added more docstrings

app.py

@@ -1,3 +1,10 @@
+"""
+Created on Fri Apr 21 2023
+@name:   app.py
+@desc:   Main file for the application
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 import sys
 from PyQt5.QtWidgets import QApplication
 from utils.gui.pyqt.main_window.MainWindow import MainWindow

utils/data_processing/data_processing.py

@@ -1,3 +1,10 @@
+"""
+Created on Mon Apr 24 2023
+@name:   data_processing.py
+@desc:   A module to process the data
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 from utils.math import data_extraction
 from utils.files.input import ScannedObject
 from utils.settings.SettingManager import SettingManager
@@ -13,6 +20,8 @@ def get_raw_data(obj:ScannedObject, ndigits:int,delta_z:float=1,update_progress_
 
     :param obj: Object to analyse
     :param ndigits: Number of digits to keep after the comma
+    :param delta_z: Delta z to use for the discretisation
+    :param update_progress_bar: Function to update the progress bar
     :return: dict(str:list) with the following keys:
         - X (en mm)     : list of x values
         - Y (en mm)     : list of y values
@@ -22,18 +31,24 @@ def get_raw_data(obj:ScannedObject, ndigits:int,delta_z:float=1,update_progress_
         - Xi-Xmoy       : list of Xi-Xmoy values
         - Yi-Ymoy       : list of Yi-Ymoy values
     """
+
+    # Create the data dict
     colones = ["X (en mm)", "Y (en mm)", "Z (en mm)", "teta (en rad)", "rayon (en mm)","Xi-Xmoy","Yi-Ymoy"]
     data = {}
     for colone in colones:
         data[colone] = []
 
+    # Select the discretisation method from the settings
     if SettingManager.get_instance().get_setting("discretisation_method") == "Z0-Zi < DeltaZ":
         get_discrete_vertices = obj.get_discrete_vertices
     else:
         get_discrete_vertices = obj.get_discrete_vertices3 
 
+    # Get the discrete vertices
     discrete_vertices = get_discrete_vertices(delta_z)
     progress = 0
+
+    # Calculate the data for each discrete vertex
     for discrete_values in discrete_vertices:
         mean_x ,mean_y, mean_z = data_extraction.get_x_y_z_mean(discrete_values)
         for x,y,z in discrete_values:
@@ -54,6 +69,8 @@ def get_discrete_data(obj:ScannedObject, ndigits:int, delta_z:float=1, update_pr
 
     :param obj: Object to analyse
     :param ndigits: Number of digits to keep after the comma
+    :param delta_z: Delta z to use for the discretisation
+    :param update_progress_bar: Function to update the progress bar
     :return: dict(str:list) with the following keys:
         - X moy (en mm)             : list of x mean values
         - Y moy (en mm)             : list of y mean values
@@ -61,15 +78,19 @@ def get_discrete_data(obj:ScannedObject, ndigits:int, delta_z:float=1, update_pr
         - Rayon moyen (en mm)       : list of mean radius values
         - Rayon ecart type (en mm)  : list of radius standard deviation values
     """
+    # Create the data dict
     colones = ["X moy (en mm)", "Y moy (en mm)", "Z moy (en mm)","Discretisation(en mm)","Rayon moyen (en mm)","Rayon ecart type (en mm)"]
     data = {}
     for colone in colones:
         data[colone] = []
+
+    # Select the discretisation method from the settings
     if SettingManager.get_instance().get_setting("discretisation_method") == "Z0-Zi < DeltaZ":
         get_discrete_vertices = obj.get_discrete_vertices
     else:
         get_discrete_vertices = obj.get_discrete_vertices3 
 
