Upload 6 files
Browse files- README.md +14 -14
- app.py +267 -0
- breast_cancer_project_finally_finished.ipynb +417 -0
- patient_report.pdf +0 -0
- requirement.txt +10 -10
- setup.sh +1 -1
README.md
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---
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title: Clinical Decision Aid Mammogram
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emoji: 💻
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colorFrom: purple
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colorTo: green
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sdk: gradio
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sdk_version: 5.7.1
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app_file: app.py
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pinned: false
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license: apache-2.0
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short_description: Diagnosis of breast type in breast cancer from mammography
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---
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Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
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---
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title: Clinical Decision Aid Mammogram
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emoji: 💻
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colorFrom: purple
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colorTo: green
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sdk: gradio
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sdk_version: 5.7.1
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app_file: app.py
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pinned: false
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license: apache-2.0
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short_description: Diagnosis of breast type in breast cancer from mammography
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---
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Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
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app.py
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import pdfkit
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# path_wkhtmltopdf = "/usr/bin/wkhtmltopdf"
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# config = pdfkit.configuration(wkhtmltopdf=path_wkhtmltopdf)
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import subprocess
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try:
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path_wkhtmltopdf = subprocess.check_output(['which', 'wkhtmltopdf']).decode('utf-8').strip()
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config = pdfkit.configuration(wkhtmltopdf=path_wkhtmltopdf)
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except subprocess.CalledProcessError:
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raise FileNotFoundError("wkhtmltopdf not found. Ensure it is installed in your environment.")
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# import tensorflow as tf
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import numpy as np
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from PIL import Image
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import cv2
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import gradio as gr
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# from numpy import asarray
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from transformers import pipeline
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from tensorflow.keras.layers import Dense, Flatten, GlobalAveragePooling2D, BatchNormalization, Dropout,AveragePooling2D
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import tensorflow as tf
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from tensorflow.keras.applications import DenseNet201
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from keras.models import Model
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from keras.models import Sequential
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from keras.regularizers import *
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from tensorflow import keras
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from tensorflow.keras import layers
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import tensorflow as tf
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import matplotlib.pyplot as plt
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from PIL import Image
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import cv2
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from transformers import pipeline
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import os
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# تابع پیشبینی
