measurement_for_sds test for negative base values

rcpchgrowth/__init__.py

@@ -1,5 +1,5 @@
 from .date_calculations import chronological_decimal_age, corrected_decimal_age, chronological_calendar_age, estimated_date_delivery, corrected_gestational_age
-from .global_functions import centile, sds_for_measurement, measurement_from_sds, percentage_median_bmi, mid_parental_height
+from .global_functions import centile, sds_for_measurement, measurement_from_sds, percentage_median_bmi, mid_parental_height, measurement_for_z
 from .centile_bands import centile_band_for_centile
 from .bmi_functions import bmi_from_height_weight, weight_for_bmi_height
 from .age_advice_strings import comment_prematurity_correction

rcpchgrowth/chart_functions.py

@@ -407,16 +407,20 @@ def create_uk_who_chart(measurement_method: str, sex: str, centile_format: Union
             # if the Cole 9 centiles were selected, these are rounded,
             # so conversion to SDS is different
             # Otherwise standard conversation of centile to z is used
+
+            z=0.0 #initialise
+            centile_value=0.0 #initialise
+
             if cole_method:
-                z = rounded_sds_for_centile(centile_sds)
-                centile_value=centile_sds
+                z = rounded_sds_for_centile(centile_sds) # a centile was provided, so convert to z
+                centile_value=centile_sds # store the original centile value 
             else:
                 if (is_sds):
-                    z=centile_sds
-                    centile_value=centile(centile_sds)
+                    z=centile_sds # an sds was supplied
+                    centile_value=centile(centile_sds) # convert the z to a centile and store
                 else:
-                    z = sds_for_centile(centile_sds)
-                    centile_value=centile_sds
+                    z = sds_for_centile(centile_sds) # a centile was provided, so convert to z
+                    centile_value=centile_sds # store the original centile value 
             centile_data = []
 
             try:
@@ -433,6 +437,7 @@ def create_uk_who_chart(measurement_method: str, sex: str, centile_format: Union
                     is_sds=is_sds
                 )
             except:
+                print(f"Not possible to generate centile data for UK-WHO {measurement_method} in {sex}s.")
                 centile_data=None
             # Store this centile for a given measurement
 