+    # Get the discrete vertices
     discrete_vertices = get_discrete_vertices(delta_z)
     progress = 0
     for discrete_values in discrete_vertices:

utils/files/input.py

@@ -1,5 +1,9 @@
 """
-This module contains the functions to parse the input files, and create a ScannedObject.
+Created on Thu Apr 20 2023
+@name:   input.py
+@desc:   This module contains the functions to parse the input files, and create a ScannedObject.
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
 """
 import numpy as np
 from utils.files.output import save_output_file
@@ -64,15 +68,12 @@ class ScannedObject:
     [(0, 1, 2), (0, 2, 3), (4, 5, 6), (4, 6, 7), (0, 1, 5), (0, 4, 5), (1, 2, 6), (1, 5, 6), (2, 3, 7), (2, 6, 7), (3, 0, 4), (3, 7, 4)]
     >>> obj.get_discrete_vertices()
     [[(0, 0, 0), (1, 0, 0), (1, 1, 0), (0, 1, 0)]],[ (0, 0, 1), (1, 0, 1), (1, 1, 1), (0, 1, 1)]]
-    #TODO Add and test exemples
     """
     def __init__(self, vertices, faces=None, result_file_path=None):
         self.vertices = np.asarray(vertices)
         self.faces = np.asarray(faces)
-        # Deprecated
+        self.result_file_path = result_file_path # Deprecated
-        self.result_file_path = result_file_path
+        self.bruteforce_discretization_result = None # Deprecated
-        self.bruteforce_discretization_result = None
-        #
         self.x = np.asarray([vertex[0] for vertex in vertices])
         self.y = np.asarray([vertex[1] for vertex in vertices])
         self.z = np.asarray([vertex[2] for vertex in vertices])
@@ -95,6 +96,7 @@ class ScannedObject:
             data = f.readlines()
             for line in data :
                 if line.startswith('f'):
+                    # Ignore the normals and textures
                     if "//" in line:
                         triangles.append([int(line.split()[1].split("//")[0])-1, int(line.split()[2].split("//")[0])-1, int(line.split()[3].split("//")[0])-1])
                     elif "/" in line:
@@ -179,19 +181,22 @@ class ScannedObject:
         """
         return self.z
 
-    def get_vertices(self, sort:bool = False):
+    def get_vertices(self, sort:bool = False)->list:
         """
         Get the vertices of the object.
         :param sort: Sort the vertices by z coordinate
+
         :return: vertices
         """
         
         vertices = self.vertices if not sort else sorted(self.vertices, key=lambda vertex: vertex[2])
         return vertices
 
-    def get_discrete_vertices(self, step:float = 1):
+    def get_discrete_vertices(self, step:float = 1)->list:
         """
-        Discretize the vertices of the object.
+        Discretize the vertices of the object using a split method.
+        This implementation will split the object at every step interval.
+
         :param step: Step of the discretization
         :return: Discretized vertices
         """
@@ -219,24 +224,30 @@ class ScannedObject:
                 L.append([])
         return L
     
-    def get_discrete_vertices3(self, step:float = 1):
+    def get_discrete_vertices3(self, step:float = 1)->list:
         """
-        Deprecated
+        Discretize the vertices of the object using a lenght method.
+        This implementation will split the object when difference between the
+        first and last point of a slice is greater or equal then the step interval.
+
+        :param step: Step of the discretization
+        :return: Discretized vertices
         """
         cpt = 0
         L = [[]]
         z = min(self.get_z())
-        sorted = self.get_vertices(sort=True)
+        sorted_vertices = self.get_vertices(sort=True)
-        for index in range(len(sorted)):
+        for index,_ in enumerate(sorted_vertices):
-            L[-1].append(sorted[index])
+            L[-1].append(sorted_vertices[index])
-            if sorted[index][2] - z > step:
+            if sorted_vertices[index][2] - z > step:
-                z = sorted[index+1][2]
+                z = sorted_vertices[index+1][2]
                 L.append([])
         return L
     
     def get_faces(self,resolved:bool = False)->list:
         """
         Get the faces of the object.
+
         :return: faces
         """
         if self.faces is None:
@@ -248,6 +259,7 @@ class ScannedObject:
     def update_from_faces(self,faces:list):
         """
         Update the object from the faces.
+
         :param faces: Faces to update the object from
         """
         cpt = 0
@@ -274,6 +286,7 @@ class ScannedObject:
     def normalise(self, axis:str = 'z'):
         """
         Normalise the object.
+
         :param axis: Axis to normalise
         """
         if 'x' in axis:
@@ -287,6 +300,7 @@ class ScannedObject:
     def get_data(self)->dict:
         """
         Get the data of the object.
+
         :return: Data of the object
         """
         return {'verticies': self.vertices, 'faces': self.faces, 'x': self.x, 'y': self.y, 'z': self.z}
@@ -329,6 +343,7 @@ class ScannedObject:
     def export_xyz(self, file_path:str,separator:str="\t"):
         """
         Export the object in a file.
+
         :param file_path: Path of the file
         :param separator: chars used to separate the values
         """
@@ -344,6 +359,7 @@ class ScannedObject:
     def export_obj(self,file_path):
         """
         Export the object in a file.
+
         :param file_path: Path of the file
         """
         string = ''

utils/files/norm.py

@@ -1,5 +1,9 @@
 """
-Deprecated
+Created on Fri Apr 14 2023
+@name:   input.py
+@desc:   x,y,z input cleaning (Deprecated)
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
 """
 
 def denormalizeXYZ(filePath:str, output:str):

utils/files/output.py

@@ -1,5 +1,9 @@
 """
-This module is used to manage the output files of the program.
+Created on Mon Apr 17 2023
+@name:   output.py
+@desc:   Output file formatting and saving
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
 """
 
 from utils.settings.SettingManager import SettingManager
@@ -10,7 +14,7 @@ def format_data(data:dict, separator:str, selected_columns:list = None) -> str:
     Format the data to be saved in the output file.
 
     :param data: Data to be formatted
-    :param selected_columns: Columns to be saved
+    :param selected_columns: Columns to be saved (in the specified order)
     :param separator: Separator of the columns
     :return: Formatted data
 
@@ -27,19 +31,24 @@ def format_data(data:dict, separator:str, selected_columns:list = None) -> str:
          3   ;6   ;9
         '
     """
-    isPrettier = SettingManager.get_instance().get_setting('pretiffy_output_file')
+    # Get the setting for the output file
+    is_prettier = SettingManager.get_instance().get_setting('pretiffy_output_file')
     output = ''
+    # If the columns are not specified, we take all the columns from dict
     if selected_columns is None:
         selected_columns = list(data.keys())
+    
+    # Write the columns headers
     for column_name in selected_columns:
-        if isPrettier:
+        if is_prettier:
             output += column_name.ljust(len(column_name) if len(column_name) > 8 else 9 )  + separator
         else:
             output += column_name + separator
     output += '\n'
+    # Write the columns values
     for i in range(len(data[selected_columns[0]])):
         for column in selected_columns:
-            if isPrettier:
+            if is_prettier:
                 output += str(data[column][i]).ljust(len(column) if len(column) > 8 else 9 ) + separator
             else:
                 output += str(data[column][i]) + separator

utils/graph2D/mpl_render.py

@@ -1,8 +1,17 @@
+"""
+Created on Fri Apr 21 2023
+@name:   mpl_render.py
+@desc:   A module to render a 2D data using matplotlib
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
+
 import matplotlib.pyplot as plt
 
 def render2D(values:list):
     """
     Render a 2D model using matplotlib
+
     :param values: A list with the values
     """
     fig = plt.figure()
@@ -13,6 +22,7 @@ def render2D(values:list):
 def cross_section(x_values:list, y_values:list):
     """
     Render a 2D cross section using matplotlib
+    
     :param x: A list with the x values
     :param y: A list with the y values
     """

utils/graph2D/visplot_render.py

@@ -1,10 +1,22 @@
+"""
+Created on Fri Apr 21 2023
+@name:   visplot_render.py
+@desc:   A module to render a 2D data using vispy
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 import vispy.plot as vp
 import numpy as np
 
-def render2D(values:list,title:str,xlabel="",ylabel="",show:bool=True):
+def render2D(values:list,title:str,xlabel="",ylabel="",show:bool=True)->vp.Fig|None:
     """
     Render a 2D plot using vispy
+
     :param values: A list with the values
+    :param title: Title of the plot
+    :param xlabel: Label of the x axis
+    :param ylabel: Label of the y axis
+    :param show: If True, show the plot, else return the canvas
     """
     fig = vp.Fig(size=(600, 500), show=False)
     plotwidget = fig[0, 0]
@@ -20,11 +32,16 @@ def render2D(values:list,title:str,xlabel="",ylabel="",show:bool=True):
     else:
         return fig
 
-def cross_section(x_values:list, y_values:list,title:str,xlabel="",ylabel="",show:bool=True  ):
+def cross_section(x_values:list, y_values:list,title:str,xlabel="",ylabel="",show:bool=True)->vp.Fig|None:
     """
     Render a 2D cross section using vispy
+
     :param x: A list with the x values
     :param y: A list with the y values
+    :param title: Title of the plot
+    :param xlabel: Label of the x axis
+    :param ylabel: Label of the y axis
+    :param show: If True, show the plot, else return the canvas
     """
     color = (0.3, 0.5, 0.8,.8)
     fig = vp.Fig(show=False)

utils/graph3D/mpl_render.py

@@ -1,3 +1,11 @@
+"""
+Created on Fri Apr 21 2023
+@name:   mpl_render.py
+@desc:   A module to render a 3D data using matplotlib
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
+
 from mpl_toolkits.mplot3d.art3d import Poly3DCollection
 import matplotlib.pyplot as plt
 import numpy as np
@@ -6,6 +14,7 @@ from utils.files.input import ScannedObject
 def render3D(obj:ScannedObject):
     """
     Render a 3D model using matplotlib's Poly3dcollection
+    
     :param obj: A ScannedObject to be rendered
     """
     fig = plt.figure()

utils/graph3D/visplot_render.py

@@ -1,3 +1,10 @@
+"""
+Created on Fri Apr 21 2023
+@name:   visplot_render.py
+@desc:   A module to render a 3D data using vispy
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 import numpy as np
 from vispy import app, scene
 from vispy.scene.visuals import Mesh
@@ -5,20 +12,27 @@ from vispy.visuals.filters import ShadingFilter, WireframeFilter
 from utils.files.input import ScannedObject
 
 
-def render3D(obj:ScannedObject,show:bool=True):
+def render3D(obj:ScannedObject,show:bool=True)->scene.SceneCanvas|None:
     """
-    Render a 3D model using vispy
+    Render a 3D model mesh using vispy
+
     :param obj: A ScannedObject to be rendered
+    :param show: If True, show the plot, else return the canvas
+    :return: A canvas with the rendered object
     """
+    # Extract the vertices and faces from the object
     vertices = np.asarray(obj.get_vertices())
     faces = np.asarray(obj.get_faces())
+    # Create the canvas
     canvas = scene.SceneCanvas(keys='interactive', bgcolor='white')
+    # Create a viewbox to display the mesh in
     view = canvas.central_widget.add_view()
     view.camera = 'arcball'
     view.camera.depth_value = 1e3
     color = (0.3, 0.5, 0.8)
     mesh = Mesh(vertices, faces, color=color)
     view.add(mesh)
+    # Add filters to the mesh
     wireframe_filter = WireframeFilter(width=0)
     shading_filter = ShadingFilter(shininess=0)
     mesh.attach(wireframe_filter)

utils/gui/pyqt/error_popup/ErrorPopup.py

@@ -1,7 +1,28 @@
-from PyQt5 import QtCore, QtGui, QtWidgets
+"""
+Created on Wed Apr 28 2023
+@name:   ErrorPopup.py
+@desc:   A class to show a popup with an error message
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 from PyQt5.QtWidgets import QMessageBox
 
 class ErrorPopup(object):
+    """
+    A class to show a popup with an error message
+
+    :param error_text: The error message
+    :param details: The details of the error
+    :param button_label: The label of the button
+    :param button_callback: The callback of the button
+
+    :ivar error_text: The error message
+    :ivar details: The details of the error
+    :ivar button_label: The label of the button
+    :ivar button_callback: The callback of the button
+
+    :method show_popup: Show the popup
+    """
 
     def __init__(self,error_text,details = None,button_label = None,button_callback=None):
         self.error_text = error_text

utils/gui/pyqt/main_window/MainWindow.py

@@ -1,3 +1,10 @@
+"""
+Created on Mon Apr 24 2023
+@name:   MainWindow.py
+@desc:   Main window of the application
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 import os
 from PyQt5 import QtWidgets
 from PyQt5.QtCore import QThread
@@ -14,7 +21,8 @@ from utils.gui.pyqt.main_window.Workers.RawDataWorker import RawDataProcessWorke
 from utils.gui.pyqt.error_popup.ErrorPopup import ErrorPopup
 class MainWindow(QtWidgets.QMainWindow, Ui_MainWindow):
     """
-    Main window of the application
+    Main window of the application, it contains all the UI elements
+
     """
 
     def __init__(self, parent=None):
@@ -133,7 +141,7 @@ class MainWindow(QtWidgets.QMainWindow, Ui_MainWindow):
 
     def start_preprocess(self):
         """
-        Start the analyse
+        Start the analyse, create the thread and connect the signals.
         """
         if not self.check_input_file():
             return
@@ -171,6 +179,9 @@ class MainWindow(QtWidgets.QMainWindow, Ui_MainWindow):
         self.start_analyse_button.setEnabled(False)
 
     def process_raw_data(self, obj:ScannedObject):
+        """
+        Start the analyse, create the thread and connect the signals.
+        """
         self.processrawdata_thread = QThread()
         self.processraw_worker = RawDataProcessWorker("RawDataProcessWorker",
                                                       obj,
@@ -195,6 +206,9 @@ class MainWindow(QtWidgets.QMainWindow, Ui_MainWindow):
         self.processrawdata_thread.start()
 
     def process_discrete_data(self, obj:ScannedObject):
+        """
+        Start the analyse, create the thread and connect the signals.
+        """
         self.processdiscrete_thread = QThread()
         self.processdiscrete_worker = DiscreteDataProcessWorker("DiscreteDataProcessWorker",
                                                                 obj,
@@ -219,15 +233,27 @@ class MainWindow(QtWidgets.QMainWindow, Ui_MainWindow):
         self.processdiscrete_thread.start()
 
     def set_obj(self,obj:ScannedObject):
+        """
+        Set the obj to the main window
+        """
         self.obj = obj
 
     def set_discrete_data(self,discrete_data:dict):
+        """
+        Set the discrete data to the main window
+        """
         self.discrete_data = discrete_data
 
     def set_raw_data(self,raw_data:dict):
+        """
+        Set the raw data to the main window
+        """
         self.raw_data = raw_data 
 
     def save_model(self):
+        """
+        Save the model to a file
+        """
         if self.obj is None:
             ErrorPopup("Aucune analyse effectuée. Aucun modèle à sauvegarder").show_popup()
             return
@@ -255,6 +281,13 @@ class MainWindow(QtWidgets.QMainWindow, Ui_MainWindow):
             self.Graphs.hide()
 
     def renderGraphs(self,obj:ScannedObject,raw_data:dict,discrete_data:dict):
+        """
+        Render the graphs
+
+        :param obj: The scanned object
+        :param raw_data: The raw data
+        :param discrete_data: The discrete data
+        """
         if not self.show_graph_checkbox.isChecked():
             return
         for slot in self.slots:

utils/gui/pyqt/main_window/Workers/DiscreteDataWorker.py

@@ -1,3 +1,10 @@
+"""
+Created on Wed Apr 26 2023
+@name:   DiscreteDataWorker.py
+@desc:   A module to process discrete data in a thread
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 from PyQt5.QtCore import pyqtSignal
 from utils.files.input import ScannedObject
 from utils.files.output import save_output_file, format_data
@@ -7,7 +14,19 @@ from utils.settings.SettingManager import SettingManager
 
 class DiscreteDataProcessWorker(Worker):
     """
-    Worker to run the analyse in a thread
+    Worker to calculate the discrete data in a thread
+
+    :param name: The name of the worker
+    :param obj: The scanned object
+    :param output_path: The path to save the output file
+    :param output_file_prefix: The prefix of the output file
+    :param delta_z: The delta z
+
+    :ivar obj: The scanned object
+    :ivar delta_z: The delta z
+    :ivar output_path: The path to save the output file
+    :ivar output_file_prefix: The prefix of the output file
+    :ivar processedData: The signal to emit the result
     """
     processedData = pyqtSignal(dict)
 
