Semapp 1.0.1__py3-none-any.whl → 1.0.3__py3-none-any.whl

semapp/Processing/processing.py

@@ -36,19 +36,20 @@ class Process:
         self.output_dir = None
         self.load_json()
     def load_json(self):
+        
         """Load the settings data from a JSON file."""
         try:
             with open(self.scale_data, "r", encoding="utf-8") as file:
                 self.settings = json.load(file)
-            print("Settings data loaded successfully.")
+            pass  # Settings loaded
         except FileNotFoundError:
-            print("Settings file not found. Starting fresh.")
+            # Settings file not found, starting fresh
             self.settings = []
         except json.JSONDecodeError as error:
-            print(f"JSON decoding error: {error}")
+            # JSON decoding error
             self.settings = []
         except OSError as error:
-            print(f"OS error when reading file: {error}")
+            # OS error when reading file
             self.settings = []   
     def extract_positions(self, filepath):
         '''Function to extract positions from a 001 file.'''
@@ -113,13 +114,13 @@ class Process:
             val3 = d["val3"]
             val4_scaled = d["val4"] * pitch_x - x_center
             val5_scaled = d["val5"] * pitch_y - y_center
-
+            defect_size = d["val8"]
             x_corr = round((val2 + val4_scaled) / 10000, 1)
             y_corr = round((val3 + val5_scaled) / 10000, 1)
 
-            corrected_positions.append({"defect_id": val1, "X": x_corr,"Y": y_corr})
+            corrected_positions.append({"defect_id": val1, "X": x_corr,"Y": y_corr, "defect_size": defect_size})
 
-        self.coordinates = pd.DataFrame(corrected_positions, columns=["X", "Y"])
+        self.coordinates = pd.DataFrame(corrected_positions, columns=["X", "Y", "defect_size"])
 
         return self.coordinates
     def rename(self):
@@ -132,7 +133,7 @@ class Process:
         self.output_dir = os.path.join(self.dirname, self.wafer_number)
 
         if not os.path.exists(self.output_dir):
-            print(f"Directory not found: {self.output_dir}")
+            pass  # Directory not found
             return
 
         matching_files = glob.glob(os.path.join(self.output_dir, '*.001'))
@@ -153,8 +154,6 @@ class Process:
         for file in tiff_files:
             # Extract page number from the file name (e.g., data_page_1.tiff)
             file_number = int(file.split('_')[2].split('.')[0])
-            print(f"Processing {file}: Page number {file_number}, Total "
-                  f"settings {len(self.settings)}")
 
             # Calculate the corresponding row in the CSV
             csv_row_index = (file_number - 1) // len(self.settings)
@@ -176,7 +175,6 @@ class Process:
 
             # Rename the file
             os.rename(old_path, new_path)
-            print(f"Renamed: {file} -> {new_name}")
             
     def split_tiff(self):
         """
@@ -193,7 +191,6 @@ class Process:
         output_files = []
         page_index = 0
         if not os.path.exists(self.tiff_path):
-            print(f"TIFF file not found: {self.tiff_path}")
             return []
 
         try:
@@ -224,7 +221,6 @@ class Process:
         self.output_dir = os.path.join(self.dirname, self.wafer_number)
 
         if not os.path.exists(self.output_dir):
-            print(f"Error: Directory does not exist: {self.output_dir}")
             return
 
         tiff_files = [f for f in os.listdir(self.output_dir)
@@ -235,7 +231,6 @@ class Process:
             if not file_name.startswith("data") or "page" in file_name.lower() or file_name.endswith("001"):
                 file_path = os.path.join(self.output_dir, file_name)
                 os.remove(file_path)
-                print(f"Deleted: {file_path}")
 
     def split_tiff_all(self):
         """
@@ -248,13 +243,10 @@ class Process:
         for subdir, _, _ in os.walk(self.dirname):
             if subdir != self.dirname:
                 self.tiff_path = os.path.join(subdir, "data.tif")
-                print(f"Processing directory: {subdir}, "
-                      f"TIFF path: {self.tiff_path}")
 
                 output_files = []
                 page_index = 0
                 if not os.path.exists(self.tiff_path):
-                    print(f"TIFF file not found: {self.tiff_path}")
                     continue
 
                 try:
@@ -287,7 +279,6 @@ class Process:
             if subdir != self.dirname:
                 self.output_dir = os.path.join(self.dirname,
                                                os.path.basename(subdir))
-                print(f"Renaming files in: {self.output_dir}")
 
                 matching_files = glob.glob(os.path.join(self.output_dir, '*.001'))
 
