Merge pull request #45 from rcpch/eatyourpeas/issue32

Eatyourpeas/issue32

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.2.3
+current_version = 4.2.4
 tag = False
 commit = True
 

rcpchgrowth/__init__.py

@@ -6,10 +6,10 @@
 from .constants import *
 from .date_calculations import chronological_decimal_age, corrected_decimal_age, chronological_calendar_age, estimated_date_delivery, corrected_gestational_age
 from .dynamic_growth import create_thrive_line, return_correlation, create_thrive_lines
-from .global_functions import centile, sds_for_measurement, measurement_from_sds, percentage_median_bmi, mid_parental_height, measurement_for_z, cubic_interpolation, linear_interpolation
+from .global_functions import centile, sds_for_measurement, measurement_from_sds, percentage_median_bmi, measurement_for_z, cubic_interpolation, linear_interpolation
 from .fictional_child import generate_fictional_child_data
 from .measurement import Measurement
-from .mid_parental_height import *
+from .mid_parental_height import mid_parental_height, mid_parental_height_z, expected_height_z_from_mid_parental_height_z, lower_and_upper_limits_of_expected_height_z
 from .trisomy_21 import select_reference_data_for_trisomy_21
 from .trisomy_21_aap import select_reference_data_for_trisomy_21_aap
 from .turner import select_reference_data_for_turner

rcpchgrowth/centile_bands.py

@@ -1,6 +1,6 @@
 # imports from rcpchgrowth
 from rcpchgrowth.constants.reference_constants import COLE_TWO_THIRDS_SDS_NINE_CENTILES, THREE_PERCENT_CENTILES, UK_WHO, CDC
-from .constants import BMI, HEAD_CIRCUMFERENCE,THREE_PERCENT_CENTILE_COLLECTION,COLE_TWO_THIRDS_SDS_NINE_CENTILE_COLLECTION ,FIVE_PERCENT_CENTILES, FIVE_PERCENT_CENTILE_COLLECTION, EIGHTY_FIVE_PERCENT_CENTILES, EIGHTY_FIVE_PERCENT_CENTILE_COLLECTION
+from .constants import BMI, HEAD_CIRCUMFERENCE,THREE_PERCENT_CENTILE_COLLECTION,COLE_TWO_THIRDS_SDS_NINE_CENTILE_COLLECTION ,FIVE_PERCENT_CENTILES, FIVE_PERCENT_CENTILE_COLLECTION, EIGHTY_FIVE_PERCENT_CENTILES, EIGHTY_FIVE_PERCENT_CENTILE_COLLECTION, MAXIMUM_HEIGHT_WEIGHT_OFC_ADVISORY_SDS, MINIMUM_HEIGHT_WEIGHT_OFC_ADVISORY_SDS, MAXIMUM_BMI_ADVISORY_SDS, MINIMUM_BMI_ADVISORY_SDS, HEIGHT, WEIGHT, HEAD_CIRCUMFERENCE, BMI
 from .global_functions import rounded_sds_for_centile, sds_for_centile
 
 # Recommendations from Project board for reporting Centiles
@@ -107,6 +107,8 @@ def centile_band_for_centile(sds: float, measurement_method: str, centile_format
         params: accepts a sds: float
         params: accepts a measurement_method as string
         params: accepts array of centiles representing the centile lines
+
+        These advice messages appear in the tooltips of the growth charts in the RCPCH Growth Chart and are advisory only. They do not reject data entry.
     """
 
     centile_collection = []
@@ -121,15 +123,19 @@ def centile_band_for_centile(sds: float, measurement_method: str, centile_format
 
     centile_band_ranges = generate_centile_band_ranges(centile_collection)
 
+    upper_threshold = MAXIMUM_HEIGHT_WEIGHT_OFC_ADVISORY_SDS
+    lower_threshold = MINIMUM_HEIGHT_WEIGHT_OFC_ADVISORY_SDS
     if measurement_method == BMI:
         measurement_method = "body mass index"
+        upper_threshold = MAXIMUM_BMI_ADVISORY_SDS
+        lower_threshold = MINIMUM_BMI_ADVISORY_SDS
     elif measurement_method == HEAD_CIRCUMFERENCE:
         measurement_method = "head circumference"
 
