Running the tutorial

Adding a tutorial with some explanation. The files generated when runing the tutorial are also added. Update Tutorial.md Update README.md Update Tutorial -Fixing support for single image simulations of the MAS -Fixed a typo in the directoy spelling of the output path Typo Fixing the paths to include the session number Update Tutorial.md -Fixing typo -Include info about Single_Image_Simulation_v11.py
LittleCoinCoin · May 20, 2021 · b5304b7 · b5304b7
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diff --git a/.gitattributes b/.gitattributes
@@ -1,2 +1,4 @@
 # Auto detect text files and perform LF normalization
 * text=auto
+*.png filter=lfs diff=lfs merge=lfs -text
+*.jpg filter=lfs diff=lfs merge=lfs -text
diff --git a/BSAS/__pycache__/bsas.cpython-37.pyc b/BSAS/__pycache__/bsas.cpython-37.pyc
diff --git a/BSAS/__pycache__/bsas_functions.cpython-37.pyc b/BSAS/__pycache__/bsas_functions.cpython-37.pyc
diff --git a/Crops_Rows_Angle_Detection/CRAD.py b/Crops_Rows_Angle_Detection/CRAD.py
@@ -68,13 +68,7 @@ def __init__(self,
                 _path_output_histogram
                ):
         """
-        _path_original_img leads to the original picture of the field
-
-        _path_txt leads to a text files which contains the coordinates of all centroids
-        obtained through bsas implementation or dbscan
-
-        _display_all_steps should be set to True if the user wants to see the results of the successive steps of the process
-        (images with the detected lines are displayed)
+        TO DO
         """
 
         self.img_id = img_id

diff --git a/Crops_Rows_Angle_Detection/__pycache__/CRAD.cpython-37.pyc b/Crops_Rows_Angle_Detection/__pycache__/CRAD.cpython-37.pyc
diff --git a/Documentation/Images/CropFields_Sample/Example_SunflowerField_1.jpg b/Documentation/Images/CropFields_Sample/Example_SunflowerField_1.jpg
diff --git a/Documentation/Images/CropFields_Sample/Example_SunflowerField_2.jpg b/Documentation/Images/CropFields_Sample/Example_SunflowerField_2.jpg
diff --git a/Documentation/Images/CropFields_Sample/Example_grapevine.jpg b/Documentation/Images/CropFields_Sample/Example_grapevine.jpg
diff --git a/Documentation/Images/FourierAnalysis_v3-1.png b/Documentation/Images/FourierAnalysis_v3-1.png
diff --git a/Documentation/Images/Logos/LOGO_TerresInnovia.jpg b/Documentation/Images/Logos/LOGO_TerresInnovia.jpg
diff --git a/Documentation/Images/Logos/ekinocs-logo.png b/Documentation/Images/Logos/ekinocs-logo.png
diff --git a/Documentation/Images/Logos/logoAPT.jpg b/Documentation/Images/Logos/logoAPT.jpg
diff --git a/Documentation/Images/MAS_Hierarchy_Structure.png b/Documentation/Images/MAS_Hierarchy_Structure.png
diff --git a/Fourier/FrequencyAnalysis.py b/Fourier/FrequencyAnalysis.py
@@ -308,6 +308,6 @@ def All_Fourier_Analysis(_path_input_output,
 
 if (__name__ == "__main__"):
 
-    All_Fourier_Analysis(_path_input_output="C:/Users/eliot/Documents/Scolarité/AgroParisTech/3A/Stage_Tournesols/Code/Ouput_General",
+    All_Fourier_Analysis(_path_input_output="../Tutorial/Output_General/Set1",
                          _session_number=1,
                          _bin_div_X=2, _bin_div_Y=4)
diff --git a/MAS/Multi_Images_Simulation_v12bis.py b/MAS/Multi_Images_Simulation_v12bis.py
@@ -111,8 +111,8 @@ def All_Simulations(_path_input_rgb_img, _path_PreTreatment_and_FA,
 
 if (__name__=="__main__"):
 
-    All_Simulations(_path_input_rgb_img="C:/Users/eliot/Documents/Scolarité/AgroParisTech/3A/Stage_Tournesols/Code/Datasets/Test",
-                    _path_PreTreatment_and_FA="C:/Users/eliot/Documents/Scolarité/AgroParisTech/3A/Stage_Tournesols/Code/Ouput_General",
+    All_Simulations(_path_input_rgb_img="../Tutorial/Data/Non-Labelled/Set1",
+                    _path_PreTreatment_and_FA="../Tutorial/Output_General/Set1",
                     _session_number=1,
                     _RAs_group_size=20, _RAs_group_steps=2, _Simulation_steps=50,
                     _RALs_fuse_factor=0.5, _RALs_fill_factor=1.5)
diff --git a/MAS/Single_Image_Simulation_v11.py b/MAS/Single_Image_Simulation_v11.py
@@ -41,30 +41,19 @@ def get_file_lines(path_csv_file):
 # =============================================================================
 #path of the images 
 ### TO BE CHANGED AS PER USER NEED
-session_number = 3
-unity_date = "2020_7_30_15_10_36"
+session_number = 1
 