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def predict_demo(image, model_name):
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if model_name == "how dense is":
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image = np.asarray(image)
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# مدل اول
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def load_model():
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model = tf.keras.models.load_model("model.h5", compile=False)
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model.compile(optimizer=tf.keras.optimizers.legacy.Adam(learning_rate=0.00001, decay=0.0001),
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metrics=["accuracy"], loss=tf.keras.losses.CategoricalCrossentropy(label_smoothing=0.1))
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model.load_weights("modeldense1.h5")
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return model
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model = load_model()
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def preprocess(image):
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image = cv2.resize(image, (224, 224))
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kernel = np.array([[0, -1, 0], [-1, 5, -1], [0, -1, 0]])
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im = cv2.filter2D(image, -1, kernel)
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if im.ndim == 3:
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# اضافه کردن بعد جدید برای ورودی مدل
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im = np.expand_dims(im, axis=0)
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elif im.ndim == 2:
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# اگر تصویر سیاه و سفید باشد
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im = np.expand_dims(im, axis=-1)
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im = np.repeat(im, 3, axis=-1)
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im = np.expand_dims(im, axis=0)
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return im
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class_name = ['Benign with Density=1', 'Malignant with Density=1', 'Benign with Density=2',
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'Malignant with Density=2', 'Benign with Density=3', 'Malignant with Density=3',
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'Benign with Density=4', 'Malignant with Density=4']
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def predict_img(img):
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img = preprocess(img)
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img = img / 255.0
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pred = model.predict(img)[0]
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return {class_name[i]: float(pred[i]) for i in range(8)}
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predict_mamo= predict_img(image)
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return predict_mamo
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elif model_name == "what kind is":
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image = cv2.cvtColor(np.array(image), cv2.COLOR_BGR2RGB)
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im_pil = Image.fromarray(image)
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pipe = pipeline("image-classification", model="DHEIVER/finetuned-BreastCancer-Classification", device=0)
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def predict(image):
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result = pipe(image)
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return {result[i]['label']: float(result[i]['score']) for i in range(2)}
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return predict(im_pil)
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def generate_fixed_size_chart(predictions, image_file, chart_width=6, chart_height=5):
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# بارگذاری تصویر ماموگرافی
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mammo_image = plt.imread(image_file)
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# تعداد مدلها
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num_models = len(predictions)
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# ایجاد figure با تنظیم عرض و ارتفاع هر زیرنمودار
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fig, axes = plt.subplots(1, num_models + 1, figsize=(chart_width * (num_models + 1), chart_height), constrained_layout=True)
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# fig.subplots_adjust(wspace=0.7) # فاصله ثابت بین نمودارها
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# نمایش تصویر ماموگرافی در subplot اول
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axes[0].imshow(mammo_image, cmap='gray')
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axes[0].axis('off')
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axes[0].set_title("Mammogram")
