@ class NewmarkBeta(ResponseSpectrum): Evaluates the response spectrum using the Newmark-Beta methodology ''' - def evaluate(self): + def __call__(self): ''' Evaluates the response spectrum :returns: @@ -188,6 +187,7 @@ def _newmark_beta(self, omega, cval, kval): a_t[j, :] = self.acceleration[j] + accel[j, :] return accel, vel, disp, a_t + class NigamJennings(ResponseSpectrum): """ Evaluate the response spectrum using the algorithm of Nigam & Jennings @@ -197,7 +197,7 @@ class NigamJennings(ResponseSpectrum): of the sampling frequency. """ - def evaluate(self): + def __call__(self): """ Define the response spectrum """ diff --git a/smtk/sm_database.py b/smtk/sm_database.py index 782e03f..41b0755 100755 --- a/smtk/sm_database.py +++ b/smtk/sm_database.py @@ -29,9 +29,12 @@ RuptureContext) from openquake.hazardlib.site import Site, SiteCollection from openquake.hazardlib.geo.point import Point +from openquake.hazardlib.scalerel import PeerMSR from smtk.trellis.configure import vs30_to_z1pt0_as08, z1pt0_to_z2pt5 from smtk.trellis.configure import vs30_to_z1pt0_cy14, vs30_to_z2pt5_cb14 +DEFAULT_MSR = PeerMSR() + class Magnitude(object): """ Class to hold magnitude attributes @@ -233,7 +236,7 @@ def get_rake_from_mechanism_type(self): Returns an idealised "rake" based on a qualitative description of the style of faulting """ - if self.mechanism_type in MECHANISM_TYPE.keys(): + if self.mechanism_type in MECHANISM_TYPE: return MECHANISM_TYPE[self.mechanism_type] else: return 0.0 @@ -486,7 +489,7 @@ def get_ec8_class(self): if self.ec8: return self.ec8 if self.vs30: - for key in EC8_VS30_BOUNDARIES.keys(): + for key in EC8_VS30_BOUNDARIES: in_group = (self.vs30 >= EC8_VS30_BOUNDARIES[key][0]) and\ (self.vs30 < EC8_VS30_BOUNDARIES[key][1]) if in_group: @@ -494,14 +497,14 @@ def get_ec8_class(self): return self.ec8 elif self.nspt: # Check to see if a site class can be determined from NSPT - for key in EC8_NSPT_BOUNDARIES.keys(): + for key in EC8_NSPT_BOUNDARIES: in_group = (self.nspt >= EC8_NSPT_BOUNDARIES[key][0]) and\ (self.nspt < EC8_NSPT_BOUNDARIES[key][1]) if in_group: self.ec8 = key return self.ec8 else: - print "Cannot determine EC8 site class - no Vs30 or NSPT measures!" + print("Cannot determine EC8 site class - no Vs30 or NSPT measures!") return None def get_nehrp_class(self): @@ -511,7 +514,7 @@ def get_nehrp_class(self): if self.nehrp: return self.nehrp if self.vs30: - for key in NEHRP_VS30_BOUNDARIES.keys(): + for key in NEHRP_VS30_BOUNDARIES: in_group = (self.vs30 >= NEHRP_VS30_BOUNDARIES[key][0]) and\ (self.vs30 < NEHRP_VS30_BOUNDARIES[key][1]) if in_group: @@ -519,14 +522,14 @@ def get_nehrp_class(self): return self.nehrp elif self.nspt: # Check to see if a site class can be determined from NSPT - for key in NEHRP_NSPT_BOUNDARIES.keys(): + for key in NEHRP_NSPT_BOUNDARIES: in_group = (self.nspt >= NEHRP_NSPT_BOUNDARIES[key][0]) and\ (self.nspt < NEHRP_NSPT_BOUNDARIES[key][1]) if in_group: self.nehrp = key return self.nehrp else: - print "Cannot determine NEHRP site class - no Vs30 or NSPT measures!" + print("Cannot determine NEHRP site class - no Vs30 or NSPT measures!") return None @@ -546,7 +549,7 @@ def vs30_from_ec8(self): if self.ec8 == 'E': return 100 else: - print "Cannot determine Vs30 from EC8 site class" + print("Cannot determine Vs30 from EC8 site class") Filter = {'Type': None, 'Order': None, @@ -906,12 +909,18 @@ def _get_event_context(self, idx, nodal_plane_index=1): setattr(rctx, 'strike', 0.0) setattr(rctx, 'dip', 90.0) rctx.rake = rup.event.mechanism.get_rake_from_mechanism_type() - if rup.event.rupture: + if rup.event.rupture.surface: setattr(rctx, 'ztor', rup.event.rupture.surface.get_top_edge_depth()) setattr(rctx, 'width', rup.event.rupture.surface.width) setattr(rctx, 'hypo_loc', rup.event.rupture.surface.get_hypo_location(1000)) else: setattr(rctx, 'ztor', rup.event.depth) + # Use the PeerMSR to define the area and assuming an aspect ratio + # of 1 get the width + setattr(rctx, 'width', + np.sqrt(DEFAULT_MSR.get_median_area(rctx.mag, 0))) + # Default hypocentre location to the middle of the rupture + setattr(rctx, 'hypo_loc', (0.5, 0.5)) setattr(rctx, 'hypo_depth', rup.event.depth) setattr(rctx, 'hypo_lat', rup.event.latitude) setattr(rctx, 'hypo_lon', rup.event.longitude) diff --git a/smtk/strong_motion_selector.py b/smtk/strong_motion_selector.py index 7c9ba8f..727e329 100755 --- a/smtk/strong_motion_selector.py +++ b/smtk/strong_motion_selector.py @@ -37,14 +37,14 @@ def rank_sites_by_record_count(database, threshold=0): name_id_list = [(rec.site.id, rec.site.name) for rec in database.records] name_id = dict([]) for name_id_pair in name_id_list: - if name_id_pair[0] in name_id.keys(): + if name_id_pair[0] in name_id: name_id[name_id_pair[0]]["Count"] += 1 else: name_id[name_id_pair[0]] = {"Count": 1, "Name": name_id_pair[1]} - counts = np.array([name_id[key]["Count"] for key in name_id.keys()]) + counts = np.array([name_id[key]["Count"] for key in name_id]) sort_id = np.flipud(np.argsort(counts)) - key_vals = name_id.keys() + key_vals = list(name_id) output_list = [] for idx in sort_id: if name_id[key_vals[idx]]["Count"] >= threshold: @@ -102,7 +102,8 @@ def select_from_record_id(self, record_id): if record_id in self.record_ids: return self.database.records[self.record_ids.index(record_id)] else: - raise ValueError("Record %s is not in database" % record_id) + raise ValueError( + "Record {:s} is not in database".format(record_id)) def select_from_record_ids(self, record_ids, as_db=False): """ @@ -111,7 +112,7 @@ def select_from_record_ids(self, record_ids, as_db=False): idx = [] for record_id in record_ids: if not record_id in self.record_ids: - print("Record %s is not in database" % record_id) + print("Record {:s} is not in database".format(record_id)) for iloc, record in enumerate(self.database.records): if record.id in record_ids: idx.append(iloc) @@ -133,7 +134,7 @@ def select_from_site_ids(self, site_ids, as_db=False): """ for site_id in site_ids: if not site_id in self.site_ids: - print("Site %s is not in database" % record_id) + print("Site {:w is not in database" % record_id) idx = [] for iloc, record in enumerate(self.database.records): if record.site.id in site_ids: @@ -158,7 +159,7 @@ def select_from_event_ids(self, event_ids, as_db=False): """ for event_id in event_ids: if not event_id in self.event_ids: - print("Event %s not found in database" % event_id) + print("Event {:s} not found in database".format(event_id)) idx = [] for iloc, record in enumerate(self.database.records): if record.event.id in event_ids: @@ -345,8 +346,8 @@ def select_within_distance_range(self, distance_type, shortest, furthest, # raise ValueError("Record %s is missing selected distance " # "metric and alternative metric" % record.id) else: - print("Record %s is missing selected distance metric" - % record.id) + print("Record {:s} is missing selected distance metric".format( + record.id)) return self.select_records(idx, as_db) # Event-based selection diff --git a/smtk/trellis/configure.py b/smtk/trellis/configure.py index 6a9578e..46abdc6 100755 --- a/smtk/trellis/configure.py +++ b/smtk/trellis/configure.py @@ -558,13 +558,11 @@ def get_gsim_contexts(self): setattr(dctx, "rvolc", np.zeros_like(self.target_sites.mesh.lons)) # Sites sctx = SitesContext() - key_list = ['_vs30', '_vs30measured', '_z1pt0', '_z2pt5', '_backarc'] + key_list = ["lons", "lats", "vs30", "vs30measured", "z1pt0", "z2pt5", + "backarc"] for key in key_list: - setattr(sctx, key[1:], getattr(self.target_sites, key)) - for key in ['lons', 'lats']: - setattr(sctx, key, getattr(self.target_sites, key)) + setattr(sctx, key, self.target_sites.array[key]) - # Rupture rctx = RuptureContext() setattr(rctx, 'mag', self.magnitude) @@ -727,7 +725,7 @@ def get_target_sites_point(self, distance, distance_type, vs30, :param floar z2pt5: Depth to 2.5 km/s interface """ - if not distance_type in POINT_AT_MAPPING.keys(): + if not distance_type in list(POINT_AT_MAPPING.keys()): raise ValueError("Distance type must be one of: Rupture ('rrup'), " "Joyner-Boore ('rjb'), Epicentral ('repi') or " "Hypocentral ('rhyp')") @@ -799,7 +797,7 @@ def filter_hanging_wall(self, filter_type=None): if not filter_type: # Considers both footwall and hanging wall return self.target_sites - elif not filter_type in ['HW', 'FW']: + elif not filter_type in ('HW', 'FW'): raise ValueError('Hanging wall filter must be either "HW" or "FW"') else: pass diff --git a/smtk/trellis/trellis_plots.py b/smtk/trellis/trellis_plots.py index 3027796..ce2a99f 100755 --- a/smtk/trellis/trellis_plots.py +++ b/smtk/trellis/trellis_plots.py @@ -21,7 +21,7 @@ Sets up a simple rupture-site configuration to allow for physical comparison of GMPEs ''' -import sys, re, os +import sys, re, os, json import numpy as np from collections import Iterable, OrderedDict from itertools import cycle @@ -32,20 +32,25 @@ from copy import deepcopy import matplotlib.pyplot as plt from openquake.hazardlib import gsim, imt +from openquake.hazardlib.gsim.base import (RuptureContext, + DistancesContext, + SitesContext) from openquake.hazardlib.gsim.gsim_table import GMPETable from openquake.hazardlib.scalerel.wc1994 import WC1994 from smtk.sm_utils import _save_image, _save_image_tight import smtk.trellis.trellis_utils as utils -from smtk.trellis.configure import GSIMRupture +from smtk.trellis.configure import GSIMRupture, DEFAULT_POINT # Default - defines a 21 color and line-type cycle matplotlib.rcParams["axes.prop_cycle"] = \ - cycler(u'color', [u'b', u'g', u'r', u'c', u'm', u'y', u'k', - u'b', u'g', u'r', u'c', u'm', u'y', u'k', - u'b', u'g', u'r', u'c', u'm', u'y', u'k']) +\ + cycler(u'color', ['b', 'g', 'r', 'c', 'm', 'y', 'k', + 'b', 'g', 'r', 'c', 'm', 'y', 'k', + 'b', 'g', 'r', 'c', 'm', 'y', 'k', + 'b', 'g', 'r', 'c', 'm', 'y', 'k']) +\ cycler(u'linestyle', ["-", "-", "-", "-", "-", "-", "-", "--", "--", "--", "--", "--", "--", "--", - "-.", "-.", "-.", "-.", "-.", "-.", "-."]) + "-.", "-.", "-.", "-.", "-.", "-.", "-.", + ":", ":", ":", ":", ":", ":", ":"]) # Get a list of the available GSIMs AVAILABLE_GSIMS = gsim.get_available_gsims() @@ -67,6 +72,7 @@ PLOT_UNITS = {'PGA': 'g', 'PGV': 'cm/s', 'SA': 'g', + 'SD': 'cm', 'IA': 'm/s', 'CSV': 'g-sec', 'RSD': 's', @@ -130,7 +136,7 @@ def _check_gsim_list(gsim_list): match = re.match(r'^GMPETable\(([^)]+?)