Source code for mpas_analysis.ocean.plot_hovmoller_subtask

# -*- coding: utf-8 -*-
# This software is open source software available under the BSD-3 license.
#
# Copyright (c) 2020 Triad National Security, LLC. All rights reserved.
# Copyright (c) 2020 Lawrence Livermore National Security, LLC. All rights
# reserved.
# Copyright (c) 2020 UT-Battelle, LLC. All rights reserved.
#
# Additional copyright and license information can be found in the LICENSE file
# distributed with this code, or at
# https://raw.githubusercontent.com/MPAS-Dev/MPAS-Analysis/master/LICENSE
#

from __future__ import absolute_import, division, print_function, \
    unicode_literals

import xarray as xr
import numpy as np
import os
import matplotlib.pyplot as plt
from geometric_features import FeatureCollection, read_feature_collection

from mpas_analysis.shared import AnalysisTask

from mpas_analysis.shared.plot import plot_vertical_section_comparison, \
    savefig, add_inset
from mpas_analysis.shared.io.utility import build_config_full_path, \
    decode_strings

from mpas_analysis.shared.html import write_image_xml


[docs]class PlotHovmollerSubtask(AnalysisTask): """ Plots a time series vs. depth Attributes ---------- controlConfig : ``MpasAnalysisConfigParser`` Configuration options for a control run (if any) regionName : str The name of the region to plot inFileName : str The file containing the time-depth data set to plot outFileLabel : str The prefix on each plot and associated XML file fieldNameInTitle : str The name of the field being plotted, as used in the plot title mpasFieldName : str The name of the variable in the MPAS timeSeriesStatsMonthly output unitsLabel : str The units of the plotted field, to be displayed on color bars sectionName : str A section in the config file where the colormap and contour values are defined regionMaskFile : str A geojson file with regions (including one corresponding to ``regionName``) that will be used to make an inset thumbnailSuffix : str The text to be displayed under the thumbnail image, to which the region name will be prepended imageCaption : str The caption when mousing over the plot or displaying it full screen galleryGroup : str The name of the group of galleries in which this plot belongs groupSubtitle : str The subtitle of the group in which this plot belongs (or blank if none) groupLink : str A short name (with no spaces) for the link to the gallery group galleryName : str The name of the gallery in which this plot belongs """ # Authors # ------- # Xylar Asay-Davis, Milena Veneziani, Greg Streletz
[docs] def __init__(self, parentTask, regionName, inFileName, outFileLabel, fieldNameInTitle, mpasFieldName, unitsLabel, sectionName, thumbnailSuffix, imageCaption, galleryGroup, groupSubtitle, groupLink, galleryName, subtaskName=None, controlConfig=None, regionMaskFile=None): # {{{ """ Construct the analysis task. Parameters ---------- parentTask : ``AnalysisTask`` The parent task of which this is a subtask regionName : str The name of the region to plot inFileName : str The file containing the time-depth data set to plot outFileLabel : str The prefix on each plot and associated XML file fieldNameInTitle : str The name of the field being plotted, as used in the plot title mpasFieldName : str The name of the variable in the MPAS timeSeriesStatsMonthly output unitsLabel : str the units of the plotted field, to be displayed on color bars sectionName : str a section in the config file where the colormap and contour values are defined thumbnailSuffix : str The text to be displayed under the thumbnail image, to which the region name will be prepended imageCaption : str the caption when mousing over the plot or displaying it full screen galleryGroup : str the name of the group of galleries in which this plot belongs groupSubtitle : str the subtitle of the group in which this plot belongs (or blank if none) groupLink : str a short name (with no spaces) for the link to the gallery group galleryName : str the name of the gallery in which this plot belongs subtaskName : str, optional The name of the subtask (``plotHovmoller<RegionName>`` by default) controlConfig : ``MpasAnalysisConfigParser``, optional Configuration options for a control run (if any) regionMaskFile : str, optional A geojson file with regions (including one corresponding to ``regionName``) that will be used to make an inset """ # Authors # ------- # Xylar Asay-Davis if subtaskName is None: suffix = regionName[0].upper() + regionName[1:] subtaskName = 'plotHovmoller{}'.format(suffix) # first, call the constructor from the base class (AnalysisTask) super(PlotHovmollerSubtask, self).__init__( config=parentTask.config, taskName=parentTask.taskName, componentName='ocean', tags=parentTask.tags, subtaskName=subtaskName) self.controlConfig = controlConfig self.regionName = regionName self.inFileName = inFileName self.outFileLabel = outFileLabel self.fieldNameInTitle = fieldNameInTitle self.mpasFieldName = mpasFieldName self.unitsLabel = unitsLabel self.sectionName = sectionName self.regionMaskFile = regionMaskFile # xml/html related variables self.thumbnailSuffix = thumbnailSuffix self.imageCaption = imageCaption self.galleryGroup = galleryGroup self.groupSubtitle = groupSubtitle self.groupLink = groupLink self.galleryName = galleryName