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# ایجاد نمودارهای پیشبینی برای هر مدل در subplots بعدی
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for i, (model_name, prediction) in enumerate(predictions.items(), start=1):
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labels, values = zip(*prediction.items())
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axes[i].barh(labels, values, color='skyblue')
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axes[i].set_xlabel('Probability (%)')
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axes[i].set_title(f'{model_name}')
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# ذخیرهی نمودار در فایل
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chart_path = f"{os.getcwd()}/{os.path.basename(image_file)}_combined_chart.png"
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plt.savefig(chart_path, bbox_inches='tight')
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plt.close(fig)
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return chart_path
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def generate_pdf(patient_info, predictions):
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all_charts = []
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for image_file, prediction in predictions:
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chart = generate_fixed_size_chart(prediction, image_file)
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all_charts.append(chart)
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# تولید محتوای HTML برای PDF
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html_content = f"""
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<html>
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<head>
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<style>
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body {{ font-family: Arial, sans-serif; }}
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h1 {{ color: #2F4F4F; text-align: center; margin-bottom: 30px; }}
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.info-container {{
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display: flex;
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flex-wrap: wrap;
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justify-content: space-between;
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margin-bottom: 20px;
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}}
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.info-item {{
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width: 45%;
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margin-bottom: 10px;
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}}
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.image-container {{
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text-align: center;
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margin-bottom: 50px;
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}}
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</style>
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</head>
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<body>
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<h1>Patient Report</h1>
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<div class="image-container">
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<h3>Patient Image:</h3>
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<img src="{patient_info.get('ImagePath', '')}" alt="Patient Image" width="300">
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</div>
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<div class="image-container">
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<h3>Patient Information:</h3>
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<div class="info-container">
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{"".join(f"<div class='info-item'><strong>{key}:</strong> {value if value else '-'}</div>" for key, value in patient_info.items() if key != "ImagePath")}
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</div>
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</div>
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<h3>Predictions:</h3>
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{"".join(f"<div ><img src='{chart}' width='80%'></div>" for chart in all_charts)}
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</body>
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</html>
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"""
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# تنظیمات PDF
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pdf_path = "patient_report.pdf"
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config = pdfkit.configuration(wkhtmltopdf='/usr/bin/wkhtmltopdf')
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options = {
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"enable-local-file-access": True,
