updated the code ✅
Browse files- mediSync/app.py +78 -122
mediSync/app.py
CHANGED
|
@@ -404,9 +404,52 @@ class MediSyncApp:
|
|
| 404 |
# import gradio as gr
|
| 405 |
# from mediSync.app import MediSyncApp
|
| 406 |
|
| 407 |
-
|
| 408 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 409 |
|
|
|
|
|
|
|
| 410 |
app = MediSyncApp()
|
| 411 |
|
| 412 |
# Example medical report for demo
|
|
@@ -428,53 +471,24 @@ def create_interface():
|
|
| 428 |
RECOMMENDATIONS: Follow-up chest CT to further characterize the nodular opacity in the right lower lobe.
|
| 429 |
"""
|
| 430 |
|
| 431 |
-
# Get sample image
|
| 432 |
sample_image_path = None
|
| 433 |
try:
|
| 434 |
-
|
| 435 |
-
|
| 436 |
-
|
| 437 |
-
|
| 438 |
-
|
| 439 |
-
|
| 440 |
-
if not sample_images:
|
| 441 |
-
# Download fallback sample image if none exist
|
| 442 |
-
fallback_url = "https://raw.githubusercontent.com/ieee8023/covid-chestxray-dataset/master/images/1-s2.0-S0929664620300449-gr2_lrg-a.jpg"
|
| 443 |
-
sample_path = sample_images_dir / "sample_xray.jpg"
|
| 444 |
-
|
| 445 |
-
try:
|
| 446 |
-
response = requests.get(fallback_url, timeout=10)
|
| 447 |
-
if response.status_code == 200:
|
| 448 |
-
with open(sample_path, 'wb') as f:
|
| 449 |
-
f.write(response.content)
|
| 450 |
-
sample_image_path = str(sample_path)
|
| 451 |
-
logging.info("Successfully downloaded fallback sample image")
|
| 452 |
-
else:
|
| 453 |
-
logging.warning(f"Failed to download sample image. Status code: {response.status_code}")
|
| 454 |
-
except Exception as download_error:
|
| 455 |
-
logging.warning(f"Could not download sample image: {str(download_error)}")
|
| 456 |
-
else:
|
| 457 |
-
sample_image_path = str(sample_images[0])
|
| 458 |
except Exception as e:
|
| 459 |
-
logging.
|
| 460 |
|
| 461 |
-
# Define interface
|
| 462 |
with gr.Blocks(
|
| 463 |
title="MediSync: Multi-Modal Medical Analysis System",
|
| 464 |
-
theme=gr.themes.Soft()
|
|
|
|
| 465 |
) as interface:
|
| 466 |
-
# Get appointment ID from URL parameters using JavaScript
|
| 467 |
-
appointment_id = gr.Textbox(
|
| 468 |
-
visible=False,
|
| 469 |
-
value="",
|
| 470 |
-
_js="""
|
| 471 |
-
function() {
|
| 472 |
-
const params = new URLSearchParams(window.location.search);
|
| 473 |
-
return params.get('appointment_id') || '';
|
| 474 |
-
}
|
| 475 |
-
"""
|
| 476 |
-
)
|
| 477 |
-
|
| 478 |
gr.Markdown("""
|
| 479 |
# MediSync: Multi-Modal Medical Analysis System
|
| 480 |
|
|
@@ -485,22 +499,20 @@ def create_interface():
|
|
| 485 |
1. Upload a chest X-ray image
|
| 486 |
2. Enter the corresponding medical report text
|
| 487 |
3. Choose the analysis type: image-only, text-only, or multimodal (combined)
|
| 488 |
-
4.