\)$', gsim) filepath = match.group(1).split("=")[1] output_gsims.append(GMPETable(gmpe_table=filepath)) - elif not gsim in AVAILABLE_GSIMS.keys(): + elif not gsim in AVAILABLE_GSIMS: raise ValueError('%s Not supported by OpenQuake' % gsim) else: output_gsims.append(AVAILABLE_GSIMS[gsim]()) @@ -241,8 +247,6 @@ def __init__(self, magnitudes, distances, gsims, imts, params, self.ylim = kwargs["ylim"] self.legend_fontsize = kwargs["legend_fontsize"] self.ncol = kwargs["ncol"] - self.create_plot() - def _preprocess_distances(self): """ @@ -255,7 +259,7 @@ def _preprocess_distances(self): for gmpe in self.gsims: gsim_distances = [dist for dist in gmpe.REQUIRES_DISTANCES] for dist in gsim_distances: - if not dist in self.distances.keys(): + if not dist in self.distances: raise ValueError('GMPE %s requires distance type %s' % (_get_gmpe_name(gmpe), dist)) # % (gmpe.__class.__.__name__, dist)) @@ -287,7 +291,7 @@ def _preprocess_ruptures(self): for param in rup_params: if param == 'mag': continue - elif not param in self.params.keys(): + elif not param in self.params: raise ValueError("GMPE %s requires rupture parameter %s" % (_get_gmpe_name(gmpe), param)) #% (gmpe.__class__.__name__, param)) @@ -312,7 +316,7 @@ def _preprocess_sites(self): for gmpe in self.gsims: site_params = [param for param in gmpe.REQUIRES_SITES_PARAMETERS] for param in site_params: - if not param in self.params.keys(): + if not param in self.params: raise ValueError("GMPE %s requires site parameter %s" % (_get_gmpe_name(gmpe), param)) #% (gmpe.__class__.__name__, param)) @@ -375,12 +379,19 @@ def from_rupture_model(cls, rupture, gsims, imts, stddevs='Total', return cls(magnitudes, distances, gsims, imts, params, stddevs, rupture=rupture, **kwargs) - def create_plot(self): + def plot(self): """ Creates the plot! """ raise NotImplementedError("Cannot create plot of base class!") + def _get_ylabel(self, imt): + """ + Returns the label for plotting on a y axis + """ + raise NotImplementedError + + class MagnitudeIMTTrellis(BaseTrellis): """ @@ -393,23 +404,76 @@ def __init__(self, magnitudes, distances, gsims, imts, params, Instantiate with list of magnitude and the corresponding distances given in a dictionary """ - for key in distances.keys(): + for key in distances: if isinstance(distances[key], float): distances[key] = np.array([distances[key]]) super(MagnitudeIMTTrellis, self).__init__(magnitudes, distances, gsims, imts, params, stddevs, **kwargs) - def create_plot(self): + @classmethod + def from_rupture_model(cls, properties, magnitudes, distance, gsims, imts, + stddevs='Total', **kwargs): + """ + Implements the magnitude trellis from a dictionary of properties, + magnitudes and distance + """ + kwargs.setdefault('filename', None) + kwargs.setdefault('filetype', "png") + kwargs.setdefault('dpi', 300) + kwargs.setdefault('plot_type', "loglog") + kwargs.setdefault('distance_type', "rjb") + kwargs.setdefault('xlim', None) + kwargs.setdefault('ylim', None) + # Properties + properties.setdefault("tectonic_region", "Active Shallow Crust") + properties.setdefault("rake", 0.) + properties.setdefault("ztor", 0.) + properties.setdefault("strike", 0.) + properties.setdefault("msr", WC1994()) + properties.setdefault("initial_point", DEFAULT_POINT) + properties.setdefault("hypocentre_location", None) + properties.setdefault("line_azimuth", 90.) + properties.setdefault("origin_point", (0.5, 0.5)) + properties.setdefault("vs30measured", True) + properties.setdefault("z1pt0", None) + properties.setdefault("z2pt5", None) + properties.setdefault("backarc", False) + properties.setdefault("distance_type", "rrup") + # Define a basic rupture configuration + rup = GSIMRupture(magnitudes[0], properties["dip"], + properties["aspect"], properties["tectonic_region"], + properties["rake"], properties["ztor"], + properties["strike"], properties["msr"], + properties["initial_point"], + properties["hypocentre_location"]) + # Add the target sites + _ = rup.get_target_sites_point(distance, properties['distance_type'], + properties["vs30"], + properties["line_azimuth"], + properties["origin_point"], + properties["vs30measured"], + properties["z1pt0"], + properties["z2pt5"], + properties["backarc"]) + # Get the contexts + sctx, rctx, dctx = rup.get_gsim_contexts() + # Create an equivalent 'params' dictionary by merging the site and + # rupture properties + sctx.__dict__.update(rctx.__dict__) + for val in dctx.__dict__: + if getattr(dctx, val) is not None: + setattr(dctx, val, getattr(dctx, val)[0]) + return cls(magnitudes, dctx.__dict__, gsims, imts, sctx.__dict__, + **kwargs) + + def plot(self): """ Creates the trellis plot! """ # Determine the optimum number of rows and columns nrow, ncol = utils.best_subplot_dimensions(len(self.imts)) # Get means and standard deviations - if self.rupture: - gmvs = self.get_ground_motion_values_from_rupture() - else: - gmvs = self.get_ground_motion_values() + gmvs = self.get_ground_motion_values() fig = plt.figure(figsize=self.figure_size) fig.set_tight_layout(True) row_loc = 0 @@ -428,14 +492,13 @@ def create_plot(self): # Add legend lgd = plt.legend(self.lines, self.labels, - loc=2, - bbox_to_anchor=(1.05, 1.), + loc=3, + bbox_to_anchor=(1.1, 0.), fontsize=self.legend_fontsize, ncol=self.ncol) _save_image_tight(fig, lgd, self.filename, self.filetype, self.dpi) plt.show() - def _build_plot(self, ax, i_m, gmvs): """ Plots the lines for a given axis @@ -449,7 +512,6 @@ def _build_plot(self, ax, i_m, gmvs): self.labels = [] self.lines = [] for gmpe in self.gsims: - #self.labels.append(gmpe.__class__.__name__) gmpe_name = _get_gmpe_name(gmpe) self.labels.append(gmpe_name) line, = ax.semilogy(self.magnitudes, @@ -470,16 +532,66 @@ def _build_plot(self, ax, i_m, gmvs): self._set_labels(i_m, ax) def _set_labels(self, i_m, ax): - """ - Sets the labels on the specified axes - """ - ax.set_xlabel("Magnitude", fontsize=16) - if 'SA(' in i_m: - units = PLOT_UNITS['SA'] - else: - units = PLOT_UNITS[i_m] - ax.set_ylabel("Mean %s (%s)" % (i_m, units), fontsize=16) - + """ + Sets the labels on the specified axes + """ + ax.set_xlabel("Magnitude", fontsize=16) + ax.set_ylabel(self._get_ylabel(i_m), fontsize=16) + + def _get_ylabel(self, i_m): + """ + Return the y-label for the magnitude IMT trellis + """ + if 'SA(' in i_m: + units = PLOT_UNITS['SA'] + else: + units = PLOT_UNITS[i_m] + return "Mean {:s} ({:s})".format(i_m, units) + + def to_dict(self): + """ + Parse the ground motion values to a dictionary + """ + gmvs = self.get_ground_motion_values() + nrow, ncol = utils.best_subplot_dimensions(len(self.imts)) + gmv_dict = OrderedDict([ + ("xvalues", self.magnitudes.tolist()), + ("xlabel", "Magnitude")]) + nvals = len(self.magnitudes) + gmv_dict["figures"] = [] + row_loc = 0 + col_loc = 0 + for imt in self.imts: + if col_loc == ncol: + row_loc += 1 + col_loc = 0 + # Set the dictionary of y-values + ydict = {"ylabel": self._get_ylabel(imt), + "row": row_loc, + "column": col_loc, + "yvalues": OrderedDict([])} + + for gsim in gmvs: + if not len(gmvs[gsim][imt]): + # GSIM missing, set None + ydict["yvalues"][gsim] = [None for i in range(nvals)] + continue + iml_to_list = [] + for val in gmvs[gsim][imt].flatten().tolist(): + if np.isnan(val) or (val < 0.0): + iml_to_list.append(None) + else: + iml_to_list.append(val) + ydict["yvalues"][gsim] = iml_to_list + gmv_dict["figures"].append(ydict) + col_loc += 1 + return gmv_dict + + def to_json(self): + """ + Serializes the ground motion values to json + """ + return json.dumps(self.to_dict()) def get_ground_motion_values(self): """ @@ -512,73 +624,6 @@ def get_ground_motion_values(self): break return gmvs - def get_ground_motion_values_from_rupture(self): - """ - """ - gmvs = OrderedDict() - rctx, dctx, sctx = self._get_context_sets() - for gmpe in self.gsims: - gmpe_name = _get_gmpe_name(gmpe) - gmvs.update([(gmpe_name, {})]) - for i_m in self.imts: - gmvs[gmpe_name][i_m] = np.zeros( - [len(self.rctx), self.nsites], dtype=float) - for iloc, (rct, dct, sct) in enumerate(zip(rctx, dctx, sctx)): - try: - means, _ = gmpe.get_mean_and_stddevs( - sct, - rct, - dct, - imt.from_string(i_m), - [self.stddevs]) - - gmvs[gmpe_name][i_m][iloc, :] = \ - np.exp(means) - except (KeyError, ValueError): - gmvs[gmpe_name][i_m] = [] - break - return gmvs - - - def _get_context_sets(self): - """ - When building from the rupture it is possible that it may be preferable - to re-build the contexts (e.g. for magnitude scaling). - """ - # Build context sets - rct = [] - dct = [] - sct = [] - for rctx in self.rctx: - temp_rup = deepcopy(self.rupture) - # Update mag - temp_rup.mag = deepcopy(rctx.mag) - temp_rup.rupture = temp_rup.get_rupture() - temp_rup.target_sites = None - # Update target sites - if temp_rup.target_sites_config["TYPE"] == "Mesh": - _ = temp_rup.get_target_sites_mesh( - *[temp_rup.target_sites_config[key] for key in - ["RMAX", "SPACING", "VS30", "VS30MEASURED", - "Z1.0", "Z2.5", "BACKARC"]]) - elif temp_rup.target_sites_config["TYPE"] == "Line": - _ = temp_rup.get_target_sites_line( - *[temp_rup.target_sites_config[key] for key in - ["RMAX", "SPACING", "VS30", "AZIMUTH", "ORIGIN", - "AS_LOG", "VS30MEASURED", "Z1.0", "Z2.5", "BACKARC"]]) - else: - _ = temp_rup.get_target_sites_point( - *[temp_rup.target_sites_config[key] for key in - ["R", "RTYPE", "VS30", "AZIMUTH", "ORIGIN", - "VS30MEASURED", "Z1.0", "Z2.5", "BACKARC"]]) - s_c, r_c, d_c = temp_rup.get_gsim_contexts() - rct.append(r_c) - dct.append(d_c) - sct.append(s_c) - return rct, dct, sct - - - def pretty_print(self, filename=None, sep=","): """ Format the ground motion for printing to file or to screen @@ -595,13 +640,10 @@ def pretty_print(self, filename=None, sep=","): self._write_pprint_header_line(fid, sep) # Print Distances distance_str = sep.join(["{:s}{:s}{:s}".format(key, sep, str(val[0])) - for (key, val) in self.dctx.__dict__.items()]) + for (key, val) in self.dctx.items()]) fid.write("Distances%s%s\n" % (sep, distance_str)) # Loop over IMTs - if self.rupture: - gmvs = self.get_ground_motion_values_from_rupture() - else: - gmvs = self.get_ground_motion_values() + gmvs = self.get_ground_motion_values() for imt in self.imts: fid.write("%s\n" % imt) header_str = "Magnitude" + sep + sep.join([_get_gmpe_name(gsim) @@ -621,8 +663,9 @@ def _write_pprint_header_line(self, fid, sep=","): Write the header lines of the pretty print function """ fid.write("Magnitude IMT Trellis\n") - fid.write("%s\n" % sep.join(["{:s}{:s}{:s}".format(key, sep, str(val)) - for (key, val) in self.params.items()])) + fid.write("%s\n" % sep.join([ + "{:s}{:s}{:s}".format(key, sep, str(val)) + for (key, val) in self.params.items()])) class MagnitudeSigmaIMTTrellis(MagnitudeIMTTrellis): @@ -719,13 +762,17 @@ def get_ground_motion_values_from_rupture(self): break return gmvs + def _get_ylabel(self, i_m): + """ + """ + return self.stddevs + " Std. Dev. ({:s})".format(str(i_m)) + def _set_labels(self, i_m, ax): """ Sets the axes labels """ ax.set_xlabel("Magnitude", fontsize=16) - ax.set_ylabel(self.stddevs + " Std. Dev. ({:s})".format(str(i_m)), - fontsize=16) + ax.set_ylabel(self._get_ylabel(i_m), fontsize=16) def _write_pprint_header_line(self, fid, sep=","): """ @@ -733,8 +780,9 @@ def _write_pprint_header_line(self, fid, sep=","): """ fid.write("Magnitude IMT %s Standard Deviations Trellis\n" % self.stddevs) - fid.write("%s\n" % sep.join(["{:s}{:s}{:s}".format(key, sep, str(val)) - for (key, val) in self.params.items()])) + fid.write("%s\n" % sep.join([ + "{:s}{:s}{:s}".format(key, sep, str(val)) + for (key, val) in self.params.items()])) class DistanceIMTTrellis(MagnitudeIMTTrellis): @@ -746,7 +794,7 @@ class DistanceIMTTrellis(MagnitudeIMTTrellis): def __init__(self, magnitudes, distances, gsims, imts, params, stddevs="Total", **kwargs): """ - Instandi + Instantiation """ if isinstance(magnitudes, float): magnitudes = [magnitudes] @@ -754,6 +802,40 @@ def __init__(self, magnitudes, distances, gsims, imts, params, super(DistanceIMTTrellis, self).__init__(magnitudes, distances, gsims, imts, params, stddevs, **kwargs) + @classmethod + def from_rupture_model(cls, rupture, gsims, imts, stddevs='Total', + **kwargs): + """ + Constructs the Base Trellis Class from a rupture model + :param rupture: + Rupture as instance of the :class: + smtk.trellis.configure.GSIMRupture + """ + kwargs.setdefault('filename', None) + kwargs.setdefault('filetype', "png") + kwargs.setdefault('dpi', 300) + kwargs.setdefault('plot_type', "loglog") + kwargs.setdefault('distance_type', "rjb") + kwargs.setdefault('xlim', None) + kwargs.setdefault('ylim', None) + assert isinstance(rupture, GSIMRupture) + magnitudes = [rupture.magnitude] + sctx, rctx, dctx = rupture.get_gsim_contexts() + # Create distances dictionary + distances = {} + for key in dctx._slots_: + distances[key] = getattr(dctx, key) + # Add all other parameters to the dictionary + params = {} + for key in rctx._slots_: + params[key] = getattr(rctx, key) + #for key in sctx.__slots__: + for key in sctx._slots_: + #for key in ['vs30', 'vs30measured', 'z1pt0', 'z2pt5']: + params[key] = getattr(sctx, key) + return cls(magnitudes, distances, gsims, imts, params, stddevs, + **kwargs) + def _build_plot(self, ax, i_m, gmvs): """ Plots the lines for a given axis @@ -802,18 +884,59 @@ def _build_plot(self, ax, i_m, gmvs): ax.set_ylim(self.ylim[0], self.ylim[1]) self._set_labels(i_m, ax) - def _set_labels(self, i_m, ax): - """ - Sets the labels on the specified axes - """ - ax.set_xlabel("%s (km)" % DISTANCE_LABEL_MAP[self.distance_type], - fontsize=16) - if 'SA(' in i_m: - units = PLOT_UNITS['SA'] - else: - units = PLOT_UNITS[i_m] - ax.set_ylabel("Mean %s (%s)" % (i_m, units), fontsize=16) + """ + Sets the labels on the specified axes + """ + ax.set_xlabel("%s (km)" % DISTANCE_LABEL_MAP[self.distance_type], + fontsize=16) + ax.set_ylabel(self._get_ylabel(i_m), fontsize=16) + + def _get_ylabel(self, i_m): + """ + Returns the y-label for the given IMT + """ + if 'SA(' in i_m: + units = PLOT_UNITS['SA'] + else: + units = PLOT_UNITS[i_m] + return "Mean {:s} ({:s})".format(i_m, units) + + def to_dict(self): + """ + Parses the ground motion values to a dictionary + """ + gmvs = self.get_ground_motion_values() + nrow, ncol = utils.best_subplot_dimensions(len(self.imts)) + dist_label = "{:s} (km)".format(DISTANCE_LABEL_MAP[self.distance_type]) + gmv_dict = OrderedDict([ + ("xvalues", self.distances[self.distance_type].tolist()), + ("xlabel", dist_label)]) + gmv_dict["figures"] = [] + row_loc = 0 + col_loc = 0 + for imt in self.imts: + if col_loc == ncol: + row_loc += 1 + col_loc = 0 + # Set the dictionary of y-values + ydict = {"ylabel": self._get_ylabel(imt), + "row": row_loc, + "column": col_loc, + "yvalues": OrderedDict([])} + for gsim in gmvs: + data = [None if np.isnan(val) else val + for val in gmvs[gsim][imt].flatten()] + ydict["yvalues"][gsim] = data + gmv_dict["figures"].append(ydict) + col_loc += 1 + return gmv_dict + + def to_json(self): + """ + Exports ground motion values to json + """ + return json.dumps(self.to_dict()) def pretty_print(self, filename=None, sep=","): """ @@ -975,15 +1098,18 @@ def _build_plot(self, ax, i_m, gmvs): self._set_labels(i_m, ax) - + def _get_ylabel(self, i_m): + """ + """ + return self.stddevs + " Std. Dev. ({:s})".format(str(i_m)) + def _set_labels(self, i_m, ax): """ Sets the labels on the specified axes """ ax.set_xlabel("%s (km)" % DISTANCE_LABEL_MAP[self.distance_type], fontsize=16) - ax.set_ylabel(self.stddevs + " Std. Dev. ({:s})".format(str(i_m)), - fontsize=16) + ax.set_ylabel(self._get_ylabel(i_m), fontsize=16) def _write_pprint_header_line(self, fid, sep=","): """ @@ -995,21 +1121,167 @@ def _write_pprint_header_line(self, fid, sep=","): for (key, val) in self.params.items()])) -class MagnitudeDistanceSpectraTrellis(MagnitudeIMTTrellis): - """ - - """ +class MagnitudeDistanceSpectraTrellis(BaseTrellis): + # In this case the preprocessor needs to be removed def __init__(self, magnitudes, distances, gsims, imts, params, stddevs="Total", **kwargs): - """ + """ + Builds the trellis plots for variation in response spectra with + magnitude and distance. + + In this case the class is instantiated with a set of magnitudes + and a dictionary indicating the different distance types. """ imts = ["SA(%s)" % i_m for i_m in imts] super(MagnitudeDistanceSpectraTrellis, self).