Final cleanup.
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@ -1,6 +1,9 @@
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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''' Utility to convert data from a glucometer into charts. '''
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__author__ = 'Timothy Allen'
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__email__ = 'tim@treehouse.org.za'
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__license__ = 'MIT'
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''' Included are the Noto Sans and IcoGluco font sets.
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Noto Sans is licensed under the SIL Open Font License version 1.1
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@ -12,11 +15,6 @@
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licensed under Creative Commons BY 3.0, <http://creativecommons.org/licenses/by/3.0/>
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'''
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__author__ = 'Timothy Allen'
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__email__ = 'tim@treehouse.org.za'
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__license__ = 'MIT'
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# TODO: comments -- unicode/images/np.array
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# TODO: weekly graph with each day's figures as a different-coloured line
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import argparse
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@ -40,30 +38,32 @@ import re
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from scipy import interpolate
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from scipy.special import binom
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import sys
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import pprint
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# Constants for units
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''' Constants for units '''
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UNIT_MGDL = 'mg/dL'
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UNIT_MMOLL = 'mmol/L'
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VALID_UNITS = [UNIT_MGDL, UNIT_MMOLL]
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# When averaging, set the period to this number of minutes
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''' When averaging, set the period to this number of minutes '''
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INTERVAL = 15
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# Maximum gluclose value to display (TODO: mmol/mg)
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GRAPH_MAX = 21
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GRAPH_MIN = 1
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''' Set the default high and low in mmol/L; it will be reset to mg/dL if neccessary '''
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DEFAULT_HIGH = 8
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DEFAULT_LOW = 4
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''' Maximum glucose value to display '''
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GRAPH_MAX_MMOLL = 21
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GRAPH_MIN_MMOLL = 0
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GRAPH_MAX_MGDL = 400
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GRAPH_MIN_MGDL = 0
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# Colour for below-target maxmins
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''' Colour for below-target maxmins '''
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RED = '#d71920'
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# Colour for above-target maxmins
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'''' Colour for above-target maxmins '''
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YELLOW = '#f1b80e'
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# Colour for graph lines
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''' Colour for graph lines '''
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BLUE = '#02538f'
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# Colour for median glucose box
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''' Colour for median glucose box '''
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GREEN = '#009e73'
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# Colour for median A1c box
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''' Colour for median A1c box '''
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BOXYELLOW = '#e69f00'
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def main():
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@ -71,8 +71,6 @@ def main():
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raise Exception(
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'Unsupported Python version, please use at least Python 3.2')
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pp = pprint.PrettyPrinter(depth=6)
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args = parse_arguments()
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''' This could be done directly from glucometerutils instead of via CSV '''
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@ -82,17 +80,17 @@ def main():
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for row in rows:
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row = parse_entry(row, args.icons)
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# If we're on the default values for units, highs and lows, check that the average
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# value is under 35 (assuming that average mmol/L < 35 and average mg/dL > 35)
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''' If we're on the default values for units, highs and lows, check that the average
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value is under 35 (assuming that average mmol/L < 35 and average mg/dL > 35) '''
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if args.units == UNIT_MMOLL and (args.high == DEFAULT_HIGH or args.low == DEFAULT_LOW):
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mean = round(np.mean([l.get('value') for l in rows]), 1)
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if mean > 35:
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args.units = UNIT_MGDL
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args.high = convert_glucose_unit(args.high, UNIT_MMOLL)
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args.low = convert_glucose_unit(args.low, UNIT_MMOLL)
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args.graph_max = convert_glucose_unit(args.graph_max, UNIT_MMOLL)
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args.graph_min = convert_glucose_unit(args.graph_min, UNIT_MMOLL)
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''' Manually specify max and min for mg/dL '''
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args.graph_max = GRAPH_MAX_MGDL
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args.graph_min = GRAPH_MIN_MGDL
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''' Fill in gaps that might exist in the data, in order to smooth the curves and fills '''
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''' We're using 8 minute gaps in order to have more accurate fills '''
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@ -111,9 +109,13 @@ def main():
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rcParams['font.sans-serif'] = ['Calibri','Verdana','Geneva','Arial','Helvetica','DejaVu Sans','Bitstream Vera Sans','sans-serif']
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rcParams['mathtext.default'] = 'regular'
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# Load custom fonts for the icon sets
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''' Load custom fonts for the icon sets
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At present, backend_pdf does not parse unicode correctly, and unicode
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characters from many fonts that lack proper glyph names are massed together
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and printed as the same character. The IcoGluco font, generated from Noto Sans and
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custom icons on IcoMoon, works around this. '''
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if args.icons:
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args.customfont = import_font('fonts/icogluco.ttf') # Works
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args.customfont = import_font('fonts/icogluco.ttf')
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#args.customfont = import_font('fonts/OpenSansEmoji.ttf') # Alternate working font
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nrows = args.graphs_per_page
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@ -302,18 +304,16 @@ def main():
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def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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pp = pprint.PrettyPrinter(depth=6)
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(x, y, z, p, q) = (list(), list(), list(), list(), list())
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for (key, value) in sorted(data.items()):
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# Time
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''' Time '''
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a = key
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if 'maxmin' in transforms:
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# If a max and a min exists, initialise them to y and z
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''' If a max and a min exists, initialise them to y and z '''
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b = value.get('max')
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c = value.get('min')
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else:
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# Glucose and comment
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''' Glucose and comment '''
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b = value.get('value')
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c = value.get('comment', '')
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x.append(a)
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@ -342,7 +342,7 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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if args.units == UNIT_MMOLL:
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y_tick_freq = 2
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else:
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y_tick_freq = convert_glucose_unit(2, UNIT_MMOLL)
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y_tick_freq = 50
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''' Formatting for axis labels, using date calculations from above '''
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ax.set_xlabel('Time', fontsize=9)
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@ -373,7 +373,8 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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''' Use SciPy's interp1d for linear transforming '''
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if not maxmin:
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f = interpolate.interp1d(x, y, kind='linear')
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x = np.linspace(x.min(), x.max(), 50) # 50 is number of points to make between x.max & x.min
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''' 50 is number of points to make between x.max & x.min '''
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x = np.linspace(x.min(), x.max(), 50)
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y = f(x)
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elif transform == 'spline' and transforms.get(transform) is True:
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@ -425,9 +426,6 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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zorder=40, bbox=dict(facecolor=BOXYELLOW, edgecolor='#e69f00', alpha=0.7, pad=8), \
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)
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# XXX At present, backend_pdf does not parse unicode correctly, and all recent
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# unicode chacters that lack proper glyph names are massed together and printed
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# as the same character
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if args.units == UNIT_MMOLL:
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y_offset = 6
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else:
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@ -454,7 +452,6 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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elif key == 'Food':
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symbol += '\N{GREEN APPLE}'
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symbol += '$'
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print(symbol)
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ax.annotate(
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symbol,
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xy=(x_pos, args.graph_max-y_offset),
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@ -495,9 +492,9 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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return ax
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def import_font(fontname):
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''' Turns a relative font path into a matplotlib font property. '''
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basedir = os.path.dirname(os.path.abspath(__file__))
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fontdir = os.path.join(basedir, 'fonts')
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fontpath = os.path.join(fontdir, fontname)
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fontpath = os.path.join(basedir, fontname)
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if not os.path.exists(fontpath):
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raise UserError("Font %s does not exist" % fontpath)
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prop = fm.FontProperties(fname=fontpath)
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@ -528,7 +525,6 @@ def parse_entry(data, icons, fmt='%Y-%m-%d %H:%M:%S'):
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ctype = relevant.group(1)
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cvalue = relevant.group(2)
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#cvalue = re.sub('(\d+)(\.\d+)?', '\g<1>', cvalue)
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''' Convert floating point-style strings (2.0) to integer-style strings (2) '''
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try:
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cvalue = int(float(cvalue))
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@ -541,13 +537,6 @@ def parse_entry(data, icons, fmt='%Y-%m-%d %H:%M:%S'):
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if re.search('Long', ctype) is not None:
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cvalue += 'L'
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# XXX At present, backend_pdf does not parse unicode correctly, and all recent
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# unicode chacters that lack proper glyph names are massed together and printed
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# as the same character
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# XXX Alternatives include replacing the glyph with an image, or a Path
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#ctype = re.sub('Food', '$\mathcal{\N{GREEN APPLE}}$', ctype, flags=re.IGNORECASE)
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#ctype = re.sub('Rapid-acting insulin', '$\mathcal{\N{SYRINGE}}^\mathrm{'+cvalue+'}$', ctype, flags=re.IGNORECASE)
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#ctype = re.sub('Long-acting insulin', '$\mathcal{\N{SYRINGE}}^\mathrm{'+cvalue+'}$', ctype, flags=re.IGNORECASE)
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ctype = re.sub('Rapid-acting insulin', 'Insulin', ctype, flags=re.IGNORECASE)
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ctype = re.sub('Long-acting insulin', 'Insulin', ctype, flags=re.IGNORECASE)
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@ -800,11 +789,15 @@ def parse_arguments():
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args.pagesize = verify_pagesize(args.pagesize)
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args.units = verify_units(args.units, args.high, args.low)
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if args.units == UNIT_MMOLL:
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args.graph_max = GRAPH_MAX
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args.graph_min = GRAPH_MIN
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args.graph_max = GRAPH_MAX_MMOLL
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args.graph_min = GRAPH_MIN_MMOLL
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else:
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args.graph_max = convert_glucose_unit(GRAPH_MAX, UNIT_MMOLL)
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args.graph_min = convert_glucose_unit(GRAPH_MIN, UNIT_MMOLL)
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args.graph_max = GRAPH_MAX_MGDL
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args.graph_min = GRAPH_MIN_MGDL
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''' If the user specified the units but not the high or low targets, set them now '''
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if args.high == DEFAULT_HIGH or args.low == DEFAULT_LOW:
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args.high = convert_glucose_unit(args.high, UNIT_MMOLL)
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args.low = convert_glucose_unit(args.low, UNIT_MMOLL)
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''' Ensure we have a valid number of graphs_per_page '''
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if not isinstance(args.graphs_per_page, int) or args.graphs_per_page < 1:
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