Merge pull request #54 from rcpch/eatyourpeas/issue41

who

Author: eatyourpeas

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.2.8
+current_version = 4.3.0
 tag = False
 commit = True
 

Dockerfile

@@ -1,7 +1,20 @@
-FROM python:3.12-bookworm
+FROM python:3.12
 
+# Set the working directory in the container
+WORKDIR /app
+
+# Copy the requirements file into the container
 COPY requirements.txt .
 
-RUN pip install -r requirements.txt
+# Create a virtual environment
+RUN python -m venv /app/venv
+
+# Upgrade pip and install the dependencies in the virtual environment
+RUN /app/venv/bin/pip install --upgrade pip
+RUN /app/venv/bin/pip install -r requirements.txt
 
+# Copy the rest of the application code
 COPY . .
+
+# Set the entrypoint to use the virtual environment's Python interpreter
+CMD ["python3"]

docker-compose.yml

@@ -1,5 +1,4 @@
-# NOTE The below is the Docker Compose specification version NOT the Python version:
-version: "3.8"
+version: "3.12"
 
 services:
   rcpchgrowth-python:
@@ -9,5 +8,4 @@ services:
     working_dir: /app
     tty: true # Allocate a pseudo-TTY
     stdin_open: true # Keep stdin open
-    command: |
-      pytest
+    container_name: rcpchgrowth-python

rcpchgrowth/age_advice_strings.py

@@ -1,4 +1,4 @@
-from rcpchgrowth.constants import CDC
+from rcpchgrowth.constants import CDC, WHO
 
 def comment_prematurity_correction(
     chronological_decimal_age: float,
@@ -17,7 +17,7 @@ def comment_prematurity_correction(
             lay_chronological_decimal_age_comment = "Your child was born on their due date."
             clinician_chronological_decimal_age_comment = "Born Term. No correction has been made for gestation."
             # These fields should only apply to CDC reference, since UK-WHO corrects for all gestations (and therefore corrected_decimal_age will never be equal to chronological_decimal_age if gestation_weeks is not 40)
-            if gestation_weeks < 42 and reference == CDC:
+            if gestation_weeks < 42 and (reference == CDC or reference == WHO):
                 if gestation_weeks < 37:
                     lay_chronological_decimal_age_comment = f"Your child was born at {gestation_weeks}+{gestation_days} weeks gestation. No correction is made for this beyond 2 years of age."
                     clinician_chronological_decimal_age_comment =f"Born preterm at {gestation_weeks}+{gestation_days} weeks gestation. No correction is made for this beyond 2 years of age."

rcpchgrowth/chart_functions.py

@@ -5,6 +5,7 @@
 from .trisomy_21_aap import select_reference_data_for_trisomy_21_aap
 from .turner import select_reference_data_for_turner
 from .uk_who import select_reference_data_for_uk_who_chart
+from .who import who_reference, select_reference_data_for_who_chart
 from .constants.reference_constants import (
     CDC_REFERENCES, 
     CDC,
@@ -25,6 +26,8 @@
     TURNERS, 
     UK_WHO, 
     UK_WHO_REFERENCES, 
+    WHO,
+    WHO_REFERENCES
 )
 
 """
@@ -70,6 +73,12 @@ def create_chart(
             sex=sex,
             centile_format=centile_format,
             is_sds=is_sds)
+    elif reference == WHO:
+        return create_who_chart(
+            measurement_method=measurement_method,
+            sex=sex,
+            centile_format=centile_format,
+            is_sds=is_sds)
     else:
         print("No reference data returned. Is there a spelling mistake in your reference?")
 