-path_input_root = "C:/Users/eliot/Documents/Scolarité/AgroParisTech/3A/Stage_Tournesols"
-# =============================================================================
-# path_input_raw = path_input_root+"/Unity/Screenshots/"+unity_date+"/virtual_reality"
-# path_input_adjusted_position_files = path_input_root+"/Travaux_Fil_Rouge/code_tournesol_4/Output_FT/Session_{0}/Adjusted_Position_Files".format(session_number)
-# path_input_OTSU = path_input_root+"/Travaux_Fil_Rouge/code_tournesol_4/Output/Session_{0}/Otsu_R".format(session_number)
-# path_input_PLANT_FT_PRED = path_input_root+"/Travaux_Fil_Rouge/code_tournesol_4/Output_FT/Session_{0}/Plant_FT_Predictions".format(session_number)
-# =============================================================================
+path_input_root = "../Tutorial"
 
-path_input_raw = path_input_root+"/Unity/Screenshots/MetaCapture_Session_{0}".format(session_number)+\
-                "/"+unity_date+"/virtual_reality"
-path_input_adjusted_position_files = path_input_root+"/Travaux_Fil_Rouge/code_tournesol_4/Output_FT/MetaCapture_Session_{0}".format(session_number)+\
-                                    "/"+unity_date+\
-                                    "/Adjusted_Position_Files"
-path_input_OTSU = path_input_root+"/Travaux_Fil_Rouge/code_tournesol_4/Output/MetaCapture_Session_{0}".format(session_number)+\
-                "/"+unity_date+"/Otsu_R"
-path_input_PLANT_FT_PRED = path_input_root+"/Travaux_Fil_Rouge/code_tournesol_4/Output_FT/MetaCapture_Session_{0}".format(session_number)+\
-                            "/"+unity_date + \
-                            "/Plant_FT_Predictions"
+path_input_raw = path_input_root+"/Data/Non-Labelled/Set1"
+#path_input_adjusted_position_files = ""
+path_input_OTSU = path_input_root+"/Output_General/Set1/Output/Session_"+\
+                            str(session_number)+"/Otsu_R"
+path_input_PLANT_FT_PRED = path_input_root+"/Output_General/Set1/Output_FA/Session_"+\
+                            str(session_number)+"/Plant_FT_Predictions"
 
 names_input_raw = os.listdir(path_input_raw)
-names_input_adjusted_position_files = os.listdir(path_input_adjusted_position_files)
+#names_input_adjusted_position_files = os.listdir(path_input_adjusted_position_files)
 names_input_OTSU = os.listdir(path_input_OTSU)
 names_input_PLANT_FT_PRED = os.listdir(path_input_PLANT_FT_PRED)
 
@@ -78,9 +67,11 @@ def get_file_lines(path_csv_file):
 data_input_raw = import_data(path_input_raw,
                              names_input_raw[:subset_size],
                              get_img_array)
-data_adjusted_position_files = import_data(path_input_adjusted_position_files,
-                                           names_input_adjusted_position_files[:subset_size],
-                                           get_file_lines)
+# =============================================================================
+# data_adjusted_position_files = import_data(path_input_adjusted_position_files,
+#                                            names_input_adjusted_position_files[:subset_size],
+#                                            get_file_lines)
+# =============================================================================
 data_input_OTSU = import_data(path_input_OTSU,
                               names_input_OTSU[:subset_size],
                               get_img_array)
@@ -103,7 +94,7 @@ def get_file_lines(path_csv_file):
 _image_index = 0
 
 print(names_input_OTSU[_image_index])
-print(names_input_adjusted_position_files[_image_index])
+#print(names_input_adjusted_position_files[_image_index])
 print(names_input_PLANT_FT_PRED[_image_index])
 
 # =============================================================================
@@ -116,7 +107,7 @@ def get_file_lines(path_csv_file):
                                     RAs_group_size, RAs_group_steps,
                                     RALs_fuse_factor, RALs_fill_factor,
                                     [0,0],
-                                    data_adjusted_position_files[_image_index])
+                                    None)#data_adjusted_position_files[_image_index])
 MAS_Simulation.Initialize_AD()
 MAS_Simulation.Perform_Simulation_newEndCrit(Simulation_steps,
                                              _coerced_X=True,
@@ -147,6 +138,6 @@ def get_file_lines(path_csv_file):
 # print("FP =", MAS_Simulation.FP)
 # =============================================================================
 
