Fix bugs that occur when switching to mg/dL units.

glucometer_graphs.py

@@ -9,7 +9,7 @@ __license__ = 'MIT'
 # TODO: comments -- unicode
 # TODO: prettify
 # TODO: weekly graph with each day's figures as a different-coloured line
-# TODO: verify either set of units (mmol,mg/dl) works with the data
+# TODO: verify either set of units (mmol/L,mg/dl) works with the data
 
 import argparse
 import csv
@@ -40,16 +40,19 @@ VALID_UNITS = [UNIT_MGDL, UNIT_MMOLL]
 INTERVAL = 15
 # Maximum gluclose value to display (TODO: mmol/mg)
 GRAPH_MAX    = 21
+GRAPH_MIN    = 1
+DEFAULT_HIGH = 8
+DEFAULT_LOW  = 4
 
-# Set colour for below-target maxmins
+# Colour for below-target maxmins
 RED = '#d71920'
-# Set colour for above-target maxmins
+# Colour for above-target maxmins
 YELLOW = '#f1b80e'
-# Set colour for graph lines
+# Colour for graph lines
 BLUE = '#02538f'
-# Set colour for median glucose box
+# Colour for median glucose box
 GREEN = '#009e73'
-# Set colour for median A1c box
+# Colour for median A1c box
 BOXYELLOW = '#e69f00'
 
 def main():
@@ -68,6 +71,18 @@ def main():
   for row in rows:
     row = parse_entry(row, args.icons)
 
+  # If we're on the default values for units, highs and lows, check that the average
+  # value is under 35 (assuming that average mmol/L < 35 and average mg/dL > 35)
+  if args.units == UNIT_MMOLL and (args.high == DEFAULT_HIGH or args.low == DEFAULT_LOW):
+    mean = round(np.mean([l['value'] for l in rows]), 1)
+    if mean > 35:
+      args.units = UNIT_MGDL
+      args.high  = convert_glucose_unit(args.high, UNIT_MMOLL)
+      args.low   = convert_glucose_unit(args.low, UNIT_MMOLL)
+      args.graph_max = convert_glucose_unit(args.graph_max, UNIT_MMOLL)
+      args.graph_min = convert_glucose_unit(args.graph_min, UNIT_MMOLL)
+
+
   ''' Fill in gaps that might exist in the data, in order to smooth the curves and fills '''
   ''' We're using 8 minute gaps in order to have more accurate fills '''
   rows = fill_gaps(rows, interval=dt.timedelta(minutes=10))
@@ -140,7 +155,7 @@ def main():
     generate_plot(data,
         ax=ax,
         transforms={'bezier':True, 'avga1c':a_median, \
-            'color':[RED, BLUE, RED], 'boundaries':[0, args.low, args.high, GRAPH_MAX]},
+            'color':[RED, BLUE, RED], 'boundaries':[args.graph_min, args.low, args.high, args.graph_max]},
         args=args,
         color=BLUE,
     )
@@ -211,7 +226,7 @@ def main():
         generate_plot(data,
             ax=ax,
             transforms={'bezier':True, \
-                'color':[RED, BLUE, RED], 'boundaries':[0, args.low, args.high, GRAPH_MAX]},
+                'color':[RED, BLUE, RED], 'boundaries':[args.graph_min, args.low, args.high, args.graph_max]},
             args=args,
             color=BLUE,
         )
@@ -308,13 +323,17 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
   x_min       =  mdates.date2num(firstminute)
   x_max       =  mdates.date2num(lastminute)
   ax.set_xlim(x_min, x_max)
-  ax.set_ylim(0, GRAPH_MAX)
+  ax.set_ylim(args.graph_min, args.graph_max)
   ''' Calculate the time intervals in 2 hour segments '''
   xtimes = []
   time = firstminute
   while time < lastminute:
       xtimes.append(time)
       time += dt.timedelta(hours=2)
+  if args.units == UNIT_MMOLL:
+    y_tick_freq = 2
+  else:
+    y_tick_freq = convert_glucose_unit(2, UNIT_MMOLL)
 
   ''' Formatting for axis labels, using date calculations from above '''
   ax.set_xlabel('Time', fontsize=9)
@@ -327,9 +346,9 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
     tick.label1.set_horizontalalignment('left')
 
   ax.set_ylabel('Blood Glucose (' + args.units + ')', fontsize=9)
-  ax.set_ybound(0, GRAPH_MAX)
+  ax.set_ybound(args.graph_min, args.graph_max)
   ax.grid(axis='y', color = '#d0d0d0', linestyle = (1,(0.5,2)), zorder=1)
-  ax.set_yticks([a for a in range(0, GRAPH_MAX, 2)])
+  ax.set_yticks([a for a in range(int(args.graph_min), int(args.graph_max), int(y_tick_freq))])
   ax.yaxis.set_major_formatter(mticker.FormatStrFormatter("%d"))
   ax.yaxis.set_ticks_position('none')
 
