3.2. covid19_create_movie_or_summary
This CLI is the main top-level CLI currently in the repository. Its purpose is to individually create COVID-19 summary movies and figures, of cumulative cases and deaths, in the Contiguous United States (CONUS) or one of the 380 defined MSAs.
It has four modes of operation. Its help output, when running covid19_create_movie_or_summary -h, produces the following,
usage: covid19_create_movie_or_summary [-h] [-d DIRNAME] [--info] {M,m,s,mcd} ...
positional arguments:
{M,m,s,mcd} 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.
M If chosen, then list all the metropolitan areas through which we can look.
m Make a movie of the COVID-19 cases and deaths trend for the specific Metropolitan Statistical Area
(MSA).
s Make a summary plot, and incident data file, of COVID-19 cases and deaths trend, for the specific
Metropolitan Statistical Area (MSA).
mcd Make a large-sized movie of either "CASES" or "DEATHS" for given MSA or CONUS.
optional arguments:
-h, --help show this help message and exit
-d DIRNAME, --dirname DIRNAME
The directory into which to store the resulting files. Default is /usr/WS2/islam5/covid19_data/nyc.
--info If chosen, then print out INFO level logging statements.
The default flags in the top level operation are,
-hshows this help screen.-dor--dirnamespecifies the output directory. Default is the current working directory.--infosays to showINFOlogging output.
3.2.1. summarize MSAs
covid19_create_movie_or_summary M (METRO flag) lists the COVID-19 stats for all, or user-selected, MSAs by population. For example, here are the statistics for the top 30 MSAs.
covid19_create_movie_or_summary M --topN=30
HERE ARE THE 30 METRO AREAS, ORDERED BY POPULATION
DATA AS OF 03 February 2021.
RANK IDENTIFIER NAME POPULATION FIRST INC. NUM DAYS NUM CASES NUM DEATHS MAX CASE COUNTY MAX CASE COUNTY NAME
------ ------------ ----------------------- ------------ ---------------- ---------- ----------- ------------ ----------------- ----------------------------------
1 nyc NYC Metro Area 19,216,182 01 March 2020 339 1,570,532 52,935 621,218 New York City, New York
2 losangeles LA Metro Area 18,711,436 25 January 2020 375 2,003,708 26,385 1,129,957 Los Angeles County, California
3 chicago Chicago Metro Area 9,458,539 24 January 2020 376 824,383 15,096 456,144 Cook County, Illinois
4 dallas Dallas Metro Area 7,573,136 09 March 2020 331 700,645 7,468 262,738 Dallas County, Texas
5 houston Houston Metro Area 7,066,141 04 March 2020 336 490,925 6,087 323,408 Harris County, Texas
6 bayarea Bay Area 6,860,207 31 January 2020 369 330,559 4,012 103,236 Santa Clara County, California
7 dc DC Metro Area 6,280,487 05 March 2020 335 367,490 5,913 68,518 Prince George's County, Maryland
8 miami Miami Metro Area 6,166,488 06 March 2020 334 660,440 9,256 376,551 Miami-Dade County, Florida
9 philadelphia Philadelphia Metro Area 6,102,434 06 March 2020 334 415,562 10,284 111,098 Philadelphia County, Pennsylvania
10 atlanta Atlanta Metro Area 6,020,364 02 March 2020 338 481,514 6,006 84,807 Gwinnett County, Georgia
11 phoenix Phoenix Metro Area 4,948,203 26 January 2020 374 523,129 8,325 479,978 Maricopa County, Arizona
12 boston Boston Metro Area 4,873,019 01 February 2020 368 353,216 9,627 103,162 Middlesex County, Massachusetts
13 detroit Detroit Metro Area 4,319,629 10 March 2020 330 248,467 8,266 97,429 Wayne County, Michigan
14 seattle Seattle Metro Area 3,979,845 21 January 2020 379 143,511 2,236 79,063 King County, Washington
15 minneapolis Minneapolis Metro Area 3,640,043 06 March 2020 334 288,879 3,840 96,262 Hennepin County, Minnesota
16 sandiego San Diego Metro Area 3,338,330 10 February 2020 359 241,081 2,683 241,081 San Diego County, California
17 tampa Tampa Metro Area 3,194,831 01 March 2020 339 202,358 3,552 101,910 Hillsborough County, Florida
18 denver Denver Metro Area 2,967,239 05 March 2020 335 209,203 3,020 56,166 Denver County, Colorado
19 stlouis St. Louis Metro Area 2,803,228 07 March 2020 333 245,406 4,217 84,254 St. Louis County, Missouri
20 baltimore Baltimore Metro Area 2,800,053 08 March 2020 332 154,795 3,111 47,768 Baltimore County, Maryland