__init__(magnitudes, - distances, gsims, imts, params, stddevs, **kwargs) + distances, gsims, imts, params, stddevs, **kwargs) + + def _preprocess_ruptures(self): + """ + In this case properties such as the rupture depth and width may change + with the magnitude. Where this behaviour is desired the use feeds + the function with a list of RuptureContext instances, in which each + rupture context contains the information specific to that magnitude. + + If this behaviour is not desired then the pre-processing of the + rupture information proceeds as in the conventional case within the + base class + """ + # If magnitudes was provided with a list of RuptureContexts + if all([isinstance(mag, RuptureContext) + for mag in self.magnitudes]): + # Get all required rupture attributes + self.rctx = [mag for mag in self.magnitudes] + for gmpe in self.gsims: + rup_params = [param + for param in gmpe.REQUIRES_RUPTURE_PARAMETERS] + for rctx in self.rctx: + for param in rup_params: + if not param in rctx.__dict__: + raise ValueError( + "GMPE %s requires rupture parameter %s" + % (_get_gmpe_name(gmpe), param)) + return + # Otherwise instantiate in the conventional way + super(MagnitudeDistanceSpectraTrellis, self)._preprocess_ruptures() + def _preprocess_distances(self): + """ + In the case of distances one can pass either a dictionary containing + the distances, or a list of dictionaries each calibrated to a specific + magnitude (the list must be the same length as the number of + magnitudes) + """ + if isinstance(self.distances, dict): + # Copy the same distances across + self.distances = [deepcopy(self.distances) + for mag in self.magnitudes] + assert (len(self.distances) == len(self.magnitudes)) + # Distances should be a list of dictionaries + self.dctx = [] + required_distances = [] + for gmpe in self.gsims: + gsim_distances = [dist for dist in gmpe.REQUIRES_DISTANCES] + for mag_distances in self.distances: + for dist in gsim_distances: + if not dist in mag_distances: + raise ValueError('GMPE %s requires distance type %s' + % (_get_gmpe_name(gmpe), dist)) + + if not dist in required_distances: + required_distances.append(dist) + + for distance in self.distances: + dctx = gsim.base.DistancesContext() + dist_check = False + for dist in required_distances: + if dist_check and not (len(distance[dist]) == self.nsites): + raise ValueError("Distances arrays not equal length!") + else: + self.nsites = len(distance[dist]) + dist_check = True + setattr(dctx, dist, distance[dist]) + self.dctx.append(dctx) - def create_plot(self): + @classmethod + def from_rupture_model(cls, properties, magnitudes, distances, + gsims, imts, stddevs='Total', **kwargs): + """ + Constructs the Base Trellis Class from a rupture model + :param dict properties: + Properties of the rupture and sites, including (* indicates + required): *dip, *aspect, tectonic_region, rake, ztor, strike, + msr, initial_point, hypocentre_location, distance_type, + vs30, line_azimuth, origin_point, vs30measured, z1pt0, + z2pt5, backarc + :param list magnitudes: + List of magnitudes + :param list distances: + List of distances (the distance type should be specified in the + properties dict - rrup, by default) + """ + kwargs.setdefault('filename', None) + kwargs.setdefault('filetype', "png") + kwargs.setdefault('dpi', 300) + kwargs.setdefault('plot_type', "loglog") + kwargs.setdefault('distance_type', "rjb") + kwargs.setdefault('xlim', None) + kwargs.setdefault('ylim', None) + # Defaults for the properties of the rupture and site configuration + properties.setdefault("tectonic_region", "Active Shallow Crust") + properties.setdefault("rake", 0.) + properties.setdefault("ztor", 0.) + properties.setdefault("strike", 0.) + properties.setdefault("msr", WC1994()) + properties.setdefault("initial_point", DEFAULT_POINT) + properties.setdefault("hypocentre_location", None) + properties.setdefault("line_azimuth", 90.) + properties.setdefault("origin_point", (0.5, 0.5)) + properties.setdefault("vs30measured", True) + properties.setdefault("z1pt0", None) + properties.setdefault("z2pt5", None) + properties.setdefault("backarc", False) + properties.setdefault("distance_type", "rrup") + distance_dicts = [] + rupture_dicts = [] + for magnitude in magnitudes: + # Generate the rupture for the specific magnitude + rup = GSIMRupture(magnitude, properties["dip"], + properties["aspect"], + properties["tectonic_region"], + properties["rake"], properties["ztor"], + properties["strike"], properties["msr"], + properties["initial_point"], + properties["hypocentre_location"]) + distance_dict = None + for distance in distances: + # Define the target sites with respect to the rupture + _ = rup.get_target_sites_point(distance, + properties["distance_type"], + properties["vs30"], + properties["line_azimuth"], + properties["origin_point"], + properties["vs30measured"], + properties["z1pt0"], + properties["z2pt5"], + properties["backarc"]) + sctx, rctx, dctx = rup.get_gsim_contexts() + if not distance_dict: + distance_dict = [] + for (key, val) in dctx.__dict__.items(): + distance_dict.append((key, val)) + distance_dict = dict(distance_dict) + else: + for (key, val) in dctx.__dict__.items(): + distance_dict[key] = np.hstack([ + distance_dict[key], val]) + distance_dicts.append(distance_dict) + rupture_dicts.append(rctx) + return cls(rupture_dicts, distance_dicts, gsims, imts, properties, + stddevs, **kwargs) + + def plot(self): """ Create plot! """ @@ -1018,8 +1290,8 @@ def create_plot(self): gmvs = self.get_ground_motion_values() fig = plt.figure(figsize=self.figure_size) fig.set_tight_layout({"pad":0.5}) - for rowloc in xrange(nrow): - for colloc in xrange(self.nsites): + for rowloc in range(nrow): + for colloc in range(self.nsites): self._build_plot( plt.subplot2grid((nrow, self.nsites), (rowloc, colloc)), gmvs, @@ -1028,13 +1300,41 @@ def create_plot(self): # Add legend lgd = plt.legend(self.lines, self.labels, - loc=2, - bbox_to_anchor=(1.1, 1.), - ncol=self.ncol) + loc=3., + bbox_to_anchor=(1.1, 0.0), + fontsize=self.legend_fontsize) + _save_image_tight(fig, lgd, self.filename, self.filetype, self.dpi) plt.show() - - + + def get_ground_motion_values(self): + """ + Runs the GMPE calculations to retreive ground motion values + :returns: + Nested dictionary of values + {'GMPE1': {'IM1': , 'IM2': }, + 'GMPE2': {'IM1': , 'IM2': }} + """ + gmvs = OrderedDict() + for gmpe in self.gsims: + gmpe_name = _get_gmpe_name(gmpe) + gmvs.update([(gmpe_name, {})]) + for i_m in self.imts: + gmvs[gmpe_name][i_m] = np.zeros( + [len(self.rctx), self.nsites], dtype=float) + for iloc, (rct, dct) in enumerate(zip(self.rctx, self.dctx)): + try: + means, _ = gmpe.get_mean_and_stddevs( + self.sctx, rct, dct, + imt.from_string(i_m), + [self.stddevs]) + + gmvs[gmpe_name][i_m][iloc, :] = \ + np.exp(means) + except (KeyError, ValueError): + gmvs[gmpe_name][i_m] = [] + break + return gmvs def _build_plot(self, ax, gmvs, rloc, cloc): """ @@ -1048,8 +1348,6 @@ def _build_plot(self, ax, gmvs, rloc, cloc): """ self.labels = [] self.lines = [] - #periods = np.array([imt.from_string(i_m).period - # for i_m in self.imts]) max_period = 0.0 min_period = np.inf for gmpe in self.gsims: @@ -1073,20 +1371,18 @@ def _build_plot(self, ax, gmvs, rloc, cloc): if self.plot_type == "loglog": line, = ax.loglog(periods, spec, - #"-", linewidth=2.0, label=gmpe_name) else: line, = ax.semilogy(periods, spec, - #"-", linewidth=2.0, label=gmpe_name) # On the top row, add the distance as a title if rloc == 0: - ax.set_title("%s = %9.3f (km)" %( + ax.set_title("%s = %9.1f (km)" %( self.distance_type, - self.distances[self.distance_type][cloc]), + self.distances[rloc][self.distance_type][cloc]), fontsize=14) # On the last column add a vertical label with magnitude if cloc == (self.nsites - 1): @@ -1103,7 +1399,6 @@ def _build_plot(self, ax, gmvs, rloc, cloc): ax.grid(True) self._set_labels(i_m, ax) - def _set_labels(self, i_m, ax): """ Sets the labels on the specified axes @@ -1111,6 +1406,55 @@ def _set_labels(self, i_m, ax): ax.set_xlabel("Period (s)", fontsize=14) ax.set_ylabel("Sa (g)", fontsize=14) + def to_dict(self): + """ + Export ground motion values to a dictionary + """ + gmvs = self.get_ground_motion_values() + periods = [float(val.split("SA(")[1].rstrip(")")) + for val in self.imts] + + gmv_dict = OrderedDict([ + ("xlabel", "Period (s)"), + ("xvalues", periods), + ("figures", []) + ]) + + mags = [rup.mag for rup in self.magnitudes] + dists = self.distances[0][self.distance_type] + for i, mag in enumerate(mags): + for j, dist in enumerate(dists): + ydict = OrderedDict([ + ("ylabel", "Sa (g)"), + ("magnitude", mag), + ("distance", np.around(dist, 3)), + ("row", i), + ("column", j), + ("yvalues", OrderedDict([(gsim, []) for gsim in gmvs])) + ]) + for gsim in gmvs: + for imt in self.imts: + if len(gmvs[gsim][imt]): + ydict["yvalues"][gsim].