rcpchgrowth/data_tables/trisomy_21.json

@@ -982,7 +982,7 @@
         },
         "bmi": {
             "male":[
-                {"decimal_age": 0, "L": 0.7975301, "M": 12.18163, "S": 0.1195348}, 
+                {"decimal_age": 0.0, "L": 0.7975301, "M": 12.18163, "S": 0.1195348}, 
                 {"decimal_age": 0.08, "L": 0.7580755, "M": 13.4406, "S": 0.1114926}, 
                 {"decimal_age": 0.17, "L": 0.7335379, "M": 14.3038, "S": 0.1068001}, 
                 {"decimal_age": 0.25, "L": 0.7154457, "M": 14.9775, "S": 0.1037158}, 
@@ -994,7 +994,7 @@
                 {"decimal_age": 0.75, "L": 0.6475536, "M": 16.8791, "S": 0.0960959}, 
                 {"decimal_age": 0.83, "L": 0.6382132, "M": 16.9882, "S": 0.0955683}, 
                 {"decimal_age": 0.92, "L": 0.628519, "M": 17.0694, "S": 0.0951506}, 
-                {"decimal_age": 1, "L": 0.6182923, "M": 17.1296, "S": 0.0948244}, 
+                {"decimal_age": 1.0, "L": 0.6182923, "M": 17.1296, "S": 0.0948244}, 
                 {"decimal_age": 1.08, "L": 0.6074216, "M": 17.1739, "S": 0.0945748}, 
                 {"decimal_age": 1.17, "L": 0.5958693, "M": 17.2059, "S": 0.0943864}, 
                 {"decimal_age": 1.25, "L": 0.5836943, "M": 17.2284, "S": 0.0942544}, 
@@ -1006,7 +1006,7 @@
                 {"decimal_age": 1.75, "L": 0.499399, "M": 17.26, "S": 0.0943826},
                 {"decimal_age": 1.83, "L": 0.4838544, "M": 17.256, "S": 0.0945339},
                 {"decimal_age": 1.92, "L": 0.4679904, "M": 17.2505, "S": 0.0947134},
-                {"decimal_age": 2, "L": 0.4518357, "M": 17.2439, "S": 0.0949221},
+                {"decimal_age": 2.0, "L": 0.4518357, "M": 17.2439, "S": 0.0949221},
                 {"decimal_age": 2.08, "L": 0.4354165, "M": 17.2361, "S": 0.0951559},
                 {"decimal_age": 2.17, "L": 0.4187565, "M": 17.2271, "S": 0.0954131},
                 {"decimal_age": 2.25, "L": 0.4018769, "M": 17.217, "S": 0.0956899},
@@ -1018,7 +1018,7 @@
                 {"decimal_age": 2.75, "L": 0.296824, "M": 17.1412, "S": 0.0976967},
                 {"decimal_age": 2.83, "L": 0.2787896, "M": 17.1284, "S": 0.0980714},
                 {"decimal_age": 2.92, "L": 0.2606286, "M": 17.1161, "S": 0.0984535},
-                {"decimal_age": 3, "L": 0.2423511, "M": 17.1044, "S": 0.0988418},
+                {"decimal_age": 3.0, "L": 0.2423511, "M": 17.1044, "S": 0.0988418},
                 {"decimal_age": 3.08, "L": 0.2239744, "M": 17.0934, "S": 0.0992357},
                 {"decimal_age": 3.17, "L": 0.2055171, "M": 17.083, "S": 0.0996345},
                 {"decimal_age": 3.25, "L": 0.186997, "M": 17.0734, "S": 0.1000371},
@@ -1030,7 +1030,7 @@
                 {"decimal_age": 3.75, "L": 0.0753428, "M": 17.0285, "S": 0.1025485},
                 {"decimal_age": 3.83, "L": 0.0567556, "M": 17.0232, "S": 0.1029832},
                 {"decimal_age": 3.92, "L": 0.038204, "M": 17.0185, "S": 0.1034228},
-                {"decimal_age": 4, "L": 0.0196991, "M": 17.0145, "S": 0.1038675},
+                {"decimal_age": 4.0, "L": 0.0196991, "M": 17.0145, "S": 0.1038675},
                 {"decimal_age": 4.08, "L": 0.0012517, "M": 17.0111, "S": 0.1043176},
                 {"decimal_age": 4.17, "L": -0.017128, "M": 17.0084, "S": 0.1047723},
                 {"decimal_age": 4.25, "L": -0.0354303, "M": 17.0063, "S": 0.1052328},
