Update app.py

app.py

@@ -61,7 +61,10 @@ class DicomAnalyzer:
         self.pan_y = 0
         self.max_pan_x = 0
         self.max_pan_y = 0
-        self.CIRCLE_COLOR = (0, 255, 255)  # BGR Yellow
+        # Main circle color remains yellow:
+        self.CIRCLE_COLOR = (0, 255, 255)  # BGR format
+        # Small circles inside the main circle will be black:
+        self.SMALL_CIRCLES_COLOR = (0, 0, 0)  # BGR black
         print("DicomAnalyzer initialized...")
 
     def save_results(self):
@@ -173,12 +176,12 @@ class DicomAnalyzer:
 
     def handle_keyboard(self, key):
         """
-        Called when the hidden textbox 'key_press' changes value.
-        key is expected to be 'ArrowLeft','ArrowRight','ArrowUp','ArrowDown'.
+        Handle arrow keys. Pan movement is increased to be more noticeable.
         """
         try:
             print(f"Handling key press: {key}")
-            pan_amount = int(5 * self.zoom_factor)
+            # Increase pan step for bigger movement:
+            pan_amount = int(10 * self.zoom_factor)
             
             if key == 'ArrowLeft':
                 self.pan_x = max(0, self.pan_x - pan_amount)
@@ -196,7 +199,8 @@ class DicomAnalyzer:
 
     def update_display(self):
         """
-        Updates the displayed image according to the current zoom/pan and draws the ROI circles.
+        Updates the displayed image according to the current zoom/pan and draws the circles.
+        The big circle is in CIRCLE_COLOR, and the small circles inside are in SMALL_CIRCLES_COLOR.
         """
         try:
             if self.original_display is None:
@@ -217,8 +221,9 @@ class DicomAnalyzer:
             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)
+                zoomed_radius = int((diameter / 2.0) * self.zoom_factor)
                 
+                # Draw the main yellow circle
                 cv2.circle(
                     zoomed_bgr,
                     (zoomed_x, zoomed_y),
@@ -228,7 +233,7 @@ class DicomAnalyzer:
                     lineType=cv2.LINE_AA
                 )
                 
-                # Draw small points along the circle
+                # Draw 8 small black circles around
                 num_points = 8
                 for i in range(num_points):
                     angle = 2 * np.pi * i / num_points
@@ -238,7 +243,7 @@ class DicomAnalyzer:
                         zoomed_bgr,
                         (point_x, point_y),
                         1,
-                        self.CIRCLE_COLOR,
+                        self.SMALL_CIRCLES_COLOR,
                         -1,
                         lineType=cv2.LINE_AA
                     )
@@ -262,8 +267,7 @@ class DicomAnalyzer:
 
     def analyze_roi(self, evt: gr.SelectData):
         """
-        Called when user clicks on the displayed image.
-        Extracts the ROI of diameter circle_diameter and computes stats.
+        Called when user clicks on the displayed image to measure an ROI.
         """
         try:
             if self.current_image is None:
@@ -272,11 +276,11 @@ class DicomAnalyzer:
             clicked_x = evt.index[0]
             clicked_y = evt.index[1]
             
-            # Adjust by current pan
+            # Adjust by pan
             x = clicked_x + self.pan_x
             y = clicked_y + self.pan_y
 
-            # Account for zoom
+            # Adjust by zoom
             if self.zoom_factor != 1.0:
                 x = x / self.zoom_factor
                 y = y / self.zoom_factor
@@ -291,7 +295,7 @@ class DicomAnalyzer:
             
             dx = X - x
             dy = Y - y
-            dist_squared = dx*dx + dy*dy
+            dist_squared = dx * dx + dy * dy
             
             mask = np.zeros((height, width), dtype=bool)
             mask[dist_squared <= r_squared] = True
@@ -345,7 +349,7 @@ class DicomAnalyzer:
             
             row1, row2 = row_pair
             
-            # SNR Formula
+            # SNR formula
             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}"]
@@ -353,7 +357,7 @@ class DicomAnalyzer:
             cell1.font = red_font
             cell1.alignment = openpyxl.styles.Alignment(horizontal='center')
             
-            # CNR Formula
+            # CNR formula
             formula2 = f"=IFERROR(({base_col}{row1}-{base_col}{row2})/{std_col}{row2},\"\")"
             cell2 = ws[f"{formula_col}{row2}"]
             cell2.value = formula2
@@ -367,10 +371,7 @@ class DicomAnalyzer:
     def save_formatted_results(self, output_path):
         """
         Creates an Excel file with results in a formatted table,
-        adding SNR/CNR formulas and averaging blocks for StdDev and CNR.
-        
-        NOTE: CNR Averages uses AVERAGE() and we skip any cell references where
-              Mean1, Mean2, StdDev2 are all zero. So we avoid AVERAGEIF complexities.
+        including SNR/CNR formulas and average calculations.
         """
         try:
             if not self.results:
@@ -381,7 +382,7 @@ class DicomAnalyzer:
             red_font = openpyxl.styles.Font(color="FF0000")
             center_alignment = openpyxl.styles.Alignment(horizontal='center')
             