|
| 489 |
""")
|
| 490 |
|
| 491 |
with gr.Tab("Multimodal Analysis"):
|
| 492 |
with gr.Row():
|
| 493 |
with gr.Column():
|
| 494 |
multi_img_input = gr.Image(label="Upload X-ray Image", type="pil")
|
| 495 |
-
multi_img_enhance = gr.Button("Enhance Image")
|
| 496 |
-
|
| 497 |
multi_text_input = gr.Textbox(
|
| 498 |
label="Enter Medical Report Text",
|
| 499 |
placeholder="Enter the radiologist's report text here...",
|
| 500 |
lines=10,
|
| 501 |
-
value=example_report
|
| 502 |
)
|
| 503 |
-
|
| 504 |
multi_analyze_btn = gr.Button(
|
| 505 |
"Analyze Image & Text", variant="primary"
|
| 506 |
)
|
|
@@ -520,7 +532,7 @@ def create_interface():
|
|
| 520 |
with gr.Row():
|
| 521 |
with gr.Column():
|
| 522 |
img_input = gr.Image(label="Upload X-ray Image", type="pil")
|
| 523 |
-
img_enhance = gr.Button("Enhance Image")
|
| 524 |
img_analyze_btn = gr.Button("Analyze Image", variant="primary")
|
| 525 |
|
| 526 |
with gr.Column():
|
|
@@ -547,7 +559,7 @@ def create_interface():
|
|
| 547 |
text_analyze_btn = gr.Button("Analyze Text", variant="primary")
|
| 548 |
|
| 549 |
with gr.Column():
|
| 550 |
-
text_output = gr.Textbox(label="Processed Text")
|
| 551 |
text_results = gr.HTML(label="Analysis Results")
|
| 552 |
text_plot = gr.HTML(label="Entity Visualization")
|
| 553 |
|
|
@@ -565,33 +577,20 @@ def create_interface():
|
|
| 565 |
|
| 566 |
### Key Features
|
| 567 |
|
| 568 |
-
- **X-ray Image Analysis**: Detects abnormalities in chest X-rays
|
| 569 |
-
- **Medical Report Processing**: Extracts key information from patient reports
|
| 570 |
-
- **Multi-modal Integration**: Combines insights from both image and text data
|
| 571 |
-
|
| 572 |
-
### Models Used
|
| 573 |
-
|
| 574 |
-
- **X-ray Analysis**: facebook/deit-base-patch16-224-medical-cxr
|
| 575 |
-
- **Medical Text Analysis**: medicalai/ClinicalBERT
|
| 576 |
|
| 577 |
### Important Disclaimer
|
| 578 |
|
| 579 |
This tool is for educational and research purposes only. It is not intended to provide medical advice or replace professional healthcare. Always consult with qualified healthcare providers for medical decisions.
|
| 580 |
""")
|
| 581 |
|
| 582 |
-
# Consultation completion section
|
| 583 |
-
with gr.Row():
|
| 584 |
-
with gr.Column():
|
| 585 |
-
end_consultation_btn = gr.Button(
|
| 586 |
-
"End Consultation",
|
| 587 |
-
variant="stop",
|
| 588 |
-
size="lg"
|
| 589 |
-
)
|
| 590 |
-
completion_status = gr.HTML()
|
| 591 |
-
|
| 592 |
# Set up event handlers
|
| 593 |
multi_img_enhance.click(
|
| 594 |
-
app.enhance_image,
|
|
|
|
|
|
|
| 595 |
)
|
| 596 |
multi_analyze_btn.click(
|
| 597 |
app.analyze_multimodal,
|
|
@@ -599,7 +598,11 @@ def create_interface():
|
|
| 599 |
outputs=[multi_results, multi_plot],
|
| 600 |
)
|
| 601 |
|
| 602 |
-
img_enhance.click(
|
|
|
|
|
|
|
|
|
|
|
|
|
| 603 |
img_analyze_btn.click(
|
| 604 |
app.analyze_image,
|
| 605 |
inputs=img_input,
|
|
@@ -612,59 +615,12 @@ def create_interface():
|
|
| 612 |
outputs=[text_output, text_results, text_plot],
|
| 613 |
)
|
| 614 |
|
| 615 |
-
|
| 616 |
-
|
| 617 |
-
|
| 618 |
-
|
| 619 |
-
|
| 620 |
-
|
| 621 |
-
# Replace with your actual Flask app URL
|
| 622 |
-
flask_app_url = "http://127.0.0.1:600/complete_consultation"
|
| 623 |
-
|
| 624 |
-
response = requests.post(
|
| 625 |
-
flask_app_url,
|
| 626 |
-
json={"appointment_id": appointment_id},
|
| 627 |
-
timeout=10
|
| 628 |
-
)
|
| 629 |
-
|
| 630 |
-
if response.status_code == 200:
|
| 631 |
-
return """
|
| 632 |
-
<div class='alert alert-success'>
|
| 633 |
-
Consultation completed successfully. Redirecting...
|
| 634 |
-
<script>
|
| 635 |
-
setTimeout(function() {
|
| 636 |
-
window.location.href = "http://127.0.0.1:600/doctors";
|
| 637 |
-
}, 2000);
|
| 638 |
-
</script>
|
| 639 |
-
</div>
|
| 640 |
-
"""
|
| 641 |
-
else:
|
| 642 |
-
return f"""
|
| 643 |
-
<div class='alert alert-error'>
|
| 644 |
-
Error completing appointment (Status: {response.status_code}).
|
| 645 |
-
Please contact support.
|
| 646 |
-
</div>
|
| 647 |
-
"""
|
| 648 |
-
|
| 649 |
-
except Exception as e:
|
| 650 |
-
return f"""
|
| 651 |
-
<div class='alert alert-error'>
|
| 652 |
-
Error: {str(e)}
|
| 653 |
-
</div>
|
| 654 |
-
"""
|
| 655 |
-
|
| 656 |
-
end_consultation_btn.click(
|
| 657 |
-
fn=complete_consultation,
|
| 658 |
-
inputs=[appointment_id],
|
| 659 |
-
outputs=completion_status
|
| 660 |
-
)
|
| 661 |
-
|
| 662 |
-
try:
|
| 663 |
-
interface.launch()
|
| 664 |
-
except Exception as e:
|
| 665 |
-
logging.error(f"Failed to launch interface: {str(e)}")
|
| 666 |
-
raise RuntimeError("Failed to launch MediSync interface") from e
|
| 667 |
-
|
| 668 |
|
| 669 |
if __name__ == "__main__":
|
| 670 |
logging.basicConfig(
|
|
|
|
| 404 |
# import gradio as gr
|
| 405 |
# from mediSync.app import MediSyncApp
|
| 406 |
|
| 407 |
+
import os
|
| 408 |
+
import logging
|
| 409 |
+
from pathlib import Path
|
| 410 |
+
import requests
|
| 411 |
+
import gradio as gr
|
| 412 |
+
from PIL import Image
|
| 413 |
+
import io
|
| 414 |
+
|
| 415 |
+
class MediSyncApp:
|
| 416 |
+
"""Mock application class for demonstration purposes."""
|
| 417 |
+
|
| 418 |
+
def enhance_image(self, image):
|
| 419 |
+
"""Mock image enhancement function."""
|
| 420 |
+
if image is None:
|
| 421 |
+
return None
|
| 422 |
+
return image
|
| 423 |
+
|
| 424 |
+
def analyze_multimodal(self, image, text):
|
| 425 |
+
"""Mock multimodal analysis function."""
|
| 426 |
+
return (
|
| 427 |
+
"<div style='color: green'>Multimodal analysis completed successfully.</div>",
|
| 428 |
+
"<div>Visualization placeholder</div>"
|
| 429 |
+
)
|
| 430 |
+
|
| 431 |
+
def analyze_image(self, image):
|
| 432 |
+
"""Mock image analysis function."""
|
| 433 |
+
if image is None:
|
| 434 |
+
return None, "<div style='color: red'>No image provided</div>", ""
|
| 435 |
+
return (
|
| 436 |
+
image,
|
| 437 |
+
"<div style='color: green'>Image analysis completed successfully.</div>",
|
| 438 |
+
"<div>Image visualization placeholder</div>"
|
| 439 |
+
)
|
| 440 |
+
|
| 441 |
+
def analyze_text(self, text):
|
| 442 |
+
"""Mock text analysis function."""
|
| 443 |
+
if not text.strip():
|
| 444 |
+
return "", "<div style='color: red'>No text provided</div>", ""
|
| 445 |
+
return (
|
| 446 |
+
text,
|
| 447 |
+
"<div style='color: green'>Text analysis completed successfully.</div>",
|
| 448 |
+
"<div>Text visualization placeholder</div>"
|
| 449 |
+
)
|
| 450 |
|
| 451 |
+
def create_interface():
|
| 452 |
+
"""Create and launch the Gradio interface for Hugging Face Spaces."""
|
| 453 |
app = MediSyncApp()
|
| 454 |
|
| 455 |
# Example medical report for demo
|
|
|
|
| 471 |
RECOMMENDATIONS: Follow-up chest CT to further characterize the nodular opacity in the right lower lobe.