@@ -109,7 +118,7 @@ def generate_custom_sds_line(
                     centile=custom_centile
                 )
             except:
-                print("Could not generate centile data.")
+                print("Could not generate centile data for UK-WHO.")
                 centile_data=[]
         # all data can now be tagged by reference_name and added to reference_data
         reference_data.append({reference: centile_data})
@@ -131,7 +140,30 @@ def generate_custom_sds_line(
                     centile=custom_centile
                 )
             except:
-                print(f"Could not generate SDS centile data.")
+                print(f"Could not generate SDS centile data for {CDC}.")
+                centile_data=[]
+        # all data can now be tagged by reference_name and added to reference_data
+        reference_data.append({reference: centile_data})
+    elif reference == WHO:
+        for reference_index, reference in enumerate(WHO_REFERENCES):
+            # the centile reference data
+            lms_array_for_measurement=select_reference_data_for_who_chart(
+                who_reference_name=reference, 
+                measurement_method=measurement_method,
+                sex=sex
+            )
+            centile_data=[]
+            try:
+                centile_data= build_centile_object(
+                    reference=WHO,
+                    measurement_method=measurement_method,
+                    sex=sex,
+                    lms_array_for_measurement=lms_array_for_measurement,
+                    z=custom_sds,
+                    centile=custom_centile
+                )
+            except:
+                print(f"Could not generate SDS centile data for WHO.")
                 centile_data=[]
         # all data can now be tagged by reference_name and added to reference_data
         reference_data.append({reference: centile_data})
@@ -219,6 +251,8 @@ def select_reference_lms_data(reference: str, measurement_method: str, sex: str)
         lms_array_for_measurement=select_reference_data_for_trisomy_21(measurement_method=measurement_method, sex=sex)
     elif reference == CDC:
         lms_array_for_measurement=select_reference_data_for_cdc_chart(measurement_method=measurement_method, sex=sex)
+    elif reference == WHO:
+        lms_array_for_measurement=select_reference_data_for_who_chart(measurement_method=measurement_method, sex=sex)
     else: 
         raise Exception("No data has been selected!")
 
@@ -907,7 +941,163 @@ def create_trisomy_21_aap_chart(measurement_method: str, sex: str, centile_forma
     ]
     """
 
-# Private functions
+def create_who_chart(
+        measurement_method: str, 
+        sex: str, 
+        centile_format: Union[str, list] = COLE_TWO_THIRDS_SDS_NINE_CENTILES, 
+        is_sds = False
+    ):
+
+    # user selects which centile collection they want, for sex and measurement_method
+    # If the Cole method is selected, conversion between centile and SDS
+    # is different as SDS is rounded to the nearest 2/3
+    # Cole method selection is stored in the cole_method flag.
+    # If no parameter is passed, default is the Cole method
+    # Alternatively it is possible to pass a custom list of values - if the is_sds flag is False (default) these are centiles
+    
+    centile_sds_collection = []
+    cole_method = False
+
+    if (type(centile_format) is list):
+        # a custom list of centiles was provided
+        centile_sds_collection = centile_format
+    else:
+        # a standard centile collection was selected
+        centile_sds_collection = select_centile_format(centile_format)
+        is_sds=False
+
+    ##
+    # iterate through the 3 references that make up CDC (Fenton, WHO, CDC  itself)
+    # There will be a list for each one
+    ##
+
+    # all data for a given reference are stored here: this is returned to the user
+    reference_data = []
+
+    for reference_index, reference_name in enumerate(WHO_REFERENCES):
+        sex_list: dict = {}  # all the data for a given sex are stored here
+        # For each reference we have 2 sexes
+        # for sex_index, sex in enumerate(SEXES):
+        # For each sex we have 4 measurement_methods
+
+        measurements: dict = {}  # all the data for a given measurement_method are stored here
+
+        # for measurement_index, measurement_method in enumerate(MEASUREMENT_METHODS):
+        # for every measurement method we have as many centiles
+        # as have been requested
+
+        centiles = []  # all generated centiles for a selected centile collection are stored here
+
+        default_youngest_reference = False
+        if reference_index == 1: # WHO children
+            default_youngest_reference = True
+
+        # the centile reference data
+        try:
+            lms_array_for_measurement=select_reference_data_for_who_chart(
+                who_reference_name=reference_name, 
+                measurement_method=measurement_method, 
+                 sex=sex, 
+                 default_youngest_reference=default_youngest_reference)
+        except:
+            lms_array_for_measurement = []
+
+        for centile_index, centile_sds in enumerate(centile_sds_collection):
+            # we must create a z for each requested centile
+            # 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) # a centile was provided, so convert to z
+                centile_value=centile_sds # store the original centile value 
+            else:
+                if (is_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) # a centile was provided, so convert to z
+                    centile_value=centile_sds # store the original centile value 
+            centile_data = []
+
+            try:
+                # Generate a centile. there will be nine of these if Cole method selected.
+                # Some data does not exist at all ages, so any error reflects missing data.
+                # If this happens, an empty list is returned.
+                centile_data = generate_centile(
+                    z=z,
+                    centile=centile_value,
+                    measurement_method=measurement_method,
+                    sex=sex,
+                    lms_array_for_measurement=lms_array_for_measurement,
+                    reference=WHO,
+                    is_sds=is_sds,
+                    default_youngest_reference=default_youngest_reference
+                )
+            except LookupError as e:
+                print(f"Not possible to generate centile data for WHO {measurement_method} in {sex}s. {e}")
+                centile_data=None
+            # Store this centile for a given measurement
+            
+            centiles.append({"sds": round(z * 100) / 100,
+                        "centile": centile_value, "data": centile_data})
+
+        # this is the end of the centile_collection for loop
+        # All the centiles for this measurement, sex and reference are added to the measurements list
+        measurements.update({measurement_method: centiles})
+
+        # this is the end of the measurement_methods loop
+        # All data for all measurement_methods for this sex are added to the sex_list list
+
+        sex_list.update({sex: measurements})
+
+        # all data can now be tagged by reference_name and added to reference_data
+        reference_data.append({reference_name: sex_list})
+
+    # returns a list of 4 references, each containing 2 lists for each sex,
+    # each sex in turn containing 4 datasets for each measurement_method
+    return reference_data
+
+    """
+    # return object structure
+    [ cdc_infant: {
+        male: {
+            height: [
+                {
+                    sds: -2.667,
+                    centile: 0.4
+                    data: [{l: , x: , y: }, ....]
+                }
+            ],
+            weight: [...],
+            bmi: [...],
+            ofc: [...]
+        },
+        female {...}
+    },
+    cdc_child: {
+        male: {
+            height: [
+                {
+                    sds: -2.667,
+                    centile: 0.4
+                    data: [{l: , x: , y: }, ....]
+                }
+            ],
+            weight: [...],
+            bmi: [...],
+            ofc: [...]
+            },
+        female {...}
+        }
+    ]
+    """
+        
+
+
 def select_centile_format(centile_format: str):
     """
     Select the centile format