-            # Define headers
+            # Column group headers
             headers = ['Area', 'Mean', 'StdDev', 'Min', 'Max']
 
             column_groups = [
@@ -394,7 +395,6 @@ class DicomAnalyzer:
                 ('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"]
@@ -411,13 +411,13 @@ class DicomAnalyzer:
                 '(4.5mm)', '(4mm)', '(3.5mm)', '(3mm)', '(2.5mm)'
             ]
             
-            # Insert Phantom size labels
+            # Set the phantom size row labels
             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
 
-            # Fill data from self.results
+            # Fill the data from self.results
             result_idx = 0
             current_col_group = 0
             current_row_pair = 0
@@ -429,19 +429,19 @@ class DicomAnalyzer:
                 cols = column_groups[current_col_group]
                 rows = row_pairs[current_row_pair]
                 
-                # First row in pair
+                # First row
                 if result_idx < len(self.results):
                     result = self.results[result_idx]
                     self._write_result_to_cells(ws, result, cols, rows[0])
                     result_idx += 1
                 
-                # Second row in pair
+                # Second row
                 if result_idx < len(self.results):
                     result = self.results[result_idx]
                     self._write_result_to_cells(ws, result, cols, rows[1])
                     result_idx += 1
                 
-                # Insert SNR/CNR formulas for these two rows
+                # Add SNR/CNR formulas
                 self.add_formulas_to_template(ws, rows, cols, red_font)
                 
                 current_col_group += 1
@@ -457,23 +457,23 @@ class DicomAnalyzer:
                         if cell.value is not None:
                             cell.alignment = center_alignment
 
-            # ---- Create tables for StdDev Averages and CNR Averages ----
+            # Additional tables: StdDev Averages and CNR Averages
             current_row = 32
 
-            # 1) StdDev Averages
+            # StdDev
             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
             
             for i, size in enumerate(phantom_sizes):
-                row_number = row_pairs[i][0]  # First row only for std
+                row_number = row_pairs[i][0]
                 stddev_values = []
                 
                 for cols in column_groups:
-                    stddev_col = cols[2]  # StdDev column
+                    stddev_col = cols[2]  # The StdDev column
                     cell_value = ws[f"{stddev_col}{row_number}"].value
-                    if cell_value not in [0, None, '']:  # Ignore zeros and empty
+                    if cell_value not in [0, None, '']:
                         stddev_values.append(float(cell_value))
                 
                 size_cell = ws.cell(row=current_row, column=1, value=size)
@@ -486,15 +486,14 @@ class DicomAnalyzer:
                     avg_cell.alignment = center_alignment
                 current_row += 1
 
-            current_row += 2  # Space between the two tables
+            current_row += 2
 
-            # 2) CNR Averages
+            # CNR
             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
             
-            # حساب متوسط CNR للصف الثاني في كل pair باستخدام AVERAGE فقط
             for i, size in enumerate(phantom_sizes):
                 row_number = row_pairs[i][1]
                 cnr_cells = []
@@ -503,7 +502,7 @@ class DicomAnalyzer:
                     formula_col = get_column_letter(column_index_from_string(cols[-1]) + 1)
                     cnr_cell_ref = f"{formula_col}{row_number}"
 
-                    # نقرأ Mean1,Mean2,Std2 للتحقق
+                    # Read Mean1, Mean2, Std2 to skip zeros
                     mean_col = cols[1]
                     std_col  = cols[2]
                     
@@ -518,7 +517,7 @@ class DicomAnalyzer:
                     except:
                         mean1_val, mean2_val, std2_val = 0, 0, 0
 
-                    # لو كلها صفر => لا نضيف الخلية
+                    # If not all zero, add the cell reference
                     if not (mean1_val == 0 and mean2_val == 0 and std2_val == 0):
                         cnr_cells.append(cnr_cell_ref)
                 