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"no-stop-slow-scripts": True,
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}
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pdfkit.from_string(html_content, pdf_path, configuration=config, options=options)
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return pdf_path
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+
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# تابع نمایش گزارش و تولید PDF
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def display_report(patient_info, predictions):
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pdf_path = generate_pdf(patient_info, predictions)
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report_content = f"<h2>Patient Report</h2><p>{patient_info}</p><h2>Predictions</h2>{predictions}"
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return report_content, pdf_path
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# رابط Gradio
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with gr.Blocks() as demo:
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gr.Markdown("## Breast Cancer Detection - Multi-Model Interface")
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# صفحه اول - اطلاعات بیمار
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with gr.Tab("Patient Info"):
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patient_image = gr.Image(label="Upload Patient Profile Image", type="pil")
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name = gr.Textbox(label="Name")
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height = gr.Number(label="Height (cm)")
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weight = gr.Number(label="Weight (kg)")
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age = gr.Number(label="Age")
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gender = gr.Radio(["Male", "Female", "Other"], label="Gender")
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residence = gr.Textbox(label="Residence")
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birth_place = gr.Textbox(label="Birth Place")
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occupation = gr.Textbox(label="Occupation")
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medical_history = gr.Textbox(label="Medical History")
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patient_info = gr.State()
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patient_info_submit = gr.Button("Next")
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# صفحه دوم - انتخاب مدلها و آپلود تصاویر ماموگرافی
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with gr.Tab("Model & Image Selection"):
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model_choice = gr.CheckboxGroup(["how dense is", "what kind is"], label="Select Model(s)", interactive=True)
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mammography_images = gr.File(label="Upload Mammography Image(s)", file_count="multiple", type="filepath")
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predictions = gr.State()
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process_button = gr.Button("Process Images")
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# صفحه سوم - نمایش اطلاعات و پیشبینی
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with gr.Tab("Results"):
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report_display = gr.HTML(label="Patient Report")
|
| 219 |
+
download_button = gr.Button("Download Report")
|
| 220 |
+
|
| 221 |
+
# جمعآوری اطلاعات بیمار و انتقال به مرحله بعدی
|
| 222 |
+
def collect_patient_info(image, name, height, weight, age, gender, residence, birth_place, occupation, medical_history):
|
| 223 |
+
# ذخیره تصویر بیمار و اضافه کردن مسیر به اطلاعات بیمار
|
| 224 |
+
image_path = "patient_image.jpg"
|
| 225 |
+
image.save(image_path)
|
| 226 |
+
return {
|
| 227 |
+
"Name": name,
|
| 228 |
+
"Gender": gender,
|
| 229 |
+
"Height": height,
|
| 230 |
+
"Weight": weight,
|
| 231 |
+
"Age": age,
|
| 232 |
+
"Residence": residence,
|
| 233 |
+
"Birth Place": birth_place,
|
| 234 |
+
"Occupation": occupation,
|
| 235 |
+
"Medical History": medical_history,
|
| 236 |
+
"ImagePath": image_path # اضافه کردن مسیر تصویر
|
| 237 |
+
}
|
| 238 |
+
|
| 239 |
+
patient_info_submit.click(
|
| 240 |
+
collect_patient_info,
|
| 241 |
+
inputs=[patient_image, name, height, weight, age, gender, residence, birth_place, occupation, medical_history],
|
| 242 |
+
outputs=patient_info
|
| 243 |
+
)
|
| 244 |
+
|
| 245 |
+
# پردازش تصاویر ماموگرافی با مدلهای انتخابی
|
| 246 |
+
def process_images(patient_info, selected_models, images):
|
| 247 |
+
all_predictions = []
|
| 248 |
+
for image_file in images:
|
| 249 |
+
image = Image.open(image_file)
|
| 250 |
+
image_predictions = {model: predict_demo(image, model) for model in selected_models}
|
| 251 |
+
all_predictions.append((image_file, image_predictions))
|
| 252 |
+
return all_predictions
|
| 253 |
+
|
| 254 |
+
process_button.click(
|
| 255 |
+