rcpchgrowth/constants/age_constants.py

@@ -7,10 +7,14 @@
 FORTY_TWO_WEEKS_GESTATION = ((42 * 7) - (40 * 7)) / 365.25  # 42 weeks as decimal age
 TWENTY_THREE_WEEKS_GESTATION = ((23 * 7) - (40 * 7)) / 365.25  # 23 weeks as decimal age
 FIFTY_WEEKS_GESTATION = ((50 * 7) - (40 * 7)) / 365.25  # 50 weeks as decimal age
+ZERO_YEARS = 0.0
 TWO_YEARS = 2.0
 THREE_YEARS = 3.0
+FIVE_YEARS = 5.0
+TEN_YEARS = 10.0
 SEVENTEEN_YEARS = 17.0
 EIGHTEEN_YEARS = 18.0
+NINETEEN_YEARS = 19.0
 TWENTY_YEARS = 20.0
 TERM_WEEKS = 40
 LOWER_THRESHOLD_PRETERM_REFERENCE_WEEKS = 23

rcpchgrowth/constants/reference_constants.py

@@ -27,6 +27,18 @@
 FENTON = "fenton" # Fenton is the reference name for preterm infants
 CDC_REFERENCES = [FENTON, CDC_INFANT, CDC_CHILD] # CDC references
 
+# WHO constants
+WHO = "who" # WHO is the overarching reference
+WHO_2006_INFANT = "who_2006_infant" # WHO 2006 infant is the reference name for children 0-2 years
+WHO_2006_CHILD = "who_2006_child" # WHO 2006 child is the reference name for children 2-5 years
+WHO_2007_CHILD = "who_2007_child" # WHO 2007 child is the reference name for children 5-19 years
+WHO_REFERENCES = [WHO_2006_INFANT, WHO_2006_CHILD, WHO_2007_CHILD] # WHO references
+
+WHO_2006_REFERENCE_LOWER_THRESHOLD = ((42 * 7) - (40 * 7)) / 365.25  # 42 weeks as decimal age  # 2 weeks as decimal age
+WHO_2006_REFERENCE_UPPER_THRESHOLD = 5.0  # 5 years as decimal age
+WHO_2007_REFERENCE_LOWER_THRESHOLD = 5.0  # 5 years as decimal age
+WHO_2007_REFERENCE_UPPER_THRESHOLD = 19.0  # 19 years as decimal age
+
 # 23 weeks is the lowest decimal age available on the UK90 charts
 UK90_REFERENCE_LOWER_THRESHOLD = (
     (23 * 7) - (40 * 7)
@@ -64,7 +76,7 @@
 WEIGHT = "weight"
 HEAD_CIRCUMFERENCE = "ofc"
 BMI = "bmi"
-REFERENCES = [UK_WHO, TRISOMY_21, TURNERS]
+REFERENCES = [UK_WHO, TRISOMY_21, TRISOMY_21_AAP, TURNERS, CDC, WHO]
 SEXES = [MALE, FEMALE]
 MEASUREMENT_METHODS = [HEIGHT, WEIGHT, HEAD_CIRCUMFERENCE, BMI]