@@ -307,8 +298,6 @@ class Process:
 
                 for file in tiff_files:
                     file_number = int(file.split('_')[2].split('.')[0])
-                    print(f"Processing {file}: Page number {file_number}, "
-                          f"Total settings {len(self.settings)}")
 
                     csv_row_index = (file_number - 1) // len(self.settings)
                     remainder = (file_number - 1) % len(self.settings)
@@ -324,7 +313,6 @@ class Process:
                     new_path = os.path.join(self.output_dir, new_name)
 
                     os.rename(old_path, new_path)
-                    print(f"Renamed: {file} -> {new_name}")
 
     def clean_all(self):
         """
@@ -337,10 +325,8 @@ class Process:
             if subdir != self.dirname:
                 self.output_dir = os.path.join(self.dirname,
                                                os.path.basename(subdir))
-                print(f"Cleaning directory: {self.output_dir}")
 
                 if not os.path.exists(self.output_dir):
-                    print(f"Error: Directory does not exist: {self.output_dir}")
                     continue
 
                 tiff_files = [f for f in os.listdir(self.output_dir)
@@ -350,7 +336,6 @@ class Process:
                             "page" in file_name.lower() or file_name.endswith("001"):
                         file_path = os.path.join(self.output_dir, file_name)
                         os.remove(file_path)
-                        print(f"Deleted: {file_path}")
 
     def organize_and_rename_files(self):
         """
@@ -359,16 +344,22 @@ class Process:
         and rename the files to 'data.tif' in their respective subfolders.
         """
         if not os.path.exists(self.dirname):
-            print(f"Error: The folder {self.dirname} does not exist.")
             return
 
+        # Check if there are subdirectories
+        subdirs = [d for d in os.listdir(self.dirname) if
+                   os.path.isdir(os.path.join(self.dirname, d))]
+        
+        # Check if there are .tif files
+        tif_files = [f for f in os.listdir(self.dirname) 
+                     if f.lower().endswith(".tif") and os.path.isfile(os.path.join(self.dirname, f))]
+
         # Iterate through files in the directory
         for file_name in os.listdir(self.dirname):
             if file_name.lower().endswith(".tif"):
                 parts = file_name.rsplit("_", 1)
                 if len(parts) < 2:
-                    print(
-                        f"Skipping file with unexpected format: {file_name}")
+                    # Skip file with unexpected format
                     continue
 
                 # Use the last part (before extension) as the subfolder name
@@ -383,14 +374,11 @@ class Process:
                 destination_path = os.path.join(subfolder_path, "data.tif")
                 shutil.move(source_path, destination_path)
 
-                print(
-                    f"Moved and renamed: {file_name} -> {destination_path}")
             
             if file_name.lower().endswith(".001"):
                 parts = file_name.rsplit("_", 1)
                 if len(parts) < 2:
-                    print(
-                        f"Skipping file with unexpected format: {file_name}")
+                    # Skip file with unexpected format
                     continue
 
                 # Use the last part (before extension) as the subfolder name
@@ -405,8 +393,53 @@ class Process:
                 destination_path = os.path.join(subfolder_path, file_name)
                 shutil.move(source_path, destination_path)
 
-                print(
-                    f"Moved and renamed: {file_name} -> {destination_path}")
+        
+        # If no subdirectories and no .tif files, create folders from KLARF files
+        if not subdirs and not tif_files:
+            wafer_ids = self.extract_wafer_ids_from_klarf()
+            
+            if wafer_ids:
+                for wafer_id in wafer_ids:
+                    subfolder_path = os.path.join(self.dirname, str(wafer_id))
+                    os.makedirs(subfolder_path, exist_ok=True)
+
+    def extract_wafer_ids_from_klarf(self):
+        """Extract wafer IDs from KLARF files (.001) that contain COMPLUS4T."""
+        wafer_ids = []
+        
+        if not self.dirname:
+            return wafer_ids
+        
+        # Chercher les fichiers .001
+        try:
+            files = [f for f in os.listdir(self.dirname) 
+                    if f.endswith('.001') and os.path.isfile(os.path.join(self.dirname, f))]
+            
+            for file in files:
+                file_path = os.path.join(self.dirname, file)
+                try:
+                    with open(file_path, 'r', encoding='utf-8', errors='ignore') as f:
+                        content = f.read()
+                        
+                        # Check if file contains "COMPLUS4T"
+                        if 'COMPLUS4T' in content:
+                            # Search for all lines with WaferID
+                            # Pattern to extract number in quotes after WaferID
+                            pattern = r'WaferID\s+"@(\d+)"'
+                            matches = re.findall(pattern, content)
+                            
+                            # Add found IDs (converted to int)
+                            for match in matches:
+                                wafer_id = int(match)
+                                if wafer_id not in wafer_ids and 1 <= wafer_id <= 26:
+                                    wafer_ids.append(wafer_id)
+                except Exception as e:
+                    pass  # Error reading file
+        
+        except Exception as e:
+            pass  # Error listing files
+        
+        return wafer_ids
 
     def rename_wo_legend_all(self):
         """
@@ -421,19 +454,15 @@ class Process:
                 if file.endswith(".001"):
                     folder_names.append(subdir)
 