process_images,
|
| 256 |
+
inputs=[patient_info, model_choice, mammography_images],
|
| 257 |
+
outputs=predictions
|
| 258 |
+
)
|
| 259 |
+
|
| 260 |
+
# نمایش گزارش بیمار و پیشبینیها در صفحه سوم
|
| 261 |
+
download_button.click(
|
| 262 |
+
display_report,
|
| 263 |
+
inputs=[patient_info, predictions],
|
| 264 |
+
outputs=[report_display, gr.File(label="Download PDF Report")] # اصلاح خروجی برای Gradio
|
| 265 |
+
)
|
| 266 |
+
|
| 267 |
+
demo.launch(debug=True, share=True)
|
breast_cancer_project_finally_finished.ipynb
ADDED
|
@@ -0,0 +1,417 @@
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|
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|
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|
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|
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|
|
|
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|
|
|
|
|
|
|
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|
|
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|
|
|
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|
|
|
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|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"cells": [
|
| 3 |
+
{
|
| 4 |
+
"cell_type": "code",
|
| 5 |
+
"execution_count": 7,
|
| 6 |
+
"metadata": {
|
| 7 |
+
"id": "GZR221V_EwiN"
|
| 8 |
+
},
|
| 9 |
+
"outputs": [],
|
| 10 |
+
"source": [
|
| 11 |
+
"import pdfkit\n",
|
| 12 |
+
"path_wkhtmltopdf = \"/usr/bin/wkhtmltopdf\"\n",
|
| 13 |
+
"config = pdfkit.configuration(wkhtmltopdf=path_wkhtmltopdf)"
|
| 14 |
+
]
|
| 15 |
+
},
|
| 16 |
+
{
|
| 17 |
+
"cell_type": "code",
|
| 18 |
+
"execution_count": 9,
|
| 19 |
+
"metadata": {
|
| 20 |
+
"id": "e6si8Vop4FjB"
|
| 21 |
+
},
|
| 22 |
+
"outputs": [],
|
| 23 |
+
"source": [
|
| 24 |
+
"# import tensorflow as tf\n",
|
| 25 |
+
"import numpy as np\n",
|
| 26 |
+
"from PIL import Image\n",
|
| 27 |
+
"import cv2\n",
|
| 28 |
+
"import gradio as gr\n",
|
| 29 |
+
"# from numpy import asarray\n",
|
| 30 |
+
"from transformers import pipeline"
|
| 31 |
+
]
|
| 32 |
+
},
|
| 33 |
+
{
|
| 34 |
+
"cell_type": "code",
|
| 35 |
+
"execution_count": null,
|
| 36 |
+
"metadata": {
|
| 37 |
+
"colab": {
|
| 38 |
+
"base_uri": "https://localhost:8080/"
|
| 39 |
+
},
|
| 40 |
+
"id": "3b-TCKUozaMn",
|
| 41 |
+
"outputId": "58f44bd4-8916-436d-e00a-1e19a4586dbc"
|
| 42 |
+
},
|
| 43 |
+
"outputs": [
|
| 44 |
+
{
|
| 45 |
+
"name": "stdout",
|
| 46 |
+
"output_type": "stream",
|
| 47 |
+
"text": [
|
| 48 |
+
"Downloading data from https://storage.googleapis.com/tensorflow/keras-applications/densenet/densenet201_weights_tf_dim_ordering_tf_kernels_notop.h5\n",
|
| 49 |
+
"74836368/74836368 [==============================] - 4s 0us/step\n"
|
| 50 |
+
]
|
| 51 |
+
},
|
| 52 |
+
{
|
| 53 |
+
"name": "stderr",
|
| 54 |
+
"output_type": "stream",
|
| 55 |
+
"text": [
|
| 56 |
+
"/usr/local/lib/python3.10/dist-packages/keras/src/engine/training.py:3103: UserWarning: You are saving your model as an HDF5 file via `model.save()`. This file format is considered legacy. We recommend using instead the native Keras format, e.g. `model.save('my_model.keras')`.\n",
|
| 57 |
+
" saving_api.save_model(\n",
|
| 58 |
+
"WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.\n"
|
| 59 |
+
]
|
| 60 |
+
}
|
| 61 |
+
],
|
| 62 |
+
"source": [
|
| 63 |
+
"from tensorflow.keras.layers import Dense, Flatten, GlobalAveragePooling2D, BatchNormalization, Dropout,AveragePooling2D\n",
|
| 64 |
+
"import tensorflow as tf\n",
|
| 65 |
+
"from tensorflow.keras.applications import DenseNet201\n",
|
| 66 |
+
"from keras.models import Model\n",
|
| 67 |
+
"from keras.models import Sequential\n",
|
| 68 |
+
"from keras.regularizers import *\n",
|
| 69 |
+
"from tensorflow import keras\n",
|
| 70 |
+
"from tensorflow.keras import layers"
|
| 71 |
+
]
|
| 72 |
+
},
|
| 73 |
+
{
|
| 74 |
+
"cell_type": "code",
|
| 75 |
+
"execution_count": 5,
|
| 76 |
+
"metadata": {
|
| 77 |
+
"colab": {
|
| 78 |
+
"base_uri": "https://localhost:8080/",
|
| 79 |
+
"height": 889
|
| 80 |
+
},
|
| 81 |
+
"id": "Ylgxw-pHiLCC",
|
| 82 |
+
"outputId": "76d5f8ed-82f4-4227-ff75-dcbba696eb14"
|
| 83 |
+
},
|
| 84 |
+
"outputs": [
|
| 85 |
+
{
|
| 86 |
+
"name": "stdout",
|
| 87 |
+
"output_type": "stream",
|
| 88 |
+
"text": [
|
| 89 |
+
"Colab notebook detected. This cell will run indefinitely so that you can see errors and logs. To turn off, set debug=False in launch().\n",
|
| 90 |
+
"* Running on public URL: https://54b3e1140167dae729.gradio.live\n",
|
| 91 |
+
"\n",
|
| 92 |
+
"This share link expires in 72 hours. For free permanent hosting and GPU upgrades, run `gradio deploy` from the terminal in the working directory to deploy to Hugging Face Spaces (https://huggingface.co/spaces)\n"
|
| 93 |
+
]
|
| 94 |
+
},
|
| 95 |
+
{
|
| 96 |
+
"data": {
|
| 97 |
+
"text/html": [
|
| 98 |
+
"<div><iframe src=\"https://54b3e1140167dae729.gradio.live\" width=\"100%\" height=\"500\" allow=\"autoplay; camera; microphone; clipboard-read; clipboard-write;\" frameborder=\"0\" allowfullscreen></iframe></div>"
