def _get_data( msa_or_conus_name ):
if msa_or_conus_name.lower( ) == 'conus':
data_conus = COVID19Database.data_conus( )
return core.get_incident_data( data_conus )
if msa_or_conus_name.lower( ) in COVID19Database.data_msas_2019( ):
data_msas_2019 = COVID19Database.data_msas_2019( )
return core.get_incident_data( data_msas_2019[ msa_or_conus_name.lower( ) ] )
raise ValueError("Error, the chosen MSA name %s not one of the %d defined." % (
msa_or_conus_name.lower( ), len( COVID19Database.data_msas_2019( ) ) ) )
def _get_data_state_or_territory( statename ):
mapping_state_rname_conus = COVID19Database.mapping_state_rname_conus( )
mapping_state_rname_nonconus = COVID19Database.mapping_state_rname_nonconus( )
data_states = COVID19Database.data_states( )
data_nonconus_states_territories = COVID19Database.data_nonconus_states_territories( )
if statename in mapping_state_rname_conus:
data_state = data_states[
mapping_state_rname_conus[ statename ] ]
return core.get_incident_data( data_state )
if statename in mapping_state_rname_nonconus:
data_state = data_nonconus_states_territories[
mapping_state_rname_nonconus[ statename ] ]
return core.get_incident_data( data_state )
raise ValueError("Error, the chosen state or territory, %s, not in one of the %d defined." % (
statename, len( mapping_state_rname_conus ) + len( mapping_state_rname_nonconus ) ) )
def main():
all_state_territory_choices = sorted(
chain.from_iterable(
map(lambda arr: arr.keys(),
(COVID19Database.mapping_state_rname_conus(),
COVID19Database.mapping_state_rname_nonconus()))))
parser = ArgumentParser()
parser.add_argument(
'-d',
'--dirname',
dest='dirname',
type=str,
action='store',
default=os.getcwd(),
help=
'The directory into which to store the resulting files. Default is %s.'
% os.getcwd())
parser.add_argument(
'--info',
dest='do_info',
action='store_true',
default=False,
help='If chosen, then print out INFO level logging statements.')
parser.add_argument(
'-n',
dest='name',
type=str,
action='store',
default='New York',
help=
'Make movies or other summary data for a state. Default is "New York".',
choices=all_state_territory_choices)
parser.add_argument(
'-M',
'--maxnum',
dest='maxnum',
type=int,
action='store',
default=None,
metavar='MAXNUM',
help=' '.join([
'The limit of cases/deaths to visualize.',
'Default is a plausible amount for the chosen state.',
'You should use a limit larger (by at least 2, no more than 10) than',
'the maximum number of cases recorded for a county in that state.'
]))
parser.add_argument('-y',
'--yes',
dest='do_yes',
action='store_true',
default=False,
help='If chosen, then do not confirm --maxnum.')
#
subparsers = parser.add_subparsers(help=' '.join([
'Choose one of three options:',
'(m) make a movie of the COVID-19 cumulative stats for the state;',
'(s) dumps summary plots of last incident date,',
'and cumulative covid-19 stats, of a state;',
'and (mcd) make a movie of either "CASES" or "DEATHS" in the state.'
]),
dest='choose_option')
#
## make summary movie (m)
parser_moviestate = subparsers.add_parser(
'm',
help=
'Make a movie of the COVID-19 cases and deaths trend for the specific state.'
)
#
## make summary plots of last day, and COVID-19 cases/deaths in pandas dataframe up to last day.
parser_sumstate = subparsers.add_parser(
's',
help=' '.join([
'Make a summary plot, and incident data file,',
'of COVID-19 cases and deaths trend,', 'for the specific state.'
]))
#
## make a movie of cases OR deaths (mcd)
parser_movcasedeath = subparsers.add_parser(
'mcd',
help=
'Make a large-sized movie of either "CASES" or "DEATHS" for given state.'
)
parser_movcasedeath.add_argument(
'-d',
'--disp',
dest='movcasedeath_display',
type=str,
action='store',
default='cases',
metavar='DISP',
choices=('cases', 'deaths'),
help=
'Whether to display the "cases" or "death" trends of the given state. Default is "cases".'
)
parser_movcasedeath.add_argument(
'-s',
'--saveimages',
dest='movcasedeath_saveimages',
action='store_true',
default=False,
help=
'If chosen, then save the images used to create the movie into a ZIP archive.'