\ + append(gmvs[gsim][imt][i, j]) + else: + ydict["yvalues"][gsim].append(None) + gmv_dict["figures"].append(ydict) + return gmv_dict + + def to_json(self): + """ + Exports the ground motion values to json + """ + return json.dumps(self.to_dict()) + + def _get_ylabel(self, i_m): + """ + In this case only the spectra are being shown, so return only the + Sa (g) label + """ + return "Sa (g)" + def pretty_print(self, filename=None, sep=","): """ Format the ground motion for printing to file or to screen @@ -1125,10 +1469,7 @@ def pretty_print(self, filename=None, sep=","): fid = sys.stdout # Print Meta information self._write_pprint_header_line(fid, sep) - # Loop over IMTs - #if self.rupture: - # gmvs = self.get_ground_motion_values_from_rupture() - #else: + # Loop over IMTs gmvs = self.get_ground_motion_values() # Get the GMPE list header string gsim_str = "IMT{:s}{:s}".format( @@ -1160,7 +1501,7 @@ def pretty_print(self, filename=None, sep=","): imt_str = imt.split("(")[1].rstrip(")") iml_str = sep.join(iml_str) fid.write("{:s}{:s}{:s}\n".format(imt_str, sep, iml_str)) - fid.write("====================================================\n") + fid.write("================================================\n") if filename: fid.close() @@ -1210,36 +1551,34 @@ def _build_plot(self, ax, gmvs, rloc, cloc): min_period = np.min(periods) if np.min(periods) < min_period else \ min_period - #spec = np.array([gmvs[gmpe.__class__.__name__][i_m][rloc, cloc] - # for i_m in self.imts]) if self.plot_type == "loglog": line, = ax.semilogx(periods, spec, - #"-", linewidth=2.0, label=gmpe_name) else: line, = ax.plot(periods, spec, - #"-", linewidth=2.0, label=gmpe_name) # On the top row, add the distance as a title if rloc == 0: ax.set_title("%s = %9.3f (km)" %( self.distance_type, - self.distances[self.distance_type][cloc]), - fontsize=12) + self.distances[0][self.distance_type][cloc]), + fontsize=14) # On the last column add a vertical label with magnitude if cloc == (self.nsites - 1): ax.annotate("M = %s" % self.rctx[rloc].mag, - (1.02, 0.5), + (1.05, 0.5), xycoords="axes fraction", - fontsize=12, + fontsize=14, rotation="vertical") self.lines.append(line) ax.set_xlim(min_period, max_period) + if isinstance(self.ylim, tuple): + ax.set_ylim(self.ylim[0], self.ylim[1]) ax.grid(True) self._set_labels(i_m, ax) @@ -1256,15 +1595,12 @@ def get_ground_motion_values(self): gmpe_name = _get_gmpe_name(gmpe) gmvs.update([(gmpe_name, {})]) for i_m in self.imts: - gmvs[gmpe_name][i_m] = np.zeros([len(self.rctx), - self.nsites], - dtype=float) - for iloc, rct in enumerate(self.rctx): + gmvs[gmpe_name][i_m] = np.zeros([len(self.rctx), self.nsites], + dtype=float) + for iloc, (rct, dct) in enumerate(zip(self.rctx, self.dctx)): try: _, sigmas = gmpe.get_mean_and_stddevs( - self.sctx, - rct, - self.dctx, + self.sctx, rct,dct, imt.from_string(i_m), [self.stddevs]) gmvs[gmpe_name][i_m][iloc, :] = sigmas[0] @@ -1272,8 +1608,7 @@ def get_ground_motion_values(self): gmvs[gmpe_name][i_m] = [] break return gmvs - - + def _set_labels(self, i_m, ax): """ Sets the labels on the specified axes @@ -1281,6 +1616,13 @@ def _set_labels(self, i_m, ax): ax.set_xlabel("Period (s)", fontsize=14) ax.set_ylabel("%s Std. Dev." % self.stddevs, fontsize=14) + def _get_ylabel(self, i_m): + """ + Returns the standard deviation term (specific to the standard deviation + type specified for the class) + """ + return "{:s} Std. Dev.".format(self.stddevs) + def _write_pprint_header_line(self, fid, sep=","): """ Write the header lines of the pretty print function @@ -1290,3 +1632,180 @@ def _write_pprint_header_line(self, fid, sep=","): fid.write("%s\n" % sep.join(["{:s}{:s}{:s}".format(key, sep, str(val)) for (key, val) in self.params.items()])) + +#class MagnitudeDistanceSpectraTrellis(MagnitudeIMTTrellis): +# """ +# +# """ +# def __init__(self, magnitudes, distances, gsims, imts, params, +# stddevs="Total", **kwargs): +# """ +# """ +# imts = ["SA(%s)" % i_m for i_m in imts] +# +# super(MagnitudeDistanceSpectraTrellis, self).__init__(magnitudes, +# distances, gsims, imts, params, stddevs, **kwargs) +# +# +# def create_plot(self): +# """ +# Create plot! +# """ +# nrow = len(self.magnitudes) +# # Get means and standard deviations +# gmvs = self.get_ground_motion_values() +# fig = plt.figure(figsize=self.figure_size) +# fig.set_tight_layout({"pad":0.5}) +# for rowloc in xrange(nrow): +# for colloc in xrange(self.nsites): +# self._build_plot( +# plt.subplot2grid((nrow, self.nsites), (rowloc, colloc)), +# gmvs, +# rowloc, +# colloc) +# # Add legend +# lgd = plt.legend(self.lines, +# self.labels, +# loc=2, +# bbox_to_anchor=(1.1, 1.), +# ncol=self.ncol) +# _save_image_tight(fig, lgd, self.filename, self.filetype, self.dpi) +# plt.show() +# +# +# +# def _build_plot(self, ax, gmvs, rloc, cloc): +# """ +# Plots the lines for a given axis +# :param ax: +# Axes object +# :param str i_m: +# Intensity Measure +# :param dict gmvs: +# Ground Motion Values Dictionary +# """ +# self.labels = [] +# self.lines = [] +# #periods = np.array([imt.from_string(i_m).period +# # for i_m in self.imts]) +# max_period = 0.0 +# min_period = np.inf +# for gmpe in self.gsims: +# periods = [] +# spec = [] +# gmpe_name = _get_gmpe_name(gmpe) +# for i_m in self.imts: +# if len(gmvs[gmpe_name][i_m]): +# periods.append(imt.from_string(i_m).period) +# spec.append(gmvs[gmpe_name][i_m][rloc, cloc]) +# periods = np.array(periods) +# spec = np.array(spec) +# max_period = np.max(periods) if np.max(periods) > max_period else \ +# max_period +# min_period = np.min(periods) if np.min(periods) < min_period else \ +# min_period +# +# +# self.labels.append(gmpe_name) +# # Get spectrum from gmvs +# if self.plot_type == "loglog": +# line, = ax.loglog(periods, +# spec, +# #"-", +# linewidth=2.0, +# label=gmpe_name) +# else: +# line, = ax.semilogy(periods, +# spec, +# #"-", +# linewidth=2.0, +# label=gmpe_name) +# # On the top row, add the distance as a title +# if rloc == 0: +# ax.set_title("%s = %9.3f (km)" %( +# self.distance_type, +# self.distances[self.distance_type][cloc]), +# fontsize=14) +# # On the last column add a vertical label with magnitude +# if cloc == (self.nsites - 1): +# ax.annotate("M = %s" % self.rctx[rloc].mag, +# (1.05, 0.5), +# xycoords="axes fraction", +# fontsize=14, +# rotation="vertical") +# +# self.lines.append(line) +# ax.set_xlim(min_period, max_period) +# if isinstance(self.ylim, tuple): +# ax.set_ylim(self.ylim[0], self.ylim[1]) +# ax.grid(True) +# self._set_labels(i_m, ax) +# +# +# def _set_labels(self, i_m, ax): +# """ +# Sets the labels on the specified axes +# """ +# ax.set_xlabel("Period (s)", fontsize=14) +# ax.set_ylabel("Sa (g)", fontsize=14) +# +# def pretty_print(self, filename=None, sep=","): +# """ +# Format the ground motion for printing to file or to screen +# :param str filename: +# Path to file +# :param str sep: +# Separator character +# """ +# if filename: +# fid = open(filename, "w") +# else: +# fid = sys.stdout +# # Print Meta information +# self._write_pprint_header_line(fid, sep) +# # Loop over IMTs +# #if self.rupture: +# # gmvs = self.get_ground_motion_values_from_rupture() +# #else: +# gmvs = self.get_ground_motion_values() +# # Get the GMPE list header string +# gsim_str = "IMT{:s}{:s}".format( +# sep, +# sep.join([_get_gmpe_name(gsim) for gsim in self.gsims])) +# for i, mag in enumerate(self.magnitudes): +# for j in range(self.nsites): +# dist_string = sep.join([ +# "{:s}{:s}{:s}".format(dist_type, sep, str(val[j])) +# for (dist_type, val) in self.distances.items()]) +# # Get M-R header string +# mr_header = "Magnitude{:s}{:s}{:s}{:s}".format(sep, str(mag), +# sep, +# dist_string) +# fid.write("%s\n" % mr_header) +# fid.write("%s\n" % gsim_str) +# for imt in self.imts: +# iml_str = [] +# for gsim in self.gsims: +# gmpe_name = _get_gmpe_name(gsim) +# # Need to deal with case that GSIMs don't define +# # values for the period +# if len(gmvs[gmpe_name][imt]): +# iml_str.append("{:.8f}".format( +# gmvs[gmpe_name][imt][i, j])) +# else: +# iml_str.append("-999.000") +# # Retreived IMT string +# imt_str = imt.split("(")[1].rstrip(")") +# iml_str = sep.join(iml_str) +# fid.write("{:s}{:s}{:s}\n".format(imt_str, sep, iml_str)) +# fid.write("====================================================\n") +# if filename: +# fid.close() +# +# def _write_pprint_header_line(self, fid, sep=","): +# """ +# Write the header lines of the pretty print function +# """ +# fid.write("Magnitude - Distance Spectra (km) IMT Trellis\n") +# fid.write("%s\n" % sep.join(["{:s}{:s}{:s}".format(key, sep, str(val)) +# for (key, val) in self.params.items()])) diff --git a/tests/hazard/__init__.py b/tests/hazard/__init__.py new file mode 100755 index 0000000..e69de29 diff --git a/tests/hazard/conditional_simulation_test.py b/tests/hazard/conditional_simulation_test.py new file mode 100644 index 0000000..f7600b1 --- /dev/null +++ b/tests/hazard/conditional_simulation_test.py @@ -0,0 +1,95 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# vim: tabstop=4 shiftwidth=4 softtabstop=4 +# +# Copyright (C) 2014-2017 GEM Foundation and G. Weatherill +# +# OpenQuake is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License as published +# by the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# OpenQuake 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 Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with OpenQuake. If not, see . +""" +Tests for execution of Conditional Simulation tools +""" +import unittest +import os +import cPickle +import smtk.hazard.conditional_simulation as csim +from smtk.residuals.gmpe_residuals import Residuals + +BASE_DATA_PATH = os.path.join(os.path.dirname(__file__), "data") + + +class