|
| 99 |
+
],
|
| 100 |
+
"text/plain": [
|
| 101 |
+
"<IPython.core.display.HTML object>"
|
| 102 |
+
]
|
| 103 |
+
},
|
| 104 |
+
"metadata": {},
|
| 105 |
+
"output_type": "display_data"
|
| 106 |
+
},
|
| 107 |
+
{
|
| 108 |
+
"name": "stderr",
|
| 109 |
+
"output_type": "stream",
|
| 110 |
+
"text": [
|
| 111 |
+
"WARNING:tensorflow:5 out of the last 5 calls to <function Model.make_predict_function.<locals>.predict_function at 0x78c970190a60> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for more details.\n"
|
| 112 |
+
]
|
| 113 |
+
},
|
| 114 |
+
{
|
| 115 |
+
"name": "stdout",
|
| 116 |
+
"output_type": "stream",
|
| 117 |
+
"text": [
|
| 118 |
+
"1/1 [==============================] - 4s 4s/step\n"
|
| 119 |
+
]
|
| 120 |
+
},
|
| 121 |
+
{
|
| 122 |
+
"name": "stderr",
|
| 123 |
+
"output_type": "stream",
|
| 124 |
+
"text": [
|
| 125 |
+
"WARNING:tensorflow:6 out of the last 6 calls to <function Model.make_predict_function.<locals>.predict_function at 0x78c97cd316c0> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for more details.\n"
|
| 126 |
+
]
|
| 127 |
+
},
|
| 128 |
+
{
|
| 129 |
+
"name": "stdout",
|
| 130 |
+
"output_type": "stream",
|
| 131 |
+
"text": [
|
| 132 |
+
"1/1 [==============================] - 4s 4s/step\n",
|
| 133 |
+
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"1/1 [==============================] - 3s 3s/step\n",
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"1/1 [==============================] - 3s 3s/step\n",
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+
"Keyboard interruption in main thread... closing server.\n",
|
| 144 |
+
"Killing tunnel 127.0.0.1:7860 <> https://54b3e1140167dae729.gradio.live\n"
|
| 145 |
+
]
|
| 146 |
+
},
|
| 147 |
+
{
|
| 148 |
+
"data": {
|
| 149 |
+
"text/plain": []
|
| 150 |
+
},
|
| 151 |
+
"execution_count": 5,
|
| 152 |
+
"metadata": {},
|
| 153 |
+
"output_type": "execute_result"
|
| 154 |
+
}
|
| 155 |
+
],
|
| 156 |
+
"source": [
|
| 157 |
+
"import tensorflow as tf\n",
|
| 158 |
+
"import matplotlib.pyplot as plt\n",
|
| 159 |
+
"import numpy as np\n",
|
| 160 |
+
"from PIL import Image\n",
|
| 161 |
+
"import cv2\n",
|
| 162 |
+
"import gradio as gr\n",
|
| 163 |
+
"from transformers import pipeline\n",
|
| 164 |
+
"import pdfkit # نیاز به نصب دارد (pip install pdfkit)\n",
|
| 165 |
+
"import os\n",
|
| 166 |
+
"\n",
|
| 167 |
+
"# تابع پیشبینی\n",
|
| 168 |
+
"def predict_demo(image, model_name):\n",
|
| 169 |
+
" if model_name == \"how dense is\":\n",
|
| 170 |
+
" image = np.asarray(image)\n",
|
| 171 |
+
"\n",
|
| 172 |
+
" # مدل اول\n",
|
| 173 |
+
" def load_model():\n",
|
| 174 |
+
" model = tf.keras.models.load_model(\"/content/model.h5\", compile=False)\n",
|
| 175 |
+
" model.compile(optimizer=tf.keras.optimizers.legacy.Adam(learning_rate=0.00001, decay=0.0001),\n",
|
| 176 |
+
" metrics=[\"accuracy\"], loss=tf.keras.losses.CategoricalCrossentropy(label_smoothing=0.1))\n",
|
| 177 |
+
" model.load_weights(\"/content/modeldense1.h5\")\n",
|
| 178 |
+
" return model\n",
|
| 179 |
+
"\n",
|
| 180 |
+
" model = load_model()\n",
|
| 181 |
+
"\n",
|
| 182 |
+
" def preprocess(image):\n",
|
| 183 |
+
" image = cv2.resize(image, (224, 224))\n",
|
| 184 |
+
" kernel = np.array([[0, -1, 0], [-1, 5, -1], [0, -1, 0]])\n",
|
| 185 |
+
" im = cv2.filter2D(image, -1, kernel)\n",
|
| 186 |
+
" if im.ndim == 3:\n",
|
| 187 |
+
" # اضافه کردن بعد جدید برای ورودی مدل\n",
|
| 188 |
+
" im = np.expand_dims(im, axis=0)\n",
|
| 189 |
+
" elif im.ndim == 2:\n",
|
| 190 |
+
" # اگر تصویر سیاه و سفید باشد\n",
|
| 191 |
+
" im = np.expand_dims(im, axis=-1)\n",
|
| 192 |
+
" im = np.repeat(im, 3, axis=-1)\n",
|
| 193 |
+
" im = np.expand_dims(im, axis=0)\n",
|
| 194 |
+
" return im\n",
|
| 195 |
+
"\n",
|
| 196 |
+
"\n",
|
| 197 |
+
" class_name = ['Benign with Density=1', 'Malignant with Density=1', 'Benign with Density=2',\n",
|
| 198 |
+
" 'Malignant with Density=2', 'Benign with Density=3', 'Malignant with Density=3',\n",
|
| 199 |
+
" 'Benign with Density=4', 'Malignant with Density=4']\n",
|
| 200 |
+
"\n",
|
| 201 |
+
" def predict_img(img):\n",
|
| 202 |
+
" img = preprocess(img)\n",
|
| 203 |
+
" img = img / 255.0\n",
|
| 204 |
+
" pred = model.predict(img)[0]\n",
|
| 205 |
+
" return {class_name[i]: float(pred[i]) for i in range(8)}\n",
|
| 206 |
+
"\n",
|
| 207 |
+
"\n",
|
| 208 |
+
" predict_mamo= predict_img(image)\n",
|
| 209 |
+
" return predict_mamo\n",
|
| 210 |
+
"\n",
|
| 211 |
+
" elif model_name == \"what kind is\":\n",
|
| 212 |
+
" image = cv2.cvtColor(np.array(image), cv2.COLOR_BGR2RGB)\n",
|
| 213 |
+
" im_pil = Image.fromarray(image)\n",
|
| 214 |
+
" pipe = pipeline(\"image-classification\", model=\"DHEIVER/finetuned-BreastCancer-Classification\", device=0)\n",
|
| 215 |
+
"\n",
|
| 216 |
+
" def predict(image):\n",
|
| 217 |
+
" result = pipe(image)\n",
|
| 218 |
+
" return {result[i]['label']: float(result[i]['score']) for i in range(2)}\n",
|
| 219 |
+
"\n",
|
| 220 |