-    if sds <= -6:
-        return f"This {measurement_method} measurement is well below the normal range. Please review its accuracy."
-    elif sds > 6:
-        return f"This {measurement_method} measurement is well above the normal range. Please review its accuracy."
+    if sds < lower_threshold:
+        return f"This {measurement_method} measurement is well outside the normal range. Please check its accuracy."
+    elif sds > upper_threshold:
+        return f"This {measurement_method} measurement is well outside the normal range. Please check its accuracy."
     elif sds <= centile_band_ranges[0][0]:
         return f"This {measurement_method} measurement is below the normal range."
     elif sds > centile_band_ranges[-1][1]:

rcpchgrowth/constants/validation_constants.py

@@ -1,11 +1,12 @@
 """
 These constants are intended to be used throughout both the rcpchgrowth module
 and the API for validation of input values and rejection of very high or low values
+
+The constants used previously drew on the Guiness Book of Records and other sources to set hard limits.
+These were replaced with SDS sds_advisory and sds_error values in the rcpchgrowth-python repository as per issue #32
 """
 
 # HEIGHT CONSTANTS
-MINIMUM_LENGTH_CM = 20
-MAXIMUM_HEIGHT_CM = 300
 # The smallest baby was report by the BBC on 9/8/2021 (https://www.bbc.co.uk/news/world-asia-58141756.amp)
 # to have a length of just 24cm and was born at 25 weeks gestation, discharged at 13 mths of age (chronological)
 # from Singapore's National University Hospital
@@ -14,8 +15,6 @@
 # https://en.wikipedia.org/wiki/Robert_Wadlow
 
 # WEIGHT CONSTANTS
-MINIMUM_WEIGHT_KG = 0.15
-MAXIMUM_WEIGHT_KG = 500
 # The smallest baby was report by the BBC on 9/8/2021 (https://www.bbc.co.uk/news/world-asia-58141756.amp)
 # to weigh just 212g and was born at 25 weeks gestation, discharged at 13 mths of age (chronological)
 # from Singapore's National University Hospital
@@ -25,16 +24,12 @@
 # https://en.wikipedia.org/wiki/Jon_Brower_Minnoch
 
 # OFC CONSTANTS
-MINIMUM_OFC_CM = 5
-MAXIMUM_OFC_CM = 100
 # We couldn't find a good answer for the 'largest human head' that we could use
 # Instead have presumed that 100 is a good maximum, given that pathological states
 # causing very large head size (eg hydrocephalus) render the OFC meaningless for
 # growth measurement and assessment purposes.
 
 # BMI CONSTANTS
-MINIMUM_BMI_KGM2 = 7.5
-MAXIMUM_BMI_KGM2 = 105
 # Again, John Brower Minnoch comes to our rescue here. HIs body mass index
 # at the time of his death was 105 kg/m2. In terms of the lowest body mass index ever recorded
 # there was nly limited web search information that suggested 7.5 kg.m2 as the lowest ever.
@@ -51,3 +46,14 @@
 # the shortest woman in the world is Jyoti Kishanji Amge at 62.8 cm
 # lower limit to paternal and maternal height here therefore set arbitrarily at 50 cm
 # (this constant was added from the API server `schemas/request_validation_classes.py`)
+
+# These constants are used to determine the range of SDS values that are considered - see discussion in issue #32 in the rcpchgrowth-python repository
+# All previous hard-coded values have been replaced with these constants
+MINIMUM_HEIGHT_WEIGHT_OFC_ADVISORY_SDS = -4
+MAXIMUM_HEIGHT_WEIGHT_OFC_ADVISORY_SDS = 4
+MINIMUM_BMI_ADVISORY_SDS = -4
+MAXIMUM_BMI_ADVISORY_SDS = 4
+MINIMUM_HEIGHT_WEIGHT_OFC_ERROR_SDS = -8
+MAXIMUM_HEIGHT_WEIGHT_OFC_ERROR_SDS = 8
+MINIMUM_BMI_ERROR_SDS = -15
+MAXIMUM_BMI_ERROR_SDS = 15

rcpchgrowth/global_functions.py

@@ -210,20 +210,6 @@ def generate_centile(
 
     return centile_measurements
 
-
-def mid_parental_height(
-    height_paternal: float, height_maternal: float, sex: str
-) -> float:
-    """
-    Calculates mid-parental height for the child.
-    All units are in cm
-    """
-    if sex == MALE:
-        return (height_paternal + height_maternal + 13) / 2
-    else:
-        return (height_paternal + height_maternal - 13) / 2
-
-
 """
 *** PUBLIC FUNCTIONS THAT CONVERT BETWEEN CENTILE AND SDS
 """

rcpchgrowth/measurement.py

@@ -1,5 +1,6 @@
 # standard imports
 from datetime import date
+from typing import Literal
 
 # rcpch imports
 from .centile_bands import centile_band_for_centile
@@ -71,13 +72,6 @@ def __init__(
         # self.height_prediction_reference = height_prediction_reference
         self.events_text = events_text
 
-        # validate the measurement method to ensure that the observation value is within the expected range - TODO this will be changed to SDS-based cutoffs
-        try:
-            self.__validate_measurement_method(
-                measurement_method=measurement_method, observation_value=observation_value)
-            observation_value_error = None
-        except Exception as err:
-            observation_value_error = f"{err}"
 
