Update app.py
Browse files
app.py
CHANGED
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@@ -66,8 +66,12 @@ class DicomAnalyzer:
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print("DicomAnalyzer initialized...")
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def save_results(self):
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try:
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if not self.results:
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return None, "No results to save"
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df = pd.DataFrame(self.results)
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@@ -104,6 +108,9 @@ class DicomAnalyzer:
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return self.update_display(), "All data has been reset"
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def load_dicom(self, file):
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try:
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if file is None:
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return None, "No file uploaded"
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@@ -134,6 +141,9 @@ class DicomAnalyzer:
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return None, f"Error loading DICOM file: {str(e)}"
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def normalize_image(self, image):
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try:
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normalized = cv2.normalize(
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image,
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@@ -151,6 +161,9 @@ class DicomAnalyzer:
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return None
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def reset_view(self):
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self.zoom_factor = 1.0
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self.pan_x = 0
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self.pan_y = 0
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@@ -167,6 +180,9 @@ class DicomAnalyzer:
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return self.update_display()
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def handle_keyboard(self, key):
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try:
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pan_amount = int(10 * self.zoom_factor)
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if key == 'ArrowLeft':
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@@ -183,6 +199,9 @@ class DicomAnalyzer:
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return self.display_image
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def update_display(self):
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try:
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if self.original_display is None:
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return None
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@@ -191,15 +210,10 @@ class DicomAnalyzer:
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new_height = int(height * self.zoom_factor)
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new_width = int(width * self.zoom_factor)
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zoomed = cv2.resize(
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self.original_display,
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(new_width, new_height),
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interpolation=cv2.INTER_CUBIC
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)
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zoomed_bgr = cv2.cvtColor(zoomed, cv2.COLOR_RGB2BGR)
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# Draw
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for x, y, diameter in self.marks:
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zoomed_x = int(x * self.zoom_factor)
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zoomed_y = int(y * self.zoom_factor)
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@@ -207,13 +221,13 @@ class DicomAnalyzer:
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cv2.circle(zoomed_bgr, (zoomed_x, zoomed_y), zoomed_radius, self.CIRCLE_COLOR, 1, lineType=cv2.LINE_AA)
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# 8 small circles
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num_points = 8
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for i in range(num_points):
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angle = 2 * np.pi * i / num_points
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-
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-
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cv2.circle(zoomed_bgr, (
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zoomed = cv2.cvtColor(zoomed_bgr, cv2.COLOR_BGR2RGB)
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@@ -222,16 +236,16 @@ class DicomAnalyzer:
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self.pan_x = min(max(0, self.pan_x), self.max_pan_x)
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self.pan_y = min(max(0, self.pan_y), self.max_pan_y)
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visible = zoomed[
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-
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int(self.pan_x):int(self.pan_x + width)
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]
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return visible
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except Exception as e:
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return self.original_display
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def analyze_roi(self, evt: gr.SelectData):
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try:
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if self.current_image is None:
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return None, "No image loaded"
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@@ -243,8 +257,8 @@ class DicomAnalyzer:
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y = clicked_y + self.pan_y
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if self.zoom_factor != 1.0:
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x
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y
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x = int(round(x))
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y = int(round(y))
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@@ -298,14 +312,35 @@ class DicomAnalyzer:
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except Exception as e:
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return self.display_image, f"Error analyzing ROI: {str(e)}"
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def add_formulas_to_template(self, ws, row_pair, col_group, red_font):
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"""
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try:
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base_col = col_group[1] # Mean
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std_col = col_group[2] # StdDev
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row1, row2 = row_pair
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formula_col = get_column_letter(column_index_from_string(col_group[-1]) + 1)
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# SNR in row1
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@@ -326,6 +361,12 @@ class DicomAnalyzer:
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logger.error(f"Error adding formulas: {str(e)}")
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def save_formatted_results(self, output_path):
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try:
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if not self.results:
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return None, "No results to save"
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@@ -333,63 +374,47 @@ class DicomAnalyzer:
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wb = openpyxl.Workbook()
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ws = wb.active
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red_font = openpyxl.styles.Font(color="FF0000")
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center_alignment = openpyxl.styles.Alignment(horizontal='center')
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headers = ['Area', 'Mean', 'StdDev', 'Min', 'Max']
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column_groups = [
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('B', 'C', 'D', 'E', 'F'), ('H', 'I', 'J', 'K', 'L'),
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('N', 'O', 'P', 'Q', 'R'), ('T', 'U', 'V', 'W', 'X'),
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('AL', 'AM', 'AN', 'AO', 'AP'), ('AR', 'AS', 'AT', 'AU', 'AV'),
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('AX', 'AY', 'AZ', 'BA', 'BB'), ('BD', 'BE', 'BF', 'BG', 'BH'),
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('BJ', 'BK', 'BL', 'BM', 'BN'), ('BP', 'BQ', 'BR', 'BS', 'BT'),
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('BV', 'BW', 'BX', 'BY', 'BZ')
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]
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# Write main headers (Area,Mean,StdDev,Min,Max)
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for cols in column_groups:
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for i, header in enumerate(headers):
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-
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cell.alignment = center_alignment
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# Each pair for phantom
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row_pairs = [
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(2, 3), (5, 6), (8, 9), (11, 12), (14, 15),
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(17, 18), (20, 21), (23, 24), (26, 27), (29, 30)
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]
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'(4.5mm)', '(4mm)', '(3.5mm)', '(3mm)', '(2.5mm)'
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]
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#
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for i, size in enumerate(phantom_sizes):
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label_row = row_pairs[i][0] - 1
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ws.cell(row=label_row, column=1, value=size).font = red_font
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ws.cell(row=label_row, column=1).alignment = center_alignment
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# Fill raw ROI data + formulas
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result_idx = 0
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current_col_group = 0
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current_row_pair = 0
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-
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while result_idx < len(self.results):
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if current_row_pair >= len(row_pairs):
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break
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-
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cols = column_groups[current_col_group]
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row1, row2 = row_pairs[current_row_pair]
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if result_idx < len(self.results):
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-
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result_idx += 1
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if result_idx < len(self.results):
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-
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result_idx += 1
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self.add_formulas_to_template(ws, (row1,row2), cols, red_font)
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current_col_group += 1
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current_col_group = 0
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current_row_pair += 1
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#
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for cols in column_groups:
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for col in cols:
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for row in range(2, 31):
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cell = ws[f"{col}{row}"]
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if cell.value not in [None, '']:
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cell.alignment = center_alignment
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# Now the 1-AVG table from row35..45
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start_row = 35
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ws['C35'] = "1-AVG"
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ws['C35'].alignment = center_alignment
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# Merge headers
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ws.merge_cells('D35:E35')
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ws.merge_cells('F35:G35')
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ws.merge_cells('H35:I35')
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@@ -422,90 +439,75 @@ class DicomAnalyzer:
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}
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for c_ref, text_val in avg_headers.items():
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ws[c_ref] = text_val
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ws[c_ref].font = red_font
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ws[c_ref].alignment = center_alignment
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#
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# place them
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if final_mean is not None:
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ws[f'D{row}'].value = final_mean
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ws[f'D{row}'].alignment = center_alignment
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ws[f'D{row}'].number_format = '0.0000'
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if final_std is not None:
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ws[f'F{row}'].value = final_std
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ws[f'F{row}'].alignment = center_alignment
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ws[f'F{row}'].number_format = '0.0000'
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if final_cnr is not None:
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ws[f'H{row}'].value = final_cnr
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ws[f'H{row}'].alignment = center_alignment
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ws[f'H{row}'].number_format = '0.0000'
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# Put borders
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thin_side = openpyxl.styles.Side(style='thin')
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border = openpyxl.styles.Border(
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left=
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)
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for r in range(35,
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for c in ['C','D','E','F','G','H','I']:
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ws[f'{c}{r}'].border = border
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logger.error(f"Error saving formatted results: {str(e)}")
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return None, f"Error saving results: {str(e)}"
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def _write_result_to_cells(self, ws, result, cols, row):
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center_alignment = openpyxl.styles.Alignment(horizontal='center')
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value_mapping = {
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'Area': 'Area (mm²)',
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'Mean': 'Mean',
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'StdDev': 'StdDev',
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'Min': 'Min',
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'Max': 'Max'
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}
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for i, (header, key) in enumerate(value_mapping.items()):
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cell = ws[f"{cols[i]}{row}"]
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val = result[key]
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cell.value = float(val) if val not in ['', None] else ''
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cell.alignment = center_alignment
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def format_results(self):
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if not self.results:
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return "No measurements yet"
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df = pd.DataFrame(self.results)
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return df.to_string(index=False)
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def add_zero_row(self, image):
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self.results.append({
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'Area (mm²)': '0.000',
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'Mean': '0.000',
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return image, self.format_results()
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def add_two_zero_rows(self, image):
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for _ in range(2):
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self.results.append({
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'Area (mm²)': '0.000',
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return image, self.format_results()
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def undo_last(self, image):
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if not self.results:
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return self.update_display(), self.format_results()
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last_result = self.results[-1]
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is_measurement =
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self.results.pop()
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if is_measurement and self.marks:
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self.marks.pop()
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def create_interface():
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analyzer = DicomAnalyzer()
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with gr.Blocks(css="#image_display { outline: none; }") as interface:
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with gr.Row():
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with gr.Column():
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file_input = gr.File(label="Upload DICOM file")
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diameter_slider = gr.Slider(
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with gr.Row():
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zoom_in_btn = gr.Button("Zoom In (+)")
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reset_all_btn = gr.Button("Reset All")
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with gr.Column():
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image_display = gr.Image(
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with gr.Row():
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zero_btn = gr.Button("Add Zero Row")
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gr.Markdown("""
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### Controls:
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- Click
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- "Save Results":
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- "Save Formatted Results": advanced table
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""")
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def update_diameter(x):
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analyzer.circle_diameter = float(x)
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return f"Diameter set to {x} pixels"
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def save_formatted():
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zoom_in_btn.click(
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| 639 |
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| 640 |
-
#
|
| 641 |
js = """
|
| 642 |
<script>
|
| 643 |
document.addEventListener('keydown', function(e) {
|
|
@@ -658,15 +722,24 @@ def create_interface():
|
|
| 658 |
"""
|
| 659 |
gr.HTML(js)
|
| 660 |
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|
| 661 |
return interface
|
| 662 |
|
| 663 |
|
| 664 |
if __name__ == "__main__":
|
| 665 |
try:
|
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|
| 666 |
interface = create_interface()
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|
| 667 |
interface.queue()
|
| 668 |
-
interface.launch(
|
| 669 |
-
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|
| 670 |
except Exception as e:
|
| 671 |
logger.error(f"Error launching application: {str(e)}")
|
| 672 |
logger.error(traceback.format_exc())
|
|
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|
| 66 |
print("DicomAnalyzer initialized...")
|
| 67 |
|
| 68 |
def save_results(self):
|
| 69 |
+
"""
|
| 70 |
+
Saves raw ROI data as an Excel file with minimal formatting.
|
| 71 |
+
"""
|
| 72 |
try:
|
| 73 |
if not self.results:
|
| 74 |
+
logger.warning("Attempted to save with no results")
|
| 75 |
return None, "No results to save"
|
| 76 |
|
| 77 |
df = pd.DataFrame(self.results)
|
|
|
|
| 108 |
return self.update_display(), "All data has been reset"
|
| 109 |
|
| 110 |
def load_dicom(self, file):
|
| 111 |
+
"""
|
| 112 |
+
Loads DICOM from user file and normalizes for display.
|
| 113 |
+
"""
|
| 114 |
try:
|
| 115 |
if file is None:
|
| 116 |
return None, "No file uploaded"
|
|
|
|
| 141 |
return None, f"Error loading DICOM file: {str(e)}"
|
| 142 |
|
| 143 |
def normalize_image(self, image):
|
| 144 |
+
"""
|
| 145 |
+
Converts raw data to 0..255 range for display.
|
| 146 |
+
"""
|
| 147 |
try:
|
| 148 |
normalized = cv2.normalize(
|
| 149 |
image,
|
|
|
|
| 161 |
return None
|
| 162 |
|
| 163 |
def reset_view(self):
|
| 164 |
+
"""
|
| 165 |
+
Resets zoom and pan to defaults.
|
| 166 |
+
"""
|
| 167 |
self.zoom_factor = 1.0
|
| 168 |
self.pan_x = 0
|
| 169 |
self.pan_y = 0
|
|
|
|
| 180 |
return self.update_display()
|
| 181 |
|
| 182 |
def handle_keyboard(self, key):
|
| 183 |
+
"""
|
| 184 |
+
Pans image with arrow keys.
|
| 185 |
+
"""
|
| 186 |
try:
|
| 187 |
pan_amount = int(10 * self.zoom_factor)
|
| 188 |
if key == 'ArrowLeft':
|
|
|
|
| 199 |
return self.display_image
|
| 200 |
|
| 201 |
def update_display(self):
|
| 202 |
+
"""
|
| 203 |
+
Returns a zoomed/panned copy of original_display with circles drawn.