)
#
##
args = parser.parse_args()
logger = logging.getLogger()
if args.do_info: logger.setLevel(logging.INFO)
statename = args.name.strip()
mapping_state_rname_conus = COVID19Database.mapping_state_rname_conus()
mapping_state_rname_nonconus = COVID19Database.mapping_state_rname_nonconus(
)
data_states = COVID19Database.data_states()
data_nonconus_states_territories = COVID19Database.data_nonconus_states_territories(
)
if statename in mapping_state_rname_conus:
data_state = data_states[mapping_state_rname_conus[statename]]
else:
data_state = data_nonconus_states_territories[
mapping_state_rname_nonconus[statename]]
inc_data = core.get_incident_data(data_state)
maxnum = args.maxnum
if maxnum is None:
max_cases = core.get_max_cases_county(inc_data)['cases']
maxnum = find_plausible_maxnum(max_cases)
if maxnum < 1:
print('Error, maximum number for visualization %d < 1.' % maxnum)
return
_summarize_data(inc_data, maxnum)
#
## quad movie summary
if args.choose_option == 'm':
if args.do_yes: status = args.do_yes
else: status = _try_continue()
if not status: return
movie_name = viz.create_summary_movie_frombeginning(
inc_data, dirname=args.dirname)
#
## cumulative COVID-19 stats up to last day
elif args.choose_option == 's':
if args.do_yes: status = args.do_yes
else: status = _try_continue()
if not status: return
viz.get_summary_demo_data(inc_data,
maxnum_colorbar=maxnum,
dirname=args.dirname)
#
## movie of only either COVID-19 cases or deaths
elif args.choose_option == 'mcd':
if args.do_yes: status = args.do_yes
else: status = _try_continue()
if not status: return
#
viz.create_summary_cases_or_deaths_movie_frombeginning(
inc_data,
type_disp=args.movcasedeath_display,
dirname=args.dirname,
save_imgfiles=args.movcasedeath_saveimages)
def main():
parser = ArgumentParser()
parser.add_argument(
'-d',
'--dirname',
dest='dirname',
type=str,
action='store',
default=os.getcwd(),
help=
'The directory into which to store the resulting files. Default is %s.'
% os.getcwd())
parser.add_argument(
'--info',
dest='do_info',
action='store_true',
default=False,
help='If chosen, then print out INFO level logging statements.')
#
subparsers = parser.add_subparsers(help=' '.join([
'Choose one of three options:', '(M) summarizes stats from metros;',
'(m) make a movie of a metro region;',
'and (s) dumps summary plots of last incident date,',
'and cumulative covid-19 stats, of a metro region.'
]),
dest='choose_option')
#
## list of metros (M)
parser_showmetros = subparsers.add_parser(
'M',
help=
'If chosen, then list all the metropolitan areas through which we can look.'
)
parser_showmetros.add_argument(
'-f',
'--format',
help=
'Format of the table that displays MSA summary. Default is "simple".',
type=str,
action='store',
choices=['simple', 'github', 'rst', 'rst-simple', 'json'],
default='simple')
parser_showmetros.add_argument(
'--metros',
help=
'If chosen, list of selected metros for which to summarize COVID-19 data.',
type=str,
action='store')
parser_showmetros.add_argument(
'--topN',
dest='topN',
type=int,
action='store',
help=
'If defined, will be the top N (N must be an integer greater than 0) population metros to get data on.'
)
#
## make summary movie (m)
parser_moviemetro = subparsers.add_parser(
'm',
help=
'Make a movie of the COVID-19 cases and deaths trend for the specific Metropolitan Statistical Area (MSA).'
)
parser_moviemetro.add_argument(
'-n',
'--name',
dest='name',
type=str,
action='store',
default='bayarea',
help='Make a movie of this metropolitan area. Default is "bayarea"')
parser_moviemetro.add_argument(
'-M',
'--maxnum',
dest='maxnum',
type=int,
action='store',
default=None,
metavar='MAXNUM',
help=' '.join([
'The limit of cases/deaths to visualize.',
'Default is a plausible amount for the chosen MSA or CONUS.',
'You should use a limit larger (by at least 2, no more than 10) than',
'the maximum number of cases recorded for a county in that MSA or CONUS.'
]))
parser_moviemetro.add_argument(
'--conus',
dest='do_conus',
action='store_true',
default=False,
help=
'If chosen, then make a movie of the COVID-19 cases and deaths trends for the Continental US (CONUS).'
)
parser_moviemetro.add_argument(
'-y',
'--yes',
dest='do_yes_moviemetro',
action='store_true',
default=False,
help='If chosen, then do not confirm --maxnum.')
