app.py

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

print("Starting imports completed...")

# 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)
    ]
)

logger = logging.getLogger(__name__)

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
        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
        self.zoom_factor = 1.0
        self.current_image = None
        self.dicom_data = None
        self.display_image = None
        self.marks = []
        self.original_image = None
        self.original_display = None
        self.pan_x = 0
        self.pan_y = 0
        self.max_pan_x = 0
        self.max_pan_y = 0
        self.CIRCLE_COLOR = (0, 255, 255)  # BGR Yellow
        print("DicomAnalyzer initialized...")

    def save_results(self):
        """
        Basic save function for raw results with improved error handling and logging
        """
        try:
            if not self.results:
                logger.warning("Attempted to save with no results")
                return None, "No results to save"

            df = pd.DataFrame(self.results)
            columns_order = ['Area (mm²)', 'Mean', 'StdDev', 'Min', 'Max', 'Point']
            df = df[columns_order]

            timestamp = time.strftime("%Y%m%d_%H%M%S")
            output_file = f"analysis_results_{timestamp}.xlsx"

            with pd.ExcelWriter(output_file, engine='openpyxl') as writer:
                df.to_excel(writer, index=False, sheet_name='Results')
                
                worksheet = writer.sheets['Results']
                for idx, col in enumerate(df.columns):
                    max_length = max(
                        df[col].astype(str).apply(len).max(),
                        len(str(col))
                    ) + 2
                    worksheet.column_dimensions[get_column_letter(idx + 1)].width = max_length

            logger.info(f"Results saved successfully to {output_file}")
            return output_file, f"Results saved successfully to {output_file}"

        except Exception as e:
            error_msg = f"Error saving results: {str(e)}"
            logger.error(error_msg)
            logger.error(traceback.format_exc())
            return None, error_msg

    def reset_all(self, image):
        self.results = []
        self.marks = []
        self.reset_view()
        return self.update_display(), "All data has been reset"

    def load_dicom(self, file):
        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)
            self.original_image = image.copy()
            
            rescale_slope = getattr(dicom_data, 'RescaleSlope', 1)
            rescale_intercept = getattr(dicom_data, 'RescaleIntercept', 0)
            image = (image * rescale_slope) + rescale_intercept
            
            self.current_image = image
            self.dicom_data = dicom_data
            self.display_image = self.normalize_image(image)
            self.original_display = self.display_image.copy()
            
            self.reset_all(None)
            print("DICOM file loaded successfully")
            
            return self.display_image, "DICOM file loaded successfully"
        except Exception as e:
            print(f"Error loading DICOM file: {str(e)}")
            return None, f"Error loading DICOM file: {str(e)}"

    def normalize_image(self, image):
        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

    def zoom_in(self, image):
        print("Zooming in...")
        self.zoom_factor = min(20.0, self.zoom_factor + 0.5)
        return self.update_display()

    def zoom_out(self, image):
        print("Zooming out...")
        self.zoom_factor = max(1.0, self.zoom_factor - 0.5)
        return self.update_display()

    def handle_keyboard(self, key):
        try:
            print(f"Handling key press: {key}")
            pan_amount = int(5 * self.zoom_factor)
            
            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)
            
            return self.update_display()
        except Exception as e:
            print(f"Error handling keyboard input: {str(e)}")
            return self.display_image

    def update_display(self):
        try:
            if self.original_display is None:
                return None

            height, width = self.original_display.shape[:2]
            new_height = int(height * self.zoom_factor)
            new_width = int(width * self.zoom_factor)

            zoomed = cv2.resize(
                self.original_display,
                (new_width, new_height),
                interpolation=cv2.INTER_CUBIC
            )

            zoomed_bgr = cv2.cvtColor(zoomed, cv2.COLOR_RGB2BGR)

            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:
            print(f"Error updating display: {str(e)}")
            return self.original_display

    def analyze_roi(self, evt: gr.SelectData):
        try:
            if self.current_image is None:
                return None, "No image loaded"

            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"

            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)

            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

            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 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)}"

    def add_formulas_to_template(self, ws, row_pair, col_group, red_font):
        try:
            base_col = col_group[1]  # Mean column
            std_col = col_group[2]   # StdDev column
            
            row1, row2 = row_pair
            
            # SNR Formula for the first row with IFERROR
            formula1 = f"=IFERROR({base_col}{row1}/{std_col}{row1},\"\")"
            formula_col = get_column_letter(column_index_from_string(col_group[-1]) + 1)
            cell1 = ws[f"{formula_col}{row1}"]
            cell1.value = formula1
            cell1.font = red_font
            cell1.alignment = openpyxl.styles.Alignment(horizontal='center')
            
