Semapp 1.0.0__tar.gz → 1.0.2__tar.gz

{semapp-1.0.0 → semapp-1.0.2}/PKG-INFO

@@ -1,21 +1,20 @@
 Metadata-Version: 2.4
 Name: Semapp
-Version: 1.0.0
+Version: 1.0.2
 Summary: Package for SEM visualization
 Author-email: Thibaut Meyer <thibaut.meyer3@gmail.com>
-License-Expression: MIT
-Project-URL: Homepage, https://github.com/pypa/sampleproject
-Project-URL: Issues, https://github.com/pypa/sampleproject/issues
+License-Expression: GPL-3.0-or-later
+Project-URL: Homepage, https://github.com/thi-mey/SEMapp
 Keywords: SEM,GUI
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: matplotlib==3.8.3
-Requires-Dist: numpy<2.0,>=1.21
-Requires-Dist: pandas>=2.2.0
-Requires-Dist: Pillow>=11.0.0
+Requires-Dist: matplotlib==3.10.3
+Requires-Dist: numpy==2.2.5
+Requires-Dist: pandas==2.2.3
+Requires-Dist: Pillow==11.2.1
 Requires-Dist: PyQt5==5.15.11
-Requires-Dist: PyQt5_sip<13.0.0,>=12.15.0
+Requires-Dist: PyQt5_sip==12.17.0
 Dynamic: license-file

{semapp-1.0.0 → semapp-1.0.2}/SEMapp.egg-info/PKG-INFO

@@ -1,21 +1,20 @@
 Metadata-Version: 2.4
 Name: Semapp
-Version: 1.0.0
+Version: 1.0.2
 Summary: Package for SEM visualization
 Author-email: Thibaut Meyer <thibaut.meyer3@gmail.com>
-License-Expression: MIT
-Project-URL: Homepage, https://github.com/pypa/sampleproject
-Project-URL: Issues, https://github.com/pypa/sampleproject/issues
+License-Expression: GPL-3.0-or-later
+Project-URL: Homepage, https://github.com/thi-mey/SEMapp
 Keywords: SEM,GUI
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: matplotlib==3.8.3
-Requires-Dist: numpy<2.0,>=1.21
-Requires-Dist: pandas>=2.2.0
-Requires-Dist: Pillow>=11.0.0
+Requires-Dist: matplotlib==3.10.3
+Requires-Dist: numpy==2.2.5
+Requires-Dist: pandas==2.2.3
+Requires-Dist: Pillow==11.2.1
 Requires-Dist: PyQt5==5.15.11
-Requires-Dist: PyQt5_sip<13.0.0,>=12.15.0
+Requires-Dist: PyQt5_sip==12.17.0
 Dynamic: license-file

semapp-1.0.2/SEMapp.egg-info/requires.txt

@@ -0,0 +1,6 @@
+matplotlib==3.10.3
+numpy==2.2.5
+pandas==2.2.3
+Pillow==11.2.1
+PyQt5==5.15.11
+PyQt5_sip==12.17.0

{semapp-1.0.0 → semapp-1.0.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = "Semapp"
-version = "1.0.0"
+version = "1.0.2"
 authors = [
   { name="Thibaut Meyer", email="thibaut.meyer3@gmail.com" },
 ]
@@ -16,23 +16,22 @@ keywords = [
     "GUI",
 ]
 dependencies = [
-    "matplotlib==3.8.3",
-    "numpy>=1.21,<2.0",
-    "pandas>=2.2.0",
-    "Pillow>=11.0.0",
+    "matplotlib==3.10.3",
+    "numpy==2.2.5",
+    "pandas==2.2.3",
+    "Pillow==11.2.1",
     "PyQt5==5.15.11",
-    "PyQt5_sip>=12.15.0,<13.0.0"
+    "PyQt5_sip==12.17.0",
 ]
 classifiers = [
     "Programming Language :: Python :: 3",
     "Operating System :: OS Independent",
 ]
-license = "MIT"
+license = "GPL-3.0-or-later"
 license-files = ["LICENSE*"]
 
 [project.gui-scripts]
 Semapp = "semapp.main:main"
 
 [project.urls]
-Homepage = "https://github.com/pypa/sampleproject"
-Issues = "https://github.com/pypa/sampleproject/issues"
+Homepage = "https://github.com/thi-mey/SEMapp"

{semapp-1.0.0 → semapp-1.0.2}/semapp/Layout/create_button.py

@@ -63,7 +63,7 @@ class ButtonFrame(QWidget):
         # Example of adding them to a layout
         self.entries = {}
         self.dirname = None
-        # self.dirname = r"C:\Users\TM273821\Desktop\SEM\Amel"
+        # self.dirname = r"C:\Users\TM273821\Desktop\SEM\TEst_complus"
 
 
         max_characters = 30  # Set character limit

{semapp-1.0.0 → semapp-1.0.2}/semapp/Plot/frame_attributes.py

@@ -114,42 +114,49 @@ class PlotFrame(QWidget):
         dans_defect_list = False
 
         with open(filepath, "r", encoding="utf-8") as f:
-            for ligne in f:
-                ligne = ligne.strip()
-
-                if ligne.startswith("SampleSize"):
-                    match = re.search(r"SampleSize\s+1\s+(\d+)", ligne)
-                    if match:
-                        data["SampleSize"] = int(match.group(1))
-
-                elif ligne.startswith("DiePitch"):
-                    match = re.search(r"DiePitch\s+([0-9.]+)\s+([0-9.]+);", ligne)
-                    if match:
-                        data["DiePitch"]["X"] = float(match.group(1))
-                        data["DiePitch"]["Y"] = float(match.group(2))
-
-                elif ligne.startswith("DieOrigin"):
-                    match = re.search(r"DieOrigin\s+([0-9.]+)\s+([0-9.]+);", ligne)
-                    if match:
-                        data["DieOrigin"]["X"] = float(match.group(1))
-                        data["DieOrigin"]["Y"] = float(match.group(2))
-
-                elif ligne.startswith("SampleCenterLocation"):
-                    match = re.search(r"SampleCenterLocation\s+([0-9.]+)\s+([0-9.]+);", ligne)
-                    if match:
-                        data["SampleCenterLocation"]["X"] = float(match.group(1))
-                        data["SampleCenterLocation"]["Y"] = float(match.group(2))
-
-                elif ligne.startswith("DefectList"):
-                    dans_defect_list = True
-                    continue
-
-                elif dans_defect_list:
-                    if re.match(r"^\d+\s", ligne):
-                        valeurs = ligne.split()
-                        if len(valeurs) >= 18:
-                            defect = {f"val{i+1}": float(val) for i, val in enumerate(valeurs[:18])}
-                            data["Defects"].append(defect)
+            lines = f.readlines()
+            
+        for i, line in enumerate(lines):
+            line = line.strip()
+
+            if line.startswith("SampleSize"):
+                match = re.search(r"SampleSize\s+1\s+(\d+)", line)
+                if match:
+                    data["SampleSize"] = int(match.group(1))
+
+            elif line.startswith("DiePitch"):
+                match = re.search(r"DiePitch\s+([0-9.e+-]+)\s+([0-9.e+-]+);", line)
+                if match:
+                    data["DiePitch"]["X"] = float(match.group(1))
+                    data["DiePitch"]["Y"] = float(match.group(2))
+
+            elif line.startswith("DieOrigin"):
+                match = re.search(r"DieOrigin\s+([0-9.e+-]+)\s+([0-9.e+-]+);", line)
+                if match:
+                    data["DieOrigin"]["X"] = float(match.group(1))
+                    data["DieOrigin"]["Y"] = float(match.group(2))
+
+            elif line.startswith("SampleCenterLocation"):
+                match = re.search(r"SampleCenterLocation\s+([0-9.e+-]+)\s+([0-9.e+-]+);", line)
+                if match:
+                    data["SampleCenterLocation"]["X"] = float(match.group(1))
+                    data["SampleCenterLocation"]["Y"] = float(match.group(2))
+
+            elif line.startswith("DefectList"):
+                dans_defect_list = True
+                continue
+
+            elif dans_defect_list:
+                if re.match(r"^\d+\s", line):
+                    value = line.split()
+                    if len(value) >= 12:
+                        # Vérifier si la ligne suivante a exactement 2 colonnes
+                        if i + 1 < len(lines):
+                            next_line = lines[i + 1].strip()
+                            next_values = next_line.split()
+                            if len(next_values) == 2:
+                                defect = {f"val{i+1}": float(val) for i, val in enumerate(value[:10])}
+                                data["Defects"].append(defect)
 
         pitch_x = data["DiePitch"]["X"]
         pitch_y = data["DiePitch"]["Y"]
@@ -164,6 +171,7 @@ class PlotFrame(QWidget):
             val3 = d["val3"]
             val4_scaled = d["val4"] * pitch_x - Xcenter
             val5_scaled = d["val5"] * pitch_y - Ycenter
+            defect_size = d["val9"]
 
             x_corr = round((val2 + val4_scaled) / 10000, 1)
             y_corr = round((val3 + val5_scaled) / 10000, 1)
@@ -171,11 +179,20 @@ class PlotFrame(QWidget):
             corrected_positions.append({
                 "defect_id": val1,
                 "X": x_corr,
-                "Y": y_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"])
+        
+        # Enregistrer le mapping en CSV dans le même dossier que filepath
+        import os
+        file_dir = os.path.dirname(filepath)
+        csv_path = os.path.join(file_dir, "mapping.csv")
+        self.coordinates.to_csv(csv_path, index=False)
+        print(f"Mapping saved to: {csv_path}")
 
         return self.coordinates
 
@@ -204,15 +221,15 @@ class PlotFrame(QWidget):
         folder_path = os.path.join(self.button_frame.folder_var_changed(), 
                                  str(self.selected_wafer))
         
-                # Recherche du fichier qui se termine par .001 dans le dossier
+        # Find the first .001 file in the selected folder
         matching_files = glob.glob(os.path.join(folder_path, '*.001'))
 
-        # Si au moins un fichier correspond, on prend le premier
+        # Sort the files to ensure consistent ordering
         if matching_files:
             recipe_path = matching_files[0]
         else:
-            recipe_path = None  # Ou tu peux lever une exception ou afficher un message d’erreur
-        # Charger les coordonnées depuis le fichier CSV (recipe)
+            recipe_path = None  
+        
         self.coordinates = self.extract_positions(recipe_path)     
         
         tiff_path = os.path.join(folder_path, "data.tif")
@@ -223,9 +240,8 @@ class PlotFrame(QWidget):
             return
 
         self._load_tiff(tiff_path)
-        self._update_plot()  # Maintenant les coordonnées seront disponibles pour le plot
+        self._update_plot() 
 
-        # Pop-up stylisé
         msg = QMessageBox()
         msg.setIcon(QMessageBox.Information)
         msg.setText(f"Wafer {self.selected_wafer} opened successfully")
@@ -303,8 +319,10 @@ class PlotFrame(QWidget):
         if self.coordinates is not None:
             x_coords = self.coordinates.iloc[:, 0]
             y_coords = self.coordinates.iloc[:, 1]
+            defect_size = self.coordinates.iloc[:, 2]
+            print(f"defect_size: {defect_size}")
 
-            # Calcul de la valeur maximale absolue parmi toutes les coordonnées
+            # Calculate the maximum value for scaling
             max_val = max(abs(x_coords).max(), abs(y_coords).max())
 
             if max_val <= 5:
@@ -316,14 +334,17 @@ class PlotFrame(QWidget):
             elif max_val <= 15:
                 radius = 15
             else:
-                radius = max_val  # fallback pour les cas supérieurs à 30
+                radius = max_val  # fallback for > 15
 
             self.radius = radius
 
-            ax.scatter(x_coords, y_coords, color='blue', marker='o',
+            # Create color array based on defect_size (values are in scientific notation)
+            colors = ['red' if size > 1.0e+01 else 'blue' for size in defect_size]
+            
+            ax.scatter(x_coords, y_coords, color=colors, marker='o',
                        s=100, label='Positions')
             
-                # Mise à l'échelle du graphique en fonction du radius
+            # Set limits based on the radius
             ax.set_xlim(-radius - 1, radius + 1)
             ax.set_ylim(-radius - 1, radius + 1)
 