21 charlotte Charlotte Metro Area 2,636,883 11 March 2020 329 217,212 2,436 88,055 Mecklenburg County, North Carolina
22 orlando Orlando Metro Area 2,608,147 12 March 2020 328 185,303 2,185 104,620 Orange County, Florida
23 sanantonio San Antonio Metro Area 2,550,960 12 February 2020 357 213,538 3,142 177,814 Bexar County, Texas
24 portland Portland Metro Area 2,492,412 28 February 2020 341 85,605 1,125 30,278 Multnomah County, Oregon
25 sacramento Sacramento Metro Area 2,363,730 21 February 2020 348 126,067 1,725 87,106 Sacramento County, California
26 pittsburgh Pittsburgh Metro Area 2,317,600 13 March 2020 327 146,373 3,414 70,165 Allegheny County, Pennsylvania
27 lasvegas Las Vegas Metro Area 2,266,715 05 March 2020 335 216,121 3,351 216,121 Clark County, Nevada
28 austin Austin Metro Area 2,227,083 13 March 2020 327 137,713 1,414 70,631 Travis County, Texas
29 cincinnati Cincinnati Metro Area 2,221,208 14 March 2020 326 186,056 1,374 68,156 Hamilton County, Ohio
30 kansascity Kansas City Metro Area 2,157,990 07 March 2020 333 132,759 1,600 50,392 Johnson County, Kansas
One can also select MSAs with the --metros flag. The -f or --format flag prints out a table of MSAs formatted in one of three ways: simple, the default, is the tabular format shown above; github is Github flavored Markdown; and rst is reStructuredText. This is described in the help output, produced by covid19_create_movie_or_summary M -h,
usage: covid19_create_movie_or_summary M [-h] [-f {simple,github,rst,rst-simple,json}] [--metros METROS] [--topN TOPN]
optional arguments:
-h, --help show this help message and exit
-f {simple,github,rst,rst-simple,json}, --format {simple,github,rst,rst-simple,json}
Format of the table that displays MSA summary. Default is "simple".
--metros METROS If chosen, list of selected metros for which to summarize COVID-19 data.
--topN TOPN If defined, will be the top N (N must be an integer greater than 0) population metros to get data on.
The standard flag is -f or --format. It asks which of the five formats to spit out the tabulated data to the console.
simpleis the default, and it means to display the tabular data in standard Markdown format. The metro summary table demonstrates this.githubmeans to display the tabular data in standard Github flavored Markdown format.rstmeans to display the tabular data in standard reStructuredText format.rst-simplemeans to display the tabular data using the fancier and better list-table reStructuredText format; its representation is much better and clearer than the standard reStructuredText to represent tables.jsonis the final one, and spits the tabular data out into JSON format.
If you don’t specify the optional arguments, --metros or --topN, then all 380 metros are tabulated.
--metroslooks for a list of MSAs that you have specified.--topNlooks for a positive integer, the top \(N \ge 1\) US metro areas by population.
3.2.2. show mode
covid19_create_movie_or_summary s (SHOW flag) summarizes the latest COVID-19 statistics for a specified MSA. The help output, while running covid19_create_movie_or_summary s -h, is shown below,
usage: covid19_create_movie_or_summary s [-h] [-n NAME] [-M MAXNUM] [--conus]
[-y]
optional arguments:
-h, --help show this help message and exit
-n NAME, --name NAME Create a summary plot and incident data file of this
metropolitan area. Default is "bayarea".
-M MAXNUM, --maxnum MAXNUM
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.
--conus If chosen, then make a movie of the COVID-19 cases and
deaths trends for the Continental US (CONUS).
-y, --yes If chosen, then do not confirm --maxnum.
The required -n or --name flag specifies the MSA. The -M or --maxnum sets the color limits of cases and deaths to this number (the default is a number that is comfortable above the maximum number of cases in a county in the MSA); and the -y or --yes flag suppresses the intermediate prompt that asks the user whether the specified or default maximum number is sufficient. For example, for the NYC metro area,
bash$ covid19_create_movie_or_summary s -n nyc
HERE ARE DETAILS FOR NYC Metro Area.
2019 EST. POP = 19,216,182.
FIRST CASE: 01 March 2020.
LATEST CASE: 30 January 2021 (335 days after first case)
MAXIMUM NUMBER OF CASES: 603,428 (in New York City, New York)
MAXIMUM NUMBER OF CASES FOR VISUALIZATION: 1,000,000.
CONTINUE (must choose one) [y/n]:
Warning
The command line output shown above for the operation of covid19_create_movie_or_summary s -n nyc is for 31 JANUARY 2021. Example images shown below are for this or later dates.
This mode of operation, for example for NYC, will output seven files:
covid19_nyc_LATEST.pkl.gzis the serializedPandas DataFrameof the COVID-19 cases and deaths, total and per county, from the date of first incident to the latest incident.covid19_nyc_cds_LATEST.pdf and covid19_nyc_cds_LATEST.png are the PDF and PNG showing the trend of COVID-19 cases and deaths in the NYC metro area.
Fig. 3.2 The latest trend lines of cumulative cases and deaths in the NYC metropolitan area.
covid19_nyc_cases_LATEST.pdf and covid19_nyc_cases_LATEST.png <plots showing the are the PDF and PNG showing the county map, colored by number of COVID-19 cases, on the LAST incident day.
Fig. 3.3 The latest image of cumulative cases in the NYC metropolitan area.
covid19_nyc_death_LATEST.pdf and covid19_nyc_death_LATEST.png are the PDF and PNG showing the county map, colored by number of COVID-19 deaths, on the LAST incident day.
Fig. 3.4 The latest image of cumulative deaths in the NYC metropolitan area.
3.2.3. movie mode
covid19_create_movie_or_summary m (MOVIE flag) creates an MP4 movie of COVID-19 cases and deaths for the MSA you specify (see the high quality GIF animations of these MP4 movies). The help output, while running covid19_create_movie_or_summary m -h, is shown below,
usage: covid19_create_movie_or_summary m [-h] [-n NAME] [-M MAXNUM] [--conus]
[-y]
optional arguments:
-h, --help show this help message and exit
-n NAME, --name NAME Make a movie of this metropolitan area. Default is
"bayarea"
-M MAXNUM, --maxnum MAXNUM
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.
--conus If chosen, then make a movie of the COVID-19 cases and
deaths trends for the Continental US (CONUS).
-y, --yes If chosen, then do not confirm --maxnum.
The meaning of the -M and -y flags are the same as in SHOW mode. This mode of operation, for example for NYC,
covid19_create_movie_or_summary m -n nyc -y
will output a quad structured movie of the cumulative COVID-19 cases and deaths for the NYC metropolitan area, covid19_nyc_LATEST.mp4. Fig. 3.5 is a GIF animation of that.
Fig. 3.5 The four-quadrant movie, that covid19_create_movie_or_summary m creates, of the cumulative COVID-19 cases and deaths in the NYC metropolitan area. Upper left quad is the summary information for the MSA. Lower left quad is the running tally of cumulative cases and deaths, by day from first incident. Upper right is logarithmic coloration of cumulative deaths, by day from first incident. Lower right is logarithmic coloration of cumulative cases, by day from first incident.
Note also that the created MP4 files have metadata associated with them. You can either inspect them using mp4info or using code in the mutagen.mp4.MP4. Here is what mp4info covid19_nyc_LATEST.mp4 returns,
mp4info version -r
covid19_nyc_LATEST.mp4:
Track Type Info
1 video H264 High@4, 67.200 secs, 160 kbps, 1590x1172 @ 5.000000 fps
Name: nyc, ALL, 30-01-2021
Artist: Tanim Islam
Encoded with: Lavf57.56.101
Release Date: 30-01-2021
Album: METROPOLITAN STATISTICAL AREA
For MSAs,
Album is
METROPOLITAN STATISTICAL AREA.Artist is Tanim Islam (duh).
Name is MSA name,
ALLif showing cases and deaths as quads in one movie (this is what covid19_nyc_LATEST.mp4 shows), and the last date of COVID-19 cases and deaths that are reported.Release Date is also the last date of COVID-19 cases and deaths that are reported.
For the CONUS, such as covid19_conus_LATEST.mp4, here is the output when running mp4info,
mp4info version -r
covid19_conus_LATEST.mp4:
Track Type Info
1 video H264 High@5, 75.200 secs, 277 kbps, 1908x1166 @ 5.000000 fps
Name: conus, ALL, 30-01-2021
Artist: Tanim Islam
Encoded with: Lavf57.56.101
Release Date: 30-01-2021
Album: CONUS
And here is its metadata,
Album is
CONUS.Name is
CONUS,ALLif showing cases and deaths as quads in one movie (this is what covid19_conus_LATEST.mp4 shows), and the last date of COVID-19 cases and deaths that are reported.