@@ -1042,7 +1042,7 @@
                 {"decimal_age": 4.75, "L": -0.143193, "M": 17.0081, "S": 0.1080977},
                 {"decimal_age": 4.83, "L": -0.1607589, "M": 17.0111, "S": 0.1085914},
                 {"decimal_age": 4.92, "L": -0.1782008, "M": 17.0149, "S": 0.1090893},
-                {"decimal_age": 5, "L": -0.1955155, "M": 17.0195, "S": 0.1095912},
+                {"decimal_age": 5.0, "L": -0.1955155, "M": 17.0195, "S": 0.1095912},
                 {"decimal_age": 5.08, "L": -0.2127001, "M": 17.0251, "S": 0.1100974},
                 {"decimal_age": 5.17, "L": -0.2297519, "M": 17.0316, "S": 0.1106068},
                 {"decimal_age": 5.25, "L": -0.2466678, "M": 17.039, "S": 0.1111201},
@@ -1054,7 +1054,7 @@
                 {"decimal_age": 5.75, "L": -0.3451413, "M": 17.1029, "S": 0.1142622},
                 {"decimal_age": 5.83, "L": -0.3610311, "M": 17.1167, "S": 0.1147954},
                 {"decimal_age": 5.92, "L": -0.3767681, "M": 17.1314, "S": 0.1153319},
-                {"decimal_age": 6, "L": -0.3923514, "M": 17.1471, "S": 0.1158704},
+                {"decimal_age": 6.0, "L": -0.3923514, "M": 17.1471, "S": 0.1158704},
                 {"decimal_age": 6.08, "L": -0.4077801, "M": 17.1636, "S": 0.1164113},
                 {"decimal_age": 6.17, "L": -0.4230534, "M": 17.1811, "S": 0.1169544},
                 {"decimal_age": 6.25, "L": -0.4381714, "M": 17.1995, "S": 0.1174995},
@@ -1066,7 +1066,7 @@
                 {"decimal_age": 6.75, "L": -0.5256538, "M": 17.3287, "S": 0.1208067},
                 {"decimal_age": 6.83, "L": -0.5397037, "M": 17.3531, "S": 0.1213627},
                 {"decimal_age": 6.92, "L": -0.5536048, "M": 17.3784, "S": 0.1219195},
-                {"decimal_age": 7, "L": -0.567358, "M": 17.4044, "S": 0.1224771},
+                {"decimal_age": 7.0, "L": -0.567358, "M": 17.4044, "S": 0.1224771},
                 {"decimal_age": 7.08, "L": -0.5809644, "M": 17.4311, "S": 0.1230351},
                 {"decimal_age": 7.17, "L": -0.5944252, "M": 17.4585, "S": 0.1235938},
                 {"decimal_age": 7.25, "L": -0.6077414, "M": 17.4866, "S": 0.1241526},
@@ -1078,7 +1078,7 @@
                 {"decimal_age": 7.75, "L": -0.6846683, "M": 17.6684, "S": 0.1274992},
                 {"decimal_age": 7.83, "L": -0.6970069, "M": 17.7008, "S": 0.1280544},
                 {"decimal_age": 7.92, "L": -0.7092117, "M": 17.7337, "S": 0.1286085},
-                {"decimal_age": 8, "L": -0.7212843, "M": 17.7671, "S": 0.1291613},
+                {"decimal_age": 8.0, "L": -0.7212843, "M": 17.7671, "S": 0.1291613},
                 {"decimal_age": 8.08, "L": -0.7332264, "M": 17.801, "S": 0.1297126},
                 {"decimal_age": 8.17, "L": -0.7450395, "M": 17.8354, "S": 0.1302625},
                 {"decimal_age": 8.25, "L": -0.7567253, "M": 17.8703, "S": 0.1308106},
@@ -1090,7 +1090,7 @@
                 {"decimal_age": 8.75, "L": -0.8242714, "M": 18.0889, "S": 0.1340562},
                 {"decimal_age": 8.83, "L": -0.8351192, "M": 18.1268, "S": 0.134589},
                 {"decimal_age": 8.92, "L": -0.8458554, "M": 18.165, "S": 0.1351193},
-                {"decimal_age": 9, "L": -0.8564819, "M": 18.2036, "S": 0.1356467},
+                {"decimal_age": 9.0, "L": -0.8564819, "M": 18.2036, "S": 0.1356467},
