Modify prep_df_nn - remove mineral filter, create missing columns wit…

…h UserWarning
sarahshi · May 15, 2024 · 3ba10bd · 3ba10bd
1 parent 423f799
commit 3ba10bd
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Showing 7 changed files with 20,409 additions and 2,812 deletions.
diff --git a/DF.csv b/DF.csv
diff --git a/mineralML_colab.ipynb b/mineralML_colab.ipynb
@@ -85,7 +85,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Read in the CSV and prepare data for analysis (fill in nans, limit to trained igneous minerals)"
+    "## Read in the CSV and prepare data for analysis (fill in nans, limit to trained igneous minerals). This CSV is an example file of minerals from LEPR. "
    ]
   },
   {

diff --git a/src/mineralML/__init__.py b/src/mineralML/__init__.py
@@ -1,6 +1,6 @@
-# %% 
+# %%
 
-__author__ = 'Sarah Shi'
+__author__ = "Sarah Shi"
 
 import os
 import copy

diff --git a/src/mineralML/confusion_matrix.py b/src/mineralML/confusion_matrix.py
@@ -1,4 +1,4 @@
-# %% 
+# %%
 
 import numpy as np
 import pandas as pd
@@ -8,12 +8,21 @@
 import matplotlib
 from matplotlib import pyplot as plt
 
-# %% 
-
-def pp_matrix(df_cm, annot=True, cmap="BuGn", fmt=".2f",
-    fz=12, lw=0.5, cbar=False, figsize=[10.5, 10.5],
-    show_null_values=0, pred_val_axis="x"):  #, savefig = None,):
-
+# %%
+
+
+def pp_matrix(
+    df_cm,
+    annot=True,
+    cmap="BuGn",
+    fmt=".2f",
+    fz=12,
+    lw=0.5,
+    cbar=False,
+    figsize=[10.5, 10.5],
+    show_null_values=0,
+    pred_val_axis="x",
+):  # , savefig = None,):
     """
 
     Creates and displays a confusion matrix visualization using Seaborn's heatmap function.
@@ -59,11 +68,21 @@ def pp_matrix(df_cm, annot=True, cmap="BuGn", fmt=".2f",
     ax1 = fig1.gca()  # Get Current Axis
     ax1.cla()  # clear existing plot
 
-    ax = sns.heatmap(df_cm, annot=annot, annot_kws={"size": fz}, linewidths=lw, ax=ax1, cbar=cbar, cmap=cmap, linecolor="w", fmt=fmt,)
+    ax = sns.heatmap(
+        df_cm,
+        annot=annot,
+        annot_kws={"size": fz},
+        linewidths=lw,
+        ax=ax1,
+        cbar=cbar,
+        cmap=cmap,
+        linecolor="w",
+        fmt=fmt,
+    )
 
     # set ticklabels rotation
-    ax.set_xticklabels(ax.get_xticklabels(), rotation=45, fontsize=13, ha='right')
-    ax.set_yticklabels(ax.get_yticklabels(), rotation=35, fontsize=13, va='top')
+    ax.set_xticklabels(ax.get_xticklabels(), rotation=45, fontsize=13, ha="right")
+    ax.set_yticklabels(ax.get_yticklabels(), rotation=35, fontsize=13, va="top")
 
     # Turn off all the ticks
     for t in ax.xaxis.get_major_ticks():
@@ -89,7 +108,9 @@ def pp_matrix(df_cm, annot=True, cmap="BuGn", fmt=".2f",
         posi += 1
 
         # set text
-        txt_res = config_cell_text_and_colors(array_df, lin, col, t, facecolors, posi, fz, fmt, show_null_values)
+        txt_res = config_cell_text_and_colors(
+            array_df, lin, col, t, facecolors, posi, fz, fmt, show_null_values
+        )
 
         text_add.extend(txt_res[0])
         text_del.extend(txt_res[1])
@@ -106,12 +127,11 @@ def pp_matrix(df_cm, annot=True, cmap="BuGn", fmt=".2f",
     ax.set_ylabel(ylbl)
     plt.tight_layout()  # set layout slim
 
-    # if savefig != None: 
+    # if savefig != None:
     #     plt.savefig(savefig + '.pdf')
 
 
 def insert_totals(df_cm):
-
     """
 
     Inserts total sums for each row and column into the confusion matrix DataFrame.
@@ -125,32 +145,35 @@ def insert_totals(df_cm):
 
     Returns:
         None: The function modifies the DataFrame in place.
-    
+
     Note:
         If 'sum_row' or 'sum_col' already exist in the DataFrame, they will be recalculated.
 