            # CNR Formula for the second row with IFERROR
            formula2 = f"=IFERROR(({base_col}{row1}-{base_col}{row2})/{std_col}{row2},\"\")"
            cell2 = ws[f"{formula_col}{row2}"]
            cell2.value = formula2
            cell2.font = red_font
            cell2.alignment = openpyxl.styles.Alignment(horizontal='center')
            
            logger.debug(f"Added formulas for rows {row1},{row2} in column {formula_col}")
        except Exception as e:
            logger.error(f"Error adding formulas: {str(e)}")

    def save_formatted_results(self, output_path):
        try:
            if not self.results:
                return None, "No results to save"

            wb = openpyxl.Workbook()
            ws = wb.active
            red_font = openpyxl.styles.Font(color="FF0000")
            center_alignment = openpyxl.styles.Alignment(horizontal='center')
            
            # Define headers
            headers = ['Area', 'Mean', 'StdDev', 'Min', 'Max']

            column_groups = [
                ('B', 'C', 'D', 'E', 'F'), ('H', 'I', 'J', 'K', 'L'),
                ('N', 'O', 'P', 'Q', 'R'), ('T', 'U', 'V', 'W', 'X'),
                ('Z', 'AA', 'AB', 'AC', 'AD'), ('AF', 'AG', 'AH', 'AI', 'AJ'),
                ('AL', 'AM', 'AN', 'AO', 'AP'), ('AR', 'AS', 'AT', 'AU', 'AV'),
                ('AX', 'AY', 'AZ', 'BA', 'BB'), ('BD', 'BE', 'BF', 'BG', 'BH'),
                ('BJ', 'BK', 'BL', 'BM', 'BN'), ('BP', 'BQ', 'BR', 'BS', 'BT'),
                ('BV', 'BW', 'BX', 'BY', 'BZ')
            ]

            # Add headers for each column group
            for cols in column_groups:
                for i, header in enumerate(headers):
                    cell = ws[f"{cols[i]}1"]
                    cell.value = header
                    cell.alignment = center_alignment

            row_pairs = [
                (2, 3), (5, 6), (8, 9), (11, 12), (14, 15),
                (17, 18), (20, 21), (23, 24), (26, 27), (29, 30)
            ]

            phantom_sizes = [
                '(7mm)', '(6.5mm)', '(6mm)', '(5.5mm)', '(5mm)',
                '(4.5mm)', '(4mm)', '(3.5mm)', '(3mm)', '(2.5mm)'
            ]
            
            for i, size in enumerate(phantom_sizes):
                header_cell = ws.cell(row=row_pairs[i][0]-1, column=1, value=size)
                header_cell.font = red_font
                header_cell.alignment = center_alignment

            result_idx = 0
            current_col_group = 0
            current_row_pair = 0
            
            while result_idx < len(self.results):
                if current_row_pair >= len(row_pairs):
                    break
                    
                cols = column_groups[current_col_group]
                rows = row_pairs[current_row_pair]
                
                if result_idx < len(self.results):
                    result = self.results[result_idx]
                    self._write_result_to_cells(ws, result, cols, rows[0])
                    result_idx += 1
                
                if result_idx < len(self.results):
                    result = self.results[result_idx]
                    self._write_result_to_cells(ws, result, cols, rows[1])
                    result_idx += 1
                
                self.add_formulas_to_template(ws, rows, cols, red_font)
                
                current_col_group += 1
                if current_col_group >= len(column_groups):
                    current_col_group = 0
                    current_row_pair += 1

            # Center align all data cells
            for cols in column_groups:
                for col in cols:
                    for row in range(2, 31):
                        cell = ws[f"{col}{row}"]
                        if cell.value is not None:
                            cell.alignment = center_alignment

            # Add space before averages tables
            current_row = 32

            # Headers for StdDev Averages
            stddev_header = ws.cell(row=current_row, column=1, value="StdDev Averages")
            stddev_header.font = red_font
            stddev_header.alignment = center_alignment
            current_row += 1
            