                 {"decimal_age": 9.08, "L": -0.8670007, "M": 18.2426, "S": 0.1361716},
                 {"decimal_age": 9.17, "L": -0.8774138, "M": 18.2819, "S": 0.1366939},
                 {"decimal_age": 9.25, "L": -0.8877229, "M": 18.3215, "S": 0.1372131},
@@ -1102,7 +1102,7 @@
                 {"decimal_age": 9.75, "L": -0.9474747, "M": 18.5658, "S": 0.1402682},
                 {"decimal_age": 9.83, "L": -0.9570971, "M": 18.6075, "S": 0.1407681},
                 {"decimal_age": 9.92, "L": -0.9666279, "M": 18.6494, "S": 0.1412629},
-                {"decimal_age": 10, "L": -0.9760686, "M": 18.6916, "S": 0.1417557},
+                {"decimal_age": 10.0, "L": -0.9760686, "M": 18.6916, "S": 0.1417557},
                 {"decimal_age": 10.08, "L": -0.9854209, "M": 18.734, "S": 0.1422454},
                 {"decimal_age": 10.17, "L": -0.9946866, "M": 18.7767, "S": 0.1427322},
                 {"decimal_age": 10.25, "L": -1.003867, "M": 18.8196, "S": 0.1432159},
@@ -1114,7 +1114,7 @@
                 {"decimal_age": 10.75, "L": -1.057258, "M": 19.0819, "S": 0.1460552},
                 {"decimal_age": 10.83, "L": -1.065889, "M": 19.1264, "S": 0.1465182},
                 {"decimal_age": 10.92, "L": -1.074447, "M": 19.1711, "S": 0.1469781},
-                {"decimal_age": 11, "L": -1.082934, "M": 19.2159, "S": 0.1474352},
+                {"decimal_age": 11.0, "L": -1.082934, "M": 19.2159, "S": 0.1474352},
                 {"decimal_age": 11.08, "L": -1.091351, "M": 19.261, "S": 0.1478893},
                 {"decimal_age": 11.17, "L": -1.0997, "M": 19.3062, "S": 0.1483408},
                 {"decimal_age": 11.25, "L": -1.107981, "M": 19.3516, "S": 0.1487894},
@@ -1126,7 +1126,7 @@
                 {"decimal_age": 11.75, "L": -1.156312, "M": 19.6269, "S": 0.1514243},
                 {"decimal_age": 11.83, "L": -1.164152, "M": 19.6732, "S": 0.1518542},
                 {"decimal_age": 11.92, "L": -1.171933, "M": 19.7196, "S": 0.1522817},
-                {"decimal_age": 12, "L": -1.179656, "M": 19.7661, "S": 0.1527067},
+                {"decimal_age": 12.0, "L": -1.179656, "M": 19.7661, "S": 0.1527067},
                 {"decimal_age": 12.08, "L": -1.187322, "M": 19.8128, "S": 0.1531295},
                 {"decimal_age": 12.17, "L": -1.194933, "M": 19.8595, "S": 0.1535494},
                 {"decimal_age": 12.25, "L": -1.20249, "M": 19.9062, "S": 0.1539673},
@@ -1138,7 +1138,7 @@
                 {"decimal_age": 12.75, "L": -1.24676, "M": 20.1882, "S": 0.1564283},
                 {"decimal_age": 12.83, "L": -1.253968, "M": 20.2353, "S": 0.1568306},
                 {"decimal_age": 12.92, "L": -1.261131, "M": 20.2824, "S": 0.1572314},
-                {"decimal_age": 13, "L": -1.268249, "M": 20.3295, "S": 0.1576303},
+                {"decimal_age": 13.0, "L": -1.268249, "M": 20.3295, "S": 0.1576303},
                 {"decimal_age": 13.08, "L": -1.275322, "M": 20.3767, "S": 0.1580272},
                 {"decimal_age": 13.17, "L": -1.282351, "M": 20.4238, "S": 0.1584224},
                 {"decimal_age": 13.25, "L": -1.289338, "M": 20.4709, "S": 0.1588158},
@@ -1150,7 +1150,7 @@
                 {"decimal_age": 13.75, "L": -1.330389, "M": 20.7528, "S": 0.1611403},
                 {"decimal_age": 13.83, "L": -1.337092, "M": 20.7996, "S": 0.1615224},