-        print(folder_names)  # debug print
 
         # Process each folder found
         for folder in folder_names:
             for subdir, _, files in os.walk(folder):
                 for file in files:
                     if file.endswith(".tiff"):
-                        print(subdir)
-                        print(f"Processing: {file}")
                         old_filepath = os.path.join(subdir, file)
 
                         matching_files = glob.glob(os.path.join(folder, '*.001'))
-                        print("Found .001 files:", matching_files)  # debug print
 
                         if matching_files:
                             recipe_path = matching_files[0]
@@ -442,14 +471,11 @@ class Process:
                             return
                         
 
-                        print(self.coordinates)
 
                         try:
                             defect_part = int(file.split("_")[1]) - 1
-                            print(f"Defect part index: {defect_part}")
                         except (IndexError, ValueError):
-                            print(
-                                f"Skipping file due to unexpected format: {file}")
+                            # Error parsing defect part index, skip file
                             continue
 
                         # Check if defect part is within the valid range
@@ -459,31 +485,28 @@ class Process:
                     
 
                         if defect_part >= len(self.coordinates):
-                            print(
-                                f"Skipping file {file} due to out-of-bounds "
-                                f"defect part.")
+                            # Error: defect part out of bounds, skip file
                             continue
 
                         x = self.coordinates.iloc[defect_part, 0]
                         y = self.coordinates.iloc[defect_part, 1]
-                        new_filename = f"{x}_{y}"
-
-                        # Add specific suffix based on the file type
-                        if "_Class_1_Internal" in file:
-                            new_filename += "_BSE.tif"
-                        elif "_Class_1_Topography" in file:
-                            topo_number = file.split("_Class_1_Topography")[1][
-                                0]  # Extract Topography number
-                            new_filename += f"_SE{topo_number}.tiff"
-                        else:
-                            print(
-                                f"Skipping file due to unexpected format: {file}")
-                            continue
+                        new_filename = f"{x}_{y}.tiff"
+
+                        # # Add specific suffix based on the file type
+                        # if "_Class_1_Internal" in file:
+                        #     new_filename += "_BSE.tif"
+                        # elif "_Class_1_Topography" in file:
+                        #     topo_number = file.split("_Class_1_merged")[1][
+                        #         0]  # Extract Topography number
+                        #     new_filename += f"_SE{topo_number}.tiff"
+                        # else:
+                        #     print(
+                        #         f"Skipping file due to unexpected format: {file}")
+                        #     continue
 
                         # Construct the new file path and rename
                         new_filepath = os.path.join(subdir, new_filename)
                         os.rename(old_filepath, new_filepath)
-                        print(f"Renamed: {old_filepath} -> {new_filepath}")
 
     def rename_wo_legend(self):
         """
@@ -493,27 +516,22 @@ class Process:
         """
         wafer_path = os.path.join(self.dirname, self.wafer_number)
         if not os.path.exists(wafer_path):
-            print(f"Error: The wafer folder {wafer_path} does not exist.")
             return
 
         for subdir, _, files in os.walk(wafer_path):
             for file in files:
                 if file.endswith(".tiff"):
-                    print(f"Processing: {file}")
 
                     old_filepath = os.path.join(subdir, file)
 
                     try:
                         defect_part = int(file.split("_")[1]) - 1
-                        print(f"Defect part index: {defect_part}")
                     except (IndexError, ValueError):
-                        print(
-                            f"Skipping file due to unexpected format: {file}")
+                        # Error parsing defect part, skip file
                         continue
                     
                     matching_files = glob.glob(os.path.join(wafer_path, '*.001'))
 
-                    print("Found .001 files:", matching_files)  # debug print
 
                     if matching_files:
                         recipe_path = matching_files[0]
@@ -523,9 +541,7 @@ class Process:
                     
                     # Check if defect part is within the valid range
                     if defect_part >= len(self.coordinates):
-                        print(
-                            f"Skipping file {file} "
-                            f"due to out-of-bounds defect part.")
+                        # Error: defect part out of bounds, skip file
                         continue
 
                     x = self.coordinates.iloc[defect_part, 0]
@@ -540,14 +556,12 @@ class Process:
                             0]  # Extract Topography number
                         new_filename += f"_SE{topo_number}.tiff"
                     else:
-                        print(
-                            f"Skipping file due to unexpected format: {file}")
+                        # Error: unexpected file format, skip file
                         continue
 
