growthcharts 0.1.0__py3-none-any.whl

growthcharts/__init__.py

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+# growthcharts/__init__.py
+
+from .patient import Patient
+from .infant import Infant
+from .child import Child
+
+__all__ = ["Patient", "Infant", "Child"]

growthcharts/child.py

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+import pandas as pd
+import matplotlib.pyplot as plt
+import math
+from scipy.stats import norm
+
+from .patient import Patient
+from pathlib import Path
+
+
+DATA_PATH = Path(__file__).parent / "data"
+
+
+class Child(Patient):
+    """
+    Represents a child patient (2–20 years) and provides growth chart analysis
+    and visualization based on CDC growth standards.
+
+    This class extends the Patient class and adds functionality for:
+    - Weight-for-age
+    - Length-for-age
+    - BMI-for-age
+
+    Supports plotting percentile curves and calculating Z-scores and percentiles
+    using the LMS method.
+    """
+
+    # Child 2 to 20 database
+    df_wtage = pd.read_csv(DATA_PATH /'wtage.csv', dtype={'Sex': str})
+    df_lenage = pd.read_csv(DATA_PATH /'lenage.csv', dtype={'Sex': str})
+    df_bmiage = pd.read_csv(DATA_PATH /'bmiage.csv', dtype={'Sex': str})
+
+    def __init__(self, sex: str, age: int, wt: float = None, length: float = None):
+        """
+        Initialize a Child object.
+
+        At least one anthropometric measurement must be provided.
+
+        Args:
+            sex (str): Child sex.
+            age (int): Age in months.
+            wt (float, optional): Weight in kilograms.
+            length (float, optional): Length/height in centimeters.
+
+        Raises:
+            ValueError: If both wt and length are None.
+        """
+        if wt is None and length is None:
+            raise ValueError("At least wt or length must be provided")
+
+        super().__init__(sex, age, wt, length)
+
+    def plot_wtage(self, title=None):
+        """
+        Plot weight-for-age growth chart with patient's measurement.
+
+        Args:
+            title (str, optional): Plot title.
+        """
+        df = self.df_wtage
+
+        self.sex = str(self.sex).lower()
+        if self.sex in ['m', '1']:
+            self.sex = '1'
+        elif self.sex in ['f', '2']:
+            self.sex = '2'
+        else:
+            raise TypeError('define sex as m or f')
+
+        data = df[df['Sex'] == self.sex]
+
+        plt.figure(figsize=(12, 7))
+        for i, col in enumerate(self.agecolumns[1:]):
+            if i in self.highlight_indices:
+                plt.plot(data['Agemos'], data[col],
+                         color='gray', linewidth=2, label=f'{title} {col}')
+            else:
+                plt.plot(data['Agemos'], data[col],
+                         color='lightgray', linewidth=1)
+
+        if self.wt is not None:
+            plt.scatter(self.age, self.wt, color='red', s=100, zorder=5)
+
+        plt.title(title)
+        plt.xlabel("age(month)")
+        plt.ylabel("Weight(Kg)")
+        plt.grid(True)
+        plt.legend()
+        plt.show()
+
+    def plot_lenage(self, title=None):
+        """
+        Plot length-for-age growth chart with patient's measurement.
+
+        Args:
+            title (str, optional): Plot title.
+        """
+        df = self.df_lenage
+
+        self.sex = str(self.sex).lower()
+        if self.sex in ['m', '1']:
+            self.sex = '1'
+        elif self.sex in ['f', '2']:
+            self.sex = '2'
+        else:
+            raise TypeError('define sex as m or f')
+
+        data = df[df['Sex'] == self.sex]
+
+        plt.figure(figsize=(14, 10))
+        for i, col in enumerate(self.agecolumns[1:]):
+            if i in self.highlight_indices:
+                plt.plot(data['Agemos'], data[col],
+                         color='gray', linewidth=2, label=f'{title} {col}')
+            else:
+                plt.plot(data['Agemos'], data[col],
+                         color='lightgray', linewidth=1)
+
+        if self.length is not None:
+            plt.scatter(self.age, self.length, color='red', s=100, zorder=5)
+
+        plt.title(title)
+        plt.xlabel("age(month)")
