Merge branch 'stable' of https://github.com/Lexi-BU/lxi_gui into stable

.gitignore

@@ -146,4 +146,7 @@ poetry.lock
 
 .flake8
 
+# Ignore the .ds store file
+.DS_Store
+
 documents_from_ff

codes/luigi.cfg

@@ -3,24 +3,24 @@ x_min_entry = -5
 x_max_entry = 5
 y_min_entry = -5
 y_max_entry = 5
-hist_bin_entry = 200
-c_min_entry = 1
-c_max_entry = None
+hist_bin_entry = 100
+c_min_entry = 5
+c_max_entry = 500
 density_status = False
-norm_type = log
+norm_type = linear
 unit_type = mcp
-v_min_thresh_entry = 1.2
-v_max_thresh_entry = 3.4
-v_sum_min_thresh_entry = 5
-v_sum_max_thresh_entry = 7
-cut_status = False
+v_min_thresh_entry = 0
+v_max_thresh_entry = 4
+v_sum_min_thresh_entry = 0
+v_sum_max_thresh_entry = 20
+cut_status = True
 curve_fit_status = False
 lin_corr_status = True
-non_lin_corr_status = True
+non_lin_corr_status = False
 cmap = viridis
 
 [time_options]
-start_time = 2023-01-01 00:00:00
-end_time = 2026-12-31 00:00:00
+start_time = 2023-11-16 10:00:00
+end_time = 2024-11-16 16:32:52
 time_threshold = 60
 

codes/lxi_file_read_funcs.py

@@ -2,6 +2,7 @@
 import datetime
 import importlib
 import os
+import platform
 import logging
 import struct
 from pathlib import Path
@@ -407,15 +408,15 @@ def read_binary_data_sci(
 
     # Split the file name in a folder and a file name
     # Format filenames and folder names for the different operating systems
-    if os.name == "posix":
+    if platform.system() == "Linux":
         output_file_name = os.path.basename(os.path.normpath(in_file_name)).split(".")[0] + "_sci_output.csv"
         output_folder_name = os.path.dirname(os.path.normpath(in_file_name)) + "/processed_data/sci"
         save_file_name = output_folder_name + "/" + output_file_name
-    elif os.name == "nt":
+    elif platform.system() == "Windows":
         output_file_name = os.path.basename(os.path.normpath(in_file_name)).split(".")[0] + "_sci_output.csv"
         output_folder_name = os.path.dirname(os.path.normpath(in_file_name)) + "\\processed_data\\sci"
         save_file_name = output_folder_name + "\\" + output_file_name
-    elif os.name == "darwin":
+    elif platform.system() == "Darwin":
         output_file_name = os.path.basename(os.path.normpath(in_file_name)).split(".")[0] + "_sci_output.csv"
         output_folder_name = os.path.dirname(os.path.normpath(in_file_name)) + "/processed_data/sci"
         save_file_name = output_folder_name + "/" + output_file_name
@@ -850,7 +851,8 @@ def read_binary_data_hk(
     for key in df.keys():
         for ii in range(1, len(df[key])):
             if np.isnan(df[key][ii]):
-                df[key][ii] = df[key][ii - 1]
+                # df[key][ii] = df[key][ii - 1]
+                df.loc[ii, key] = df.loc[ii - 1, key]
 
     # Set the date column to the Date_datetime
     df["Date"] = Date_datetime
@@ -881,15 +883,15 @@ def read_binary_data_hk(
     df.set_index("Date", inplace=True, drop=False)
     # Split the file name in a folder and a file name
     # Format filenames and folder names for the different operating systems
-    if os.name == "posix":
+    if platform.system() == "Linux":
         output_folder_name = os.path.dirname(os.path.normpath(in_file_name)) + "/processed_data/hk"
         output_file_name = os.path.basename(os.path.normpath(in_file_name)).split(".")[0] + "_hk_output.csv"
         save_file_name = output_folder_name + "/" + output_file_name
-    elif os.name == "nt":
+    elif platform.system() == "Windows":
         output_folder_name = os.path.dirname(os.path.normpath(in_file_name)) + "\\processed_data\\hk"
         output_file_name = os.path.basename(os.path.normpath(in_file_name)).split(".")[0] + "_hk_output.csv"
         save_file_name = output_folder_name + "\\" + output_file_name
-    elif os.name == "darwin":
+    elif platform.system() == "Darwin":
         output_folder_name = os.path.dirname(os.path.normpath(in_file_name)) + "/processed_data/hk"
         output_file_name = os.path.basename(os.path.normpath(in_file_name)).split(".")[0] + "_hk_output.csv"
         save_file_name = output_folder_name + "/" + output_file_name
@@ -916,11 +918,11 @@ def open_file_sci(start_time=None, end_time=None):
     )
 