-MAS_Simulation.Show_Adjusted_And_RALs_positions()
-MAS_Simulation.Show_nb_RALs()
-MAS_Simulation.Show_RALs_Deicision_Scores()
+MAS_Simulation.Show_RALs_Position(_recorded_position_indeces=[-1], _colors=['g'])
+#MAS_Simulation.Show_nb_RALs()
+#MAS_Simulation.Show_RALs_Deicision_Scores()
diff --git a/MAS/__pycache__/MAS_v16.cpython-37.pyc b/MAS/__pycache__/MAS_v16.cpython-37.pyc
diff --git a/Pre_Treatments/Process_image_for_FT.py b/Pre_Treatments/Process_image_for_FT.py
@@ -174,8 +174,8 @@ def All_Pre_Treatment(_path_input_rgb_img, _path_output_root,
 
 if (__name__=="__main__"):
 
-    All_Pre_Treatment(_path_input_rgb_img="C:/Users/eliot/Documents/Scolarité/AgroParisTech/3A/Stage_Tournesols/Code/Datasets/Test",
-                      _path_output_root="C:/Users/eliot/Documents/Scolarité/AgroParisTech/3A/Stage_Tournesols/Code/Ouput_General",
+    All_Pre_Treatment(_path_input_rgb_img="../Tutorial/Data/Non-Labelled/Set1",
+                      _path_output_root="../Tutorial/Output_General/Set1",
                       _make_unique_folder_per_session=True, _session=1,
                       _do_Otsu=True, _do_AD=True,
                       _save_AD_score_images=False, _save_BSAS_images=False,

diff --git a/README.md b/README.md
@@ -20,6 +20,7 @@ the procedure will consist in [Pre-Processing](https://github.com/LittleCoinCoin
 Plants](https://github.com/LittleCoinCoin/Plant_Counting/blob/Pre-Release/Documentation/MAS/Multi_Images_Simulation_v12bis.md) (with the MAS). It is possible to Rune all three steps in one go with the script named *WholeProcess.py*; or 
 all three steps separately with the scripts *Process_image_for_FT.py*, *FrequencyAnalysis.py* and *Multi_Images_Simulation_v12bis.py*.
 Further details about each scripts are available in the Documentation.
+A little [tutorial](https://github.com/LittleCoinCoin/Plant_Counting/blob/Pre-Release/Tutorial/Tutorial.md) is available
 
 # References
  * The paper presenting the method:

diff --git a/Segmentation_Otsu/__pycache__/data.cpython-37.pyc b/Segmentation_Otsu/__pycache__/data.cpython-37.pyc
diff --git a/Segmentation_Otsu/__pycache__/otsu.cpython-37.pyc b/Segmentation_Otsu/__pycache__/otsu.cpython-37.pyc
diff --git a/Segmentation_Otsu/data.py b/Segmentation_Otsu/data.py
@@ -2,7 +2,11 @@
 """
 Created on Wed Jan 29 13:36:47 2020
 
-@author: Le groupe tournesol
+@author:
+    Naomie Berda
+    Léa Courteille
+    Grison William
+    Lucas Mathieu
 """
 
 import os

diff --git a/Tutorial/Data/Non-Labelled/Set1/rgb_83.png b/Tutorial/Data/Non-Labelled/Set1/rgb_83.png
diff --git a/Tutorial/Data/Non-Labelled/Set1/rgb_85.png b/Tutorial/Data/Non-Labelled/Set1/rgb_85.png
diff --git a/Tutorial/Data/Non-Labelled/Set1/rgb_87.png b/Tutorial/Data/Non-Labelled/Set1/rgb_87.png
diff --git a/Tutorial/Data/Non-Labelled/Set1/rgb_89.png b/Tutorial/Data/Non-Labelled/Set1/rgb_89.png
diff --git a/Tutorial/Data/Non-Labelled/Set2/rgb_91.png b/Tutorial/Data/Non-Labelled/Set2/rgb_91.png
diff --git a/Tutorial/Data/Non-Labelled/Set2/rgb_93.png b/Tutorial/Data/Non-Labelled/Set2/rgb_93.png
diff --git a/Tutorial/Data/Non-Labelled/Set2/rgb_95.png b/Tutorial/Data/Non-Labelled/Set2/rgb_95.png
diff --git a/Tutorial/Data/Non-Labelled/Set2/rgb_97.png b/Tutorial/Data/Non-Labelled/Set2/rgb_97.png