@@ -526,7 +525,7 @@ class DicomAnalyzer:
                 size_cell.alignment = center_alignment
 
                 if cnr_cells:
-                    # نبني صيغة Excel: =IFERROR(AVERAGE(G3,M3,...),"")
+                    # Using AVERAGE(...) instead of AVERAGEIF
                     average_formula = f'=IFERROR(AVERAGE({",".join(cnr_cells)}), "")'
                     
                     avg_cell = ws.cell(row=current_row, column=2)
@@ -536,7 +535,7 @@ class DicomAnalyzer:
                 
                 current_row += 1
 
-            # تنسيق العناوين الأخيرة
+            # Align the extra rows
             for row in range(32, current_row):
                 for col in range(1, 3):
                     cell = ws.cell(row=row, column=col)
@@ -550,7 +549,7 @@ class DicomAnalyzer:
             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 (dict) into a row of cells."""
+        """Helper method to write a single result to worksheet cells."""
         center_alignment = openpyxl.styles.Alignment(horizontal='center')
         
         value_mapping = {
@@ -564,7 +563,6 @@ class DicomAnalyzer:
         for i, (header, key) in enumerate(value_mapping.items()):
             cell = ws[f"{cols[i]}{row}"]
             val = result[key]
-            # Handle empty strings
             cell.value = float(val) if val not in ['', None] else ''
             cell.alignment = center_alignment
 
@@ -577,18 +575,10 @@ class DicomAnalyzer:
         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):
+        """
+        Adds one row with zero-values.
+        """
         self.results.append({
             'Area (mm²)': '0.000',
             'Mean': '0.000',
@@ -601,7 +591,7 @@ class DicomAnalyzer:
 
     def add_two_zero_rows(self, image):
         """
-        Adds two consecutive rows of zeros.
+        Adds two consecutive rows with zero-values.
         """
         for _ in range(2):
             self.results.append({
@@ -653,10 +643,10 @@ def create_interface():
                     elem_id="image_display"
                 )
                 
+        # Removed the "Add Blank Row" button
         with gr.Row():
-            blank_btn = gr.Button("Add Blank Row")
             zero_btn = gr.Button("Add Zero Row")
-            zero2_btn = gr.Button("Add Two Zero Rows")  # <-- New button
+            zero2_btn = gr.Button("Add Two Zero Rows")
             undo_btn = gr.Button("Undo Last")
             save_btn = gr.Button("Save Results")
             save_formatted_btn = gr.Button("Save Formatted Results")
@@ -667,26 +657,24 @@ def create_interface():
         
         gr.Markdown("""
         ### Controls:
-        - Use arrow keys to pan when zoomed in (multiple times).
+        - Use arrow keys to pan when zoomed in. Movement is now larger.
         - Click points to measure ROI.
         - Use Zoom In/Out buttons or Reset View to adjust zoom level.
         - Use Reset All to clear all measurements.
-        - "Save Results" => Basic Excel with raw data.
-        - "Save Formatted Results" => Excel with advanced formatting & formulas.
+        - "Save Results": basic Excel with raw data.
+        - "Save Formatted Results": Excel with advanced formatting & formulas.
         """)
 
-        # Update diameter callback
         def update_diameter(x):
             analyzer.circle_diameter = float(x)
             print(f"Diameter updated to: {x}")
             return f"Diameter set to {x} pixels"
 
-        # Save formatted callback
         def save_formatted():
             output_path = "analysis_results_formatted.xlsx"
             return analyzer.save_formatted_results(output_path)
 
-        # Event handlers
+        # Handlers
         file_input.change(
             fn=analyzer.load_dicom,
             inputs=file_input,
@@ -735,19 +723,13 @@ def create_interface():
             outputs=image_display
         )
         
-        blank_btn.click(
-            fn=analyzer.add_blank_row,
-            inputs=image_display,
-            outputs=[image_display, results_display]
-        )
-        
+        # Removed blank_btn
         zero_btn.click(
             fn=analyzer.add_zero_row,
             inputs=image_display,
             outputs=[image_display, results_display]
         )
-
-        # زر إضافة صفين صفر
+        
         zero2_btn.click(
             fn=analyzer.add_two_zero_rows,
             inputs=image_display,
@@ -771,7 +753,6 @@ def create_interface():
         )
 
         # JavaScript snippet to allow multiple arrow key presses
-        # by resetting the value in key_press.
         js = """
         <script>
         document.addEventListener('keydown', function(e) {
@@ -779,11 +760,8 @@ def create_interface():
                 e.preventDefault();
                 const keyPressElement = document.querySelector('#key_press textarea');
                 if (keyPressElement) {
-                    // Set the value to the pressed key and dispatch
                     keyPressElement.value = e.key;
                     keyPressElement.dispatchEvent(new Event('input'));
-
-                    // Clear value after short delay so next press is recognized
                     setTimeout(() => {
                       keyPressElement.value = '';
                       keyPressElement.dispatchEvent(new Event('input'));