                 {"decimal_age": 13.92, "L": -1.343757, "M": 20.8463, "S": 0.1619024},
-                {"decimal_age": 14, "L": -1.350385, "M": 20.893, "S": 0.1622812},
+                {"decimal_age": 14.0, "L": -1.350385, "M": 20.893, "S": 0.1622812},
                 {"decimal_age": 14.08, "L": -1.356975, "M": 20.9395, "S": 0.1626586},
                 {"decimal_age": 14.17, "L": -1.363529, "M": 20.9859, "S": 0.1630346},
                 {"decimal_age": 14.25, "L": -1.370047, "M": 21.0323, "S": 0.1634091},
@@ -1162,7 +1162,7 @@
                 {"decimal_age": 14.75, "L": -1.408424, "M": 21.308, "S": 0.1656287},
                 {"decimal_age": 14.83, "L": -1.414703, "M": 21.3536, "S": 0.1659941},
                 {"decimal_age": 14.92, "L": -1.420949, "M": 21.399, "S": 0.1663585},
-                {"decimal_age": 15, "L": -1.427164, "M": 21.4442, "S": 0.166722},
+                {"decimal_age": 15.0, "L": -1.427164, "M": 21.4442, "S": 0.166722},
                 {"decimal_age": 15.08, "L": -1.433347, "M": 21.4894, "S": 0.1670836},
                 {"decimal_age": 15.17, "L": -1.439499, "M": 21.5344, "S": 0.1674444},
                 {"decimal_age": 15.25, "L": -1.44562, "M": 21.5792, "S": 0.1678042},
@@ -1174,7 +1174,7 @@
                 {"decimal_age": 15.75, "L": -1.481732, "M": 21.8454, "S": 0.1699412},
                 {"decimal_age": 15.83, "L": -1.487652, "M": 21.8892, "S": 0.1702935},
                 {"decimal_age": 15.92, "L": -1.493545, "M": 21.9329, "S": 0.1706453},
-                {"decimal_age": 16, "L": -1.499411, "M": 21.9765, "S": 0.170996},
+                {"decimal_age": 16.0, "L": -1.499411, "M": 21.9765, "S": 0.170996},
                 {"decimal_age": 16.08, "L": -1.505251, "M": 22.0199, "S": 0.1713459},
                 {"decimal_age": 16.17, "L": -1.511065, "M": 22.0631, "S": 0.171695},
                 {"decimal_age": 16.25, "L": -1.516854, "M": 22.1062, "S": 0.1720431},
@@ -1186,7 +1186,7 @@
                 {"decimal_age": 16.75, "L": -1.551072, "M": 22.3614, "S": 0.1741151},
                 {"decimal_age": 16.83, "L": -1.556692, "M": 22.4034, "S": 0.1744578},
                 {"decimal_age": 16.92, "L": -1.562289, "M": 22.4453, "S": 0.1747996},
-                {"decimal_age": 17, "L": -1.567864, "M": 22.487, "S": 0.1751407},
+                {"decimal_age": 17.0, "L": -1.567864, "M": 22.487, "S": 0.1751407},
                 {"decimal_age": 17.08, "L": -1.573416, "M": 22.5285, "S": 0.1754814},
                 {"decimal_age": 17.17, "L": -1.578946, "M": 22.5699, "S": 0.1758212},
                 {"decimal_age": 17.25, "L": -1.584454, "M": 22.6112, "S": 0.17616},
@@ -1198,7 +1198,7 @@
                 {"decimal_age": 17.75, "L": -1.617057, "M": 22.8555, "S": 0.17818},
                 {"decimal_age": 17.83, "L": -1.622419, "M": 22.8957, "S": 0.1785144},
                 {"decimal_age": 17.92, "L": -1.62776, "M": 22.9357, "S": 0.1788482},
-                {"decimal_age": 18, "L": -1.633082, "M": 22.9756, "S": 0.1791814},
+                {"decimal_age": 18.0, "L": -1.633082, "M": 22.9756, "S": 0.1791814},
                 {"decimal_age": 18.08, "L": -1.638384, "M": 23.0154, "S": 0.1795139},
                 {"decimal_age": 18.17, "L": -1.643667, "M": 23.055, "S": 0.179846},
                 {"decimal_age": 18.25, "L": -1.64893, "M": 23.0945, "S": 0.1801772},