+
" return predict(im_pil)\n",
|
| 221 |
+
"\n",
|
| 222 |
+
"\n",
|
| 223 |
+
"\n",
|
| 224 |
+
"def generate_fixed_size_chart(predictions, image_file, chart_width=6, chart_height=5):\n",
|
| 225 |
+
" # بارگذاری تصویر ماموگرافی\n",
|
| 226 |
+
" mammo_image = plt.imread(image_file)\n",
|
| 227 |
+
"\n",
|
| 228 |
+
" # تعداد مدلها\n",
|
| 229 |
+
" num_models = len(predictions)\n",
|
| 230 |
+
"\n",
|
| 231 |
+
" # ایجاد figure با تنظیم عرض و ارتفاع هر زیرنمودار\n",
|
| 232 |
+
" fig, axes = plt.subplots(1, num_models + 1, figsize=(chart_width * (num_models + 1), chart_height), constrained_layout=True)\n",
|
| 233 |
+
" # fig.subplots_adjust(wspace=0.7) # فا��له ثابت بین نمودارها\n",
|
| 234 |
+
"\n",
|
| 235 |
+
" # نمایش تصویر ماموگرافی در subplot اول\n",
|
| 236 |
+
" axes[0].imshow(mammo_image, cmap='gray')\n",
|
| 237 |
+
" axes[0].axis('off')\n",
|
| 238 |
+
" axes[0].set_title(\"Mammogram\")\n",
|
| 239 |
+
"\n",
|
| 240 |
+
" # ایجاد نمودارهای پیشبینی برای هر مدل در subplots بعدی\n",
|
| 241 |
+
" for i, (model_name, prediction) in enumerate(predictions.items(), start=1):\n",
|
| 242 |
+
" labels, values = zip(*prediction.items())\n",
|
| 243 |
+
" axes[i].barh(labels, values, color='skyblue')\n",
|
| 244 |
+
" axes[i].set_xlabel('Probability (%)')\n",
|
| 245 |
+
" axes[i].set_title(f'{model_name}')\n",
|
| 246 |
+
"\n",
|
| 247 |
+
" # ذخیرهی نمودار در فایل\n",
|
| 248 |
+
" chart_path = f\"/content/{os.path.basename(image_file)}_combined_chart.png\"\n",
|
| 249 |
+
" plt.savefig(chart_path, bbox_inches='tight')\n",
|
| 250 |
+
" plt.close(fig)\n",
|
| 251 |
+
"\n",
|
| 252 |
+
" return chart_path\n",
|
| 253 |
+
"\n",
|
| 254 |
+
"def generate_pdf(patient_info, predictions):\n",
|
| 255 |
+
" all_charts = []\n",
|
| 256 |
+
" for image_file, prediction in predictions:\n",
|
| 257 |
+
" chart = generate_fixed_size_chart(prediction, image_file)\n",
|
| 258 |
+
" all_charts.append(chart)\n",
|
| 259 |
+
"\n",
|
| 260 |
+
" # تولید محتوای HTML برای PDF\n",
|
| 261 |
+
" html_content = f\"\"\"\n",
|
| 262 |
+
" <html>\n",
|
| 263 |
+
" <head>\n",
|
| 264 |
+
" <style>\n",
|
| 265 |
+
" body {{ font-family: Arial, sans-serif; }}\n",
|
| 266 |
+
" h1 {{ color: #2F4F4F; text-align: center; margin-bottom: 30px; }}\n",
|
| 267 |
+
" .info-container {{\n",
|
| 268 |
+
" display: flex;\n",
|
| 269 |
+
" flex-wrap: wrap;\n",
|
| 270 |
+
" justify-content: space-between;\n",
|
| 271 |
+
" margin-bottom: 20px;\n",
|
| 272 |
+
" }}\n",
|
| 273 |
+
" .info-item {{\n",
|
| 274 |
+
" width: 45%;\n",
|
| 275 |
+
" margin-bottom: 10px;\n",
|
| 276 |
+
" }}\n",
|
| 277 |
+
" .image-container {{\n",
|
| 278 |
+
" text-align: center;\n",
|
| 279 |
+
" margin-bottom: 50px;\n",
|
| 280 |
+
" }}\n",
|
| 281 |
+
" </style>\n",
|
| 282 |
+
" </head>\n",
|
| 283 |
+
" <body>\n",
|
| 284 |
+
" <h1>Patient Report</h1>\n",
|
| 285 |
+
" <div class=\"image-container\">\n",
|
| 286 |
+
" <h3>Patient Image:</h3>\n",
|
| 287 |
+
" <img src=\"{patient_info.get('ImagePath', '')}\" alt=\"Patient Image\" width=\"300\">\n",
|
| 288 |
+
" </div>\n",
|
| 289 |
+
" <div class=\"image-container\">\n",
|
| 290 |
+
" <h3>Patient Information:</h3>\n",
|
| 291 |
+
" <div class=\"info-container\">\n",
|
| 292 |
+
" {\"\".join(f\"<div class='info-item'><strong>{key}:</strong> {value if value else '-'}</div>\" for key, value in patient_info.items() if key != \"ImagePath\")}\n",
|
| 293 |
+
" </div>\n",
|
| 294 |
+
" </div>\n",
|
| 295 |
+
" <h3>Predictions:</h3>\n",
|
| 296 |
+
" {\"\".join(f\"<div ><img src='{chart}' width='80%'></div>\" for chart in all_charts)}\n",
|
| 297 |
+
" </body>\n",
|
| 298 |
+
" </html>\n",
|
| 299 |
+
" \"\"\"\n",
|
| 300 |
+
"\n",
|
| 301 |
+
" # تنظیمات PDF\n",
|
| 302 |
+
" pdf_path = \"/content/patient_report.pdf\"\n",
|
| 303 |
+
" config = pdfkit.configuration(wkhtmltopdf='/usr/bin/wkhtmltopdf')\n",
|
| 304 |
+
" options = {\n",
|
| 305 |
+
" \"enable-local-file-access\": True,\n",
|
| 306 |
+
" \"no-stop-slow-scripts\": True,\n",
|
| 307 |
+
" }\n",
|
| 308 |
+
" pdfkit.from_string(html_content, pdf_path, configuration=config, options=options)\n",
|
| 309 |
+
"\n",
|
| 310 |
+
" return pdf_path\n",
|
| 311 |
+
"\n",
|
| 312 |
+
"\n",
|
| 313 |
+
"\n",
|
| 314 |
+
"# تابع نمایش گزارش و تولید PDF\n",
|
| 315 |
+
"def display_report(patient_info, predictions):\n",
|
| 316 |
+
" pdf_path = generate_pdf(patient_info, predictions)\n",
|
| 317 |
+
" report_content = f\"<h2>Patient Report</h2><p>{patient_info}</p><h2>Predictions</h2>{predictions}\"\n",
|
| 318 |
+
" return report_content, pdf_path\n",
|
| 319 |
+
"\n",
|
| 320 |
+
"# رابط Gradio\n",
|
| 321 |
+
"with gr.Blocks() as demo:\n",
|
| 322 |
+
" gr.Markdown(\"## Breast Cancer Detection - Multi-Model Interface\")\n",
|
| 323 |
+
"\n",
|
| 324 |
+
" # صفحه اول - اطلاعات بیمار\n",
|
| 325 |
+
" with gr.Tab(\"Patient Info\"):\n",
|
| 326 |
+
" patient_image = gr.Image(label=\"Upload Patient Profile Image\", type=\"pil\")\n",
|
| 327 |
+
" name = gr.Textbox(label=\"Name\")\n",
|
| 328 |
