From be34b9cd87b2987d99e9936758a48cd7d6cd3000 Mon Sep 17 00:00:00 2001
From: kgao <kenny.gao@ssec.wisc.edu>
Date: Tue, 23 Aug 2016 15:35:06 +0000
Subject: [PATCH] Code that creates quicklooks creates aoss tower quicklooks
---
aosstower/tower_quicklooks/.DS_Store | Bin 0 -> 6148 bytes
.../tower_quicklooks/create_quicklook.py | 590 ++++++++++++++++++
aosstower/tower_quicklooks/test_cases.txt | 7 +
3 files changed, 597 insertions(+)
create mode 100644 aosstower/tower_quicklooks/.DS_Store
create mode 100644 aosstower/tower_quicklooks/create_quicklook.py
create mode 100644 aosstower/tower_quicklooks/test_cases.txt
diff --git a/aosstower/tower_quicklooks/.DS_Store b/aosstower/tower_quicklooks/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
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diff --git a/aosstower/tower_quicklooks/create_quicklook.py b/aosstower/tower_quicklooks/create_quicklook.py
new file mode 100644
index 0000000..d799d64
--- /dev/null
+++ b/aosstower/tower_quicklooks/create_quicklook.py
@@ -0,0 +1,590 @@
+import os
+from datetime import datetime as dt
+from datetime import timedelta as delta
+import logging
+import pandas as pd
+from netCDF4 import MFDataset, MFTime
+import numpy as np
+import matplotlib.pyplot as plt
+import math
+
+CHOICES = ['air_temp', 'dewpoint',
+ 'rh', 'pressure', 'wind_speed', 'wind_dir', 'accum_precip', 'solar_flux']
+
+TITLES = {'air_temp': 'Temperature and Dewpoint(°C)',
+ 'rh': 'Relative Humidity(%)', 'pressure': 'Pressure(hpa)',
+ 'wind_speed': 'Wind Speed(m/s)', 'wind_dir': 'Wind Direction(°)',
+ 'accum_precip': 'Accumulated Precipitation Since 00Z (mm)',
+ 'solar_flux': 'Solar Flux(W/m^2)'}
+
+IND_TITLES = {'air_temp': 'Temperature and Dewpoint',
+ 'rh': 'Relative Humidity', 'pressure': 'Pressure',
+ 'wind_speed': 'Wind Speed', 'wind_dir': 'Wind Direction',
+ 'accum_precip': 'Accumulated Precipitation Since 00Z',
+ 'solar_flux': 'Solar Flux'}
+
+# The purpose of this method is to take a string in the format
+# YYYY-MM-DDTHH:MM:SS and convert that to a datetime object
+# or a string in the format YY-MM-DD and convert that to a datetime object
+# used in coordination with argparse -s and -e params
+# @param datetime string
+# @return datetime object
+
+def _dt_convert(datetime_str):
+ #parse datetime string, return datetime object
+ try:
+ return dt.strptime(datetime_str, '%Y-%m-%dT%H:%M:%S')
+
+ except:
+ return dt.strptime(datetime_str, '%Y-%m-%d')
+
+# The purpose of this method is to take a list of level_b1 filepaths
+# and convert those into a pandas frame with only good data
+# @param input_files - list of level_b1 filepaths
+# @return frame - pandas dataframe with only good data
+
+def get_data(input_files):
+ files = MFDataset(input_files)
+
+ #dictionary with var_name: good data pairs
+ dataDict = {}
+
+ #get the data from the files
+ for name in CHOICES:
+ data = files.variables[name][:]
+
+ qc_data = files.variables['qc_' + name][:]
+
+ dataDict[name] = data
+ dataDict['qc_' + name] = qc_data
+
+ #for some reason, time has floating point precision issues
+ #so I'm using base_time and offsets instead
+ #might need to fix later
+ base_time = files.variables['base_time'][:]
+
+ #convert base_time epoch format into date_time object
+ base_time_obj = dt(1970,1,1) + delta(seconds=int(base_time))
+
+ #get offsets from files
+ off_sets = files.variables['time_offset']
+
+ #convert that into offsets from the first file's base_time
+ off_sets = MFTime(off_sets)[:]