# }}} def setup_and_check(self): # {{{ """ Perform steps to set up the analysis and check for errors in the setup. """ # Authors # ------- # Xylar Asay-Davis, Greg Streletz # first, call setup_and_check from the base class (AnalysisTask), # which will perform some common setup, including storing: # self.runDirectory , self.historyDirectory, self.plotsDirectory, # self.namelist, self.runStreams, self.historyStreams, # self.calendar super(PlotHovmollerSubtask, self).setup_and_check() config = self.config if self.controlConfig is not None: assert(not os.path.isabs(self.inFileName)) baseDirectory = build_config_full_path( self.controlConfig, 'output', 'timeSeriesSubdirectory') self.controlFileName = '{}/{}'.format(baseDirectory, self.inFileName) else: self.controlFileName = None if not os.path.isabs(self.inFileName): baseDirectory = build_config_full_path( config, 'output', 'timeSeriesSubdirectory') self.inFileName = '{}/{}'.format(baseDirectory, self.inFileName) mainRunName = self.config.get('runs', 'mainRunName') self.filePrefix = '{}_{}_{}'.format(self.outFileLabel, self.regionName, mainRunName) self.xmlFileNames = ['{}/{}.xml'.format( self.plotsDirectory, self.filePrefix)] return # }}} def run_task(self): # {{{ """ Make the Hovmoller plot from the time series. """ # Authors # ------- # Xylar Asay-Davis, Milena Veneziani, Greg Streletz self.logger.info("\nPlotting {} time series vs. depth...".format( self.fieldNameInTitle)) config = self.config mainRunName = config.get('runs', 'mainRunName') self.logger.info(' Load ocean data...') ds = xr.open_dataset(self.inFileName) if 'regionNames' in ds.coords: allRegionNames = decode_strings(ds.regionNames) regionIndex = allRegionNames.index(self.regionName) regionNameInTitle = self.regionName.replace('_', ' ') regionDim = ds.regionNames.dims[0] else: plotTitles = config.getExpression('regions', 'plotTitles') allRegionNames = config.getExpression('regions', 'regions') regionIndex = allRegionNames.index(self.regionName) regionNameInTitle = plotTitles[regionIndex] regionDim = 'nOceanRegionsTmp' ds = ds.isel(**{regionDim: regionIndex}) # Note: restart file, not a mesh file because we need refBottomDepth, # not in a mesh file try: restartFile = self.runStreams.readpath('restart')[0] except ValueError: raise IOError('No MPAS-O restart file found: need at least one ' 'restart file for plotting time series vs. depth') # Define/read in general variables self.logger.info(' Read in depth...') with xr.open_dataset(restartFile) as dsRestart: # reference depth [m] depths = dsRestart.refBottomDepth.values z = np.zeros(depths.shape) z[0] = -0.5 * depths[0] z[1:] = -0.5 * (depths[0:-1] + depths[1:]) Time = ds.Time.values field = ds[self.mpasFieldName].values.transpose() xLabel = 'Time (years)' yLabel = 'Depth (m)' title = '{}\n{}'.format(self.fieldNameInTitle, regionNameInTitle) outFileName = '{}/{}.png'.format(self.plotsDirectory, self.filePrefix) if config.has_option(self.sectionName, 'firstYearXTicks'): firstYearXTicks = config.getint(self.sectionName, 'firstYearXTicks') else: firstYearXTicks = None if config.has_option(self.sectionName, 'yearStrideXTicks'): yearStrideXTicks = config.getint(self.sectionName, 'yearStrideXTicks') else: yearStrideXTicks = None movingAverageMonths = config.getWithDefault( self.sectionName, 'movingAverageMonths', 1) if config.has_option(self.sectionName, 'yLim'): yLim = config.getExpression(self.sectionName, 'yLim') else: yLim = None if self.controlConfig is None: refField = None diff = None refTitle = None diffTitle = None else: controlConfig = self.controlConfig dsRef = xr.open_dataset(self.controlFileName) if 'regionNames' in dsRef.coords: allRegionNames = decode_strings(dsRef.regionNames) regionIndex = allRegionNames.index(self.regionName) regionNameInTitle = self.regionName.replace('_', ' ') regionDim = dsRef.regionNames.dims[0] else: plotTitles = controlConfig.getExpression('regions', 'plotTitles') allRegionNames = controlConfig.getExpression('regions', 'regions') regionIndex = allRegionNames.index(self.regionName) regionNameInTitle = plotTitles[regionIndex] regionDim = 'nOceanRegionsTmp' dsRef = dsRef.isel(**{regionDim: regionIndex}) refField = dsRef[self.mpasFieldName].values.transpose() assert(field.shape == refField.shape) diff = field - refField refTitle = self.controlConfig.get('runs', 'mainRunName') diffTitle = 'Main - Control' fig, _, suptitle = plot_vertical_section_comparison( config, Time, z, field, refField, diff, self.sectionName, colorbarLabel=self.unitsLabel, title=title, modelTitle=mainRunName, refTitle=refTitle, diffTitle=diffTitle, xlabel=xLabel, ylabel=yLabel, lineWidth=1, xArrayIsTime=True, movingAveragePoints=movingAverageMonths, calendar=self.calendar, firstYearXTicks=firstYearXTicks, yearStrideXTicks=yearStrideXTicks, yLim=yLim, invertYAxis=False) if self.regionMaskFile is not None: # shift the super-title a little to the left to make room for the # inset pos = suptitle.get_position() suptitle.set_position((pos[0] - 0.05, pos[1])) fcAll = read_feature_collection(self.regionMaskFile) fc = FeatureCollection() for feature in fcAll.features: if feature['properties']['name'] == self.regionName: fc.add_feature(feature) break add_inset(fig, fc, width=1.0, height=1.0, xbuffer=0.1, ybuffer=0.1) savefig(outFileName, tight=False) else: savefig(outFileName) write_image_xml( config=config, filePrefix=self.filePrefix, componentName='Ocean', componentSubdirectory='ocean', galleryGroup=self.galleryGroup, groupSubtitle=self.groupSubtitle, groupLink=self.groupLink, gallery=self.galleryName, thumbnailDescription='{} {}'.format( regionNameInTitle, self.thumbnailSuffix), imageDescription=self.imageCaption, imageCaption=self.imageCaption)
# }}} # }}} # vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python