Fix bugs that occur when switching to mg/dL units.
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@ -9,7 +9,7 @@ __license__ = 'MIT'
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# TODO: comments -- unicode
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# TODO: prettify
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# TODO: weekly graph with each day's figures as a different-coloured line
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# TODO: verify either set of units (mmol,mg/dl) works with the data
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# TODO: verify either set of units (mmol/L,mg/dl) works with the data
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import argparse
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import csv
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@ -39,17 +39,20 @@ VALID_UNITS = [UNIT_MGDL, UNIT_MMOLL]
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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_MAX = 21
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GRAPH_MIN = 1
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DEFAULT_HIGH = 8
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DEFAULT_LOW = 4
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# Set colour for below-target maxmins
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# Colour for below-target maxmins
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RED = '#d71920'
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# Set colour for above-target maxmins
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# Colour for above-target maxmins
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YELLOW = '#f1b80e'
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# Set colour for graph lines
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# Colour for graph lines
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BLUE = '#02538f'
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# Set colour for median glucose box
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# Colour for median glucose box
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GREEN = '#009e73'
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# Set 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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@ -68,6 +71,18 @@ 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 args.units == UNIT_MMOLL and (args.high == DEFAULT_HIGH or args.low == DEFAULT_LOW):
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mean = round(np.mean([l['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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''' 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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rows = fill_gaps(rows, interval=dt.timedelta(minutes=10))
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@ -140,7 +155,7 @@ def main():
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generate_plot(data,
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ax=ax,
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transforms={'bezier':True, 'avga1c':a_median, \
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'color':[RED, BLUE, RED], 'boundaries':[0, args.low, args.high, GRAPH_MAX]},
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'color':[RED, BLUE, RED], 'boundaries':[args.graph_min, args.low, args.high, args.graph_max]},
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args=args,
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color=BLUE,
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)
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@ -211,7 +226,7 @@ def main():
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generate_plot(data,
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ax=ax,
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transforms={'bezier':True, \
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'color':[RED, BLUE, RED], 'boundaries':[0, args.low, args.high, GRAPH_MAX]},
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'color':[RED, BLUE, RED], 'boundaries':[args.graph_min, args.low, args.high, args.graph_max]},
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args=args,
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color=BLUE,
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)
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@ -308,13 +323,17 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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x_min = mdates.date2num(firstminute)
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x_max = mdates.date2num(lastminute)
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ax.set_xlim(x_min, x_max)
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ax.set_ylim(0, GRAPH_MAX)
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ax.set_ylim(args.graph_min, args.graph_max)
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''' Calculate the time intervals in 2 hour segments '''
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xtimes = []
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time = firstminute
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while time < lastminute:
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xtimes.append(time)
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time += dt.timedelta(hours=2)
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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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''' Formatting for axis labels, using date calculations from above '''
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ax.set_xlabel('Time', fontsize=9)
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@ -327,9 +346,9 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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tick.label1.set_horizontalalignment('left')
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ax.set_ylabel('Blood Glucose (' + args.units + ')', fontsize=9)
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ax.set_ybound(0, GRAPH_MAX)
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ax.set_ybound(args.graph_min, args.graph_max)
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ax.grid(axis='y', color = '#d0d0d0', linestyle = (1,(0.5,2)), zorder=1)
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ax.set_yticks([a for a in range(0, GRAPH_MAX, 2)])
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ax.set_yticks([a for a in range(int(args.graph_min), int(args.graph_max), int(y_tick_freq))])
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ax.yaxis.set_major_formatter(mticker.FormatStrFormatter("%d"))
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ax.yaxis.set_ticks_position('none')
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@ -350,15 +369,13 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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elif transform == 'spline' and transforms[transform] is True:
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''' Use SciPy's UnivariateSpline for transforming (s is transforming factor) '''
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if args.units == UNIT_MMOLL:
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s = 8
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else:
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s = convert_glucose_unit(12, UNIT_MMOLL)
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if not maxmin:
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curve = interpolate.UnivariateSpline(x=x, y=y, k=3, s=8)
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curve = interpolate.UnivariateSpline(x=x, y=y, k=3, s=s)
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y = curve(x)
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#else:
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# TODO Apply spline to each curve?