ConditionalSimulationTestCase(unittest.TestCase): + """ + Test suite for the conditional simulation + + Currently only testing execution - not correctness of values + """ + @classmethod + def setUpClass(cls): + """ + Import the database and the rupture before tests + """ + input_db = os.path.join(BASE_DATA_PATH, "LAquila_Database") + with open(os.path.join(input_db, "metadatafile.pkl"), "r") as fid: + cls.db = cPickle.load(fid) + input_rupture_file = os.path.join(BASE_DATA_PATH, + "laquila_rupture.xml") + cls.rupture = csim.build_rupture_from_file(input_rupture_file) + cls.gsims = ["AkkarEtAlRjb2014"] + cls.imts = ["PGA", "SA(1.0)"] + for rec in cls.db: + rec.datafile = os.path.join(os.path.dirname(__file__), + rec.datafile) + print(rec.datafile) + # Generate the residuals + cls.residuals = Residuals(cls.gsims, cls.imts) + cls.residuals.get_residuals(cls.db) + + def test_generation_residual_fields(self): + """ + Executes the site collection + """ + observed_sites = self.db.get_site_collection() + self.assertEqual(len(observed_sites), 13) + # Get the target sites + limits = [12.5, 15.0, 0.05, 40.5, 43.0, 0.05] + vs30 = 800.0 + unknown_sites = csim.get_regular_site_collection(limits, vs30) + # Generate a conditional field of residuals + pga_residuals = self.residuals.residuals["AkkarEtAlRjb2014"]\ + ["PGA"]["Intra event"] + sa1_residuals = self.residuals.residuals["AkkarEtAlRjb2014"]\ + ["SA(1.0)"]["Intra event"] + pga_field1 = csim.conditional_simulation(observed_sites, + pga_residuals, + unknown_sites, "PGA", 1) + sa1_field1 = csim.conditional_simulation(observed_sites, + sa1_residuals, + unknown_sites, "SA(1.0)", 1) + + def tests_generation_gmfs(self): + """ + Tests the generation of the full ground motion fields + """ + limits = [12.5, 15.0, 0.05, 40.5, 43.0, 0.05] + vs30 = 800.0 + unknown_sites = csim.get_regular_site_collection(limits, vs30) + gmfs = csim.get_conditional_gmfs(self.db, + self.rupture, + sites=unknown_sites, + gsims=self.gsims, + imts=self.imts, + number_simulations=5, + truncation_level=3.0) + self.assertEqual(gmfs["AkkarEtAlRjb2014"]["PGA"].shape[1], 5) + self.assertEqual(gmfs["AkkarEtAlRjb2014"]["SA(1.0)"].shape[1], 5) diff --git a/tests/hazard/data/LAquila_Database/metadatafile.pkl b/tests/hazard/data/LAquila_Database/metadatafile.pkl new file mode 100644 index 0000000..64e5a6b --- /dev/null +++ b/tests/hazard/data/LAquila_Database/metadatafile.pkl @@ -0,0 +1,5162 @@ +ccopy_reg +_reconstructor +p1 +(csmtk.sm_database +GroundMotionDatabase +p2 +c__builtin__ +object +p3 +NtRp4 +(dp5 +S'directory' +p6 +NsS'records' +p7 +(lp8 +g1 +(csmtk.sm_database +GroundMotionRecord +p9 +g3 +NtRp10 +(dp11 +S'distance' +p12 +g1 +(csmtk.sm_database +RecordDistance +p13 +g3 +NtRp14 +(dp15 +S'r_x' +p16 +NsS'rhypo' +p17 +F10 +sS'hanging_wall' +p18 +NsS'flag' +p19 +I0 +sS'rjb' +p20 +F0 +sS'repi' +p21 +F4 +sS'azimuth' +p22 +NsS'ry0' +p23 +NsS'rrup' +p24 +NsbsS'datafile' +p25 +S'data/LAquila_Database/records/16833.hdf5' +p26 +sS'directivity' +p27 +NsS'vertical' +p28 +g1 +(csmtk.sm_database +Component +p29 +g3 +NtRp30 +(dp31 +S'lup' +p32 +NsS'baseline' +p33 +S'Zeroth Order Baseline Correction' +p34 +sS'filter' +p35 +(dp36 +S'Passes' +p37 +I2 +sS'NRoll' +p38 +I2 +sS'Low-Cut' +p39 +F0.10000000000000001 +sS'High-Cut' +p40 +F50 +sS'Type' +p41 +S'Acausal Butterworth (Bandpass)' +p42 +sS'Order' +p43 +S'4-pole/4-pole' +p44 +ssS'ims' +p45 +(dp46 +S'PGV' +p47 +F10.4174934 +sS'PGD' +p48 +NsS'PGA' +p49 +F258.50007199999999 +ssS'units' +p50 +NsS'id' +p51 +S'16833' +p52 +sS'orientation' +p53 +S'UP' +p54 +sbsS'yrecord' +p55 +g1 +(g29 +g3 +NtRp56 +(dp57 +g32 +Nsg33 +S'Zeroth Order Baseline Correction' +p58 +sg35 +(dp59 +g37 +I2 +sg38 +I2 +sg39 +F0.10000000000000001 +sg40 +F50 +sg41 +S'Acausal Butterworth (Bandpass)' +p60 +sg43 +S'4-pole/4-pole' +p61 +ssg45 +(dp62 +g47 +F31.139098700000002 +sg48 +Nsg49 +F467.56410800000003 +ssg50 +Nsg51 +g52 +sg53 +S'WE' +p63 +sbsS'site' +p64 +g1 +(csmtk.sm_database +RecordSite +p65 +g3 +NtRp66 +(dp67 +S'instrument_type' +p68 +S'Digital' +p69 +sS'code' +p70 +S'L Aquila - V. 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b/tests/hazard/data/LAquila_Database/records/16889.hdf5 differ diff --git a/tests/hazard/data/laquila_rupture.xml b/tests/hazard/data/laquila_rupture.xml new file mode 100644 index 0000000..b5f7708 --- /dev/null +++ b/tests/hazard/data/laquila_rupture.xml @@ -0,0 +1,20 @@ + + + + 6.3 + -98.0 + + + + + 13.3976 42.4371 + 13.5571 42.3012 + + + 50.0 + 0.8 + 12.69 + + + diff --git a/tests/intensity_measures_test.py b/tests/intensity_measures_test.py new file mode 100644 index 0000000..19f49fd --- /dev/null +++ b/tests/intensity_measures_test.py @@ -0,0 +1,244 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# vim: tabstop=4 shiftwidth=4 softtabstop=4 +# +# Copyright (C) 2014-2017 GEM Foundation and G. Weatherill +# +# OpenQuake is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License as published +# by the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# OpenQuake 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 Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with OpenQuake. If not, see . +""" +Tests for generation of data for trellis plots +""" +import unittest +import os +import h5py +import numpy as np +import smtk.response_spectrum as rsp +import smtk.intensity_measures as ims + + +BASE_DATA_PATH = os.path.dirname(__file__) + + +class BaseIMSTestCase(unittest.TestCase): + """ + Base test case for Response Spectra and Intensity Measure functions + """ + + @staticmethod + def arr_diff(x, y, percent): + """ + Retrieving data from hdf5 leads to precision differences use relative + error (i.e. < X % difference) + """ + idx = np.logical_and(x > 0.0, y > 0.0) + diff = np.zeros_like(x) + diff[idx] = ((x[idx] / y[idx]) - 1.0) * 100 + if np.all(np.fabs(diff) < percent): + return True + else: + iloc = np.argmax(diff) + print(x, y, diff, x[iloc], y[iloc], diff[iloc]) + return False + + def _compare_sa_sets(self, sax, fle_loc, disc=1.0): + """ + When data is stored in a dictionary of arrays, compare by keys + """ + for key in sax: + if not isinstance(sax[key], np.ndarray) or len(sax[key]) == 1: + continue + reference_data = self.fle[fle_loc + "/{:s}".format(key)][:] + self.assertTrue(self.arr_diff(sax[key], reference_data, disc)) + + def setUp(self): + """ + Connect to hdf5 data store + """ + self.fle = h5py.File(os.path.join(BASE_DATA_PATH, + "smtk_ims_test_data.hdf5"), "r") + self.periods = self.fle["INPUTS/periods"][:] + + def tearDown(self): + """ + Close hdf5 connection + """ + self.fle.close() + + +class ResponseSpectrumTestCase(BaseIMSTestCase): + """ + Tests the response spectrum methods + """ + + def test_response_spectrum(self): + """ + Tests the Nigam & Jennings Response Spectrum + """ + x_record = self.fle["INPUTS/RECORD1/XRECORD"][:] + x_time_step = self.fle["INPUTS/RECORD1/XRECORD"].attrs["timestep"] + nigam_jennings = rsp.NigamJennings(x_record, x_time_step, self.periods, + damping=0.05, units="cm/s/s") + sax, timeseries, acc, vel, dis = nigam_jennings() + self._compare_sa_sets(sax, "TEST1/X/spectra") + for key in ["Acceleration", "Velocity", "Displacement"]: + if not isinstance(timeseries[key], np.ndarray): + continue + self.assertTrue( + self.arr_diff(timeseries[key], + self.fle["TEST1/X/timeseries/{:s}".format(key)][:], + 1.0) + ) + + def test_get_response_spectrum_pair(self): + """ + Tests the call to the response spectrum via ims + """ + sax, say = ims.get_response_spectrum_pair( + self.fle["INPUTS/RECORD1/XRECORD"][:], + self.fle["INPUTS/RECORD1/XRECORD"].attrs["timestep"], + self.fle["INPUTS/RECORD1/YRECORD"][:], + self.fle["INPUTS/RECORD1/YRECORD"].attrs["timestep"], + self.periods, damping=0.05, units="cm/s/s", + method="Nigam-Jennings") + self._compare_sa_sets(sax, "TEST1/X/spectra") + self._compare_sa_sets(say, "TEST1/Y/spectra") + + def test_get_geometric_mean_spectrum(self): + """ + Tests the geometric mean spectrum + """ + sax, say = ims.get_response_spectrum_pair( + self.fle["INPUTS/RECORD1/XRECORD"][:], + self.fle["INPUTS/RECORD1/XRECORD"].attrs["timestep"], + self.fle["INPUTS/RECORD1/YRECORD"][:], + self.fle["INPUTS/RECORD1/YRECORD"].attrs["timestep"], + self.periods, damping=0.05, units="cm/s/s", + method="Nigam-Jennings") + sa_gm = ims.geometric_mean_spectrum(sax, say) + self._compare_sa_sets(sa_gm, "TEST1/GM/spectra") + + def test_envelope_spectrum(self): + """ + Tests the envelope spectrum + """ + sax, say = ims.get_response_spectrum_pair( + self.fle["INPUTS/RECORD1/XRECORD"][:], + self.fle["INPUTS/RECORD1/XRECORD"].attrs["timestep"], + self.fle["INPUTS/RECORD1/YRECORD"][:], + self.fle["INPUTS/RECORD1/YRECORD"].attrs["timestep"], + self.periods, damping=0.05, units="cm/s/s", + method="Nigam-Jennings") + sa_env = ims.envelope_spectrum(sax, say) + self._compare_sa_sets(sa_env, "TEST1/ENV/spectra") + + def test_gmrotd50(self): + """ + Tests the function to get GMRotD50 + """ + gmrotd50 = ims.gmrotdpp( + self.fle["INPUTS/RECORD1/XRECORD"][:], + self.fle["INPUTS/RECORD1/XRECORD"].attrs["timestep"], + self.fle["INPUTS/RECORD1/YRECORD"][:], + self.fle["INPUTS/RECORD1/YRECORD"].attrs["timestep"], + self.periods, percentile=50.0, damping=0.05, units="cm/s/s", + method="Nigam-Jennings") + self._compare_sa_sets(gmrotd50, "TEST1/GMRotD50/spectra") + + def test_gmroti50(self): + """ + Tests the function to get GMRotI50 + """ + gmroti50 = ims.gmrotipp( + self.fle["INPUTS/RECORD1/XRECORD"][:], + self.fle["INPUTS/RECORD1/XRECORD"].attrs["timestep"], + self.fle["INPUTS/RECORD1/YRECORD"][:], + self.fle["INPUTS/RECORD1/YRECORD"].attrs["timestep"], + self.periods, percentile=50.0, damping=0.05, units="cm/s/s", + method="Nigam-Jennings") + self._compare_sa_sets(gmroti50, "TEST1/GMRotI50/spectra") + + +class ScalarIntensityMeasureTestCase(BaseIMSTestCase): + """ + Tests the functions returning scalar intensity measures + """ + def test_get_peak_measures(self): + """ + Tests the PGA, PGV, PGD functions + """ + pga_x, pgv_x, pgd_x, _, _ = ims.get_peak_measures( + self.fle["INPUTS/RECORD1/XRECORD"].attrs["timestep"], + self.fle["INPUTS/RECORD1/XRECORD"][:], + True, + True) + self.assertAlmostEqual(pga_x, 523.6900024, 3) + self.assertAlmostEqual(pgv_x, 46.7632261, 3) + self.assertAlmostEqual(pgd_x, 13.6729804, 3) + + def test_get_durations(self): + """ + Tests the bracketed, uniform and significant duration + """ + x_record = self.fle["INPUTS/RECORD1/XRECORD"][:] + x_timestep = self.fle["INPUTS/RECORD1/XRECORD"].attrs["timestep"] + self.assertAlmostEqual( + ims.get_bracketed_duration(x_record, x_timestep, 5.0), + 19.7360000, 3) + + self.assertAlmostEqual( + ims.get_uniform_duration(x_record, x_timestep, 5.0), + 14.6820000, 3) + + self.assertAlmostEqual( + ims.get_significant_duration(x_record, x_timestep, 0.05, 0.95), + 4.0320000, 3) + + def test_arias_cav_arms(self): + """ + Tests the functions for Ia, CAV, CAV5 and Arms + """ + x_record = self.fle["INPUTS/RECORD1/XRECORD"][:] + x_timestep = self.fle["INPUTS/RECORD1/XRECORD"].attrs["timestep"] + # Arias intensity + self.assertAlmostEqual( + ims.get_arias_intensity(x_record, x_timestep), + 111.1540091, 3) + # 5 - 95 % Arias Intensity + self.assertAlmostEqual( + ims.get_arias_intensity(x_record, x_timestep, 0.05, 0.95), + 99.9621952, 3) + # CAV + self.assertAlmostEqual( + ims.get_cav(x_record, x_timestep), + 509.9941624, 3) + # CAV5 + self.assertAlmostEqual( + ims.get_cav(x_record, x_timestep, threshold=5.0), + 496.7741956, 3) + # Arms + self.assertAlmostEqual( + ims.get_arms(x_record, x_timestep), + 56.8495087, 3) + + def test_spectrum_intensities(self): + """ + Tests Housner Intensity and Acceleration Spectrum Intensity + """ + x_record = self.fle["INPUTS/RECORD1/XRECORD"][:] + x_timestep = self.fle["INPUTS/RECORD1/XRECORD"].attrs["timestep"] + sax = ims.get_response_spectrum(x_record, x_timestep, self.periods)[0] + housner = ims.get_response_spectrum_intensity(sax) + self.assertAlmostEqual(housner, 121.3103787, 3) + asi = ims.get_acceleration_spectrum_intensity(sax) + self.assertAlmostEqual(asi, 432.5134666, 3) diff --git a/tests/residuals/__init__.py b/tests/residuals/__init__.py new file mode 100755 index 0000000..e69de29 diff --git a/tests/residuals/data/residual_tests_esm_data.csv b/tests/residuals/data/residual_tests_esm_data.csv new file mode 100644 index 0000000..d49db6b --- /dev/null +++ b/tests/residuals/data/residual_tests_esm_data.csv @@ -0,0 +1,42 @@ 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diff --git a/tests/residuals/residuals_tests.py b/tests/residuals/residuals_tests.py new file mode 100644 index 0000000..11bf057 --- /dev/null +++ b/tests/residuals/residuals_tests.py @@ -0,0 +1,149 @@ +""" +Core test suite for the database and residuals construction +""" +import os +import subprocess +import unittest +import cPickle +import numpy as np +from smtk.parsers.esm_flatfile_parser import (ESMFlatfileParser, + HEADERS, + COUNTRY_CODES) +import smtk.residuals.gmpe_residuals as res + + +BASE_DATA_PATH = os.path.join(os.path.dirname(__file__), "data") + + +EXPECTED_IDS = [ +"EMSC_20040918_0000026_RA_PYAS_0", "EMSC_20040918_0000026_RA_PYAT_0", +"EMSC_20040918_0000026_RA_PYLI_0", "EMSC_20040918_0000026_RA_PYLL_0", +"EMSC_20041205_0000033_CH_BNALP_0", "EMSC_20041205_0000033_CH_BOURR_0", +"EMSC_20041205_0000033_CH_DIX_0", "EMSC_20041205_0000033_CH_EMV_0", +"EMSC_20041205_0000033_CH_LIENZ_0", "EMSC_20041205_0000033_CH_LLS_0", +"EMSC_20041205_0000033_CH_MMK_0", "EMSC_20041205_0000033_CH_SENIN_0", +"EMSC_20041205_0000033_CH_SULZ_0", "EMSC_20041205_0000033_CH_VDL_0", +"EMSC_20041205_0000033_CH_ZUR_0", "EMSC_20041205_0000033_RA_STBO_0", +"EMSC_20130103_0000020_HL_SIVA_0", "EMSC_20130103_0000020_HL_ZKR_0", +"EMSC_20130108_0000044_HL_ALNA_0", "EMSC_20130108_0000044_HL_AMGA_0", +"EMSC_20130108_0000044_HL_DLFA_0", "EMSC_20130108_0000044_HL_EFSA_0", +"EMSC_20130108_0000044_HL_KVLA_0", "EMSC_20130108_0000044_HL_LIA_0", +"EMSC_20130108_0000044_HL_NOAC_0", "EMSC_20130108_0000044_HL_PLG_0", +"EMSC_20130108_0000044_HL_PRK_0", "EMSC_20130108_0000044_HL_PSRA_0", +"EMSC_20130108_0000044_HL_SMTH_0", "EMSC_20130108_0000044_HL_TNSA_0", +"EMSC_20130108_0000044_HL_YDRA_0", "EMSC_20130108_0000044_KO_ENZZ_0", +"EMSC_20130108_0000044_KO_FOCM_0", "EMSC_20130108_0000044_KO_GMLD_0", +"EMSC_20130108_0000044_KO_GOKC_0", "EMSC_20130108_0000044_KO_GOMA_0", +"EMSC_20130108_0000044_KO_GPNR_0", "EMSC_20130108_0000044_KO_KIYI_0", +"EMSC_20130108_0000044_KO_KRBN_0", "EMSC_20130108_0000044_KO_ORLT_0", +"EMSC_20130108_0000044_KO_SHAP_0"] + + +class ResidualsTestCase(unittest.TestCase): + """ + Core test case for the residuals objects + """ + + @classmethod + def setUpClass(cls): + """ + Setup constructs the database from the ESM test data + """ + ifile = os.path.join(BASE_DATA_PATH, "residual_tests_esm_data.csv") + cls.out_location = os.path.join(BASE_DATA_PATH, "residual_tests") + if os.path.exists(cls.out_location): + subprocess.call(["rm", "-r", cls.out_location]) + parser = ESMFlatfileParser.autobuild("000", "ESM ALL", + cls.out_location, ifile) + cls.database_file = os.path.join(cls.out_location, + "metadatafile.pkl") + cls.database = None + with open(cls.database_file, "r") as f: + cls.database = cPickle.load(f) + cls.gsims = ["AkkarEtAlRjb2014", "ChiouYoungs2014"] + cls.imts = ["PGA", "SA(1.0)"] + + def test_correct_build_load(self): + """ + Verifies that the database has been built and loaded correctly + """ + self.assertEqual(len(self.database), 41) + self.assertListEqual([rec.id for rec in self.database], + EXPECTED_IDS) + + def _check_residual_dictionary_correctness(self, res_dict): + """ + Basic check for correctness of the residual dictionary + """ + for i, gsim in enumerate(res_dict): + self.assertEqual(gsim, self.gsims[i]) + for j, imt in enumerate(res_dict[gsim]): + self.assertEqual(imt, self.imts[j]) + if gsim == "AkkarEtAlRjb2014": + # For Akkar et al - inter-event residuals should have + # 4 elements and the intra-event residuals 41 + self.assertEqual( + len(res_dict[gsim][imt]["Inter event"]), 4) + elif gsim == "ChiouYoungs2014": + # For Chiou & Youngs - inter-event residuals should have + # 41 elements and the intra-event residuals 41 too + self.assertEqual( + len(res_dict[gsim][imt]["Inter event"]), 41) + else: + pass + self.assertEqual( + len(res_dict[gsim][imt]["Intra event"]), 41) + self.assertEqual( + len(res_dict[gsim][imt]["Total"]), 41) + + def tests_residuals_execution(self): + """ + Tests basic execution of residuals - not correctness of values + """ + residuals = res.Residuals(self.gsims, self.imts) + residuals.get_residuals(self.database, component="Geometric") + self._check_residual_dictionary_correctness(residuals.residuals) + _ = residuals.get_residual_statistics() + + def tests_likelihood_execution(self): + """ + Tests basic execution of residuals - not correctness of values + """ + lkh = res.Likelihood(self.gsims, self.imts) + lkh.get_residuals(self.database, component="Geometric") + self._check_residual_dictionary_correctness(lkh.residuals) + _ = lkh.get_likelihood_values() + + def tests_llh_execution(self): + """ + Tests execution of LLH - not correctness of values + """ + llh = res.LLH(self.gsims, self.imts) + llh.get_residuals(self.database, component="Geometric") + self._check_residual_dictionary_correctness(llh.residuals) + _ = llh.get_loglikelihood_values(self.imts) + + def tests_multivariate_llh_execution(self): + """ + Tests execution of multivariate llh - not correctness of values + """ + multi_llh = res.MultivariateLLH(self.gsims, self.imts) + multi_llh.get_residuals(self.database, component="Geometric") + self._check_residual_dictionary_correctness(multi_llh.residuals) + _ = multi_llh.get_likelihood_values() + + def tests_edr_execution(self): + """ + Tests execution of EDR - not correctness of values + """ + edr = res.EDR(self.gsims, self.imts) + edr.get_residuals(self.database, component="Geometric") + self._check_residual_dictionary_correctness(edr.residuals) + _ = edr.get_edr_values() + + @classmethod + def tearDownClass(cls): + """ + Deletes the database + """ + subprocess.call(["rm", "-r", cls.out_location]) diff --git a/tests/smtk_ims_test_data.hdf5 