                     # Construct the new file path and rename
                     new_filepath = os.path.join(subdir, new_filename)
                     os.rename(old_filepath, new_filepath)
-                    print(f"Renamed: {old_filepath} -> {new_filepath}")
 
     def clean_folders_and_files(self):
         """
@@ -565,21 +579,59 @@ class Process:
                     # Avoid name conflicts
                     if not os.path.exists(new_path):
                         os.rename(old_path, new_path)
-                        print(f"Renamed: {old_path} -> {new_path}")
                     else:
-                        print(f"Conflict: {new_path} already exists. Skipped renaming.")
+                        pass  # Conflict: file already exists, skip
     
         for folder, subfolders, files in os.walk(self.dirname):
             # Delete .tiff files that contain "Raw" in their name
             for file in files:
                 if file.endswith(".tiff") and "Raw" in file:
-                    print(file)
                     file_path = os.path.join(folder, file)
                     os.remove(file_path)
-                    print(f"Deleted: {file_path}")
+
+
+    def ajouter_extension_tiff(self):
+        """
+        Add .tiff extension to all files in parent folder and subfolders,
+        EXCEPT those ending with .001.
+        Uses os.walk to traverse all subfolders.
+        """
+        fichiers_renommes = 0
+        
+        # Traverse all subfolders with os.walk
+        for root, dirs, files in os.walk(self.dirname):
+            for file in files:
+                # Ignore files ending with .001
+                if file.endswith('.001'):
+                    continue
+                
+                # Check if file has no extension or has different extension than .tiff
+                if '.' not in file or not file.endswith('.tiff'):
+                    old_filepath = os.path.join(root, file)
+                    
+                    # If file has no extension, add .tiff
+                    if '.' not in file:
+                        new_filename = file + '.tiff'
+                    else:
+                        # If file has different extension, replace with .tiff
+                        base_name = file.rsplit('.', 1)[0]  # Take everything except last extension
+                        new_filename = base_name + '.tiff'
+                    
+                    new_filepath = os.path.join(root, new_filename)
+                    
+                    # Check that new name doesn't already exist
+                    if not os.path.exists(new_filepath):
+                        try:
+                            os.rename(old_filepath, new_filepath)
+                            fichiers_renommes += 1
+                        except Exception as e:
+                            pass  # Error renaming file
+        
+        return fichiers_renommes
+
 
 if __name__ == "__main__":
-    DIRNAME = r"C:\Users\TM273821\Desktop\SEM\RAW"
+    DIRNAME = r"C:\Users\TM273821\Desktop\SEM\D25S2039_200_MOS2_SIO2_API"
     SCALE = r"C:\Users\TM273821\SEM\settings_data.json"
 
     processor = Process(DIRNAME, wafer=18, scale=SCALE)
@@ -588,11 +640,14 @@ if __name__ == "__main__":
     # processor.organize_and_rename_files()  # Organize and rename files
     # processor.rename_wo_legend_all()  # Preprocess all files in the directory
     # processor.clean_folders_and_files()
-    processor.rename_wo_legend()  # Preprocess specific wafer
+    # processor.rename_wo_legend()  # Preprocess specific wafer
 
     # processor.split_tiff_all()  # Preprocess specific wafer
     # processor.split_tiff_all()  # Preprocess specific wafer
     # processor.split_tiff()  # Preprocess specific wafer
-    # processor.rename_all()  # Preprocess specific wafer
+    processor.rename_all()  # Preprocess specific wafer
+    
+    # # Ajouter l'extension .tiff aux fichiers qui n'en ont pas
+    # processor.ajouter_extension_tiff()
     
 

semapp/__init__.py

@@ -0,0 +1,10 @@
+"""
+SEMapp - SEM Data Visualization Application
+
+A PyQt5-based application for visualizing and analyzing Scanning Electron Microscope (SEM) data.
+Supports both standard and COMPLUS4T KLARF file formats.
+"""
+
+__version__ = "1.0.2"
+__author__ = "Your Name"
+

semapp/main.py

@@ -6,8 +6,13 @@ for the SEM data visualization application.
 """
 
 import sys
+import os
 from PyQt5.QtCore import QTimer
 from PyQt5.QtWidgets import QApplication, QWidget, QGridLayout
+
+# Add parent directory to path to allow imports
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
+
 from semapp.Layout.main_window_att import LayoutFrame
 from semapp.Layout.create_button import ButtonFrame
 from semapp.Plot.frame_attributes import PlotFrame
@@ -76,7 +81,11 @@ class MainWindow(QWidget):  # pylint: disable=R0903
 
 
 def main():
-    print("SEMapp launched")
+    """
+    Main entry point for the SEMapp application.
+    
+    Creates and displays the main window, then starts the Qt event loop.
+    """
     app = QApplication(sys.argv)
     window = MainWindow()
     window.show()