Update app.py

app.py

@@ -232,237 +232,344 @@ class DicomAnalyzer:
         except Exception as e:
             print(f"Error analyzing ROI: {str(e)}")
             return self.display_image, f"Error analyzing ROI: {str(e)}"
-import gradio as gr
-import cv2
-import numpy as np
-import pandas as pd
-import pydicom
-import io
-from PIL import Image
-import openpyxl
-from openpyxl.utils import get_column_letter, column_index_from_string
-import logging
-import time
-import traceback
-from functools import wraps
-import sys
+    def update_display(self):
+        try:
+            if self.original_display is None:
+                return None
 
-print("Starting imports completed...")
+            height, width = self.original_display.shape[:2]
+            new_height = int(height * self.zoom_factor)
+            new_width = int(width * self.zoom_factor)
 
-# Set up logging
-logging.basicConfig(
-    level=logging.DEBUG,
-    format='%(asctime)s - %(levelname)s - %(message)s',
-    handlers=[
-        logging.FileHandler('dicom_analyzer_debug.log'),
-        logging.StreamHandler(sys.stdout)
-    ]
-)
+            zoomed = cv2.resize(self.original_display, (new_width, new_height), 
+                              interpolation=cv2.INTER_CUBIC)
 
-logger = logging.getLogger(__name__)
+            zoomed_bgr = cv2.cvtColor(zoomed, cv2.COLOR_RGB2BGR)
 
-def debug_decorator(func):
-    @wraps(func)
-    def wrapper(*args, **kwargs):
-        logger.debug(f"Entering {func.__name__}")
-        start_time = time.time()
-        try:
-            result = func(*args, **kwargs)
-            logger.debug(f"Function {func.__name__} completed successfully")
-            return result
+            for x, y, diameter in self.marks:
+                zoomed_x = int(x * self.zoom_factor)
+                zoomed_y = int(y * self.zoom_factor)
+                zoomed_radius = int((diameter/2.0) * self.zoom_factor)
+                
+                cv2.circle(zoomed_bgr,
+                          (zoomed_x, zoomed_y),
+                          zoomed_radius,
+                          self.CIRCLE_COLOR,
+                          1,
+                          lineType=cv2.LINE_AA)
+                
+                num_points = 8
+                for i in range(num_points):
+                    angle = 2 * np.pi * i / num_points
+                    point_x = int(zoomed_x + zoomed_radius * np.cos(angle))
+                    point_y = int(zoomed_y + zoomed_radius * np.sin(angle))
+                    cv2.circle(zoomed_bgr,
+                              (point_x, point_y),
+                              1,
+                              self.CIRCLE_COLOR,
+                              -1,
+                              lineType=cv2.LINE_AA)
+
+            zoomed = cv2.cvtColor(zoomed_bgr, cv2.COLOR_BGR2RGB)
+
+            self.max_pan_x = max(0, new_width - width)
+            self.max_pan_y = max(0, new_height - height)
+            self.pan_x = min(max(0, self.pan_x), self.max_pan_x)
+            self.pan_y = min(max(0, self.pan_y), self.max_pan_y)
+
+            visible = zoomed[
+                int(self.pan_y):int(self.pan_y + height),
+                int(self.pan_x):int(self.pan_x + width)
+            ]
+
+            return visible
         except Exception as e:
-            logger.error(f"Error in {func.__name__}: {str(e)}")
-            logger.error(traceback.format_exc())
-            raise
-        finally:
-            end_time = time.time()
-            logger.debug(f"Execution time: {end_time - start_time:.4f} seconds")
-    return wrapper
-
-class DicomAnalyzer:
-    def __init__(self):
-        self.results = []
-        self.circle_diameter = 9.0  # Changed to float for precise calculations
-        self.zoom_factor = 1.0
-        self.current_image = None
-        self.dicom_data = None
-        self.display_image = None
-        self.marks = []  # Store (x, y, diameter) for each mark
-        self.original_image = None
-        self.original_display = None
-        # Pan position
-        self.pan_x = 0
-        self.pan_y = 0
-        self.max_pan_x = 0
-        self.max_pan_y = 0
-        # Circle color in BGR
-        self.CIRCLE_COLOR = (0, 255, 255)  # BGR Yellow
-        print("DicomAnalyzer initialized...")
-
-    def load_dicom(self, file):
+            print(f"Error updating display: {str(e)}")
+            return self.original_display
+
+    def format_results(self):
+        if not self.results:
+            return "No measurements yet"
+        df = pd.DataFrame(self.results)
+        columns_order = ['Area (mm²)', 'Mean', 'StdDev', 'Min', 'Max', 'Point']
+        df = df[columns_order]
+        return df.to_string(index=False)
+
+    def save_results(self):
         try:
-            if file is None:
-                return None, "No file uploaded"
-            
-            if hasattr(file, 'name'):
-                dicom_data = pydicom.dcmread(file.name)
-            else:
-                dicom_data = pydicom.dcmread(file)
-                
-            image = dicom_data.pixel_array.astype(np.float32)
+            if not self.results:
+                return None, "No results to save"
             
-            # Store original pixel values before any scaling
-            self.original_image = image.copy()
+            df = pd.DataFrame(self.results)
+            columns_order = ['Area (mm²)', 'Mean', 'StdDev', 'Min', 'Max', 'Point']
+            df = df[columns_order]
             
-            # Apply DICOM scaling for display
-            rescale_slope = getattr(dicom_data, 'RescaleSlope', 1)
-            rescale_intercept = getattr(dicom_data, 'RescaleIntercept', 0)
-            image = (image * rescale_slope) + rescale_intercept
+            temp_file = "analysis_results.xlsx"
+            df.to_excel(temp_file, index=False)
             
-            self.current_image = image
-            self.dicom_data = dicom_data
-            
-            self.display_image = self.normalize_image(image)
-            self.original_display = self.display_image.copy()
-            
-            # Reset view on new image
-            self.reset_view()
-            print("DICOM file loaded successfully")
-            
-            return self.display_image, "DICOM file loaded successfully"
+            return temp_file, "Results saved successfully"
         except Exception as e:
-            print(f"Error loading DICOM file: {str(e)}")
-            return None, f"Error loading DICOM file: {str(e)}"
+            print(f"Error saving results: {str(e)}")
+            return None, f"Error saving results: {str(e)}"
 
-    def normalize_image(self, image):
+    def save_results_to_template(self, template_path, output_path):
         try:
-            normalized = cv2.normalize(
-                image, 
-                None, 
-                alpha=0,
-                beta=255,
-                norm_type=cv2.NORM_MINMAX,
-                dtype=cv2.CV_8U
-            )
-            if len(normalized.shape) == 2:
-                normalized = cv2.cvtColor(normalized, cv2.COLOR_GRAY2BGR)
-            return normalized
-        except Exception as e:
-            print(f"Error normalizing image: {str(e)}")
-            return None
-
-    def reset_view(self):
-        self.zoom_factor = 1.0
-        self.pan_x = 0
-        self.pan_y = 0
-        if self.original_display is not None:
-            return self.update_display()
-        return None
+            if not self.results:
+                return None, "No results to save"
+
+            # Load the Excel template
+            wb = openpyxl.load_workbook(template_path)
+            ws = wb.active
+
+            # Define row groups and phantom sizes
+            row_groups = {
+                "7mm": [41, 42],
+                "6.5mm": [67, 68],
+                "6mm": [93, 94],
+                "5.5mm": [119, 120],
+                "5mm": [145, 146],
+                "4.5mm": [171, 172],
+                "4mm": [197, 198],
+                "3.5mm": [223, 224],
+                "3mm": [249, 250],
+                "2.5mm": [275, 276]
+            }
 
-    def zoom_in(self, image):
-        print("Zooming in...")
-        self.zoom_factor = min(20.0, self.zoom_factor + 0.5)
-        return self.update_display()
+            # Define columns for measurements
+            columns = {
+                'Area (mm²)': "B",
+                'Mean': "C",
+                'StdDev': "D",
+                'Min': "E",
+                'Max': "F"
+            }
 
-    def zoom_out(self, image):
-        print("Zooming out...")
-        self.zoom_factor = max(1.0, self.zoom_factor - 0.5)
-        return self.update_display()
+            # Map results to phantom sizes (assuming results are ordered for each size)
+            result_idx = 0
 
-    def handle_keyboard(self, key):
-        try:
-            print(f"Handling key press: {key}")
-            pan_amount = int(5 * self.zoom_factor)
-            
-            original_pan_x = self.pan_x
-            original_pan_y = self.pan_y
-            
-            if key == 'ArrowLeft':
-                self.pan_x = max(0, self.pan_x - pan_amount)
-            elif key == 'ArrowRight':
-                self.pan_x = min(self.max_pan_x, self.pan_x + pan_amount)
-            elif key == 'ArrowUp':
-                self.pan_y = max(0, self.pan_y - pan_amount)
-            elif key == 'ArrowDown':
-                self.pan_y = min(self.max_pan_y, self.pan_y + pan_amount)
-            
-            print(f"Pan X: {self.pan_x} (was {original_pan_x})")
-            print(f"Pan Y: {self.pan_y} (was {original_pan_y})")
-            print(f"Max Pan X: {self.max_pan_x}")
-            print(f"Max Pan Y: {self.max_pan_y}")
-            
-            return self.update_display()
-        except Exception as e:
-            print(f"Error handling keyboard input: {str(e)}")
-            return self.display_image
+            for size, rows in row_groups.items():
+                for row in rows:
+                    if result_idx >= len(self.results):
+                        break
 
-    def analyze_roi(self, evt: gr.SelectData):
-        try:
-            if self.current_image is None:
-                return None, "No image loaded"
+                    result = self.results[result_idx]
 
-            clicked_x = evt.index[0]
-            clicked_y = evt.index[1]
-            
-            x = clicked_x + self.pan_x
-            y = clicked_y + self.pan_y
-            if self.zoom_factor != 1.0:
-                x = x / self.zoom_factor
-                y = y / self.zoom_factor
-            
-            x = int(round(x))
-            y = int(round(y))
-            
-            height, width = self.original_image.shape[:2]
-            
-            Y, X = np.ogrid[:height, :width]
-            
-            radius = self.circle_diameter / 2.0
-            r_squared = radius * radius
-            
-            dx = X - x
-            dy = Y - y
-            dist_squared = dx*dx + dy*dy
-            
-            mask = np.zeros((height, width), dtype=bool)
-            mask[dist_squared <= r_squared] = True
-            
-            roi_pixels = self.original_image[mask]
-            
-            if len(roi_pixels) == 0:
-                return self.display_image, "Error: No pixels selected"
+                    # Write each metric to the appropriate cell
+                    for metric, col in columns.items():
+                        cell = f"{col}{row}"
+                        value = result.get(metric, '')
+                        if value:
+                            try:
+                                ws[cell] = float(value)
+                            except ValueError:
+                                ws[cell] = value
 
-            pixel_spacing = float(self.dicom_data.PixelSpacing[0])
-            
-            n_pixels = np.sum(mask)
-            area = n_pixels * (pixel_spacing ** 2)
-            
-            mean_value = np.mean(roi_pixels)
-            std_dev = np.std(roi_pixels, ddof=1)
-            min_val = np.min(roi_pixels)
-            max_val = np.max(roi_pixels)
+                    result_idx += 1
 
-            rescale_slope = getattr(self.dicom_data, 'RescaleSlope', 1)
-            rescale_intercept = getattr(self.dicom_data, 'RescaleIntercept', 0)
-            
-            mean_value = (mean_value * rescale_slope) + rescale_intercept
-            std_dev = std_dev * rescale_slope
-            min_val = (min_val * rescale_slope) + rescale_intercept
-            max_val = (max_val * rescale_slope) + rescale_intercept
+            # Save the workbook
+            wb.save(output_path)
 
-            result = {
-                'Area (mm²)': f"{area:.3f}",
-                'Mean': f"{mean_value:.3f}",
-                'StdDev': f"{std_dev:.3f}",
-                'Min': f"{min_val:.3f}",
-                'Max': f"{max_val:.3f}",
-                'Point': f"({x}, {y})"
-            }
-            
-            self.results.append(result)
-            self.marks.append((x, y, self.circle_diameter))
+            return output_path, "Results saved successfully in the template format"
 
-            return self.update_display(), self.format_results()
         except Exception as e:
-            print(f"Error analyzing ROI: {str(e)}")
-            return self.display_image, f"Error analyzing ROI: {str(e)}"
+            print(f"Error saving results to template: {str(e)}")
+            return None, f"Error saving results to template: {str(e)}"
+
+    def add_blank_row(self, image):
+        self.results.append({
+            'Area (mm²)': '',
+            'Mean': '',
+            'StdDev': '',
+            'Min': '',
+            'Max': '',
+            'Point': ''
+        })
+        return image, self.format_results()
+
+    def add_zero_row(self, image):
+        self.results.append({
+            'Area (mm²)': '0.000',
+            'Mean': '0.000',
+            'StdDev': '0.000',
+            'Min': '0.000',
+            'Max': '0.000',
+            'Point': '(0, 0)'
+        })
+        return image, self.format_results()
+
+    def undo_last(self, image):
+        if self.results:
+            self.results.pop()
+        if self.marks:
+            self.marks.pop()
+        return self.update_display(), self.format_results()
+
+def create_interface():
+    print("Creating interface...")
+    analyzer = DicomAnalyzer()
+    
+    with gr.Blocks(css="#image_display { outline: none; }") as interface:
+        gr.Markdown("# DICOM Image Analyzer")
+        
+        with gr.Row():
+            with gr.Column():
+                file_input = gr.File(label="Upload DICOM file")
+                template_input = gr.File(label="Upload Excel Template")
+                diameter_slider = gr.Slider(
+                    minimum=1,
+                    maximum=20,
+                    value=9,
+                    step=1,
+                    label="ROI Diameter (pixels)"
+                )
+                
+                with gr.Row():
+                    zoom_in_btn = gr.Button("Zoom In (+)")
+                    zoom_out_btn = gr.Button("Zoom Out (-)")
+                    reset_btn = gr.Button("Reset View")
+                
+            with gr.Column():
+                image_display = gr.Image(
+                    label="DICOM Image",
+                    interactive=True,
+                    elem_id="image_display"
+                )
+                
+        with gr.Row():
+            blank_btn = gr.Button("Add Blank Row")
+            zero_btn = gr.Button("Add Zero Row")
+            undo_btn = gr.Button("Undo Last")
+            save_btn = gr.Button("Save Results")
+            save_template_btn = gr.Button("Save to Template")
+            
+        results_display = gr.Textbox(label="Results", interactive=False)
+        file_output = gr.File(label="Download Results")
+        key_press = gr.Textbox(visible=False, elem_id="key_press")
+        
+        gr.Markdown("""
+        ### Controls:
+        - Use arrow keys to pan when zoomed in
+        - Click points to measure
+        - Use Zoom In/Out buttons or Reset View to adjust zoom level
+        - Upload template and use Save to Template for formatted results
+        """)
+        
+        def update_diameter(x):
+            analyzer.circle_diameter = float(x)
+            print(f"Diameter updated to: {x}")
+            return f"Diameter set to {x} pixels"
+
+        def save_to_template(template_file):
+            if template_file is None:
+                return None, "No template file provided"
+            
+            output_path = "analysis_results_from_template.xlsx"
+            return analyzer.save_results_to_template(template_file.name, output_path)
+
+        # Event handlers
+        file_input.change(
+            fn=analyzer.load_dicom,
+            inputs=file_input,
+            outputs=[image_display, results_display]
+        )
+        
+        image_display.select(
+            fn=analyzer.analyze_roi,
+            outputs=[image_display, results_display]
+        )
+        
+        diameter_slider.change(
+            fn=update_diameter,
+            inputs=diameter_slider,
+            outputs=gr.Textbox(label="Status")
+        )
+        
+        zoom_in_btn.click(
+            fn=analyzer.zoom_in,
+            inputs=image_display,
+            outputs=image_display,
+            queue=False
+        )
+        
+        zoom_out_btn.click(
+            fn=analyzer.zoom_out,
+            inputs=image_display,
+            outputs=image_display,
+            queue=False
+        )
+        
+        reset_btn.click(
+            fn=analyzer.reset_view,
+            outputs=image_display
+        )
+        
+        key_press.change(
+            fn=analyzer.handle_keyboard,
+            inputs=key_press,
+            outputs=image_display
+        )
+        
+        blank_btn.click(
+            fn=analyzer.add_blank_row,
+            inputs=image_display,
+            outputs=[image_display, results_display]
+        )
+        
+        zero_btn.click(
+            fn=analyzer.add_zero_row,
+            inputs=image_display,
+            outputs=[image_display, results_display]
+        )
+        
+        undo_btn.click(
+            fn=analyzer.undo_last,
+            inputs=image_display,
+            outputs=[image_display, results_display]
+        )
+        
+        save_btn.click(
+            fn=analyzer.save_results,
+            outputs=[file_output, results_display]
+        )
+
+        save_template_btn.click(
+            fn=save_to_template,
+            inputs=[template_input],
+            outputs=[file_output, results_display]
+        )
+
+        js = """
+        <script>
+        document.addEventListener('keydown', function(e) {
+            if (['ArrowUp', 'ArrowDown', 'ArrowLeft', 'ArrowRight'].includes(e.key)) {
+                e.preventDefault();
+                const keyPressElement = document.querySelector('#key_press textarea');
+                if (keyPressElement) {
+                    keyPressElement.value = e.key;
+                    keyPressElement.dispatchEvent(new Event('input'));
+                }
+            }
+        });
+        </script>
+        """
+        gr.HTML(js)
+    
+    print("Interface created successfully")
+    return interface
+
+if __name__ == "__main__":
+    try:
+        print("Starting application...")
+        interface = create_interface()
+        print("Launching interface...")
+        interface.launch(
+            server_name="0.0.0.0",
+            server_port=7860,
+            share=True,
+            debug=True
+        )
+    except Exception as e:
+        print(f"Error launching application: {str(e)}")
+        logger.error(f"Error launching application: {str(e)}")
+        logger.error(traceback.format_exc())
+        raise e