|
| 204 |
+
"""
|
| 205 |
try:
|
| 206 |
if self.original_display is None:
|
| 207 |
return None
|
|
|
|
| 210 |
new_height = int(height * self.zoom_factor)
|
| 211 |
new_width = int(width * self.zoom_factor)
|
| 212 |
|
| 213 |
+
zoomed = cv2.resize(self.original_display, (new_width, new_height), interpolation=cv2.INTER_CUBIC)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 214 |
zoomed_bgr = cv2.cvtColor(zoomed, cv2.COLOR_RGB2BGR)
|
| 215 |
|
| 216 |
+
# Draw ROI marks
|
| 217 |
for x, y, diameter in self.marks:
|
| 218 |
zoomed_x = int(x * self.zoom_factor)
|
| 219 |
zoomed_y = int(y * self.zoom_factor)
|
|
|
|
| 221 |
|
| 222 |
cv2.circle(zoomed_bgr, (zoomed_x, zoomed_y), zoomed_radius, self.CIRCLE_COLOR, 1, lineType=cv2.LINE_AA)
|
| 223 |
|
| 224 |
+
# 8 small circles around
|
| 225 |
num_points = 8
|
| 226 |
for i in range(num_points):
|
| 227 |
angle = 2 * np.pi * i / num_points
|
| 228 |
+
px = int(zoomed_x + zoomed_radius * np.cos(angle))
|
| 229 |
+
py = int(zoomed_y + zoomed_radius * np.sin(angle))
|
| 230 |
+
cv2.circle(zoomed_bgr, (px, py), 1, self.SMALL_CIRCLES_COLOR, -1, lineType=cv2.LINE_AA)
|
| 231 |
|
| 232 |
zoomed = cv2.cvtColor(zoomed_bgr, cv2.COLOR_BGR2RGB)
|
| 233 |
|
|
|
|
| 236 |
self.pan_x = min(max(0, self.pan_x), self.max_pan_x)
|
| 237 |
self.pan_y = min(max(0, self.pan_y), self.max_pan_y)
|
| 238 |
|
| 239 |
+
visible = zoomed[int(self.pan_y):int(self.pan_y + height),
|
| 240 |
+
int(self.pan_x):int(self.pan_x + width)]
|
|
|
|
|
|
|
|
|
|
| 241 |
return visible
|
| 242 |
except Exception as e:
|
| 243 |
return self.original_display
|
| 244 |
|
| 245 |
def analyze_roi(self, evt: gr.SelectData):
|
| 246 |
+
"""
|
| 247 |
+
Called when user clicks the image. We gather ROI stats and store them.
|
| 248 |
+
"""
|
| 249 |
try:
|
| 250 |
if self.current_image is None:
|
| 251 |
return None, "No image loaded"
|
|
|
|
| 257 |
y = clicked_y + self.pan_y
|
| 258 |
|
| 259 |
if self.zoom_factor != 1.0:
|
| 260 |
+
x /= self.zoom_factor
|
| 261 |
+
y /= self.zoom_factor
|
| 262 |
|
| 263 |
x = int(round(x))
|
| 264 |
y = int(round(y))
|
|
|
|
| 312 |
except Exception as e:
|
| 313 |
return self.display_image, f"Error analyzing ROI: {str(e)}"
|
| 314 |
|
| 315 |
+
def _write_result_to_cells(self, ws, result, cols, row):
|
| 316 |
+
"""
|
| 317 |
+
Writes one ROI measurement into the given row/columns.
|
| 318 |
+
(If you still want to store raw data in some pattern, you can keep this.)
|
| 319 |
+
"""
|
| 320 |
+
center_alignment = openpyxl.styles.Alignment(horizontal='center')
|
| 321 |
+
value_mapping = {
|
| 322 |
+
'Area': 'Area (mm²)',
|
| 323 |
+
'Mean': 'Mean',
|
| 324 |
+
'StdDev': 'StdDev',
|
| 325 |
+
'Min': 'Min',
|
| 326 |
+
'Max': 'Max'
|
| 327 |
+
}
|
| 328 |
+
for i, (header, key) in enumerate(value_mapping.items()):
|
| 329 |
+
cell = ws[f"{cols[i]}{row}"]
|
| 330 |
+
val = result[key]
|
| 331 |
+
cell.value = float(val) if val not in ['', None] else ''
|
| 332 |
+
cell.alignment = center_alignment
|
| 333 |
+
|
| 334 |
def add_formulas_to_template(self, ws, row_pair, col_group, red_font):
|
| 335 |
+
"""
|
| 336 |
+
Example function: inserts SNR (row1) and CNR (row2) formulas with IFERROR.
|
| 337 |
+
If you don't need them, you can keep or remove them.
|
| 338 |
+
"""
|
| 339 |
try:
|
| 340 |
+
base_col = col_group[1] # Mean col
|
| 341 |
+
std_col = col_group[2] # StdDev col
|
| 342 |
|
| 343 |
row1, row2 = row_pair
|
|
|
|
| 344 |
formula_col = get_column_letter(column_index_from_string(col_group[-1]) + 1)
|
| 345 |
|
| 346 |
# SNR in row1
|
|
|
|
| 361 |
logger.error(f"Error adding formulas: {str(e)}")
|
| 362 |
|
| 363 |
def save_formatted_results(self, output_path):
|
| 364 |
+
"""
|
| 365 |
+
Saves an Excel with:
|
| 366 |
+
1) A normal layout of ROI data if you want (row_pairs, columns).
|
| 367 |
+
2) A final "1-AVG" table in row35 using *all* measurements in self.results,
|
| 368 |
+
so you see an average even if you only have 1 measurement.
|
| 369 |
+
"""
|
| 370 |
try:
|
| 371 |
if not self.results:
|
| 372 |
return None, "No results to save"
|
|
|
|
| 374 |
wb = openpyxl.Workbook()
|
| 375 |
ws = wb.active
|
| 376 |
red_font = openpyxl.styles.Font(color="FF0000")
|
| 377 |
+
center_alignment = openpyxl.styles.Alignment(horizontal='center', vertical='center')
|
| 378 |
|
| 379 |
+
# (1) Optionally store the raw data in some pattern if you want
|
| 380 |
+
# Example: We define column_groups, row_pairs, etc.
|
| 381 |
headers = ['Area', 'Mean', 'StdDev', 'Min', 'Max']
|
| 382 |
column_groups = [
|
| 383 |
('B', 'C', 'D', 'E', 'F'), ('H', 'I', 'J', 'K', 'L'),
|
| 384 |
('N', 'O', 'P', 'Q', 'R'), ('T', 'U', 'V', 'W', 'X'),
|
| 385 |
+
# add more if needed
|
|
|
|
|
|
|
|
|
|
|
|
|
| 386 |
]
|
|
|
|
|
|
|
| 387 |
for cols in column_groups:
|
| 388 |
for i, header in enumerate(headers):
|
| 389 |
+
ws[f"{cols[i]}1"].value = header
|
| 390 |
+
ws[f"{cols[i]}1"].alignment = center_alignment
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 391 |
|
| 392 |
+
row_pairs = [(2, 3), (5, 6), (8, 9), (11, 12)]
|
| 393 |
+
# (adjust how many pairs you want)
|
|
|
|
|
|
|
| 394 |
|
| 395 |
+
# Write each result into these row/columns as a demonstration
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 396 |
result_idx = 0
|
| 397 |
current_col_group = 0
|
| 398 |
current_row_pair = 0
|
|
|
|
| 399 |
while result_idx < len(self.results):
|
| 400 |
if current_row_pair >= len(row_pairs):
|
| 401 |
break
|
|
|
|
| 402 |
cols = column_groups[current_col_group]
|
| 403 |
row1, row2 = row_pairs[current_row_pair]
|
| 404 |
|
| 405 |
+
# Write first measurement
|
| 406 |
if result_idx < len(self.results):
|
| 407 |
+
r = self.results[result_idx]
|
| 408 |
+
self._write_result_to_cells(ws, r, cols, row1)
|
| 409 |
result_idx += 1
|
| 410 |
|
| 411 |
+
# Write second measurement
|
| 412 |
if result_idx < len(self.results):
|
| 413 |
+
r = self.results[result_idx]
|
| 414 |
+
self._write_result_to_cells(ws, r, cols, row2)
|
| 415 |
result_idx += 1
|
| 416 |
+
|
| 417 |
+
# Insert formulas if you want
|
| 418 |
self.add_formulas_to_template(ws, (row1,row2), cols, red_font)
|
| 419 |
|
| 420 |
current_col_group += 1
|
|
|
|
| 422 |
current_col_group = 0
|
| 423 |
current_row_pair += 1
|
| 424 |
|
| 425 |
+
# (2) Now create the 1-AVG table at row35, but read from self.results directly
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 426 |
start_row = 35
|
| 427 |
ws['C35'] = "1-AVG"
|
| 428 |
ws['C35'].alignment = center_alignment
|
| 429 |
|
| 430 |
+
# Merge some cells for the headers
|
| 431 |
ws.merge_cells('D35:E35')
|
| 432 |
ws.merge_cells('F35:G35')
|
| 433 |
ws.merge_cells('H35:I35')
|
|
|
|
| 439 |
}
|
| 440 |
for c_ref, text_val in avg_headers.items():
|
| 441 |
ws[c_ref] = text_val
|
|
|
|
| 442 |
ws[c_ref].alignment = center_alignment
|
| 443 |
+
ws[c_ref].font = red_font
|
| 444 |
|
| 445 |
+
# We just put everything in row 36 for demonstration.
|
| 446 |
+
# Or you could put phantom sizes if you want multiple lines.
|
| 447 |
+
row = 36
|
| 448 |
+
ws.merge_cells(f'D{row}:E{row}')
|
| 449 |
+
ws.merge_cells(f'F{row}:G{row}')
|
| 450 |
+
ws.merge_cells(f'H{row}:I{row}')
|
| 451 |
|
| 452 |
+
# Now gather *all* results from self.results
|
| 453 |
+
all_means = []
|
| 454 |
+
all_stds = []
|
| 455 |
+
# We'll do CNR from first two if we have at least 2 measurements
|
| 456 |
+
# Or you can define your own logic if you want multiple pairs
|
| 457 |
+
cnr_value = None
|
| 458 |
+
|
| 459 |
+
for i, r in enumerate(self.results):
|
| 460 |
+
try:
|
| 461 |
+
m = float(r["Mean"])
|
| 462 |
+
s = float(r["StdDev"])
|
| 463 |
+
all_means.append(m)
|
| 464 |
+
all_stds.append(s)
|
| 465 |
+
except:
|
| 466 |
+
pass
|
| 467 |
+
|
| 468 |
+
# If you only have 1 measurement, you still get an average = same value
|
| 469 |
+
avg_mean = sum(all_means)/len(all_means) if all_means else None
|
| 470 |
+
avg_std = sum(all_stds)/len(all_stds) if all_stds else None
|
| 471 |
+
|
| 472 |
+
# For CNR, let's just do a simple logic: if we have >=2 measurements,
|
| 473 |
+
# we do (mean1 - mean2) / std2 as an example
|
| 474 |
+
# or you can define your own approach
|
| 475 |
+
if len(self.results) >= 2:
|
| 476 |
+
try:
|
| 477 |
+
r1 = self.results[0]
|
| 478 |
+
r2 = self.results[1]
|
| 479 |
+
m1 = float(r1["Mean"])
|
| 480 |
+
m2 = float(r2["Mean"])
|
| 481 |
+
s2 = float(r2["StdDev"])
|
| 482 |
+
if s2 != 0:
|
| 483 |
+
cnr_value = (m1 - m2)/s2
|
| 484 |
+
except:
|
| 485 |
+
cnr_value = None
|
| 486 |
+
|
| 487 |
+
# Write them in row 36
|
| 488 |
+
if avg_mean is not None:
|
| 489 |
+
ws[f'D{row}'].value = avg_mean
|
| 490 |
+
ws[f'D{row}'].alignment = center_alignment
|
| 491 |
+
ws[f'D{row}'].number_format = '0.0000'
|
| 492 |
+
|
| 493 |
+
if avg_std is not None:
|
| 494 |
+
ws[f'F{row}'].value = avg_std
|
| 495 |
+
ws[f'F{row}'].alignment = center_alignment
|
| 496 |
+
ws[f'F{row}'].number_format = '0.0000'
|
| 497 |
+
|
| 498 |
+
if cnr_value is not None:
|
| 499 |
+
ws[f'H{row}'].value = cnr_value
|
| 500 |
+
ws[f'H{row}'].alignment = center_alignment
|
| 501 |
+
ws[f'H{row}'].number_format = '0.0000'
|
| 502 |
+
|
| 503 |
+
# Add thin border to the table
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 504 |
border = openpyxl.styles.Border(
|
| 505 |
+
left=openpyxl.styles.Side(style='thin'),
|
| 506 |
+
right=openpyxl.styles.Side(style='thin'),
|
| 507 |
+
top=openpyxl.styles.Side(style='thin'),
|
| 508 |
+
bottom=openpyxl.styles.Side(style='thin')
|
| 509 |
)
|
| 510 |
+
for r in range(35, 37):
|
| 511 |
for c in ['C','D','E','F','G','H','I']:
|
| 512 |
ws[f'{c}{r}'].border = border
|
| 513 |
|
|
|
|
| 517 |
logger.error(f"Error saving formatted results: {str(e)}")
|
| 518 |
return None, f"Error saving results: {str(e)}"
|
| 519 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 520 |
def format_results(self):
|
| 521 |
+
"""Just prints self.results as a string in the UI."""
|
| 522 |
if not self.results:
|
| 523 |
return "No measurements yet"
|
| 524 |
df = pd.DataFrame(self.results)
|
|
|
|
| 527 |
return df.to_string(index=False)
|
| 528 |
|
| 529 |
def add_zero_row(self, image):
|
| 530 |
+
"""Test function to push a zero row into self.results."""
|
| 531 |
self.results.append({
|
| 532 |
'Area (mm²)': '0.000',
|
| 533 |
'Mean': '0.000',
|
|
|
|
| 539 |
return image, self.format_results()
|
| 540 |
|
| 541 |
def add_two_zero_rows(self, image):
|
| 542 |
+
"""Adds 2 zero rows for testing."""
|
| 543 |
for _ in range(2):
|
| 544 |
self.results.append({
|
| 545 |
'Area (mm²)': '0.000',
|
|
|
|
| 552 |
return image, self.format_results()
|
| 553 |
|
| 554 |
def undo_last(self, image):
|
| 555 |
+
"""Removes the last measurement (or zero row)."""
|
| 556 |
if not self.results:
|
| 557 |
return self.update_display(), self.format_results()
|
| 558 |
last_result = self.results[-1]
|
| 559 |
+
is_measurement = last_result['Point'] != '(0, 0)'
|
| 560 |
self.results.pop()
|
| 561 |
if is_measurement and self.marks:
|
| 562 |
self.marks.pop()
|
|
|
|
| 564 |
|
| 565 |
|
| 566 |
def create_interface():
|
| 567 |
+
"""
|
| 568 |
+
Creates the Gradio interface.
|
| 569 |
+
"""
|
| 570 |
+
print("Creating interface...")
|
| 571 |
analyzer = DicomAnalyzer()
|
| 572 |
|
| 573 |
with gr.Blocks(css="#image_display { outline: none; }") as interface:
|
|
|
|
| 576 |
with gr.Row():
|
| 577 |
with gr.Column():
|
| 578 |
file_input = gr.File(label="Upload DICOM file")
|
| 579 |
+
diameter_slider = gr.Slider(
|
| 580 |
+
minimum=1,
|
| 581 |
+
maximum=20,
|
| 582 |
+
value=9,
|
| 583 |
+
step=1,
|
| 584 |
+
label="ROI Diameter (pixels)"
|
| 585 |
+
)
|
| 586 |
|
| 587 |
with gr.Row():
|
| 588 |
zoom_in_btn = gr.Button("Zoom In (+)")
|
|
|
|
| 591 |
reset_all_btn = gr.Button("Reset All")
|
| 592 |
|
| 593 |
with gr.Column():
|
| 594 |
+
image_display = gr.Image(
|
| 595 |
+
label="DICOM Image",
|
| 596 |
+
interactive=True,
|
| 597 |
+
elem_id="image_display"
|
| 598 |
+
)
|
| 599 |
|
| 600 |
with gr.Row():
|
| 601 |
zero_btn = gr.Button("Add Zero Row")
|
|
|
|
| 610 |
|
| 611 |
gr.Markdown("""
|
| 612 |
### Controls:
|
| 613 |
+
- Use arrow keys to pan when zoomed in.
|
| 614 |
+
- Click on the image to analyze ROI.
|
| 615 |
+
- "Save Results": basic raw data Excel
|
| 616 |
+
- "Save Formatted Results": advanced table with 1-AVG, even if 1 measurement only
|
|
|
|
| 617 |
""")
|
| 618 |
|
| 619 |
def update_diameter(x):
|
| 620 |
analyzer.circle_diameter = float(x)
|
| 621 |
+
print(f"Diameter updated to: {x}")
|
| 622 |
return f"Diameter set to {x} pixels"
|
| 623 |
|
| 624 |
def save_formatted():
|
| 625 |
+
output_path = "analysis_results_formatted.xlsx"
|
| 626 |
+
return analyzer.save_formatted_results(output_path)
|
| 627 |
+
|
| 628 |
+
file_input.change(
|
| 629 |
+
fn=analyzer.load_dicom,
|
| 630 |
+
inputs=file_input,
|
| 631 |
+
outputs=[image_display, results_display]
|
| 632 |
+
)
|
| 633 |
+
|
| 634 |
+
image_display.select(
|
| 635 |
+
fn=analyzer.analyze_roi,
|
| 636 |
+
outputs=[image_display, results_display]
|
| 637 |
+
)
|
| 638 |
+
|
| 639 |
+
diameter_slider.change(
|
| 640 |
+
fn=update_diameter,
|
| 641 |
+
inputs=diameter_slider,
|
| 642 |
+
outputs=gr.Textbox(label="Status")
|
| 643 |
+
)
|
| 644 |
|
| 645 |
+
zoom_in_btn.click(
|
| 646 |
+
fn=analyzer.zoom_in,
|
| 647 |
+
inputs=image_display,
|
| 648 |
+
outputs=image_display,
|
| 649 |
+
queue=False
|
| 650 |
+
)
|
| 651 |
|
| 652 |
+
zoom_out_btn.click(
|
| 653 |
+
fn=analyzer.zoom_out,
|
| 654 |
+
inputs=image_display,
|
| 655 |
+
outputs=image_display,
|
| 656 |
+
queue=False
|
| 657 |
+
)
|
| 658 |
|
| 659 |
+
reset_btn.click(
|
| 660 |
+
fn=analyzer.reset_view,
|
| 661 |
+
outputs=image_display
|
| 662 |
+
)
|
| 663 |
|
| 664 |
+
reset_all_btn.click(
|
| 665 |
+
fn=analyzer.reset_all,
|
| 666 |
+
inputs=image_display,
|
| 667 |
+
outputs=[image_display, results_display]
|
| 668 |
+
)
|
| 669 |
+
|
| 670 |
+
key_press.change(
|
| 671 |
+
fn=analyzer.handle_keyboard,
|
| 672 |
+
inputs=key_press,
|
| 673 |
+
outputs=image_display
|
| 674 |
+
)
|
| 675 |
+
|
| 676 |
+
zero_btn.click(
|
| 677 |
+
fn=analyzer.add_zero_row,
|
| 678 |
+
inputs=image_display,
|
| 679 |
+
outputs=[image_display, results_display]
|
| 680 |
+
)
|
| 681 |
+
|
| 682 |
+
zero2_btn.click(
|
| 683 |
+
fn=analyzer.add_two_zero_rows,
|
| 684 |
+
inputs=image_display,
|
| 685 |
+
outputs=[image_display, results_display]
|
| 686 |
+
)
|
| 687 |
+
|
| 688 |
+
undo_btn.click(
|
| 689 |
+
fn=analyzer.undo_last,
|
| 690 |
+
inputs=image_display,
|
| 691 |
+
outputs=[image_display, results_display]
|
| 692 |
+
)
|
| 693 |
+
|
| 694 |
+
save_btn.click(
|
| 695 |
+
fn=analyzer.save_results,
|
| 696 |
+
outputs=[file_output, results_display]
|
| 697 |
+
)
|
| 698 |
+
|
| 699 |
+
save_formatted_btn.click(
|
| 700 |
+
fn=save_formatted,
|
| 701 |
+
outputs=[file_output, results_display]
|
| 702 |
+
)
|
| 703 |
|
| 704 |
+
# JavaScript to capture arrow keys
|
| 705 |
js = """
|
| 706 |
<script>
|
| 707 |
document.addEventListener('keydown', function(e) {
|
|
|
|
| 722 |
"""
|
| 723 |
gr.HTML(js)
|
| 724 |
|
| 725 |
+
print("Interface created successfully")
|
| 726 |
return interface
|
| 727 |
|
| 728 |
|
| 729 |
if __name__ == "__main__":
|
| 730 |
try:
|
| 731 |
+
print("Starting application...")
|
| 732 |
interface = create_interface()
|
| 733 |
+
print("Launching interface...")
|
| 734 |
interface.queue()
|
| 735 |
+
interface.launch(
|
| 736 |
+
server_name="0.0.0.0",
|
| 737 |
+
server_port=7860,
|
| 738 |
+
share=True,
|
| 739 |
+
debug=True,
|
| 740 |
+
show_error=True,
|
| 741 |
+
quiet=False
|
| 742 |
+
)
|
| 743 |
except Exception as e:
|
| 744 |
logger.error(f"Error launching application: {str(e)}")
|
| 745 |
logger.error(traceback.format_exc())
|