+
+ #for each offset, convert that into a datetime object
+ stamps = [base_time_obj + delta(seconds=int(s)) for s in off_sets]
+
+ #append all stamps into the data frame
+ dataDict['stamps'] = stamps
+
+ return pd.DataFrame(dataDict).set_index(['stamps'])
+
+# The purpose of this method is to use the qc mask
+# to only get the good data
+# @param qc_data - np array with nan for good values and various set bits for others
+# @param stamps - all stamps corresponding to data
+# @param data - data
+# @return good data and their corresponding stamps
+
+def get_good_data(qc_data, stamps, data):
+ #all good data and stamps associated with them
+ good_data = []
+ good_stamps = []
+
+ #get good indices
+ good_indices = np.where(np.isnan(qc_data))[0]
+
+ for idx in good_indices:
+ #get good_data
+ good_data.append(data[idx])
+ good_stamps.append(stamps[idx])
+
+ return [good_data, good_stamps]
+
+# The purpose of this method is to determines all the 12:00:00 days
+# within a start and end date
+# @param cur_dt - start time
+# @param dates - end time
+# @return dates in lists
+
+def get_dates_in_range(cur_dt, end):
+ curr = cur_dt
+ while curr <= end:
+ yield curr
+ curr += delta(days=1)
+
+# The purpose of this method is to get the min and max of
+# an array of stamps and determines all the 12:00:00 days
+# in that array
+# @param dewpoint stamps - time stamps for valid dewpoint data. Only specified if
+# air temp and dew point need to be ploted in the same plot
+# @param dates - time stamps for data
+# @return datesInRange - all days with 12:00:00
+def find_half_days(dewpoint_stamps, dates):
+ date_max = np.amax(dates)
+ date_min = np.amin(dates)
+
+ if(dewpoint_stamps):
+ dew_max = np.amax(dewpoint_stamps)
+ dew_min = np.amin(dewpoint_stamps)
+
+ date_max = max(date_max, dew_max)
+ date_min = min(date_min, dew_min)
+
+ cur_dt = date_min.replace(hour=12, minute=0, second=0)
+
+ if cur_dt < date_min:
+ cur_dt += delta(days=1)
+
+ datesInRange = list(get_dates_in_range(cur_dt, date_max))
+
+ return datesInRange
+
+# The purpose of this method is to create a thumbnail plot
+# @param frame - all data I need in a data frame
+# @param ymin - lower limit of the y axis if specified. set only when --daily is given
+# @param ymax - upper limit of yaxis if specified. Set only when --daily is given
+# @param dewpoint_stamps - timestamps for valid dewpoint data. Only specified if
+# air temp and dew point need to be plotted in the same plot
+# @param dewpoint_data - valid dewpoint data. Only specified if
+# air temp and dew point need to be plotted in the same plot
+#@param output - output filename pattern
+def thumbnail_plot(dates, data, ymin, ymax,
+ dewpoint_stamps, dewpoint_data, output, wind_dir):
+
+ if(dewpoint_stamps):
+ plt.plot(dates, data, 'r', dewpoint_stamps, dewpoint_data, 'b')
+ plt.axis([min(dates), max(dates), ymin, ymax])
+ #plt.plot(dewpoint_stamps, dewpoint_data, 'b')
+
+ elif(wind_dir):
+ plt.plot(dates, data, 'ko', markersize=0.1)
+ plt.axis([min(dates), max(dates), 0, 360])
+
+ else:
+ plt.plot(dates, data, 'k')
+ plt.axis([min(dates), max(dates), ymin, ymax])
+
+ #scale
+ fig = plt.gcf()
+ dpi = fig.get_dpi()
+ fig.set_size_inches(80/float(dpi), 80/float(dpi))
+
+ #create axes
+ axes = plt.gca()
+ axes.axes.get_xaxis().set_ticklabels([])
+ axes.axes.get_xaxis().set_tick_params(length=7)
+ axes.axes.get_yaxis().set_ticklabels([])
+ axes.axes.get_yaxis().set_visible(False)
+ axes.spines['right'].set_visible(False)
+ axes.spines['bottom'].set_visible(False)
+
+ #got the basic shape of the plot
+ #still need to draw a line in the middle
+ datesInRange = find_half_days(dewpoint_stamps, dates)
+
+ for date in datesInRange:
+ plt.axvline(x=date, color='k')
+
+# The purpose of this method is to create a thumbnail
+# @param frame - all data I need in a data frame
+# @param ymin - lower limit of the y axis if specified. set only when --daily is given
+# @param ymax - upper limit of yaxis if specified. Set only when --daily is given
+# @param create_air_dew_plot - boolean specifying if air temp and dewpoint
+# @param output - output filename pattern
+# should be in same plot
+def create_thumbnail(frame, ymin, ymax, create_air_dew_plot, output):
+ #see if we're going to need subplots
+ #subplots needed when len is greater than 2 for one variable
+ #or greater than 4 for two variables
+
+ need_subplots = len(list(frame.columns.values)) > 2 and not create_air_dew_plot
+ need_subplots = need_subplots or len(list(frame.columns.values)) > 4 and create_air_dew_plot
+
+ if need_subplots:
+ plots_created = 1
+
+ if create_air_dew_plot:
+ numberPlots = (len(list(frame.columns.values)) - 2) / 2
+ plotNumber = numberPlots * 100 + 10
+
+ else:
+ numberPlots = len(list(frame.columns.values)) / 2
+ plotNumber = numberPlots * 100 + 10
+
+ stamps = list(frame.index)
+
+ #get dewpoint data
+ if create_air_dew_plot:
+ all_data = frame['dewpoint']
+ qc_data = frame['qc_dewpoint']
+
+ good_list = get_good_data(qc_data, stamps, all_data)
+ dewpoint_data = good_list[0]
+ dewpoint_stamps= good_list[1]
+
+ for name in CHOICES:
+ if name == 'dewpoint' and create_air_dew_plot:
+ continue
+
+ if name not in list(frame.columns.values):
+ continue
+
+ elif need_subplots:
+ plt.subplot(plotNumber + plots_created)
+ plots_created += 1
+
+
+ all_data = frame[name]
+ qc_data = frame['qc_' + name]
+
+ good_list = get_good_data(qc_data, stamps, all_data)
+ good_data = good_list[0]
+ good_stamps= good_list[1]
+
+ #if we don't need two lines in same plot, plot
+ if not (create_air_dew_plot and name == 'air_temp'):
+ if name != 'wind_dir':
+ thumbnail_plot(good_stamps, good_data, ymin[name], ymax[name],
+ None, None, output, False)
+
+ if name == 'wind_dir':
+ thumbnail_plot(good_stamps, good_data, ymin[name], ymax[name],
+ None, None, output, True)
+
+ else:
+ thumbnail_plot(good_stamps, good_data, ymin[name], ymax[name],
+ dewpoint_stamps, dewpoint_data, output, False)
+
+ plt.savefig(output + '.thumbnail.png')
+
+def full_plot_stamps(stamps):
+ first_stamp = np.sort(stamps)[0]
+
+ first_stamp = first_stamp.replace(hour=0, minute=0, second=0)
+
+ #print([((s - first_stamp).total_seconds()/3600) for s in stamps])
+
+ #print([(int((s - first_stamp).total_seconds()) / 3600) for s in stamps])
+
+ return [((s - first_stamp).total_seconds()/3600) for s in stamps]
+
+# The purpose of this method is to change how the y ticks are shown
+# @param min - minimum of the y range right now
+# @param max - maximum of the y range right now
+# @return new tick labels
+
+def get_new_labels(mini, maxi):
+ delta = math.ceil((maxi - mini) / 6)
+
+ return np.arange(mini, (mini + delta*6), delta)
+
+# The purpose of this method is to create a full_size plot
+# @param frame - all data I need in a data frame
+# @param ymin - lower limit of the y axis if specified. set only when --daily is given
+# @param ymax - upper limit of yaxis if specified. Set only when --daily is given