     """
 
     # Check if 'sum_row' and 'sum_col' already exist and remove them if they do
-    if 'sum_row' in df_cm.columns:
-        df_cm.drop('sum_row', axis=1, inplace=True)
-    if 'sum_col' in df_cm.index:
-        df_cm.drop('sum_col', axis=0, inplace=True)
-    
+    if "sum_row" in df_cm.columns:
+        df_cm.drop("sum_row", axis=1, inplace=True)
+    if "sum_col" in df_cm.index:
+        df_cm.drop("sum_col", axis=0, inplace=True)
+
     # Calculate the sum of each column to create 'sum_row'
     sum_col = df_cm.sum(axis=0).astype(int)  # sum columns
     sum_lin = df_cm.sum(axis=1).astype(int)  # sum rows
-
-    # Add 'sum_row' and 'sum_col' to the dataframe
-    df_cm['sum_row'] = sum_lin
-    df_cm.loc['sum_col'] = sum_col
-    df_cm.at['sum_col', 'sum_row'] = sum_lin.sum()  # Set the bottom right cell to the grand total
 
+    # Add 'sum_row' and 'sum_col' to the dataframe
+    df_cm["sum_row"] = sum_lin
+    df_cm.loc["sum_col"] = sum_col
+    df_cm.at[
+        "sum_col", "sum_row"
+    ] = sum_lin.sum()  # Set the bottom right cell to the grand total
 
-def config_cell_text_and_colors(array_df, lin, col, oText, facecolors, posi, fz, fmt, show_null_values=0):
 
+def config_cell_text_and_colors(
+    array_df, lin, col, oText, facecolors, posi, fz, fmt, show_null_values=0
+):
     """
-    
+
     Configures cell text and colors for confusion matrix visualization.
 
     Adjusts the text and background colors of cells in the confusion matrix based on their values.
@@ -173,7 +196,7 @@ def config_cell_text_and_colors(array_df, lin, col, oText, facecolors, posi, fz,
     Note:
         The function modifies text and background colors based on the value in each cell.
 
-            """
+    """
 
     import matplotlib.font_manager as fm
 
@@ -208,12 +231,18 @@ def config_cell_text_and_colors(array_df, lin, col, oText, facecolors, posi, fz,
 
         # text to DEL
         text_del.append(oText)
-        
-        warnings.filterwarnings("ignore", category=DeprecationWarning) 
+
+        warnings.filterwarnings("ignore", category=DeprecationWarning)
 
         # text to ADD
         font_prop = fm.FontProperties(weight="bold", size=fz)
-        text_kwargs = dict(color="k", ha="center",va="center", gid="sum", fontproperties=font_prop,)
+        text_kwargs = dict(
+            color="k",
+            ha="center",
+            va="center",
+            gid="sum",
+            fontproperties=font_prop,
+        )
         lis_txt = ["%d" % (cell_val), per_ok_s, "%.1f%%" % (per_err)]
         lis_kwa = [text_kwargs]
         dic = text_kwargs.copy()
@@ -222,9 +251,18 @@ def config_cell_text_and_colors(array_df, lin, col, oText, facecolors, posi, fz,
         dic = text_kwargs.copy()
         dic["color"] = "r"
         lis_kwa.append(dic)
-        lis_pos = [(oText._x, oText._y - 0.3), (oText._x, oText._y), (oText._x, oText._y + 0.3),]
+        lis_pos = [
+            (oText._x, oText._y - 0.3),
+            (oText._x, oText._y),
+            (oText._x, oText._y + 0.3),
+        ]
         for i in range(len(lis_txt)):
-            newText = dict(x=lis_pos[i][0], y=lis_pos[i][1], text=lis_txt[i], kw=lis_kwa[i],)
+            newText = dict(
+                x=lis_pos[i][0],
+                y=lis_pos[i][1],
+                text=lis_txt[i],
+                kw=lis_kwa[i],
+            )
             text_add.append(newText)
 
         # set background color for sum cells (last line and last column)
@@ -255,4 +293,3 @@ def config_cell_text_and_colors(array_df, lin, col, oText, facecolors, posi, fz,
             oText.set_color("r")
 
     return text_add, text_del
-