|
| 472 |
"""
|
| 473 |
|
| 474 |
+
# Get sample image - simplified for Hugging Face Spaces
|
| 475 |
sample_image_path = None
|
| 476 |
try:
|
| 477 |
+
# Try to use a sample image from the web
|
| 478 |
+
sample_url = "https://raw.githubusercontent.com/ieee8023/covid-chestxray-dataset/master/images/1-s2.0-S0929664620300449-gr2_lrg-a.jpg"
|
| 479 |
+
response = requests.get(sample_url, timeout=10)
|
| 480 |
+
if response.status_code == 200:
|
| 481 |
+
sample_image = Image.open(io.BytesIO(response.content))
|
| 482 |
+
sample_image_path = sample_image
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 483 |
except Exception as e:
|
| 484 |
+
logging.warning(f"Could not load sample image: {str(e)}")
|
| 485 |
|
| 486 |
+
# Define interface
|
| 487 |
with gr.Blocks(
|
| 488 |
title="MediSync: Multi-Modal Medical Analysis System",
|
| 489 |
+
theme=gr.themes.Soft(),
|
| 490 |
+
css=".alert {padding: 10px; border-radius: 5px;} .alert-error {background-color: #ffebee;} .alert-success {background-color: #e8f5e9;}"
|
| 491 |
) as interface:
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 492 |
gr.Markdown("""
|
| 493 |
# MediSync: Multi-Modal Medical Analysis System
|
| 494 |
|
|
|
|
| 499 |
1. Upload a chest X-ray image
|
| 500 |
2. Enter the corresponding medical report text
|
| 501 |
3. Choose the analysis type: image-only, text-only, or multimodal (combined)
|
| 502 |
+
4. View the analysis results
|
| 503 |
""")
|
| 504 |
|
| 505 |
with gr.Tab("Multimodal Analysis"):
|
| 506 |
with gr.Row():
|
| 507 |
with gr.Column():
|
| 508 |
multi_img_input = gr.Image(label="Upload X-ray Image", type="pil")
|
| 509 |
+
multi_img_enhance = gr.Button("Enhance Image", variant="secondary")
|
|
|
|
| 510 |
multi_text_input = gr.Textbox(
|
| 511 |
label="Enter Medical Report Text",
|
| 512 |
placeholder="Enter the radiologist's report text here...",
|
| 513 |
lines=10,
|
| 514 |
+
value=example_report,
|
| 515 |
)
|
|
|
|
| 516 |
multi_analyze_btn = gr.Button(
|
| 517 |
"Analyze Image & Text", variant="primary"
|
| 518 |
)
|
|
|
|
| 532 |
with gr.Row():
|
| 533 |
with gr.Column():
|
| 534 |
img_input = gr.Image(label="Upload X-ray Image", type="pil")
|
| 535 |
+
img_enhance = gr.Button("Enhance Image", variant="secondary")
|
| 536 |
img_analyze_btn = gr.Button("Analyze Image", variant="primary")
|
| 537 |
|
| 538 |
with gr.Column():
|
|
|
|
| 559 |
text_analyze_btn = gr.Button("Analyze Text", variant="primary")
|
| 560 |
|
| 561 |
with gr.Column():
|
| 562 |
+
text_output = gr.Textbox(label="Processed Text", interactive=False)
|
| 563 |
text_results = gr.HTML(label="Analysis Results")
|
| 564 |
text_plot = gr.HTML(label="Entity Visualization")
|
| 565 |
|
|
|
|
| 577 |
|
| 578 |
### Key Features
|
| 579 |
|
| 580 |
+
- **X-ray Image Analysis**: Detects abnormalities in chest X-rays
|
| 581 |
+
- **Medical Report Processing**: Extracts key information from patient reports
|
| 582 |
+
- **Multi-modal Integration**: Combines insights from both image and text data
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 583 |
|
| 584 |
### Important Disclaimer
|
| 585 |
|
| 586 |
This tool is for educational and research purposes only. It is not intended to provide medical advice or replace professional healthcare. Always consult with qualified healthcare providers for medical decisions.
|
| 587 |
""")
|
| 588 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 589 |
# Set up event handlers
|
| 590 |
multi_img_enhance.click(
|
| 591 |
+
app.enhance_image,
|
| 592 |
+
inputs=multi_img_input,
|
| 593 |
+
outputs=multi_img_input
|
| 594 |
)
|
| 595 |
multi_analyze_btn.click(
|
| 596 |
app.analyze_multimodal,
|
|
|
|
| 598 |
outputs=[multi_results, multi_plot],
|
| 599 |
)
|
| 600 |
|
| 601 |
+
img_enhance.click(
|
| 602 |
+
app.enhance_image,
|
| 603 |
+
inputs=img_input,
|
| 604 |
+
outputs=img_output
|
| 605 |
+
)
|
| 606 |
img_analyze_btn.click(
|
| 607 |
app.analyze_image,
|
| 608 |
inputs=img_input,
|
|
|
|
| 615 |
outputs=[text_output, text_results, text_plot],
|
| 616 |
)
|
| 617 |
|
| 618 |
+
# Launch configuration for Hugging Face Spaces
|
| 619 |
+
interface.launch(
|
| 620 |
+
server_name="0.0.0.0",
|
| 621 |
+
server_port=int(os.getenv("PORT", "7860")),
|
| 622 |
+
share=False
|
| 623 |
+
)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 624 |
|
| 625 |
if __name__ == "__main__":
|
| 626 |
logging.basicConfig(
|