rcpchgrowth/global_functions.py

@@ -36,10 +36,10 @@ def measurement_from_sds(
     observation_value = None
     try:
         observation_value = measurement_for_z(z=requested_sds, l=l, m=m, s=s)
-        return observation_value
     except Exception as e:
         print(e) 
         return None
+    return observation_value
 
 def sds_for_measurement(
     reference: str,
@@ -98,32 +98,34 @@ def generate_centile(z: float, centile: float, measurement_method: str, sex: str
     Takes the z-score equivalent of the centile, the centile to be used as a label, the sex and measurement method.
     """
 
+    if (len(lms_array_for_measurement)==0):
+        raise Exception(f"No reference data available for {measurement_method} in {sex} in {reference}")
+
     min_age = lms_array_for_measurement[0]["decimal_age"]
     max_age = lms_array_for_measurement[-1]["decimal_age"]
 
     # if this is an sds line, the label reflects the sds value. The default is to reflect the centile
     label_value = centile
     if is_sds:
-        label_value=round(z, 3)        
+        label_value=round(z, 3)
 
     centile_measurements = []
     age = min_age
     while age <= max_age:
+        measurement=0.0 #initialise
         # loop through the reference in steps of 0.1y
         try:
             measurement = measurement_from_sds(
                 reference=reference, measurement_method=measurement_method, requested_sds=z, sex=sex, age=age)
         except Exception as err:
-            print(err)
-            measurement = None
+            print(f"Measurement Calculation Error: {err}")
 
         # creates a data point
         if measurement is not None:
             try:
-                rounded = round(measurement, 4)
-            except Exception as err:
-                # cannot round a complex number: set that as zero
-                rounded = None
+                rounded = round(measurement*10000)/10000
+            except Exception as e:
+                print(f"{e} z:{z} age:{age} measurement: {measurement}")
         else:
             rounded = None
         value = {
@@ -278,10 +280,22 @@ def linear_interpolation(age: float, age_one_below: float, age_one_above: float,
 def measurement_for_z(z: float, l: float, m: float, s: float) -> float:
     """
     Returns a measurement for a z score, L, M and S
+    x = M (1 + L S z)^(1/L)
+    Note, in some circumstances, 1 + l * s * z will be negative, and 
+    it will not be possible to calculate a power.
+    In these circumstances, None is returned
     """
+    measurement_value=0.0
     if l != 0.0:
-        # measurement_value = math.pow((1 + l * s * z), 1 / l) * m
-        measurement_value = ((1 + l * s * z) ** (1 / l)) * m
+        first_step= (1 + l * s * z)
+        exponent= 1 / l
+        if first_step < 0:
+            return None
+        try:
+            measurement_value= (first_step ** (1/exponent)) * m
+        except Exception as e:
+            print(e)
+            return
     else:
         measurement_value = math.exp(s * z) * m
     return measurement_value
@@ -292,7 +306,6 @@ def z_score(l: float, m: float, s: float, observation: float):
     """
     sds = 0.0
     if l != 0.0:
-        # sds = (((math.pow((observation / m), l)) - 1) / (l * s))
         sds = (((observation / m) ** l) - 1) / (l*s)
     else:
         sds = (math.log(observation / m) / s)

rcpchgrowth/trisomy_21.py

@@ -69,7 +69,7 @@ def trisomy_21_lms_array_for_measurement_and_sex(
     if data_invalid:
         raise LookupError(data_error)
     else:
-         return TRISOMY_21_DATA["measurement"][measurement_method][sex]
+        return TRISOMY_21_DATA["measurement"][measurement_method][sex]
 
 def select_reference_data_for_trisomy_21(measurement_method:str, sex:str):
     try: