# Import the libraries
import numpy as np
import pandas as pd
from tensorflow.keras.models import load_model
from tensorflow.keras.preprocessing.image import load_img, img_to_array
from tensorflow.keras.applications.convnext import preprocess_input
import gradio as gr
# Load the model
model = load_model('models/TropiCam-AI_ConvNeXtBase')
# Load the taxonomy .csv
taxo_df = pd.read_csv('taxonomy/taxonomy_mapping.csv')
taxo_df['species'] = taxo_df['species'].str.replace('_', ' ')
# Available taxonomic levels for prediction
taxonomic_levels = ['species', 'genus', 'family', 'order', 'class']
# Function to map predicted class index to class name at the selected taxonomic level
def get_class_name(predicted_class, taxonomic_level):
unique_labels = sorted(taxo_df[taxonomic_level].unique())
return unique_labels[predicted_class]
# Function to aggregate predictions to a higher taxonomic level
def aggregate_predictions(predicted_probs, taxonomic_level, class_names):
unique_labels = sorted(taxo_df[taxonomic_level].unique())
aggregated_predictions = np.zeros((predicted_probs.shape[0], len(unique_labels)))
for idx, row in taxo_df.iterrows():
species = row['species']
higher_level = row[taxonomic_level]
species_index = class_names.index(species) # Index of the species in the prediction array
higher_level_index = unique_labels.index(higher_level)
aggregated_predictions[:, higher_level_index] += predicted_probs[:, species_index]
return aggregated_predictions, unique_labels
# Function to load and preprocess the image
def load_and_preprocess_image(image, target_size=(224, 224)):
# Resize the image
img_array = img_to_array(image.resize(target_size))
# Expand the dimensions to match model input
img_array = np.expand_dims(img_array, axis=0)
# Preprocess the image
img_array = preprocess_input(img_array)
return img_array
# Function to make predictions
def make_prediction(image, taxonomic_decision, taxonomic_level):
# Preprocess the image
img_array = load_and_preprocess_image(image)
# Get the class names from the 'species' column
class_names = sorted(taxo_df['species'].unique())
# Make a prediction
prediction = model.predict(img_array)
# Initialize variables for aggregated predictions and level index
aggregated_predictions = None
current_level_index = 0 # Start from the species level
# Determine the initial taxonomic level based on the user's decision
if taxonomic_decision == "No, I will let the model decide":
current_level_index = 0 # Start at species level if letting the model decide
else:
current_level_index = taxonomic_levels.index(taxonomic_level) # Use specified level
# Aggregate predictions based on the current taxonomic level
aggregated_predictions, aggregated_class_labels = aggregate_predictions(prediction, taxonomic_levels[current_level_index], class_names)
# If the user specified a taxonomic level, simply get the highest prediction at that level
if taxonomic_decision == "Yes, I want to specify the taxonomic level":
# Get the predicted class index for the current level
predicted_class_index = np.argmax(aggregated_predictions)
predicted_class_name = aggregated_class_labels[predicted_class_index]
# Check if common name should be displayed (only at species level)
if taxonomic_levels[current_level_index] == "species":
predicted_common_name = taxo_df[taxo_df[taxonomic_levels[current_level_index]] == predicted_class_name]['common_name'].values[0]
output_text = f"{predicted_class_name} ({predicted_common_name})
"
else:
output_text = f"{predicted_class_name}
"
# Add the top 5 predictions
output_text += "Top-5 predictions:
"
top_indices = np.argsort(aggregated_predictions[0])[-5:][::-1] # Get top 5 predictions
for i in top_indices:
class_name = aggregated_class_labels[i]
confidence_percentage = aggregated_predictions[0][i] * 100
output_text += f"" \
f"{class_name}" \
f"{confidence_percentage:.2f}%
"
return output_text
# Confidence checking for the automatic model decision
# Loop through taxonomic levels if the user lets the model decide
while current_level_index < len(taxonomic_levels):
# Aggregate predictions for the next level
aggregated_predictions, aggregated_class_labels = aggregate_predictions(prediction, taxonomic_levels[current_level_index], class_names)
# Check if the confidence of the top prediction meets the threshold
top_prediction_index = np.argmax(aggregated_predictions)
top_prediction_confidence = aggregated_predictions[0][top_prediction_index]
if top_prediction_confidence >= 0.75:
break # Confidence threshold met, exit loop
current_level_index += 1 # Move to the next taxonomic level
# Check if a valid prediction was made
if current_level_index == len(taxonomic_levels):
return "Unknown animal
" # No valid predictions met the confidence criteria
# Get the predicted class name for the top prediction
predicted_class_index = np.argmax(aggregated_predictions)
predicted_class_name = aggregated_class_labels[predicted_class_index]
# Check if common name should be displayed (only at species level)
if taxonomic_levels[current_level_index] == "species":
predicted_common_name = taxo_df[taxo_df[taxonomic_levels[current_level_index]] == predicted_class_name]['common_name'].values[0]
output_text = f"{predicted_class_name} ({predicted_common_name})
"
else:
output_text = f"{predicted_class_name}
"
# Add the top 5 predictions
output_text += "Top-5 predictions:
"
top_indices = np.argsort(aggregated_predictions[0])[-5:][::-1] # Get top 5 predictions
for i in top_indices:
class_name = aggregated_class_labels[i]
if taxonomic_levels[current_level_index] == "species":
# Display common names only at species level and make it italic
common_name = taxo_df[taxo_df[taxonomic_levels[current_level_index]] == class_name]['common_name'].values[0]
confidence_percentage = aggregated_predictions[0][i] * 100
output_text += f"" \
f"{class_name} ({common_name})" \
f"{confidence_percentage:.2f}%
"
else:
# No common names at higher taxonomic levels
confidence_percentage = aggregated_predictions[0][i] * 100
output_text += f"" \
f"{class_name}" \
f"{confidence_percentage:.2f}%
"
return output_text
# Confidence checking for the automatic model decision
# Loop through taxonomic levels if the user lets the model decide
while current_level_index < len(taxonomic_levels):
# Aggregate predictions for the next level
aggregated_predictions, aggregated_class_labels = aggregate_predictions(prediction, taxonomic_levels[current_level_index], class_names)
# Check if the confidence of the top prediction meets the threshold
top_prediction_index = np.argmax(aggregated_predictions)
top_prediction_confidence = aggregated_predictions[0][top_prediction_index]
if top_prediction_confidence >= 0.75:
break # Confidence threshold met, exit loop
current_level_index += 1 # Move to the next taxonomic level
# Check if a valid prediction was made
if current_level_index == len(taxonomic_levels):
return "Unknown animal
" # No valid predictions met the confidence criteria
# Get the predicted class name for the top prediction
predicted_class_index = np.argmax(aggregated_predictions)
predicted_class_name = aggregated_class_labels[predicted_class_index]
# Check if common name should be displayed (only at species level)
if taxonomic_levels[current_level_index] == "species":
predicted_common_name = taxo_df[taxo_df[taxonomic_levels[current_level_index]] == predicted_class_name]['common_name'].values[0]
output_text = f"{predicted_class_name} ({predicted_common_name})
"
else:
output_text = f"{predicted_class_name}
"
# Add the top-5 predictions
output_text += "Top-5 predictions:
"
top_indices = np.argsort(aggregated_predictions[0])[-5:][::-1] # Get top 5 predictions
for i in top_indices:
class_name = aggregated_class_labels[i]
if taxonomic_levels[current_level_index] == "species":
# Display common names only at species level and make it italic
common_name = taxo_df[taxo_df[taxonomic_levels[current_level_index]] == class_name]['common_name'].values[0]
confidence_percentage = aggregated_predictions[0][i] * 100
output_text += f"" \
f"{class_name} ({common_name})" \
f"{confidence_percentage:.2f}%
"
else:
# No common names at higher taxonomic levels
confidence_percentage = aggregated_predictions[0][i] * 100
output_text += f"" \
f"{class_name}" \
f"{confidence_percentage:.2f}%
"
return output_text
# Define the Gradio interface
interface = gr.Interface(
fn=make_prediction, # Function to be called for predictions
inputs=[
gr.Image(type="pil", label="Upload Image"), # Input type: Image (PIL format)
gr.Radio(choices=["Yes, I want to specify the taxonomic level", "No, I will let the model decide"],
label="Do you want to specify the taxonomic resolution for predictions? If you select 'No', the 'Taxonomic level' drop-down menu will be bypassed.",
value="No, I will let the model decide"), # Radio button for taxonomic resolution choice
gr.Dropdown(choices=taxonomic_levels, label="Taxonomic level:", value="species") # Dropdown for taxonomic level
],
outputs="html", # Output type: HTML for formatting
title="Neotropical arboreal species classification",
description="Upload an image and our AI will classify the animal. NOTE: it's best not to feed the whole image but just the cropped animal (in the final model this will be done automatically)."
)
# Launch the Gradio interface with authentication for the specified users
interface.launch()