Merge pull request #3 from staskh/fix_auc

Fix auc and clarify CGMS2DayByDay issues

Author: staskh

README.md

@@ -33,7 +33,7 @@ Unless noted, iglu-r test is considered successful if it achieves precision of 0
 | cv_glu | ✅ |
 | cv_measures | ✅ |
 | ea1c | ✅ |
-| episode_calculation |  ✅| || no match in lv1_hypo_excl and lv1_hyper_excl|
+| episode_calculation |  ✅| || |
 | gmi | ✅ |
 | grade_eugly | ✅ |
 | grade_hyper | ✅ |
@@ -49,7 +49,7 @@ Unless noted, iglu-r test is considered successful if it achieves precision of 0
 | lbgi | ✅ |
 | mad_glu | ✅ |
 | mag |  ✅ | || IMHO, Original R implementation has an error |
-| mage | ✅ | || See algorithm at [MAGE](https://github.com/irinagain/iglu/blob/master/vignettes/MAGE.Rmd) |
+| mage | ✅ | || See algorithm at [MAGE](https://irinagain.github.io/iglu/articles/MAGE.html) |
 | mean_glu | ✅ |
 | median_glu | ✅ |
 | modd | ✅ |

R_REVIEW.md

@@ -7,6 +7,13 @@
       (length(na.omit(diffs))*n/60)
 ```
 
+## AUC
+
+```
+        day = rep(data_ip[[2]], 1440/dt0),
+```
+Generate sequence of days repeated 1440/dt0, while it has to have each day repeated by 1440/dt0 and followed by the next
+
 ## CGMS2DayByDay
 
 [ndays = ceiling(as.double(difftime(max(tr), min(tr), units = "days")) + 1)](https://github.com/irinagain/iglu/blob/82e4d1a39901847881d5402d1ac61b3e678d2a5e/R/utils.R#L208) has to be ndays = ceiling(as.double(difftime(max(tr), min(tr), units = "days")))`

iglu_python/__init__.py

@@ -37,7 +37,7 @@
 from .sd_measures import sd_measures
 from .sd_roc import sd_roc
 from .summary_glu import summary_glu
-from .utils import IGLU_R_COMPATIBLE, CGMS2DayByDay, check_data_columns, gd2d_to_df
+from .utils import set_iglu_r_compatible, is_iglu_r_compatible, CGMS2DayByDay, check_data_columns, gd2d_to_df
 
 __all__ = [
     "above_percent",
@@ -62,7 +62,8 @@
     "hyper_index",
     "hypo_index",
     "igc",
-    "IGLU_R_COMPATIBLE",
+    "set_iglu_r_compatible",
+    "is_iglu_r_compatible",
     "in_range_percent",
     "iqr_glu",
     "j_index",

iglu_python/auc.py

@@ -2,7 +2,8 @@
 import numpy as np
 import pandas as pd
 
-from .utils import CGMS2DayByDay, check_data_columns, gd2d_to_df, IGLU_R_COMPATIBLE
+from .utils import CGMS2DayByDay, check_data_columns, gd2d_to_df, is_iglu_r_compatible
+
 
 
 def auc(data: pd.DataFrame, tz: str = "") -> pd.DataFrame:
@@ -65,7 +66,7 @@ def auc_single(subject_data: pd.DataFrame) -> float:
 
         # Convert gd2d to DataFrame
         input_data = gd2d_to_df(gd2d, actual_dates, dt0)
-        if IGLU_R_COMPATIBLE:
+        if is_iglu_r_compatible():
             input_data['day'] = input_data['time'].dt.floor('d')
             input_data['gl_next'] = input_data['gl'].shift(-1)
             each_day_area = input_data.groupby("day").apply(

iglu_python/episode_calculation.py

@@ -3,7 +3,7 @@
 import numpy as np
 import pandas as pd
 
-from .utils import IGLU_R_COMPATIBLE, CGMS2DayByDay, check_data_columns, gd2d_to_df, get_local_tz
+from .utils import CGMS2DayByDay, check_data_columns, gd2d_to_df, get_local_tz, is_iglu_r_compatible
 
 
 def episode_calculation(
@@ -235,7 +235,7 @@ def episode_single(
     if dt0 is None:
         dt0 = gd2d_tuple[2]
 
-    if IGLU_R_COMPATIBLE:
+    if is_iglu_r_compatible():
         day_one = pd.to_datetime(gd2d_tuple[1][0]).tz_localize(None) # make in naive-timezone
         day_one = day_one.tz_localize('UTC') # this is how IGLU_R works
         if tz and tz!="":

iglu_python/mag.py

@@ -3,7 +3,8 @@
 import numpy as np
 import pandas as pd
 
-from .utils import CGMS2DayByDay, check_data_columns, IGLU_R_COMPATIBLE
+from .utils import CGMS2DayByDay, check_data_columns, is_iglu_r_compatible
+
 
 
 def mag(
@@ -93,7 +94,7 @@ def mag_single(data: pd.DataFrame, n: int) -> float:
         # Calculate absolute differences between readings n minutes apart
         lag = readings_per_interval
 
-        if IGLU_R_COMPATIBLE:
+        if is_iglu_r_compatible():
             idx = np.arange(0,len(gl_values),lag)
             gl_values_idx = gl_values[idx]
             diffs = gl_values_idx[1:] - gl_values_idx[:-1]

iglu_python/utils.py

@@ -9,7 +9,15 @@
 
 local_tz = get_localzone()  # get the local timezone
 
-IGLU_R_COMPATIBLE = True
+_IGLU_R_COMPATIBLE = True
+
+def set_iglu_r_compatible(value: bool) -> None:
+    global _IGLU_R_COMPATIBLE
+    _IGLU_R_COMPATIBLE = value
+
+def is_iglu_r_compatible() -> bool:
+    global _IGLU_R_COMPATIBLE
+    return _IGLU_R_COMPATIBLE
 
 def localize_naive_timestamp(timestamp: datetime) -> datetime:
     """
@@ -180,7 +188,7 @@ def CGMS2DayByDay(
     time_grid = pd.date_range(
         start=start_time, end=end_time, freq=f"{dt0}min"
     )
-    if IGLU_R_COMPATIBLE:
+    if is_iglu_r_compatible():
         # remove the first time point
         time_grid = time_grid[1:]
     else:
@@ -234,7 +242,7 @@ def CGMS2DayByDay(
     interp_data = interp_data.reshape(n_days, n_points_per_day)
 
     # Get actual dates
-    if IGLU_R_COMPATIBLE:
+    if is_iglu_r_compatible():
         # convert start_time into naive datetime
         start_time = start_time.tz_localize(None)
 
@@ -254,7 +262,7 @@ def gd2d_to_df(gd2d, actual_dates, dt0):
         time.extend(day_time)
 
     df = pd.DataFrame({
-            "time": pd.Series(time, dtype='datetime64[ns]'),
+            "time": pd.Series(time),
             "gl": pd.Series(gl, dtype='float64')
         })