         # the ages_object receives birth_data and measurement_dates objects
         self.ages_object = self.__calculate_ages(
@@ -87,6 +81,13 @@ def __init__(
             gestation_weeks=self.gestation_weeks,
             gestation_days=self.gestation_days)
 
+        # validate the measurement method to ensure that the observation value is within the expected range - changed to SDS-based cutoffs - issue #32
+        try:
+            self.__validate_measurement_method(
+                measurement_method=measurement_method, observation_value=observation_value, corrected_decimal_age=self.ages_object['measurement_dates']['corrected_decimal_age'], reference=reference, sex=sex)
+            observation_value_error = None
+        except Exception as err:
+            observation_value_error = f"{err}"
 
         # the calculate_measurements_object receives the child_observation_value and measurement_calculated_values objects
         self.calculated_measurements_object = self.sds_and_centile_for_measurement_method(
@@ -598,17 +599,31 @@ def __create_measurement_object(
     def __validate_measurement_method(
             self,
             measurement_method: str,
-            observation_value: float):
+            observation_value: float,
+            corrected_decimal_age: float,
+            sex: Literal["male", "female"],
+            reference: Literal['uk-who', 'turners-syndrome', 'trisomy-21', 'trisomy-21-aap', 'cdc'] = 'uk-who'):
 
-        # Private method which accepts a measurement_method (height, weight, bmi or ofc) and
+        # Private method which accepts a measurement_method (height, weight, bmi or ofc), reference and age as well as observation value
         # and returns True if valid
 
         is_valid = False
 
+        observation_value_z_score = None
+        if observation_value is not None:
+            observation_value_z_score = sds_for_measurement(
+                reference=reference, age=corrected_decimal_age, measurement_method=measurement_method, observation_value=observation_value, sex=sex)
+
         if measurement_method == 'bmi':
             if observation_value is None:
                 raise ValueError(
-                    'Missing observation_value for Body Mass Index. Please pass a Body Mass Index in kilograms per metre squared (kg/m2)')
+                    'Missing observation_value for Body Mass Index. Please pass a Body Mass Index in kilograms per metre squared (kg/m²)')
+            elif observation_value_z_score < MINIMUM_BMI_ERROR_SDS:
+                raise ValueError(
+                    f'The Body Mass Index measurement of {observation_value} kg/m² is below -15 SD and considered to be an error.')
+            elif observation_value_z_score > MAXIMUM_BMI_KGM2:
+                raise ValueError(
+                    f'The Body Mass Index measurement of {observation_value} kg/m² is above +15 SD and considered to be an error.')
             else:
                 is_valid = True
 
@@ -620,40 +635,39 @@ def __validate_measurement_method(
                 # most likely metres passed instead of cm.
                 raise ValueError(
                     'Height/length must be passed in cm, not metres')
-            elif observation_value < MINIMUM_LENGTH_CM:
-                # a baby is unlikely to be < 30 cm long - probably a data entry error
+            elif observation_value_z_score < MINIMUM_HEIGHT_WEIGHT_OFC_ERROR_SDS:
                 raise ValueError(
-                    f'The height/length you have entered is very low and likely to be an error. Are you sure you meant a height of {observation_value} centimetres?')
-            elif observation_value > MAXIMUM_HEIGHT_CM:
+                    f'The height/length of {observation_value} cm is below -8 SD and considered to be an error.')
+            elif observation_value_z_score > MAXIMUM_HEIGHT_WEIGHT_OFC_ERROR_SDS:
                 raise ValueError(
-                    f'The height/length you have entered is very high and likely to be an error. Are you sure you meant a height of {observation_value} centimetres?')
+                    f'The height/length of {observation_value} cm is above +8 SD and considered to be an error.')
             else:
                 is_valid = True
 
         elif measurement_method == 'weight':
             if observation_value is None:
                 raise ValueError(
                     'Missing observation_value for weight. Please pass a weight in kilograms.')
-            elif observation_value < MINIMUM_WEIGHT_KG:
+            elif observation_value_z_score < MINIMUM_HEIGHT_WEIGHT_OFC_ERROR_SDS:
                 raise ValueError(
-                    f'Error. {observation_value} kilograms is very low. Please pass an accurate weight in kilograms')
-            elif observation_value > MAXIMUM_WEIGHT_KG:
+                    f'The weight of {observation_value} kg is below -8 SD and considered to be an error.')
+            elif observation_value_z_score > MAXIMUM_HEIGHT_WEIGHT_OFC_ERROR_SDS:
                 # it is likely the weight is passed in grams, not kg.
                 raise ValueError(
-                    f'{observation_value} kilograms is very high. Weight must be passed in kilograms.')
+                    f'The weight of {observation_value} kg is above +8 SD and considered to be an error. Note that the weight should be supplied in kilograms.')
             else:
                 is_valid = True
 