#
## make summary plots of last day, and COVID-19 cases/deaths in pandas dataframe up to last day.
parser_summmetro = subparsers.add_parser(
's',
help=' '.join([
'Make a summary plot, and incident data file,',
'of COVID-19 cases and deaths trend,',
'for the specific Metropolitan Statistical Area (MSA).'
]))
parser_summmetro.add_argument(
'-n',
'--name',
dest='summmetro_name',
type=str,
action='store',
default='bayarea',
metavar='NAME',
help=' '.join([
'Create a summary plot and incident data file of this metropolitan area.',
'Default is "bayarea".'
]))
parser_summmetro.add_argument(
'-M',
'--maxnum',
dest='summmetro_maxnum',
type=int,
action='store',
default=None,
metavar='MAXNUM',
help=' '.join([
'The limit of cases/deaths to visualize.',
'Default is a plausible amount for the chosen MSA or CONUS.',
'You should use a limit larger (by at least 2, no more than 10) than',
'the maximum number of cases recorded for a county in that MSA or CONUS.'
]))
parser_summmetro.add_argument(
'--conus',
dest='do_conus_summmetro',
action='store_true',
default=False,
help=
'If chosen, then make a movie of the COVID-19 cases and deaths trends for the Continental US (CONUS).'
)
parser_summmetro.add_argument(
'-y',
'--yes',
dest='do_yes_summmetro',
action='store_true',
default=False,
help='If chosen, then do not confirm --maxnum.')
#
## make a movie of cases OR deaths
parser_movcasedeath = subparsers.add_parser(
'mcd',
help=
'Make a large-sized movie of either "CASES" or "DEATHS" for given MSA or CONUS.'
)
parser_movcasedeath.add_argument(
'-n',
'--name',
dest='movcasedeath_name',
type=str,
action='store',
default='bayarea',
metavar='NAME',
help=' '.join([
'Create a summary plot and incident data file of this metropolitan area.',
'Default is "bayarea".'
]))
parser_movcasedeath.add_argument(
'-d',
'--disp',
dest='movcasedeath_display',
type=str,
action='store',
default='cases',
metavar='DISP',
choices=('cases', 'deaths'),
help=
'Whether to display the "cases" or "death" trends of the MSA or CONUS. Default is "cases".'
)
parser_movcasedeath.add_argument(
'-M',
'--maxnum',
dest='movcasedeath_maxnum',
type=int,
action='store',
default=None,
metavar='MAXNUM',
help=' '.join([
'The limit of cases/deaths to visualize.',
'Default is a plausible amount for the chosen MSA or CONUS.',
'You should use a limit larger (by at least 2, no more than 10) than',
'the maximum number of cases recorded for a county in that MSA or CONUS.'
]))
parser_movcasedeath.add_argument(
'-s',
'--saveimages',
dest='movcasedeath_saveimages',
action='store_true',
default=False,
help=
'If chosen, then save the images used to create the movie into a ZIP archive.'
)
parser_movcasedeath.add_argument(
'--conus',
dest='do_conus_movcasedeath',
action='store_true',
default=False,
help=
'If chosen, then make a movie of the COVID-19 cases and deaths trends for the Continental US (CONUS).'
)
parser_movcasedeath.add_argument(
'-y',
'--yes',
dest='do_yes_movcasedeath',
action='store_true',
default=False,
help='If chosen, then do not confirm --maxnum.')
#
##
args = parser.parse_args()
logger = logging.getLogger()
if args.do_info: logger.setLevel(logging.INFO)
#
## just show the metros
if args.choose_option == 'M':
metros = None
if args.metros is not None:
metros = set(
list(map(lambda tok: tok.strip(), args.metros.split(','))))
if args.topN is not None:
assert (args.topN >= 1)
metros = list(
map(
lambda entry: entry['prefix'],
sorted(COVID19Database.data_msas_2019().values(),
key=lambda entry: entry['population'])[::-1]
[:args.topN]))
# logging.info('top %d metros: %s.' % ( args.topN, metros ) )
if args.format != 'json':
core.display_tabulated_metros(form=args.format,
selected_metros=metros)
else:
json_data = core.display_tabulated_metros(form=args.format,
selected_metros=metros)
print('%s' % json.dumps(json_data, indent=1))
return
elif args.choose_option == 'm':
#
## now create the following stuff...
if not args.do_conus:
msaname = args.name.strip()
data_msas_2019 = COVID19Database.data_msas_2019()
if msaname not in data_msas_2019:
print(
'Error, the chosen MSA name %s not one of the %d defined.'