+# @param dewpoint_stamps - timestamps for valid dewpoint data. Only specified if
+# air temp and dew point need to be plotted in the same plot
+# @param dewpoint_data - valid dewpoint data. Only specified if
+# air temp and dew point need to be plotted in the same plot
+# @param output - output filename pattern
+# @param wind_direction - says different yaxis labels
+# @param accum_precip - different yaxis handling
+# @param see if we need subplots
+def full_plot(dates, data, ymin, ymax,
+ dewpoint_stamps, dewpoint_data, output, wind_dir,
+ accum_precip, need_subplots):
+
+ dates = full_plot_stamps(dates)
+
+ if(dewpoint_stamps):
+ dewpoint_stamps = full_plot_stamps(dewpoint_stamps)
+
+ plt.plot(dates, data, 'r', dewpoint_stamps, dewpoint_data, 'b')
+ plt.axis([min(dates), max(dates), ymin, ymax])
+
+
+ #labels = [math.ceil(float(item.get_text())) for item in ticks]
+ #plt.plot(dewpoint_stamps, dewpoint_data, 'b')
+
+
+ elif(wind_dir):
+ plt.plot(dates, data, 'ko', markersize=1)
+ plt.axis([min(dates), max(dates), 0, 360])
+
+ axes = plt.gca()
+ axes.get_yaxis().set_ticks([0,90,180,270])
+
+
+ else:
+ plt.plot(dates, data, 'k')
+ plt.axis([min(dates), max(dates), ymin, ymax])
+
+ if not need_subplots:
+ return
+
+ #get axes
+ axes = plt.gca()
+
+ #if not wind_direction, reset yaxis ticks
+ if not wind_dir:
+ if not accum_precip:
+ mini, maxi = axes.get_ylim()
+ new_labels = get_new_labels(mini, maxi)
+
+ else:
+ mini, maxi = axes.get_ylim()
+ delta = ((maxi - mini)/6)
+ new_labels = np.arange(mini, (mini + delta*6), delta)
+
+ if len(new_labels) == 0:
+ new_labels = [0, 0.05, 0.1]
+
+ plt.yticks(new_labels)
+ axes.get_yaxis().get_major_ticks()[-1].set_visible(False)
+
+ #hid last tick because for subplots above the last one, it's peeping out...
+ # will show for the last subplot or when subplots are not needed
+ # in other words, this code should only affect plots above the last plot
+ # only when sublots are needed
+ axes.get_xaxis().get_major_ticks()[-1].set_visible(False)
+ axes.get_xaxis().get_major_ticks()[0].set_visible(False)
+
+# The purpose of this method is to get the subtitle's y coordinate
+# based upon how many subplots there are
+# @param numSubPlots - number of subplots
+# @return y-coordinate of subtitle
+def get_subtitle_location(numSubPlots):
+ return 1 - 0.05*numSubPlots
+
+# The purpose of this method is to create a full size quicklook
+# @param frame - all data I need in a data frame
+# @param ymin - lower limit of the y axis if specified. set only when --daily is given
+# @param ymax - upper limit of yaxis if specified. Set only when --daily is given
+# @param create_air_dew_plot - boolean specifying if air temp and dewpoint
+# should be in same plot
+def create_full_plot(frame, ymin, ymax, create_air_dew_plot, output):
+ #see if we're going to need subplots
+ #subplots needed when len is greater than 2 for one variable
+ #or greater than 4 for two variables
+
+ need_subplots = len(list(frame.columns.values)) > 2 and not create_air_dew_plot
+ need_subplots = need_subplots or len(list(frame.columns.values)) > 4 and create_air_dew_plot
+
+ #get need supplot vars
+ if need_subplots:
+ plots_created = 1
+
+ if create_air_dew_plot:
+ numberPlots = (len(list(frame.columns.values)) - 2) / 2
+ plotNumber = numberPlots * 100 + 10
+
+ else:
+ numberPlots = len(list(frame.columns.values)) / 2
+ plotNumber = numberPlots * 100 + 10
+
+ stamps = list(frame.index)
+
+ #get dewpoint data
+ if create_air_dew_plot:
+ all_data = frame['dewpoint']
+ qc_data = frame['qc_dewpoint']
+
+ good_list = get_good_data(qc_data, stamps, all_data)
+ dewpoint_data = good_list[0]
+ dewpoint_stamps= good_list[1]
+
+ for name in CHOICES:
+ #if dewpoint with temp or a name not in frame
+ # continue
+ if name == 'dewpoint' and create_air_dew_plot:
+ continue
+
+ if name not in list(frame.columns.values):
+ continue
+
+ all_data = frame[name]
+ qc_data = frame['qc_' + name]
+
+ good_list = get_good_data(qc_data, stamps, all_data)
+ good_data = good_list[0]
+ good_stamps= good_list[1]
+
+ dateString = good_stamps[0].strftime('%m/%d/%Y')
+
+ # create plots
+ if need_subplots:
+ if plots_created == 1:
+ plt.figure().suptitle('AO&SS Building Tower Meteorogram ' + dateString)
+ ax1 = plt.subplot(plotNumber + plots_created)
+ ax1.set_title(TITLES[name], x=0.5, y=get_subtitle_location(numberPlots), fontsize=8)
+
+
+ else:
+ curr_plot = plt.subplot(plotNumber + plots_created, sharex=ax1)
+ curr_plot.set_title(TITLES[name], x=0.5, y=get_subtitle_location(numberPlots), fontsize=8)
+
+ plots_created += 1
+
+ else:
+ plt.figure().suptitle('AO&SS Building Tower ' + IND_TITLES[name] + ' ' + dateString)
+ plt.ylabel(TITLES[name])
+
+ #if we don't need two lines in same plot, plot
+ if not (create_air_dew_plot and name == 'air_temp'):
+ full_plot(good_stamps, good_data, ymin[name], ymax[name],
+ None, None, output, name == 'wind_dir',
+ name == 'accum_precip', need_subplots)
+
+ else:
+ full_plot(good_stamps, good_data, ymin[name], ymax[name],
+ dewpoint_stamps, dewpoint_data, output, False, False,
+ need_subplots)
+
+ if need_subplots:
+ plt.subplots_adjust(hspace=0, bottom=0.125)
+
+ plt.xlabel('Time (UTC)')
+
+ #reverse code done in create_full_plot
+ axes = plt.gca()
+ axes.get_xaxis().get_major_ticks()[-1].set_visible(True)
+ axes.get_xaxis().get_major_ticks()[0].set_visible(True)
+
+ plt.savefig(output + '.png')
+
+def main():
+ import argparse
+
+ #argparse description
+ parser = argparse.ArgumentParser(description="Use data from level_b1 netCDF files to create netCDF files")
+
+ #argparse verbosity info
+ parser.add_argument('-v', '--verbose', action='count',
+ default=int(os.environ.get("VERBOSITY", 2)),
+ dest='verbosity',
+ help=('each occurence increases verbosity 1 level through'
+ + ' ERROR-WARNING-INFO-DEBUG (default INFO)'))
+
+ #argparse start and end times
+ parser.add_argument('-s', '--start-time', type=_dt_convert,
+ help="Start time of plot. If only -s is given, a plot of " +
+ "only that day is created. Formats allowed: \'YYYY-MM-DDTHH:MM:SS\', \'YYYY-MM-DD\'")
+
+ parser.add_argument('-e', '--end-time', type=_dt_convert,
+ help="End time of plot. If only -e is given, a plot of only that day is " +
+ "created. Formats allowed: \'YYYY-MM-DDTHH:MM:SS\', \'YYYY-MM-DD\'")
+
+ #netcdf file paths
+ parser.add_argument("input_files", nargs="+", help="aoss_tower_level_b1 paths")
+
+ #output filename pattern
+ parser.add_argument('-o', '--output', help="filename pattern")
+
+ #thumbnail or full
+ parser.add_argument('-t', '--thumb-nail', action='store_true', help="if specified, script creates a thumbnail")
+
+ #plot names
+ parser.add_argument('--varnames', nargs="+", choices=CHOICES,
+ required=True,
+ help="the variable names for the desired plot. Valid choices: air_temp, " +
+ "dewpoint, rh, pressure, wind_speed, wind_dir, accum_precip, solar_flux")
+
+ #--daily flag
+ parser.add_argument('-d', '--daily', action='store_true',