            # Calculate StdDev averages for each row pair (top row only)
            for i, size in enumerate(phantom_sizes):
                row_number = row_pairs[i][0]  # First row
                stddev_values = []
                
                for cols in column_groups:
                    stddev_col = cols[2]  # StdDev column
                    cell_value = ws[f"{stddev_col}{row_number}"].value
                    if cell_value not in [0, None, '']:  # Ignore zeros and empty
                        stddev_values.append(float(cell_value))
                
                if stddev_values:
                    avg = sum(stddev_values) / len(stddev_values)
                    size_cell = ws.cell(row=current_row, column=1, value=size)
                    size_cell.alignment = center_alignment
                    
                    avg_cell = ws.cell(row=current_row, column=2, value=avg)
                    avg_cell.number_format = '0.000'
                    avg_cell.alignment = center_alignment
                current_row += 1

            current_row += 2  # Space between tables

            # Headers for CNR Averages
            cnr_header = ws.cell(row=current_row, column=1, value="CNR Averages")
            cnr_header.font = red_font
            cnr_header.alignment = center_alignment
            current_row += 1
            
            # Calculate CNR averages for each row pair (second row)
            for i, size in enumerate(phantom_sizes):
                row_number = row_pairs[i][1]  # second row for CNR
                valid_cnr_refs = []
                
                # Build references only if Mean and StdDev are not all zero
                for cols in column_groups:
                    formula_col = get_column_letter(column_index_from_string(cols[-1]) + 1)
                    mean_col = cols[1]
                    std_col = cols[2]
                    
                    mean1 = ws[f"{mean_col}{row_pairs[i][0]}"].value
                    mean2 = ws[f"{mean_col}{row_pairs[i][1]}"].value
                    std2 = ws[f"{std_col}{row_pairs[i][1]}"].value
                    
                    # Convert potential string values to float
                    try:
                        mean1 = float(mean1) if mean1 not in [None, ''] else 0
                        mean2 = float(mean2) if mean2 not in [None, ''] else 0
                        std2 = float(std2) if std2 not in [None, ''] else 0
                    except (ValueError, TypeError):
                        continue
                    
                    # If not all zero, we consider the cell for average
                    if not (mean1 == 0 and mean2 == 0 and std2 == 0):
                        valid_cnr_refs.append(f"{formula_col}{row_number}")
                
                size_cell = ws.cell(row=current_row, column=1, value=size)
                size_cell.alignment = center_alignment
                
                if valid_cnr_refs:
                    refs = ",".join(valid_cnr_refs)
                    array_formula = f'=IFERROR(AVERAGE(IF(ISNUMBER({refs}),{refs})),"")'
                    
                    avg_cell = ws.cell(row=current_row, column=2)
                    avg_cell.value = array_formula
                    avg_cell.number_format = '0.000'
                    avg_cell.alignment = center_alignment
                
                current_row += 1

            # Format the tables
            for row in range(32, current_row):
                for col in range(1, 3):
                    cell = ws.cell(row=row, column=col)
                    cell.alignment = center_alignment

            wb.save(output_path)
            return output_path, f"Results saved successfully ({result_idx} measurements)"

        except Exception as e:
            logger.error(f"Error saving formatted results: {str(e)}")
            return None, f"Error saving results: {str(e)}"

    def _write_result_to_cells(self, ws, result, cols, row):
        """Helper method to write a single result to worksheet cells"""
        center_alignment = openpyxl.styles.Alignment(horizontal='center')
        
        # Map the headers to the result keys
        value_mapping = {
            'Area': 'Area (mm²)',
            'Mean': 'Mean',
            'StdDev': 'StdDev',
            'Min': 'Min',
            'Max': 'Max'
        }
        
        for i, (header, key) in enumerate(value_mapping.items()):
            cell = ws[f"{cols[i]}{row}"]
            cell.value = float(result[key]) if result[key] != '' else ''
            cell.alignment = center_alignment

    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 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")
                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")
                    reset_all_btn = gr.Button("Reset All")
                
            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_formatted_btn = gr.Button("Save Formatted Results")
            
        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
        - Use Reset All to clear all measurements
        - Save Formatted Results will create Excel file with formulas
        """)

        def update_diameter(x):
            analyzer.circle_diameter = float(x)
            print(f"Diameter updated to: {x}")
            return f"Diameter set to {x} pixels"

        def save_formatted():
            output_path = "analysis_results_formatted.xlsx"
            return analyzer.save_formatted_results(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
        )
        
        reset_all_btn.click(
            fn=analyzer.reset_all,
            inputs=image_display,
            outputs=[image_display, results_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_formatted_btn.click(
            fn=save_formatted,
            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.queue()
        interface.launch(
            server_name="0.0.0.0",
            server_port=7860,
            share=True,
            debug=True,
            show_error=True,
            quiet=False
        )
    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