{semapp-1.0.0 → semapp-1.0.2}/semapp/Processing/processing.py

@@ -113,13 +113,13 @@ 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):
@@ -217,7 +217,6 @@ class Process:
     def clean(self):
         """
         Clean up the output directory by deleting any non-conforming TIFF files.
-
         This method deletes any files that do not follow the expected naming
         conventions (files not starting with "data" or
         containing the word "page").
@@ -467,19 +466,19 @@ class Process:
 
                         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)
@@ -579,21 +578,78 @@ class Process:
                     os.remove(file_path)
                     print(f"Deleted: {file_path}")
 
+
+    def ajouter_extension_tiff(self):
+        """
+        Ajoute l'extension .tiff à tous les fichiers du dossier parent et ses sous-dossiers,
+        SAUF ceux qui se terminent par .001.
+        Utilise os.walk pour parcourir tous les sous-dossiers.
+        """
+        fichiers_renommes = 0
+        
+        print(f"Scan du dossier parent: {self.dirname}")
+        
+        # Parcourir tous les sous-dossiers avec os.walk
+        for root, dirs, files in os.walk(self.dirname):
+            print(f"\nTraitement du dossier: {root}")
+            
+            for file in files:
+                # Ignorer les fichiers qui se terminent par .001
+                if file.endswith('.001'):
+                    print(f"Fichier ignoré (extension .001): {file}")
+                    continue
+                
+                # Vérifier si le fichier n'a pas d'extension ou a une extension différente de .tiff
+                if '.' not in file or not file.endswith('.tiff'):
+                    old_filepath = os.path.join(root, file)
+                    
+                    # Si le fichier n'a pas d'extension, ajouter .tiff
+                    if '.' not in file:
+                        new_filename = file + '.tiff'
+                    else:
+                        # Si le fichier a une extension différente, remplacer par .tiff
+                        base_name = file.rsplit('.', 1)[0]  # Prendre tout sauf la dernière extension
+                        new_filename = base_name + '.tiff'
+                    
+                    new_filepath = os.path.join(root, new_filename)
+                    
+                    # Vérifier que le nouveau nom n'existe pas déjà
+                    if not os.path.exists(new_filepath):
+                        try:
+                            os.rename(old_filepath, new_filepath)
+                            print(f"Extension ajoutée: '{file}' -> '{new_filename}'")
+                            fichiers_renommes += 1
+                        except Exception as e:
+                            print(f"Erreur lors du renommage de '{file}': {e}")
+                    else:
+                        print(f"Erreur: Le fichier '{new_filename}' existe déjà, impossible de renommer '{file}'")
+        
+        print(f"\n{'='*50}")
+        print(f"RÉSUMÉ DE L'AJOUT D'EXTENSIONS")
+        print(f"{'='*50}")
+        print(f"Fichiers renommés: {fichiers_renommes}")
+        
+        return fichiers_renommes
+
+
 if __name__ == "__main__":
-    DIRNAME = r"C:\Users\TM273821\Desktop\SEM\RAW"
+    DIRNAME = r"C:\Users\TM273821\Desktop\SEM\lD25S1556"
     SCALE = r"C:\Users\TM273821\SEM\settings_data.json"
 
     processor = Process(DIRNAME, wafer=18, scale=SCALE)
 
     # Process files
     # processor.organize_and_rename_files()  # Organize and rename files
-    # processor.rename_wo_legend_all()  # Preprocess all files in the directory
+    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
     
+    # Ajouter l'extension .tiff aux fichiers qui n'en ont pas
+    processor.ajouter_extension_tiff()
+    
 

{semapp-1.0.0 → semapp-1.0.2}/semapp/main.py

@@ -52,7 +52,7 @@ class MainWindow(QWidget):  # pylint: disable=R0903
         Configures the main layout, creates frames for different sections,
         and initializes the update timer.
         """
-        self.setWindowTitle("Data Visualization")
+        self.setWindowTitle("SEMapp")
         self.setStyleSheet(f"background-color: {BACKGROUND_COLOR};")
 
         # Create the main layout (canvas_layout)

semapp-1.0.0/SEMapp.egg-info/requires.txt

@@ -1,6 +0,0 @@
-matplotlib==3.8.3
-numpy<2.0,>=1.21
-pandas>=2.2.0
-Pillow>=11.0.0
-PyQt5==5.15.11
-PyQt5_sip<13.0.0,>=12.15.0