AeroViz 0.1.3__py3-none-any.whl → 0.1.4__py3-none-any.whl

AeroViz/plot/templates/metal_heatmap.py

@@ -2,56 +2,154 @@ import matplotlib.pyplot as plt
 import numpy as np
 import seaborn as sns
 from matplotlib.pyplot import Figure, Axes
-from pandas import DataFrame, date_range
+from pandas import DataFrame, date_range, concat
 from sklearn.preprocessing import StandardScaler
 
 from AeroViz.plot.utils import *
 
+__all__ = ['metal_heatmaps', 'process_data_with_two_df']
 
-def process_data(df):
-	# detected_limit = 0.0001
-	df = df.where(df >= 0.0001, np.nan)
-	# Normalize the data
-	df = DataFrame(StandardScaler().fit_transform(df), index=df.index, columns=df.columns)
-	# Remove outliers
-	df = df[(np.abs(df) < 6)]
-	# Interpolate the missing values
-	df = df.interpolate(method='linear')
-	# Smooth the data
-	df = df.rolling(window=3, min_periods=1).mean()
 
-	return df
+def process_data(df, detected_limit=True, outlier_threshold=5, smoothing_window=6, fill_method='MDL'):
+    # Fill missing values based on the specified method
+    df = fill_missing_values(df.copy(), method=fill_method)
+
+    # Normalize the data
+    df = normalize_data(df)
+
+    # Remove outliers
+    df = remove_outliers(df, threshold=outlier_threshold)
+
+    # Interpolate missing values
+    df = df.interpolate(method='linear')
+
+    # Smooth the data
+    df = smooth_data(df, window=smoothing_window)
+
+    return df
+
+
+def process_data_with_two_df(df, df2, outlier_threshold=5, smoothing_window=6, fill_method='MDL'):
+    # Shift the first DataFrame by 30 minutes
+    df = df.shift(freq='30min')
+
+    # Fill missing values for both DataFrames
+    df = fill_missing_values(df.copy(), method=fill_method)
+    df2 = fill_missing_values(df2.copy(), method=fill_method)
+
+    # Normalize both DataFrames together
+    df, df2 = normalize_and_split(df, df2)
+
+    # Shift the first DataFrame back by 30 minutes
+    df = df.shift(freq='-30min')
+
+    # Remove outliers for both DataFrames
+    df = remove_outliers(df, threshold=outlier_threshold)
+    df2 = remove_outliers(df2, threshold=outlier_threshold)
+
+    # Interpolate missing values
+    df = df.interpolate(method='linear')
+    df2 = df2.interpolate(method='linear')
+
+    # Smooth the data
+    df = smooth_data(df, window=smoothing_window)
+    df2 = smooth_data(df2, window=smoothing_window)
+
+    return df, df2
+
+
+def fill_missing_values(df, method='MDL'):
+    if method == 'interpolate':
+        return df.interpolate(method='linear')
+    else:
+        return fill_with_mdl(df)
+
+
+def fill_with_mdl(df):
+    # Minimum detection limit (MDL) dictionary
+    MDL = {
+        'Al': 100, 'Si': 18, 'P': 5.2, 'S': 3.2,
+        'Cl': 1.7, 'K': 1.2, 'Ca': 0.3, 'Ti': 1.6,
+        'V': 0.12, 'Cr': 0.12, 'Mn': 0.14, 'Fe': 0.17,
+        'Co': 0.14, 'Ni': 0.096, 'Cu': 0.079, 'Zn': 0.067,
+        'Ga': 0.059, 'Ge': 0.056, 'As': 0.063, 'Se': 0.081,
+        'Br': 0.1, 'Rb': 0.19, 'Sr': 0.22, 'Y': 0.28,
+        'Zr': 0.33, 'Nb': 0.41, 'Mo': 0.48, 'Pd': 2.2,
+        'Ag': 1.9, 'Cd': 2.5, 'In': 3.1, 'Sn': 4.1,
+        'Sb': 5.2, 'Te': 0.6, 'I': 0.49, 'Cs': 0.37,
+        'Ba': 0.39, 'La': 0.36, 'Ce': 0.3, 'Pt': 0.12,
+        'Au': 0.1, 'Hg': 0.12, 'Tl': 0.12, 'Pb': 0.13,
+        'Bi': 0.13
+    }
+
+    # Replace values below MDL with 5/6 * MDL
+    for element, threshold in MDL.items():
+        if element in df.columns:
+            df.loc[:, element] = df[element].where(df[element] >= threshold, 5 / 6 * threshold)
+
+    return df
+
+
+def normalize_data(df):
+    # Standardize the data (z-score normalization)
+    return DataFrame(StandardScaler().fit_transform(df), index=df.index, columns=df.columns)
+
+
+def remove_outliers(df, threshold=5):
+    # Remove rows where any column value exceeds the threshold
+    return df[(np.abs(df) < threshold)]
+
+
+def smooth_data(df, window=6):
+    # Apply rolling mean to smooth the data
+    return df.rolling(window=window, min_periods=1).mean()
+
+
+def normalize_and_split(df, df2):
+    # Concatenate DataFrames for combined normalization
+    combined_df = concat([df, df2])
+    normalized_combined_df = normalize_data(combined_df)
+
+    # Split the normalized DataFrame back into df and df2
+    df = normalized_combined_df.loc[df.index]
+    df2 = normalized_combined_df.loc[df2.index]
+
+    return df, df2
 