         elif measurement_method == 'ofc':
             if observation_value is None:
                 raise ValueError(
                     'Missing observation_value for head circumference. Please pass a head circumference in centimetres.')
-            elif observation_value < MINIMUM_OFC_CM:
+            elif observation_value_z_score < MINIMUM_HEIGHT_WEIGHT_OFC_ERROR_SDS:
                 raise ValueError(
-                    f'Please check this value: {observation_value}. A head circumference less than 5 centimetres is likely an error. Please pass an accurate head circumference in centimetres.')
-            elif observation_value > MAXIMUM_OFC_CM:
+                    f'The head circumference of {observation_value} cm is below -8 SD and considered to be an error.')
+            elif observation_value_z_score > MAXIMUM_HEIGHT_WEIGHT_OFC_ERROR_SDS:
                 raise ValueError(
-                    f'Please check this value: {observation_value}. A head circumference > 150 centimetres is likely an error. Please pass an accurate head circumference in cm.')
+                    f'The head circumference of {observation_value} cm is above +8 SD and considered to be an error.')
             else:
                 is_valid = True
 

rcpchgrowth/mid_parental_height.py

@@ -26,7 +26,7 @@ def mid_parental_height_z(maternal_height, paternal_height, reference=UK_WHO):
     maternal_height_z = sds_for_measurement(reference=reference, age=20.0, measurement_method=HEIGHT, observation_value=maternal_height, sex=FEMALE)
     paternal_height_z = sds_for_measurement(reference=reference, age=20.0, measurement_method=HEIGHT, observation_value=paternal_height, sex=MALE)
 
-    # take the measn of the z-scores and apply the regression coefficient of 0.5 - simplifed: (MatHtz +PatHtz)/4
+    # take the means of the z-scores and apply the regression coefficient of 0.5 - simplifed: (MatHtz +PatHtz)/4
     mid_parental_height_z_score = (maternal_height_z + paternal_height_z) / 4.0
 
     return mid_parental_height_z_score

rcpchgrowth/tests/sds_age_validation_2021.json

@@ -51998,5 +51998,31 @@
     "observation_value": 53.9,
     "corrected_sds": -0.577332795,
     "chronological_sds": -0.628501058
+  },
+  {
+    "birth_date": "26/10/2015",
+    "observation_date": "01/09/2018",
+    "gestation_weeks": 40,
+    "gestation_days": 0,
+    "sex": "male",
+    "measurement_method": "height",
+    "observation_value": 180.0,
+    "chronological_age": 2.8501026694045173,
+    "corrected_sds": 23.499259393398773,
+    "corrected_age": 2.8501026694045173,
+    "chronological_sds": 23.499259393398773
+  },
+  {
+    "birth_date": "26/10/2015",
+    "observation_date": "01/09/2030",
+    "gestation_weeks": 40,
+    "gestation_days": 0,
+    "sex": "male",
+    "measurement_method": "bmi",
+    "observation_value": 7.0,
+    "chronological_age": 14.850102669404517,
+    "corrected_sds": -22.21786749424378,
+    "corrected_age": 14.850102669404517,
+    "chronological_sds": -22.21786749424378
   }
 ]

rcpchgrowth/tests/test_centile_band_for_centile.py

@@ -373,4 +373,12 @@ def test_centile_band_for_centile_eighty_five_percent():
     #on eighty-five-percent-centiles (85th, 98th, 99.9th, 99.99th)
     for centile in on_eighty_five_percent_centiles_bmi:
         sds = sds_for_centile(centile['centile'])
-        assert centile_band_for_centile(sds=sds, measurement_method="bmi", centile_format=EIGHTY_FIVE_PERCENT_CENTILES) == f"This body mass index measurement is on or near the {centile['text']} centile."
+        assert centile_band_for_centile(sds=sds, measurement_method="bmi", centile_format=EIGHTY_FIVE_PERCENT_CENTILES) == f"This body mass index measurement is on or near the {centile['text']} centile."
+
+def test_advisory_thresholds():
+    for measurement in measurements:
+        for centile in beyond_eighty_five_percent_thresholds:
+            sds = 5 # above 4 and less than 8
+            if measurement == BMI:
+                sds = 10
+            assert centile_band_for_centile(sds=sds, measurement_method=measurement, centile_format=COLE_TWO_THIRDS_SDS_NINE_CENTILES) == f"This {measurement_texts[measurements.index(measurement)]} measurement is well outside the normal range. Please check its accuracy."