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quick script to visualize blood pressure measurements
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README.rst

BP Diag

Parses Blood Pressure Statistics

BP Diag parses blood pressure statistics from data files. It generates some statistics and prints them to STDERR. You can export the collected data (and the gathered statistics) to JSON (dump to STDOUT). And you can also generate SVG or PNG charts from it.:

bpdiag [OPTIONS] [OUTPUT [OUTPUT OPTIONS]].. [PARSER [PARSER OPTIONS]] FILENAME..

To see a list of possible command line options run:

bpdiag.py --help

Examples

Lets say we got a file called bloodpressure.txt containing the following values in a simple format. This is a good job for our default parser (there are other parsers, but more on this later):

136/83/65, 132/82/70
144/82/86, 137/81/75, -,         143/80/68
131/82/60, 144/82/64, 136/79/67, 140/80/62
136/83/68, 138/80/99, -,         133/74/65
136/79/67, 131/76/64, 135/81/72, 136/75/61
127/79/72

So if we run BP Diag over the file like this:

bpdiag.py bloodpressure.txt

We got the following results:

Parsed 17 value(s)...
Statistics (min, max, avg):
:: SYS...: 127, 144, 136
:: DIA...:  74,  83,  79
:: PULSE.:  60,  99,  69

We can also dump the results to JSON with --json or generate a line chart from it with --chart (for more options see below).

[[136,83,65],[132,82,70],[144,82,86],[137,81,75],[143,80,68],[131,82,60],[144,82,64],[136,79,67],[140,80,62],[136,83,68],[138,80,99],[133,74,65],[136,79,67],[131,76,64],[135,81,72],[136,75,61],[127,79,72]]
http://brutus.github.com/bpdiag/images/bp.png

Features

Modular Input: Parsers

Parsers define how the input from the given files is transformed into instances of the Measurements class. Those contain containing the data for each parsed measurement.

BP Diag comes with a couple of parsers, but it's easy to write your own if they don't fit your needs (just take a look at the source documentation of the module).

Parser: Plaintext [plain]

The plaintext parser is good to grab values from simple text files, like copied from a note taking app or whatever. It's for files that just store a couple of SYS, DIA and PULSE values.

For each line the --delimiter (default is ,) is used to split multiple entries on the line. And --separator (default: /) is used to split the entries into the SYS, DIA and PULSE values. Entries that just contain the --skip string (default: -) are skipped.

Number of measurements per line

Per default all values are gathered one after the other. But you can use the --entries option to set a fixed number of measurements per line.

What this means is that only that much values are used per line (even if there are more) and if a line contains less than entries values, the remaining ones are filled with None values. Also values that are the skip string are not ignored, but stored as a None value too.

This can be helpful in cases where you have a given number of measurements per line and you want to keep them aligned even if sometimes a measurement is skipped / missing (eg. because you take three measures a day and keep them on a line).:

bpdiag.py --json --compact --entries 4 bloodpressure.txt

Will result in the following JSON:

[[136,83,65],[132,82,70],null,null,[144,82,86],[137,81,75],null,[143,80,68],[131,82,60],[144,82,64],[136,79,67],[140,80,62],[136,83,68],[138,80,99],null,[133,74,65],[136,79,67],[131,76,64],[135,81,72],[136,75,61],[127,79,72],null,null,null]

Parser: Regular Expression [regex]

Parses each line with a regular expression. Every named group becomes an attribute of the resulting Measurement instance. A named group looks like this: (?P<name-of-the-grp>), and you need at least a group for SYS, DIA and PULSE, but you can grab as many info from the line as you want, it will get stored in the Measurement instance.

\b((?P<date>\d{4}-\d{1,2}-\d{1,2})\s+)?((?P<time>\d{1,2}:\d{1,2})\s+)?(?P<sys>\d{2,3})\s*([-+.:,:\/])\s*(?P<dia>\d{2,3})\s*\6\s*(?P<pulse>\d{2,3})\b/

This is the default regex, it captures date, time, sys, dia and pulse. But you can give set any regular expression with the --regex argument.

Parser: JSON [json]

Parses one JSON array from all given files. Each entry in the array needs to be either an array with exactly three values for SYS, DIA and PULSE or - if --as-obj is used - a JSON object, in which case all key/value pairs get stored.

Output

As we already seen, you will always get some statistics-output to STDERR. But you can also export the gathered data to a number of formats:

Export JSON

There are a couple of ways to do this, but always the JSON dump is written to STDOUT, so you can redirect the dump to a file.

You can dump the data as an array of SYS, DIA, PULS arrays with the --json option. Or as an array of objects with the --json-obj option (this will include all attributes of the Measurement instances, not just SYS, DIA and PULSE). If you want the gathered statistics too, use --json-stats.

There are a couple of options to govern how the dump is formated, see the --help output for info on that.

Export Chart

To generate SVG charts, you need to have PyGal installed (see below). Other than that, just use the --chart option to have a chart called bp.svg generated in your current directory. There are more options to this, take a look at the --help output.

Instead of the interactive SVG charts you can use PNG as output format. Just use the --png option along with --chart. You need a couple more dependencies for that though, take a look below.

Install

You can install BP Diag with pip or from source.

Install with pip

pip is "a tool for installing and managing Python packages". If you don't have it installed, see the pip install instructions:

pip install --user bpdiag

Install from source

You can fetch the latest sourceball from github and unpack it, or just clone this repository: git clone git://github.com/brutus/bpdiag. If you got the source, change into the directory and use setup.py:

python setup.py --user install

Dependencies

PyGal is used to generate the charts. If you want to generate charts, you need to install it. With pip it's as easy as this:

pip install --user pygal

If you want to export to PNG files, you need CairoSVG, tinycss and cssselect too. You can install them like this:

pip install --user CairoSVG tinycss cssselect

Bugs and Contribution

BP Diag is at home at: https://github.com/brutus/bpdiag/

If you want to run the test cases, see that you got nose installed and run nosetests from the bpdiag directory (the one containing the module). If you got bpdiag already installed, run them like this: nosetest test_bpdiag.

If something fails, please get in touch.

If you find any bugs, issues or anything, please use the issue tracker.

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