3.2.4. movie cases deaths mode
This is similar to movie mode, except now we can visualize movies of cases or deaths, and optionally save, the collection of PNG images used to create the movie, into a zip file. The help output, while running covid19_create_movie_or_summary mcd -h, is shown below,
usage: covid19_create_movie_or_summary mcd [-h] [-n NAME] [-d DISP] [-M MAXNUM] [-s] [--conus] [-y]
optional arguments:
-h, --help show this help message and exit
-n NAME, --name NAME Create a summary plot and incident data file of this metropolitan area. Default is "bayarea".
-d DISP, --disp DISP Whether to display the "cases" or "death" trends of the MSA or CONUS. Default is "cases".
-M MAXNUM, --maxnum MAXNUM
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.
-s, --saveimages If chosen, then save the images used to create the movie into a ZIP archive.
--conus If chosen, then make a movie of the COVID-19 cases and deaths trends for the Continental US (CONUS).
-y, --yes If chosen, then do not confirm --maxnum.
The usage of four flags – -n, -M or --maxnum, --conus, and -y or --yes – are the same as described in Section 3.2.2 and Section 3.2.3.
-dor-displets you choose whether to create a movie of thecasesordeathswithin the CONUS or a specific MSA.-sor--saveimagesoptionally lets you choose to save the PNG images into a zip archive.
Fig. 3.6 and Fig. 3.7 demonstrates this operation to create COVID-19 cases and deaths summary movies for the NYC metropolitan area. The command line syntax to generate these two movies is shown in each of their captions.
Fig. 3.6 The trend of latest COVID-19 cumulative cases (lower right quadrant in Fig. 3.5) in the NYC metropolitan area. The underlying MP4 file is covid19_nyc_cases_LATEST.mp4. The syntax used to create this movie is,
covid19_create_movie_or_summary mcd -n nyc -d cases -y
Fig. 3.7 The trend of latest COVID-19 cumulative deaths (upper right quadrant in Fig. 3.5) in the NYC metropolitan area. The underlying MP4 file is covid19_nyc_deaths_LATEST.mp4. The syntax used to create this movie is,
covid19_create_movie_or_summary mcd -n nyc -d death -y
Finally, Fig. 3.8 demonstrates the latest trend of COVID-19 cases in the CONUS. I generate it by running,
covid19_create_movie_or_summary mcd --conus -d cases -y
Fig. 3.8 The trend of latest COVID-19 cumulative cases for the CONUS. The underlying MP4 file is covid19_conus_cases_LATEST.mp4. I deliberately limit the maximum value of cases, in the colorbar, to the maximum cumulative COVID-19 deaths in a county in the region, for psychological effect; it’s distressing to see the COVID-19 cumulative case map fill up with red as time goes on.
Note also that the created MP4 files have metadata associated with them. You can either inspect them using mp4info or using code in the mutagen.mp4.MP4. Here is what mp4info covid19_nyc_cases_LATEST.mp4 returns,
mp4info version -r
covid19_nyc_cases_LATEST.mp4:
Track Type Info
1 video H264 High@5, 67.800 secs, 133 kbps, 2004x1470 @ 5.000000 fps
Name: nyc, CASES, 02-02-2021
Artist: Tanim Islam
Encoded with: Lavf57.56.101
Release Date: 02-02-2021
Album: METROPOLITAN STATISTICAL AREA
Its metadata is similar to those MP4 movies that show COVID-19 cases and deaths for MSAs. The difference is in the second element of the Name: it is CASES if the movie shows cumulative COVID-19 cases, and DEATHS if the movie shows cumulative COVID-19 deaths.
For the CONUS, here is what mp4info covid19_conus_cases_LATEST.mp4 returns,
mp4info version -r
covid19_conus_cases_LATEST.mp4:
Track Type Info
1 video H264 High@4.2, 75.800 secs, 395 kbps, 2010x1056 @ 5.000000 fps
Name: conus, CASES, 02-02-2021
Artist: Tanim Islam
Encoded with: Lavf57.56.101
Release Date: 02-02-2021
Album: CONUS
Its metadata is similar to those MP4 movies that show COVID-19 cases and deaths for the CONUS. The difference is in the second element of the Name: it is CASES if the movie shows cumulative COVID-19 cases, and DEATHS if the movie shows cumulative COVID-19 deaths.