     # Get the file name from the file path for different operating systems
-    if os.name == "posix":
+    if platform.system() == "Linux":
         file_name_sci = file_val.split("/")[-1]
-    elif os.name == "nt":
+    elif platform.system() == "Windows":
         file_name_sci = file_val.split("\\")[-1]
-    elif os.name == "darwin":
+    elif platform.system() == "Darwin":
         file_name_sci = file_val.split("/")[-1]
     else:
         raise OSError("Operating system not supported.")
@@ -945,11 +947,11 @@ def open_file_hk(start_time=None, end_time=None):
     )
 
     # Get the file name from the file path for different operating systems
-    if os.name == "posix":
+    if platform.system() == "Linux":
         file_name_hk = file_val.split("/")[-1]
-    elif os.name == "nt":
+    elif platform.system() == "Windows":
         file_name_hk = file_val.split("\\")[-1]
-    elif os.name == "darwin":
+    elif platform.system() == "Darwin":
         file_name_hk = file_val.split("/")[-1]
     else:
         raise OSError("Operating system not supported.")
@@ -1451,7 +1453,7 @@ def read_binary_file(file_val=None, t_start=None, t_end=None, multiple_files=Fal
         ):
             raise ValueError(
                 "when multiple_files is True, both t_start and t_end must either be"
-                f"None or a valid time value. The vlaues provided are t_start ="
+                f"None or a valid time value. The values provided are t_start ="
                 f"{t_start} and t_end = {t_end}."
             )
         # If both t_start and t_end are None, raise a warning stating that the times are set to none
@@ -1467,7 +1469,6 @@ def read_binary_file(file_val=None, t_start=None, t_end=None, multiple_files=Fal
             # Convert t_start and t_end from string to datetime in UTC timezone
             t_start = pd.to_datetime(t_start, utc=True)
             t_end = pd.to_datetime(t_end, utc=True)
-
             try:
                 # Convert t_start and t_end from string to unix time in seconds in UTC timezone
                 t_start_unix = t_start.timestamp()
@@ -1485,6 +1486,7 @@ def read_binary_file(file_val=None, t_start=None, t_end=None, multiple_files=Fal
 
         # Make sure that file_val is a directory
         if not os.path.isdir(file_val):
+            print(f"\n \x1b[1;31;255m WARNING: {file_val} is not a directory. \x1b[0m")
             raise ValueError("file_val should be a directory.")
 
         # Get the names of all the files in the directory with*.dat or *.txt extension
@@ -1555,7 +1557,7 @@ def read_binary_file(file_val=None, t_start=None, t_end=None, multiple_files=Fal
             os.makedirs(save_dir)
 
         # Get the file name based on the os path
-        if os.name == "nt":
+        if platform.system() == "Windows":
             file_name_hk = save_dir + "\\processed_data\\hk\\" + \
                 file_name_hk_list[0].split("\\")[-1].split('.')[0].split('_')[0] + '_' + \
                 file_name_hk_list[0].split("\\")[-1].split('.')[0].split('_')[1] + '_' + \
@@ -1571,7 +1573,7 @@ def read_binary_file(file_val=None, t_start=None, t_end=None, multiple_files=Fal
                 file_name_hk_list[0].split("\\")[-1].split('.')[0].split('_')[3] + '_' + \
                 file_name_sci_list[-1].split("\\")[-1].split('.')[0].split('_')[-4] + '_' + \
                 file_name_sci_list[-1].split("\\")[-1].split('.')[0].split('_')[-3] + '_sci_output.csv'
-        elif os.name == "posix":
+        elif platform.system() == "Linux":
             file_name_hk = save_dir + "/processed_data/hk/" + \
                 file_name_hk_list[0].split("/")[-1].split('.')[0].split('_')[0] + '_' + \
                 file_name_hk_list[0].split("/")[-1].split('.')[0].split('_')[1] + '_' + \
@@ -1587,7 +1589,7 @@ def read_binary_file(file_val=None, t_start=None, t_end=None, multiple_files=Fal
                 file_name_hk_list[0].split("/")[-1].split('.')[0].split('_')[3] + '_' + \
                 file_name_sci_list[-1].split("/")[-1].split('.')[0].split('_')[-4] + '_' + \
                 file_name_sci_list[-1].split("/")[-1].split('.')[0].split('_')[-3] + '_sci_output.csv'
-        elif os.name == "darwin":
+        elif platform.system() == "Darwin":
             file_name_hk = save_dir + "/processed_data/hk/" + \
                 file_name_hk_list[0].split("/")[-1].split('.')[0].split('_')[0] + '_' + \
                 file_name_hk_list[0].split("/")[-1].split('.')[0].split('_')[1] + '_' + \