3.3. covid19_state_summary

This CLI behaves very similarly to covid19_create_movie_or_summary, except it operates on US states or territories instead of the CONUS or US MSAs. It has three modes of operation. Its help output, when running covid19_state_summary -h, produces the following hard-to-read output,

usage: covid19_state_summary [-h] [-d DIRNAME] [--info]
                             [-n {Alabama,Alaska,Arizona,Arkansas,California,Colorado,Connecticut,Delaware,District of Columbia,Florida,Georgia,Hawaii,Idaho,Illinois,Indiana,Iowa,Kansas,Kentucky,Louisiana,Maine,Maryland,Massachusetts,Michigan,Minnesota,Mississippi,Missouri,Montana,Nebraska,Nevada,New Hampshire,New Jersey,New Mexico,New York,North Carolina,North Dakota,Ohio,Oklahoma,Oregon,Pennsylvania,Puerto Rico,Rhode Island,South Carolina,South Dakota,Tennessee,Texas,Utah,Vermont,Virginia,Washington,West Virginia,Wisconsin,Wyoming}]
                             [-M MAXNUM] [-y]
                             {m,s,mcd} ...

positional arguments:
  {m,s,mcd}             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.
    m                   Make a movie of the COVID-19 cases and deaths trend for the specific state.
    s                   Make a summary plot, and incident data file, of COVID-19 cases and deaths trend, for the specific state.
    mcd                 Make a large-sized movie of either "CASES" or "DEATHS" for given state.

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 /g/g12/islam5/.local/src/covid19_stats/docsrc.
  --info                If chosen, then print out INFO level logging statements.
  -n {Alabama,Alaska,Arizona,Arkansas,California,Colorado,Connecticut,Delaware,District of Columbia,Florida,Georgia,Hawaii,Idaho,Illinois,Indiana,Iowa,Kansas,Kentucky,Louisiana,Maine,Maryland,Massachusetts,Michigan,Minnesota,Mississippi,Missouri,Montana,Nebraska,Nevada,New Hampshire,New Jersey,New Mexico,New York,North Carolina,North Dakota,Ohio,Oklahoma,Oregon,Pennsylvania,Puerto Rico,Rhode Island,South Carolina,South Dakota,Tennessee,Texas,Utah,Vermont,Virginia,Washington,West Virginia,Wisconsin,Wyoming}
                        Make movies or other summary data for a state. Default is "New York".
  -M MAXNUM, --maxnum MAXNUM
                        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.
  -y, --yes             If chosen, then do not confirm --maxnum.

Instead of what covid19_create_movie_or_summary does, we first specify these common elements,

• the state (with the -n flag),

• the optional legend or color maximum (with -M or --maxnum),

• the optional specific output directory (with -d or --directory),

• the forcing flag (with the -y or --yes flag),

before moving to the three operations. The functionality of -M or --maxnum, -d or --directory, and -y or --yes, is identical to what covid19_create_movie_or_summary does.

The --info flag prints out INFO level debugging statements.

3.3.1. show mode

covid19_state_summary s (SHOW flag) summarizes the latest COVID-19 statistics for a specified US state or territory. Here is what happens when we run the SHOW flag on California,

bash$ covid19_state_summary -n California s

HERE ARE DETAILS FOR California.
2019 EST. POP = 39,239,334.
FIRST CASE:  25 January 2020.
LATEST CASE: 03 February 2021 (375 days after first case)
MAXIMUM NUMBER OF CASES: 1,129,957 (in Los Angeles County, California)
MAXIMUM NUMBER OF CASES FOR VISUALIZATION: 1,700,000.
CONTINUE (must choose one) [y/n]:

Warning

The command line output shown above for the operation of covid19_state_summary -n California s is for 03 FEBRUARY 2021. Example images shown below are for this or later dates.

This mode of operation, for example for California, will output seven files:

• covid19_california_LATEST.pkl.gz is the Pandas DataFrame of the COVID-19 cases and deaths, total and per county, from the date of first incident to the latest incident.

• covid19_california_cds_LATEST.pdf and covid19_california_cds_LATEST.png are the PDF and PNG showing the trend of COVID-19 cases and deaths in California.

  

  Fig. 3.9 The latest trend lines of cumulative cases and deaths in California.

• covid19_california_cases_LATEST.pdf and covid19_california_cases_LATEST.png are the PDF and PNG showing the county map, colored by number of COVID-19 cases, on the LAST incident day.

  

  Fig. 3.10 The latest image of cumulative cases in California.

• covid19_california_death_LATEST.pdf and covid19_california_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. 3.11 The latest image of cumulative deaths in California.

3.3.2. movie mode

covid19_state_summary m (MOVIE flag) creates an MP4 movie of COVID-19 cases and deaths for the US state or territory you specify. Its functionality is very similar to movie mode in covid19_create_movie_or_summary.

This mode of operation for California,

covid19_state_summary -n California -y m

will output a quad structured movie of the cumulative COVID-19 cases and deaths for California, covid19_california_LATEST.mp4. Fig. 3.12 is a GIF animation of that.

Fig. 3.12 The four-quadrant movie, that covid19_state_summary m creates, of the cumulative COVID-19 cases and deaths in the state of California. Upper left quad is the summary information for the state. 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. Its structure matches that of Fig. 3.5.

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_california_LATEST.mp4 returns,

mp4info version -r
covid19_california_LATEST.mp4:
Track   Type    Info
1       video   H264 High@4, 75.000 secs, 153 kbps, 1330x1168 @ 5.000000 fps
 Name: california, ALL, 02-02-2021
 Artist: Tanim Islam
 Encoded with: Lavf57.56.101
 Release Date: 02-02-2021
 Album: STATE

For US states and territories,

• Album is STATE.

• Artist is Tanim Islam (duh).

• Name is the name of the US state or territory, ALL if showing cases and deaths as quads in one movie (this is what covid19_california_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.

3.3.3. movie cases deaths mode

This is similar to movie mode, except now we can visualize movies of cases or deaths. The help output, while running covid19_state_summary mcd -h, is shown below,

usage: covid19_state_summary mcd [-h] [-d DISP]

optional arguments:
  -h, --help            show this help message and exit
  -d DISP, --disp DISP  Whether to display the "cases" or "death" trends of the given state. Default is "cases".
  -s, --saveimages      If chosen, then save the images used to create the movie into a ZIP archive.

• -d or --disp lets you choose whether to create a movie of the cases or deaths within the specified US state or territory.

• -s or --saveimages optionally lets you choose to save the PNG images into a zip archive.

Fig. 3.13 and Fig. 3.14 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. 3.13 The trend of latest COVID-19 cumulative cases (lower right quadrant in Fig. 3.12) in California. The underlying MP4 file is covid19_california_cases_LATEST.mp4. The syntax used to create this movie is,

covid19_state_summary -n california -y mcd -d cases

Fig. 3.14 The trend of latest COVID-19 cumulative deaths (upper right quadrant in Fig. 3.12) in California. The underlying MP4 file is covid19_california_deaths_LATEST.mp4. The syntax used to create this movie is,

covid19_state_summary -n california -y mcd -d death

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_california_cases_LATEST.mp4 returns,

mp4info version -r
covid19_california_cases_LATEST.mp4:
Track   Type    Info
1       video   H264 High@4, 75.000 secs, 170 kbps, 1408x1468 @ 5.000000 fps
 Name: california, CASES, 02-02-2021
 Artist: Tanim Islam
 Encoded with: Lavf57.56.101
 Release Date: 02-02-2021
 Album: STATE

Its metadata is similar to those MP4 movies that show COVID-19 cases and deaths for states. 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.