+
" height = gr.Number(label=\"Height (cm)\")\n",
|
| 329 |
+
" weight = gr.Number(label=\"Weight (kg)\")\n",
|
| 330 |
+
" age = gr.Number(label=\"Age\")\n",
|
| 331 |
+
" gender = gr.Radio([\"Male\", \"Female\", \"Other\"], label=\"Gender\")\n",
|
| 332 |
+
" residence = gr.Textbox(label=\"Residence\")\n",
|
| 333 |
+
" birth_place = gr.Textbox(label=\"Birth Place\")\n",
|
| 334 |
+
" occupation = gr.Textbox(label=\"Occupation\")\n",
|
| 335 |
+
" medical_history = gr.Textbox(label=\"Medical History\")\n",
|
| 336 |
+
" patient_info = gr.State()\n",
|
| 337 |
+
" patient_info_submit = gr.Button(\"Next\")\n",
|
| 338 |
+
"\n",
|
| 339 |
+
" # صفحه دوم - انتخاب مدلها و آپلود تصاویر ماموگرافی\n",
|
| 340 |
+
" with gr.Tab(\"Model & Image Selection\"):\n",
|
| 341 |
+
" model_choice = gr.CheckboxGroup([\"how dense is\", \"what kind is\"], label=\"Select Model(s)\", interactive=True)\n",
|
| 342 |
+
" mammography_images = gr.File(label=\"Upload Mammography Image(s)\", file_count=\"multiple\", type=\"filepath\")\n",
|
| 343 |
+
" predictions = gr.State()\n",
|
| 344 |
+
" process_button = gr.Button(\"Process Images\")\n",
|
| 345 |
+
"\n",
|
| 346 |
+
" # صفحه سوم - نمایش اطلاعات و پیشبینی\n",
|
| 347 |
+
" with gr.Tab(\"Results\"):\n",
|
| 348 |
+
" report_display = gr.HTML(label=\"Patient Report\")\n",
|
| 349 |
+
" download_button = gr.Button(\"Download Report\")\n",
|
| 350 |
+
"\n",
|
| 351 |
+
" # جمعآوری اطلاعات بیمار و انتقال به مرحله بعدی\n",
|
| 352 |
+
" def collect_patient_info(image, name, height, weight, age, gender, residence, birth_place, occupation, medical_history):\n",
|
| 353 |
+
" # ذخیره تصویر بیمار و اضافه کردن مسیر به اطلاعات بیمار\n",
|
| 354 |
+
" image_path = \"/content/patient_image.jpg\"\n",
|
| 355 |
+
" image.save(image_path)\n",
|
| 356 |
+
" return {\n",
|
| 357 |
+
" \"Name\": name,\n",
|
| 358 |
+
" \"Gender\": gender,\n",
|
| 359 |
+
" \"Height\": height,\n",
|
| 360 |
+
" \"Weight\": weight,\n",
|
| 361 |
+
" \"Age\": age,\n",
|
| 362 |
+
" \"Residence\": residence,\n",
|
| 363 |
+
" \"Birth Place\": birth_place,\n",
|
| 364 |
+
" \"Occupation\": occupation,\n",
|
| 365 |
+
" \"Medical History\": medical_history,\n",
|
| 366 |
+
" \"ImagePath\": image_path # اضافه کردن مسیر تصویر\n",
|
| 367 |
+
" }\n",
|
| 368 |
+
"\n",
|
| 369 |
+
" patient_info_submit.click(\n",
|
| 370 |
+
" collect_patient_info,\n",
|
| 371 |
+
" inputs=[patient_image, name, height, weight, age, gender, residence, birth_place, occupation, medical_history],\n",
|
| 372 |
+
" outputs=patient_info\n",
|
| 373 |
+
" )\n",
|
| 374 |
+
"\n",
|
| 375 |
+
" # پردازش تصاویر ماموگرافی با مدلهای انتخابی\n",
|
| 376 |
+
" def process_images(patient_info, selected_models, images):\n",
|
| 377 |
+
" all_predictions = []\n",
|
| 378 |
+
" for image_file in images:\n",
|
| 379 |
+
" image = Image.open(image_file)\n",
|
| 380 |
+
" image_predictions = {model: predict_demo(image, model) for model in selected_models}\n",
|
| 381 |
+
" all_predictions.append((image_file, image_predictions))\n",
|
| 382 |
+
" return all_predictions\n",
|
| 383 |
+
"\n",
|
| 384 |
+
" process_button.click(\n",
|
| 385 |
+
" process_images,\n",
|
| 386 |
+
" inputs=[patient_info, model_choice, mammography_images],\n",
|
| 387 |
+
" outputs=predictions\n",
|
| 388 |
+
" )\n",
|
| 389 |
+
"\n",
|
| 390 |
+
" # نمایش گزارش بیمار و پیشبینیها در صفحه سوم\n",
|
| 391 |
+
" download_button.click(\n",
|
| 392 |
+
" display_report,\n",
|
| 393 |
+
" inputs=[patient_info, predictions],\n",
|
| 394 |
+
" outputs=[report_display, gr.File(label=\"Download PDF Report\")] # اصلاح خروجی برای Gradio\n",
|
| 395 |
+
" )\n",
|
| 396 |
+
"\n",
|
| 397 |
+
"demo.launch(debug=True, share=True)\n"
|
| 398 |
+
]
|
| 399 |
+
}
|
| 400 |
+
],
|
| 401 |
+
"metadata": {
|
| 402 |
+
"accelerator": "GPU",
|
| 403 |
+
"colab": {
|
| 404 |
+
"gpuType": "T4",
|
| 405 |
+
"provenance": []
|
| 406 |
+
},
|
| 407 |
+
"kernelspec": {
|
| 408 |
+
"display_name": "Python 3",
|
| 409 |
+
"name": "python3"
|
| 410 |
+
},
|
| 411 |
+
"language_info": {
|
| 412 |
+
"name": "python"
|
| 413 |
+
}
|
| 414 |
+
},
|
| 415 |
+
"nbformat": 4,
|
| 416 |
+
"nbformat_minor": 0
|
| 417 |
+
}
|
patient_report.pdf
ADDED
|
Binary file (645 kB). View file
|
|
|
requirement.txt
CHANGED
|
@@ -1,11 +1,11 @@
|
|
| 1 |
-
tensorflow==2.15.1
|
| 2 |
-
gradio
|
| 3 |
-
diffusers
|
| 4 |
-
accelerate
|
| 5 |
-
git+https://github.com/TencentARC/PhotoMaker.git
|
| 6 |
-
pdfkit
|
| 7 |
-
wkhtmltopdf
|
| 8 |
-
transformers
|
| 9 |
-
numpy
|
| 10 |
-
pandas
|
| 11 |
matplotlib
|
|
|
|
| 1 |
+
tensorflow==2.15.1
|
| 2 |
+
gradio
|
| 3 |
+
diffusers
|
| 4 |
+
accelerate
|
| 5 |
+
git+https://github.com/TencentARC/PhotoMaker.git
|
| 6 |
+
pdfkit
|
| 7 |
+
wkhtmltopdf
|
| 8 |
+
transformers
|
| 9 |
+
numpy
|
| 10 |
+
pandas
|
| 11 |
matplotlib
|
setup.sh
CHANGED
|
@@ -1,2 +1,2 @@
|
|
| 1 |
-
#!/bin/bash
|
| 2 |
apt-get update && apt-get install -y wkhtmltopdf
|
|
|
|
| 1 |
+
#!/bin/bash
|
| 2 |
apt-get update && apt-get install -y wkhtmltopdf
|