@@ -350,15 +369,13 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
 
     elif transform == 'spline' and transforms[transform] is True:
       ''' Use SciPy's UnivariateSpline for transforming (s is transforming factor) '''
+      if args.units == UNIT_MMOLL:
+        s = 8
+      else:
+        s = convert_glucose_unit(12, UNIT_MMOLL)
       if not maxmin:
-        curve = interpolate.UnivariateSpline(x=x, y=y, k=3, s=8)
+        curve = interpolate.UnivariateSpline(x=x, y=y, k=3, s=s)
         y = curve(x)
-      #else:
-        # TODO Apply spline to each curve?
-        #curve1 = interpolate.UnivariateSpline(x=x, y=y, k=3, s=5)
-        #curve2 = interpolate.UnivariateSpline(x=x, y=z, k=3, s=5)
-        #y = curve1(x)
-        #z = curve2(x)
 
     elif transform == 'bezier' and transforms[transform] is True:
       ''' Create bezier function for transforming (s is transforming factor) '''
@@ -374,8 +391,6 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
           For large arrays, get a smaller slice of the full array.
           Do this by removing every nth element from the array '''
       n = 5
-      while len(p) > 1000:
-        p = np.delete(p, np.arange(0, len(p), n), axis=0)
       while len(x) > 1000:
         x = np.delete(x, np.arange(0, len(x), n), axis=0)
         y = np.delete(y, np.arange(0, len(y), n), axis=0)
@@ -383,18 +398,15 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
       if not maxmin:
         curve = np.array([c for _, c in bezier(np.array([x,y]).T, 250)])
         (x, y) = (curve[:,0], curve[:,1])
-      #else:
-        # TODO Apply bezier to each curve? Will this work for x?
-        #while len(q) > 1000:
-        #  q = np.delete(q, np.arange(0, len(q), n), axis=0)
-        #curve1 = np.array([c for _, c in bezier(p[:], 250)])
-        #curve2 = np.array([c for _, c in bezier(q[:], 250)])
-        #(x, y) = (curve1[:,0], curve1[:,1])
-        #(x, z) = (curve2[:,0], curve2[:,1])
 
     ''' Add the mean or median glucose and A1c values '''
     if transform == 'avgglucose' and isinstance(transforms[transform], (int, float)):
-      ax.annotate('Median glucose: %.1f%s' % (round(transforms['avgglucose'], 1), args.units), fontsize=9, \
+      if args.units == UNIT_MMOLL:
+        gmtext = 'Median glucose: %.1f%s' % (round(transforms['avgglucose'], 1), args.units)
+      else:
+        gmtext = 'Median glucose: %.0f%s' % (round(transforms['avgglucose'], 1), args.units)
+
+      ax.annotate(gmtext, fontsize=9, \
           xy=(0.95, 0.85), xycoords='axes fraction', verticalalignment='top', horizontalalignment='right', \
           zorder=40, bbox=dict(facecolor=GREEN, edgecolor='#009e73', alpha=0.7, pad=8), \
       )
@@ -413,7 +425,7 @@ def generate_plot(data, ax=None, transforms={}, args=[], **plot_args):
           #print(label)
           ax.annotate(
             label,
-            xy=(a, GRAPH_MAX-6), 
+            xy=(a, args.graph_max-6),
             rotation=45,
             zorder=25,
             )
@@ -511,6 +523,9 @@ def parse_entry(data, icons, fmt='%Y-%m-%d %H:%M:%S'):
   ''' Convert value from string to float '''
   data['value'] = float(data.get('value'))
 
+  # XXX convert everything to mg/dL for testing
+  #data['value'] = float(round(data.get('value') * 18.0, 0))
+
   return data
 
 def list_days_and_weeks(data, trim_weeks=192):
@@ -726,16 +741,22 @@ def parse_arguments():
     default='mmol/L', choices=(UNIT_MGDL, UNIT_MMOLL),
     help=('The measurement units used (mmol/L or mg/dL).'))
   parser.add_argument(
-    '--low', action='store', required=False, type=float, default=4,
+    '--low', action='store', required=False, type=float, default=DEFAULT_LOW,
     help=('Minimum of target glucose range.'))
   parser.add_argument(
-    '--high', action='store', required=False, type=float, default=8,
+    '--high', action='store', required=False, type=float, default=DEFAULT_HIGH,
     help=('Maximum of target glucose range.'))
 
   args = parser.parse_args()
 
   args.pagesize = verify_pagesize(args.pagesize)
   args.units = verify_units(args.units, args.high, args.low)
+  if args.units == UNIT_MMOLL:
+    args.graph_max = GRAPH_MAX
+    args.graph_min = GRAPH_MIN
+  else:
+    args.graph_max = convert_glucose_unit(GRAPH_MAX, UNIT_MMOLL)
+    args.graph_min = convert_glucose_unit(GRAPH_MIN, UNIT_MMOLL)
 
   ''' Ensure we have a valid number of graphs_per_page '''
   if not isinstance(args.graphs_per_page, int) or args.graphs_per_page < 1:
@@ -753,6 +774,34 @@ def from_csv(csv_file, newline=''):
     rows.append(item)
   return rows
 
+def convert_glucose_unit(value, from_unit, to_unit=None):
+  """Convert the given value of glucose level between units.
+
+  Args:
+    value: The value of glucose in the current unit
+    from_unit: The unit value is currently expressed in
+    to_unit: The unit to conver the value to: the other if empty.
+
+  Returns:
+    The converted representation of the blood glucose level.
+
+  Raises:
+    exceptions.InvalidGlucoseUnit: If the parameters are incorrect.
+  """
+  if from_unit not in VALID_UNITS:
+    raise exceptions.InvalidGlucoseUnit(from_unit)
+
+  if from_unit == to_unit:
+    return value
+
+  if to_unit is not None:
+    if to_unit not in VALID_UNITS:
+      raise exceptions.InvalidGlucoseUnit(to_unit)
+
+  if from_unit is UNIT_MGDL:
+    return round(value / 18.0, 2)
+  else:
+    return round(value * 18.0, 0)
 
 
 if __name__ == "__main__":