b/tests/smtk_ims_test_data.hdf5 new file mode 100644 index 0000000..798f762 Binary files /dev/null and b/tests/smtk_ims_test_data.hdf5 differ diff --git a/tests/trellis/__init__.py b/tests/trellis/__init__.py new file mode 100755 index 0000000..e69de29 diff --git a/tests/trellis/data/test_distance_imt_trellis.json b/tests/trellis/data/test_distance_imt_trellis.json new file mode 100644 index 0000000..f0d29cf --- /dev/null +++ b/tests/trellis/data/test_distance_imt_trellis.json @@ -0,0 +1 @@ +{"xvalues": [2.905237004115861, 2.905237004115861, 3.7714199905221903, 4.6375245285039455, 5.503550596721652, 6.369498173832653, 7.2353672385152095, 8.101157769424844, 8.96686974523709, 9.832503144626116, 10.698057946257904, 11.563534128814808, 12.42893167097327, 13.294250551407458, 14.159490748804274, 15.02465224184698, 15.889735009214746, 16.754739029599023, 17.619664281691257, 18.484510744178806, 19.349278395752208, 20.21396721511246, 21.078577180956472, 21.943108271976143, 22.807560466875657, 23.673889542782646, 24.549505104583496, 25.434223006030635, 26.327125595396005, 27.2274076314169, 28.13436068879643, 29.04735988000737, 29.965852548112004, 30.88934863090005, 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Dev. (SA(3.0))"}]} \ No newline at end of file diff --git a/tests/trellis/trellis_test.py b/tests/trellis/trellis_test.py new file mode 100644 index 0000000..a2a5421 --- /dev/null +++ b/tests/trellis/trellis_test.py @@ -0,0 +1,236 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# vim: tabstop=4 shiftwidth=4 softtabstop=4 +# +# Copyright (C) 2014-2017 GEM Foundation and G. Weatherill +# +# OpenQuake is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License as published +# by the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# OpenQuake 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 Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with OpenQuake. If not, see . +""" +Tests for generation of data for trellis plots +""" +import unittest +import os +import json +import numpy as np +import smtk.trellis.trellis_plots as trpl +import smtk.trellis.configure as rcfg + + +BASE_DATA_PATH = os.path.join(os.path.dirname(__file__), "data") + + +class BaseTrellisTest(unittest.TestCase): + """ + This core test is designed to run a series of trellis plot calculations + and ensure compatibility with previously generated results + """ + + TEST_FILE = None + + def setUp(self): + self.imts = ["PGA", "SA(0.2)", "SA(2.0)", "SA(3.0)"] + self.periods = [0.05, 0.075, 0.1, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, + 0.17, 0.18, 0.19, 0.20, 0.22, 0.24, 0.26, 0.28, 0.30, + 0.32, 0.34, 0.36, 0.38, 0.40, 0.42, 0.44, 0.46, 0.48, + 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, + 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, + 3.0, 4.001, 5.0, 7.5, 10.0] + + self.gsims = ["AkkarBommer2010", "CauzziFaccioli2008", + "ChiouYoungs2008", "ZhaoEtAl2006Asc", "AkkarEtAlRjb2014", + "BindiEtAl2014Rjb", "CauzziEtAl2014", "DerrasEtAl2014", + "AbrahamsonEtAl2014", "BooreEtAl2014", "ChiouYoungs2014", + "CampbellBozorgnia2014", "KothaEtAl2016Italy", + "KothaEtAl2016Other", "KothaEtAl2016Turkey", + "ZhaoEtAl2016Asc", "BindiEtAl2017Rjb"] + + def compare_jsons(self, old, new): + """ + Compares the json data from file with the new data from trellis plot + + This version works with the magnitude IMT and distance IMT trellis + plots. Magnitude-distance Spectra has a slightly different means of + comparison, so this will be over-ridden in that test + """ + # Check x-labels are the same + self.assertEqual(old["xlabel"], new["xlabel"]) + # Check x-values are the same + np.testing.assert_array_almost_equal(old["xvalues"], new["xvalues"], 7) + for i in range(len(old["figures"])): + self.assertEqual(old["figures"][i]["ylabel"], + new["figures"][i]["ylabel"]) + self.assertEqual(old["figures"][i]["column"], + new["figures"][i]["column"]) + self.assertEqual(old["figures"][i]["row"], + new["figures"][i]["row"]) + + for gsim in old["figures"][i]["yvalues"]: + np.testing.assert_array_almost_equal( + old["figures"][i]["yvalues"][gsim], + new["figures"][i]["yvalues"][gsim], 7) + + +class DistanceTrellisTest(BaseTrellisTest): + TEST_FILE = "test_distance_imt_trellis.json" + + def _run_trellis(self, rupture): + """ + Executes the trellis plotting - for mean + """ + return trpl.DistanceIMTTrellis.from_rupture_model(rupture, + self.gsims, + self.imts, + distance_type="rrup") + + def test_distance_imt_trellis(self): + """ + Tests the DistanceIMT trellis data generation + """ + reference = json.load(open( + os.path.join(BASE_DATA_PATH, self.TEST_FILE), "r")) + # Setup rupture + rupture = rcfg.GSIMRupture(6.5, 60., 1.5, + hypocentre_location=(0.5, 0.5)) + _ = rupture.get_target_sites_line(250.0, 1.0, 800.0) + # Get trellis calculations + trl = self._run_trellis(rupture) + # Parse the json formatted string to a dictionary string + results = json.loads(trl.to_json()) + # Compare the two dictionaries + self.compare_jsons(reference, results) + + +class DistanceSigmaTrellisTest(DistanceTrellisTest): + TEST_FILE = "test_distance_sigma_imt_trellis.json" + + def _run_trellis(self, rupture): + """ + Executes the trellis plotting - for standard deviation + """ + return trpl.DistanceSigmaIMTTrellis.from_rupture_model( + rupture, + self.gsims, + self.imts, + distance_type="rrup") + + +class MagnitudeTrellisTest(BaseTrellisTest): + TEST_FILE = "test_magnitude_imt_trellis.json" + + def _run_trellis(self, magnitudes, distance, properties): + """ + Executes the trellis plotting - for mean + """ + return trpl.MagnitudeIMTTrellis.from_rupture_model(properties, + magnitudes, + distance, + self.gsims, + self.imts) + + def test_magnitude_imt_trellis(self): + """ + Tests the MagnitudeIMT trellis data generation + """ + reference = json.load(open( + os.path.join(BASE_DATA_PATH, self.TEST_FILE), "r")) + magnitudes = np.arange(4., 8.1, 0.1) + distance = 20. + properties = {"dip": 60.0, "rake": -90.0, "aspect": 1.5, "ztor": 0.0, + "vs30": 800.0, "backarc": False, "z1pt0": 50.0, + "z2pt5": 1.0, "line_azimuth": 90.0} + trl = self._run_trellis(magnitudes, distance, properties) + results = json.loads(trl.to_json()) + self.compare_jsons(reference, results) + + +class MagnitudeSigmaTrellisTest(MagnitudeTrellisTest): + TEST_FILE = "test_magnitude_sigma_imt_trellis.json" + + def _run_trellis(self, magnitudes, distance, properties): + """ + Executes the trellis plotting - for standard deviation + """ + return trpl.MagnitudeSigmaIMTTrellis.from_rupture_model(properties, + magnitudes, + distance, + self.gsims, + self.imts) + + +class MagnitudeDistanceSpectraTrellisTest(BaseTrellisTest): + TEST_FILE = "test_magnitude_distance_spectra_trellis.json" + + def compare_jsons(self, old, new): + """ + Compares the MagnitudeDistanceSpectra jsons + """ + self.assertEqual(old["xlabel"], new["xlabel"]) + np.testing.assert_array_almost_equal(old["xvalues"], new["xvalues"], 7) + for i in range(len(old["figures"])): + self.assertAlmostEqual(old["figures"][i]["magnitude"], + new["figures"][i]["magnitude"], 7) + self.assertAlmostEqual(old["figures"][i]["distance"], + new["figures"][i]["distance"], 7) + self.assertEqual(old["figures"][i]["row"], + new["figures"][i]["row"]) + self.assertEqual(old["figures"][i]["column"], + new["figures"][i]["column"]) + for gsim in old["figures"][i]["yvalues"]: + old_vals = np.array(old["figures"][i]["yvalues"][gsim]) + new_vals = np.array(new["figures"][i]["yvalues"][gsim]) + if old_vals.dtype == "O": + # Has None Values - compare element by element + for old_val, new_val in zip(old_vals, new_vals): + if old_val and new_val: + self.assertAlmostEqual(old_val, new_val, 7) + else: + self.assertEqual(old_val, new_val) + else: + np.testing.assert_array_almost_equal(old_vals, new_vals, 7) + + def _run_trellis(self, magnitudes, distances, properties): + """ + Executes the trellis plotting - for mean + """ + return trpl.MagnitudeDistanceSpectraTrellis.from_rupture_model( + properties, magnitudes, distances, self.gsims, self.periods, + distance_type="rrup") + + def test_magnitude_distance_spectra_trellis(self): + """ + Tests the MagnitudeDistanceSpectra Trellis data generation + """ + reference = json.load(open( + os.path.join(BASE_DATA_PATH, self.TEST_FILE), "r")) + properties = {"dip": 60.0, "rake": -90.0, "aspect": 1.5, "ztor": 0.0, + "vs30": 800.0, "backarc": False, "z1pt0": 50.0, + "z2pt5": 1.0} + magnitudes = [4.0, 5.0, 6.0, 7.0] + distances = [5., 20., 50., 150.0] + trl = self._run_trellis(magnitudes, distances, properties) + results = json.loads(trl.to_json()) + self.compare_jsons(reference, results) + + +class MagnitudeDistanceSpectraSigmaTrellisTest( + MagnitudeDistanceSpectraTrellisTest): + TEST_FILE = "test_magnitude_distance_spectra_sigma_trellis.json" + + def _run_trellis(self, magnitudes, distances, properties): + """ + Executes the trellis plotting - for standard deviation + """ + return trpl.MagnitudeDistanceSpectraSigmaTrellis.from_rupture_model( + properties, magnitudes, distances, self.gsims, self.periods, + distance_type="rrup")