@@ -24,11 +43,14 @@ class DiscreteDataProcessWorker(Worker):
         Run the analyse
         """
         self.set_status("Calculating discrete data...")
+        # Execute the analyse
         discrete_data = get_discrete_data(self.obj, 6,self.delta_z,self.update_progress)
+        # Emit the result
         self.processedData.emit(discrete_data)
         self.set_weight(100)
         self.set_status("Saving data...")
         self.update_progress(10)
+        # Save the result
         suffix = SettingManager.get_instance().get_setting('discrete_data_suffix').replace('{delta_z}',str(self.delta_z))
         extension = SettingManager.get_instance().get_setting('output_file_extension')
         separator = SettingManager.get_instance().get_setting('output_file_separator')

utils/gui/pyqt/main_window/Workers/PreProcessWorker.py

@@ -1,3 +1,10 @@
+"""
+Created on Wed Apr 26 2023
+@name:   PreProcessWorker.py
+@desc:   A module to pre process the 3d object in a thread
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 from utils.gui.pyqt.main_window.Workers.Worker import Worker
 from PyQt5.QtCore import pyqtSignal
 from utils.files.input import ScannedObject
@@ -5,7 +12,17 @@ from utils.math.position_manipulation import verticalise
 
 class PreProcessWorker(Worker):
     """
-    Worker to run the analyse in a thread
+    Worker to pre process the 3d object in a thread
+
+    :param name: The name of the worker
+    :param objpath: The path to the 3d object
+
+    :ivar objpath: The path to the 3d object
+    :ivar progress_value: The current progress value
+    :ivar progress_weight: The weight of the progress bar
+    :ivar processed_obj: The signal to emit the processed object
+
+    :method run: Pre process the object, read the file, verticalise it and normalise it
     """
     processed_obj = pyqtSignal(ScannedObject)
 
@@ -17,19 +34,24 @@ class PreProcessWorker(Worker):
 
     def run(self):
         """
-        Run the analyse
+        Pre process the object, read the file, verticalise it and normalise it
+        Emit the processed object in the processed_obj signal
         """
+        # Read the file
         self.set_status("Loading file...")
         obj = ScannedObject.from_obj_file(self.objpath)
         self.update_progress(5)
 
+        # Verticalise the object
         self.set_status("Verticalising object...")
         verticalise(obj)
         self.update_progress(5)
 
+        # Normalise the object
         self.set_status("Normalising object...")
         obj.normalise()
         self.update_progress(5)
 
+        # Emit the processed object
         self.processed_obj.emit(obj)
         self.finished.emit()

utils/gui/pyqt/main_window/Workers/RawDataWorker.py

@@ -1,3 +1,10 @@
+"""
+Created on Wed Apr 26 2023
+@name:   RawDataWorker.py
+@desc:   A module to process the raw data in a thread
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 from PyQt5.QtCore import pyqtSignal
 from utils.files.input import ScannedObject
 from utils.files.output import save_output_file, format_data
@@ -7,7 +14,19 @@ from utils.settings.SettingManager import SettingManager
 
 class RawDataProcessWorker(Worker):
     """
-    Worker to run the analyse in a thread
+    Worker to calculate the raw data in a thread
+
+    :param name: The name of the worker
+    :param obj: The scanned object
+    :param output_path: The path to save the output file
+    :param output_file_prefix: The prefix of the output file
+    :param delta_z: The delta z
+
+    :ivar obj: The scanned object
+    :ivar delta_z: The delta z
+    :ivar output_path: The path to save the output file
+    :ivar output_file_prefix: The prefix of the output file
+    :ivar processedData: The signal to emit the result
     """
     processedData = pyqtSignal(dict)
 

utils/gui/pyqt/main_window/Workers/Worker.py

@@ -1,6 +1,25 @@
+"""
+Created on Wed Apr 26 2023
+@name:   Worker.py
+@desc:   Base class for the workers
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 from PyQt5.QtCore import pyqtSignal, QObject
 