+        plt.ylabel("Length(cm)")
+        plt.grid(True)
+        plt.legend()
+        plt.show()
+
+    def plot_bmiage(self, title=None):
+        """
+        Plot BMI-for-age growth chart with patient's measurement.
+
+        Args:
+            title (str, optional): Plot title.
+        """
+        df = self.df_bmiage
+
+        self.sex = str(self.sex).lower()
+        if self.sex in ['m', '1']:
+            self.sex = '1'
+        elif self.sex in ['f', '2']:
+            self.sex = '2'
+        else:
+            raise TypeError('define sex as m or f')
+
+        data = df[df['Sex'] == self.sex]
+
+        plt.figure(figsize=(12, 7))
+        for i, col in enumerate(self.agecolumns[1:]):
+            if i in self.highlight_indices:
+                plt.plot(data['Agemos'], data[col],
+                         color='gray', linewidth=2, label=f'{title} {col}')
+            else:
+                plt.plot(data['Agemos'], data[col],
+                         color='lightgray', linewidth=1)
+
+        if self.wt is not None and self.length is not None and self.length > 0:
+            plt.scatter(self.age, self.bmi, color='red', s=100, zorder=5)
+
+        plt.title(title)
+        plt.xlabel("age(month)")
+        plt.ylabel("BMI")
+        plt.grid(True)
+        plt.legend()
+        plt.show()
+
+    def analyze_wtage(self):
+        """
+        Analyze weight-for-age using LMS method.
+
+        Returns:
+            dict: Z-score and percentile.
+        """
+        df = self.df_wtage
+        self.sex = str(self.sex).lower()
+        if self.sex in ['m', '1']:
+            self.sex = '1'
+        elif self.sex in ['f', '2']:
+            self.sex = '2'
+        else:
+            raise TypeError('define sex as m or f')
+
+        df2 = df[df['Sex'] == self.sex]
+        row = df2.iloc[(df2['Agemos'] - self.age).abs().argsort()[:1]]
+
+        L = float(row['L'].values[0])
+        M = float(row['M'].values[0])
+        S = float(row['S'].values[0])
+
+        if L != 0:
+            z = ((self.wt / M) ** L - 1) / (L * S)
+        else:
+            z = math.log(self.wt / M) / S
+
+        percentile = norm.cdf(z) * 100
+
+        return {
+            "Z": round(z, 2),
+            "Percentile": round(percentile, 2)
+        }
+
+    def analyze_lenage(self):
+        """
+        Analyze length-for-age using LMS method.
+
+        Returns:
+            dict: Z-score and percentile.
+        """
+        df = self.df_lenage
+        self.sex = str(self.sex).lower()
+        if self.sex in ['m', '1']:
+            self.sex = '1'
+        elif self.sex in ['f', '2']:
+            self.sex = '2'
+        else:
+            raise TypeError('define sex as m or f')
+
+        df2 = df[df['Sex'] == self.sex]
+        row = df2.iloc[(df2['Agemos'] - self.age).abs().argsort()[:1]]
+
+        L = float(row['L'].values[0])
+        M = float(row['M'].values[0])
+        S = float(row['S'].values[0])
+
+        if L != 0:
+            z = ((self.length / M) ** L - 1) / (L * S)
+        else:
+            z = math.log(self.length / M) / S
+
+        percentile = norm.cdf(z) * 100
+
+        return {
+            "Z": round(z, 2),
+            "Percentile": round(percentile, 2)
+        }
+
+    def analyze_bmiage(self):
+        """
+        Analyze BMI-for-age using LMS method.
+
+        Returns:
+            dict: Z-score and percentile.
+        """
+        df = self.df_bmiage
+        self.sex = str(self.sex).lower()
+        if self.sex in ['m', '1']:
+            self.sex = '1'
+        elif self.sex in ['f', '2']:
+            self.sex = '2'
+        else:
+            raise TypeError('define sex as m or f')
+
+        df2 = df[df['Sex'] == self.sex]
+        row = df2.iloc[(df2['Agemos'] - self.age).abs().argsort()[:1]]
+
+        L = float(row['L'].values[0])
+        M = float(row['M'].values[0])
+        S = float(row['S'].values[0])
+
+        if L != 0:
+            z = ((self.bmi / M) ** L - 1) / (L * S)
+        else:
+            z = math.log(self.bmi / M) / S
+
+        percentile = norm.cdf(z) * 100
+
+        return {
+            "Z": round(z, 2),
+            "Percentile": round(percentile, 2)
+        }