+ help="creates a plot for every day. Usually used to create plots " +
+ "that will line up for aoss tower quicklooks page")
+
+ args = parser.parse_args()
+
+ levels = [logging.ERROR, logging.WARN, logging.INFO, logging.DEBUG]
+
+ level = levels[min(3, args.verbosity)]
+
+ logging.basicConfig(level=level)
+
+ var_names = args.varnames
+
+ create_air_dew_plot = False
+
+ #see if we need to plot air_temp and dewpoint on the same plot
+ if 'air_temp' in var_names and 'dewpoint' in var_names:
+ create_air_dew_plot = True
+ var_names.remove('dewpoint')
+
+ #get data
+ frame = get_data(args.input_files)
+
+ #only have the data we need
+ for name in CHOICES:
+ if name == 'dewpoint' and create_air_dew_plot:
+ continue
+
+ if name not in var_names:
+ del frame[name]
+ del frame['qc_' + name]
+
+ #frame only contains data from start-end times
+ if(args.start_time and args.end_time):
+ start_filter = args.start_time.strftime('%Y-%m-%d %H:%M:%S')
+ end_filter = args.end_time.strftime('%Y-%m-%d %H:%M:%S')
+ frame = frame[start_filter: end_filter]
+
+ #frame only contains data from start-end of that day
+ elif(args.start_time):
+ end_time = args.start_time.replace(hour=23, minute=59, second=59)
+ start_filter = args.start_time.strftime('%Y-%m-%d %H:%M:%S')
+ end_filter = end_time.strftime('%Y-%m-%d %H:%M:%S')
+ frame = frame[start_filter: end_filter]
+
+ ymin = {}
+ ymax = {}
+
+ if not args.daily:
+ for name in CHOICES:
+ if name == 'dewpoint' and create_air_dew_plot:
+ continue
+
+ if name not in frame:
+ continue
+
+ ymin[name] = None
+ ymax[name] = None
+
+ if(args.thumb_nail):
+ create_thumbnail(frame, ymin, ymax, create_air_dew_plot, args.output)
+
+ else:
+ create_full_plot(frame, ymin, ymax, create_air_dew_plot, args.output)
+
+ else:
+ for name in CHOICES:
+ if name == 'dewpoint' and create_air_dew_plot:
+ continue
+
+ if name not in frame:
+ continue
+
+ if name == 'accum_precip':
+ ymin[name] = frame[name].min()
+ ymax[name] = frame[name].max()
+
+ else:
+ ymin[name] = math.floor(frame[name].min())
+ ymax[name] = math.ceil(frame[name].max())
+
+ frameList = [(group[1]) for group in frame.groupby(frame.index.day)]
+
+ counter = 0
+
+ for frame in frameList:
+ if args.thumb_nail:
+ create_thumbnail(frame, ymin, ymax, create_air_dew_plot, args.output.format(str(counter)))
+ else:
+ create_full_plot(frame, ymin, ymax, create_air_dew_plot, args.output.format(str(counter)))
+ counter += 1
+ plt.gcf().clear()
+
+if __name__ == "__main__":
+ main()
diff --git a/aosstower/tower_quicklooks/test_cases.txt b/aosstower/tower_quicklooks/test_cases.txt
new file mode 100644
index 0000000..f39ab64
--- /dev/null
+++ b/aosstower/tower_quicklooks/test_cases.txt
@@ -0,0 +1,7 @@
+time python create_quicklook.py /Users/kgao/Desktop/ncFiles/05/aoss_tower.2013-05-01.day.nc /Users/kgao/Desktop/ncFiles/05/aoss_tower.2013-05-02.day.nc -o test --varnames air_temp dewpoint rh pressure wind_speed wind_dir accum_precip solar_flux --daily
+
+time python create_quicklook.py -s 2013-05-01 /Users/kgao/Desktop/ncFiles/05/aoss_tower.2013-05-01.day.nc -o test --varnames air_temp dewpoint rh pressure wind_speed wind_dir accum_precip solar_flux
+
+time python create_quicklook.py -s 2013-05-01 /Users/kgao/Desktop/ncFiles/05/aoss_tower.2013-05-01.day.nc -o test --varnames air_temp dewpoint
+
+time python create_quicklook.py -s 2013-05-01 /Users/kgao/Desktop/ncFiles/05/aoss_tower.2013-05-01.day.nc -o test --varnames pressure
--
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