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#curve1 = interpolate.UnivariateSpline(x=x, y=y, k=3, s=5)
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#curve2 = interpolate.UnivariateSpline(x=x, y=z, k=3, s=5)
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#y = curve1(x)
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#z = curve2(x)
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elif transform == 'bezier' and transforms[transform] is True:
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''' Create bezier function for transforming (s is transforming factor) '''
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@ -374,8 +391,6 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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For large arrays, get a smaller slice of the full array.
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Do this by removing every nth element from the array '''
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n = 5
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while len(p) > 1000:
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p = np.delete(p, np.arange(0, len(p), n), axis=0)
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while len(x) > 1000:
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x = np.delete(x, np.arange(0, len(x), n), axis=0)
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y = np.delete(y, np.arange(0, len(y), n), axis=0)
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@ -383,18 +398,15 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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if not maxmin:
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curve = np.array([c for _, c in bezier(np.array([x,y]).T, 250)])
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(x, y) = (curve[:,0], curve[:,1])
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#else:
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# TODO Apply bezier to each curve? Will this work for x?
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#while len(q) > 1000:
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# q = np.delete(q, np.arange(0, len(q), n), axis=0)
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#curve1 = np.array([c for _, c in bezier(p[:], 250)])
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#curve2 = np.array([c for _, c in bezier(q[:], 250)])
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#(x, y) = (curve1[:,0], curve1[:,1])
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#(x, z) = (curve2[:,0], curve2[:,1])
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''' Add the mean or median glucose and A1c values '''
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if transform == 'avgglucose' and isinstance(transforms[transform], (int, float)):
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ax.annotate('Median glucose: %.1f%s' % (round(transforms['avgglucose'], 1), args.units), fontsize=9, \
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if args.units == UNIT_MMOLL:
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gmtext = 'Median glucose: %.1f%s' % (round(transforms['avgglucose'], 1), args.units)
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else:
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gmtext = 'Median glucose: %.0f%s' % (round(transforms['avgglucose'], 1), args.units)
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ax.annotate(gmtext, fontsize=9, \
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xy=(0.95, 0.85), xycoords='axes fraction', verticalalignment='top', horizontalalignment='right', \
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zorder=40, bbox=dict(facecolor=GREEN, edgecolor='#009e73', alpha=0.7, pad=8), \
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)
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@ -413,7 +425,7 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
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#print(label)
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ax.annotate(
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label,
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xy=(a, GRAPH_MAX-6),
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xy=(a, args.graph_max-6),
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rotation=45,
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zorder=25,
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)
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@ -511,6 +523,9 @@ def parse_entry(data, icons, fmt='%Y-%m-%d %H:%M:%S'):
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''' Convert value from string to float '''
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data['value'] = float(data.get('value'))
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# XXX convert everything to mg/dL for testing
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#data['value'] = float(round(data.get('value') * 18.0, 0))
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return data
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def list_days_and_weeks(data, trim_weeks=192):
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@ -726,16 +741,22 @@ def parse_arguments():
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default='mmol/L', choices=(UNIT_MGDL, UNIT_MMOLL),
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help=('The measurement units used (mmol/L or mg/dL).'))
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parser.add_argument(
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'--low', action='store', required=False, type=float, default=4,
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'--low', action='store', required=False, type=float, default=DEFAULT_LOW,
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help=('Minimum of target glucose range.'))
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parser.add_argument(
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'--high', action='store', required=False, type=float, default=8,
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'--high', action='store', required=False, type=float, default=DEFAULT_HIGH,
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help=('Maximum of target glucose range.'))
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args = parser.parse_args()
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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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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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''' 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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@ -753,6 +774,34 @@ def from_csv(csv_file, newline=''):
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rows.append(item)
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return rows
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def convert_glucose_unit(value, from_unit, to_unit=None):
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"""Convert the given value of glucose level between units.
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Args:
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value: The value of glucose in the current unit
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from_unit: The unit value is currently expressed in
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to_unit: The unit to conver the value to: the other if empty.
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Returns:
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The converted representation of the blood glucose level.
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Raises:
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exceptions.InvalidGlucoseUnit: If the parameters are incorrect.
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"""
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if from_unit not in VALID_UNITS:
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raise exceptions.InvalidGlucoseUnit(from_unit)
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if from_unit == to_unit:
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return value
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if to_unit is not None:
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if to_unit not in VALID_UNITS:
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raise exceptions.InvalidGlucoseUnit(to_unit)
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if from_unit is UNIT_MGDL:
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return round(value / 18.0, 2)
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else:
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return round(value * 18.0, 0)
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if __name__ == "__main__":
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