% (msaname, len(data_msas_2019)))
return
data = data_msas_2019[msaname]
else:
data = COVID19Database.data_conus()
inc_data = core.get_incident_data(data)
maxnum = args.maxnum
if maxnum is None: maxnum = _get_default_maxnum(inc_data)
if maxnum < 1:
print('Error, maximum number for visualization %d < 1.' % maxnum)
return
_summarize_data(inc_data, maxnum)
if args.do_yes_moviemetro: status = args.do_yes_moviemetro
else: status = _try_continue()
if status:
movie_name = viz.create_summary_movie_frombeginning(
inc_data, dirname=args.dirname)
return
elif args.choose_option == 's':
#
## now create the following stuff...
if not args.do_conus_summmetro:
msaname = args.summmetro_name.strip()
data_msas_2019 = COVID19Database.data_msas_2019()
if msaname not in data_msas_2019:
print(
'Error, the chosen MSA name %s not one of the %d defined.'
% (msaname, len(data_msas_2019)))
return
data = data_msas_2019[msaname]
else:
data = COVID19Database.data_conus()
inc_data = core.get_incident_data(data)
maxnum = args.summmetro_maxnum
if maxnum is None: maxnum = _get_default_maxnum(inc_data)
if maxnum < 1:
print('Error, maximum number for visualization %d < 1.' % maxnum)
return
_summarize_data(inc_data, maxnum)
if args.do_yes_summmetro: status = args.do_yes_summmetro
else: status = _try_continue()
if status:
viz.get_summary_demo_data(inc_data, dirname=args.dirname)
return
elif args.choose_option == 'mcd':
#
## now create the following stuff...
if not args.do_conus_movcasedeath:
msaname = args.movcasedeath_name.strip()
data_msas_2019 = COVID19Database.data_msas_2019()
if msaname not in data_msas_2019:
print(
'Error, the chosen MSA name %s not one of the %d defined.'
% (msaname, len(data_msas_2019)))
return
data = data_msas_2019[msaname]
else:
data = COVID19Database.data_conus()
inc_data = core.get_incident_data(data)
maxnum = args.movcasedeath_maxnum
if maxnum is None: maxnum = _get_default_maxnum(inc_data)
if maxnum < 1:
print('Error, maximum number for visualization %d < 1.' % maxnum)
return
_summarize_data(inc_data, maxnum)
if args.do_yes_movcasedeath: status = args.do_yes_movcasedeath
else: status = _try_continue()
if status:
viz.create_summary_cases_or_deaths_movie_frombeginning(
inc_data,
type_disp=args.movcasedeath_display,
dirname=args.dirname,
save_imgfiles=args.movcasedeath_saveimages)
return
def main():
rank = MPI.COMM_WORLD.Get_rank()
time0 = _get_min_time0()
parser = ArgumentParser()
parser.add_argument('-r',
'--region',
metavar='region',
type=str,
required=True,
help='region as JSON file.')
parser.add_argument(
'-d',
'--dirname',
dest='dirname',
type=str,
action='store',
default=os.getcwd(),
help=
'The name of the directory to which to put all this stuff. Default is %s.'
% os.getcwd())
parser.add_argument('-i',
'--info',
dest='do_info',
action='store_true',
default=False,
help='If chosen, then turn on INFO logging.')
args = parser.parse_args()
assert (os.path.isdir(args.dirname))
assert (os.path.isfile(os.path.expanduser(args.region)))
assert (os.path.basename(os.path.expanduser(
args.region)).endswith('.json'))
#
## I do four things
ntasks = 4
nprocs = min(MPI.COMM_WORLD.Get_size(), ntasks)
if rank >= ntasks: return
#
## check on whether to turn on INFO logging
logger = logging.getLogger()
if args.do_info: logger.setLevel(logging.INFO)
#
## get incident data for the region
region_filename = os.path.abspath(os.path.expanduser(args.region))
region_data = _get_region_data(region_filename)
inc_data = core.get_incident_data(region_data)
#
## now do the thing...
all_tuples_to_process = list(range(4))
tuples_to_process = all_tuples_to_process[rank::nprocs]
for thing_to_do in tuples_to_process:
if thing_to_do == 0: _summarize(inc_data, args.dirname, time0)
elif thing_to_do == 1: _movie(inc_data, args.dirname, time0)
elif thing_to_do == 2:
_movie_casedeaths(inc_data, args.dirname, time0, type_disp='cases')
elif thing_to_do == 3:
_movie_casedeaths(inc_data,
args.dirname,
time0,
type_disp='deaths')
MPI.COMM_WORLD.Barrier()
if rank != 0: return
logging.info(
'processed all FOUR operations on %s (%s) in %0.3f seconds.' %
(inc_data['prefix'], inc_data['region name'], time.time() - time0))