 class Worker(QObject):
+    """
+    Base class for the workers
+
+    :param name: The name of the worker
+
+    :ivar name: The name of the worker
+    :ivar progress_value: The current progress value
+    :ivar progress_weight: The weight of the progress bar
+    :ivar finished: The signal to emit when the worker is finished
+    :ivar progress: The signal to emit the progress value
+    :ivar status: The signal to emit the status of the worker
+    """
     finished = pyqtSignal()
     progress = pyqtSignal(int)
     status = pyqtSignal(str)

utils/gui/pyqt/settings/Settings.py

@@ -1,11 +1,19 @@
+"""
+Created on Thu Apr 27 2023
+@name:   Settings.py
+@desc:   Settings window
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 import os
 from PyQt5 import QtWidgets
-from PyQt5.QtWidgets import QWidget
-from utils.files.input import ScannedObject
 from utils.gui.pyqt.settings.UI_Settings import Ui_Settings
 from utils.settings.SettingManager import SettingManager
 
 class Settings(QtWidgets.QMainWindow,Ui_Settings):
+    """
+    Settings window
+    """
 
     def __init__(self, parent=None):
         super().__init__(parent)

utils/math/data_extraction.py

@@ -1,5 +1,9 @@
 """
-This module contains some utility functions for math operations.
+Created on Mon Apr 17 2023
+@name:   data_extraction.py
+@desc:   This module contains some utility functions for math operations.
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
 """
 import numpy as np
 import math

utils/math/position_manipulation.py

@@ -1,3 +1,10 @@
+"""
+Created on Fri Apr 21 2023
+@name:   position_manipulation.py
+@desc:   This module contains some utility functions for position manipulation.
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 import numpy as np
 from utils.files.input import ScannedObject
 from utils.math.data_extraction import get_mean

utils/settings/SettingManager.py

@@ -1,3 +1,10 @@
+"""
+Created on Fri Apr 21 2023
+@name:   SettingManager.py
+@desc:   A module to manage the settings
+@auth:   Djalim Simaila
+@e-mail: djalim.simaila@inrae.fr
+"""
 from yaml import load, dump
 try:
     from yaml import CLoader as Loader, CDumper as Dumper
@@ -5,6 +12,12 @@ except ImportError:
     from yaml import Loader, Dumper
 
 class SettingManager:
+    """
+    A class to manage the settings
+
+    :ivar settings: The settings
+    :ivar instance: The instance of the class
+    """
     instance = None
 
     def __init__(self):
@@ -16,13 +29,21 @@ class SettingManager:
             self.createInitialSettings()
 
     @staticmethod
-    def get_instance():
+    def get_instance()->'SettingManager':
+        """
+        Get the instance of the class
+
+        :return: The instance of the class
+        """
         if SettingManager.instance is None:
             SettingManager.instance = SettingManager()
         return SettingManager.instance
 
 
     def save(self):
+        """
+        Save the settings to the config file
+        """
         with open('config.yml', 'w') as f:
             f.write(dump(self.settings, Dumper=Dumper))
 
@@ -42,19 +63,45 @@ class SettingManager:
         self.settings['pretiffy_output_file'] = True
         self.save()
 
-    def get_last_graph(self, graph_number):
+    def get_last_graph(self, graph_number)->str:
+        """
+        Get the last graph name for the specified slot
+        """
         return self.settings['lastGraph'][graph_number]
 
     def set_last_graph(self, graph_number, graph_name):
+        """
+        Set the last graph name for the specified slot
+        
+        :param graph_number: The slot number
+        :param graph_name: The graph name
+        """
         self.settings['lastGraph'][graph_number] = graph_name
         self.save()
 
-    def get_setting(self, setting_name):
+    def get_setting(self, setting_name)->any:
+        """
+        Get the value of the specified setting
+
+        :param setting_name: The name of the setting
+        :return: The value of the setting
+        """
         return self.settings[setting_name]
     
-    def get_settings(self):
+    def get_settings(self)->dict:
+        """
+        Get the settings
+
+        :return: The settings
+        """
         return self.settings
     
     def set_setting(self, setting_name, setting_value):
+        """
+        Set the value of the specified setting
+
+        :param setting_name: The name of the setting
+        :param setting_value: The value of the setting
+        """
         self.settings[setting_name] = setting_value
         self.save()