 
 @set_figure(figsize=(12, 3), fs=6)
-def metal_heatmaps(df, major_freq='24h', minor_freq='12h', ax: Axes | None = None, title=None, **kwargs
-				   ) -> tuple[Figure, Axes]:
-	items = ['Al', 'Zr', 'Si', 'Ca', 'Ti', 'Mn', 'Fe', 'V', 'Cl', 'K',
-			 'Sr', 'Ba', 'Bi', 'Pd', 'Sn', 'Cr', 'W', 'Cu', 'Zn',
-			 'As', 'Co', 'Se', 'Br', 'Cd', 'Sb', 'In', 'Pb', 'Ni']
+def metal_heatmaps(df,
+                   process=True,
+                   major_freq='24h',
+                   minor_freq='12h',
+                   cmap='jet',
+                   ax: Axes | None = None,
+                   **kwargs
+                   ) -> tuple[Figure, Axes]:
+    if process:
+        df = process_data(df)
 
-	df = df[items]
+    fig, ax = plt.subplots(**kwargs.get('fig_kws', {})) if ax is None else (ax.get_figure(), ax)
 
-	fig, ax = plt.subplots(**kwargs.get('fig_kws', {})) if ax is None else (ax.get_figure(), ax)
+    sns.heatmap(df.T, vmin=None, vmax=3, cmap=cmap, xticklabels=False, yticklabels=True,
+                cbar_kws={'label': 'Z score', "pad": 0.02})
+    ax.grid(color='gray', linestyle='-', linewidth=0.3)
 
-	sns.heatmap(df.T, vmax=3, cmap="jet", xticklabels=False, yticklabels=True,
-				cbar_kws={'label': 'Z score'})
-	ax.grid(color='gray', linestyle='-', linewidth=0.3)
-	# Set x-tick positions and labels
-	major_tick = date_range(start=df.index[0], end=df.index[-1], freq=major_freq)
-	minor_tick = date_range(start=df.index[0], end=df.index[-1], freq=minor_freq)
+    # Set x-tick positions and labels
+    major_tick = date_range(start=df.index[0], end=df.index[-1], freq=major_freq)
+    minor_tick = date_range(start=df.index[0], end=df.index[-1], freq=minor_freq)
 
-	# Set the major and minor ticks
-	ax.set_xticks(ticks=[df.index.get_loc(t) for t in major_tick])
-	ax.set_xticks(ticks=[df.index.get_loc(t) for t in minor_tick], minor=True)
-	ax.set_xticklabels(major_tick.strftime('%F'))
-	ax.tick_params(axis='y', rotation=0)
+    # Set the major and minor ticks
+    ax.set_xticks(ticks=[df.index.get_loc(t) for t in major_tick])
+    ax.set_xticks(ticks=[df.index.get_loc(t) for t in minor_tick], minor=True)
+    ax.set_xticklabels(major_tick.strftime('%F'))
+    ax.tick_params(axis='y', rotation=0)
 
-	ax.set_title(f"{title}", fontsize=10)
-	ax.set(xlabel='',
-		   ylabel='',
-		   )
+    ax.set(xlabel='',
+           ylabel='',
+           title=kwargs.get('title', None)
+           )
 
-	plt.show()
+    plt.show()
 
-	return fig, ax
+    return fig, ax

AeroViz/plot/timeseries/__init__.py

@@ -1 +1,2 @@
+from .template import *
 from .timeseries import *

AeroViz/plot/timeseries/template.py

@@ -0,0 +1,47 @@
+import matplotlib.pyplot as plt
+from matplotlib.pyplot import Figure, Axes
+from pandas import DataFrame
+
+from AeroViz.plot.timeseries import timeseries
+
+
+def timeseries_template(df: DataFrame) -> tuple[Figure, Axes]:
+    fig, ax = plt.subplots(5, 1, figsize=(len(df.index) * 0.01, 4))
+    (ax1, ax2, ax3, ax4, ax5) = ax
+
+    timeseries(df,
+               y=['Extinction', 'Scattering', 'Absorption'],
+               rolling=30,
+               ax=ax1,
+               ylabel='Coefficient',
+               ylim=[0., None],
+               set_xaxis_visible=False,
+               legend_ncol=3,
+               )
+
+    # Temp, RH
+    timeseries(df,
+               y='AT',
+               y2='RH',
+               rolling=30,
+               ax=ax2,
+               ax_plot_kws=dict(color='r'),
+               ax2_plot_kws=dict(color='b'),
+               ylim=[10, 30],
+               ylim2=[20, 100],
+               set_xaxis_visible=False,
+               legend_ncol=2,
+               )
+
+    timeseries(df, y='WS', color='WD', style='scatter', ax=ax3, scatter_kws=dict(cmap='hsv'),
+               cbar_kws=dict(ticks=[0, 90, 180, 270, 360]),
+               ylim=[0, None], set_xaxis_visible=False)
+
+    timeseries(df, y='VC', color='PBLH', style='bar', ax=ax4, bar_kws=dict(cmap='Blues'), set_xaxis_visible=False,
+               ylim=[0, 5000])
+
+    timeseries(df, y='PM25', color='PM1/PM25', style='scatter', ax=ax5, ylim=[0, None])
+
+    plt.show()
+
+    return fig, ax