Distance from ABS to free surface is added so that depth represents distance to the free surace in plots and not distance from transducers.

settings.py

@@ -6,87 +6,119 @@ import datetime
 
 # --- load raw data ---
 
-ABS_name = []
+# =========================================================
+#                 --- ACOUSTIC DATA TAB ---
+# =========================================================
 
-path_BS_raw_data = []
-filename_BS_raw_data = []
-BS_raw_data = []      # BS raw data : all measurement (go and back)
-depth = []
-depth_2D = []
-freq = []
-freq_text = []
-time = []
+# Variables names               # Description                                                               # Type
+
+ABS_name = []                   # Acoustic Backscatter System name : ["Aquascat 1000R", "UB-SediFlow"]      # List of strings
+temperature = 0                 # Temperature of measurements (One temperature for all measurements)        # Float
+water_velocity = 0              # Speed of sound in water (One speed of sound for all measurements)         # Float
+
+# --- Acoustic raw data ---
+path_BS_raw_data = []           # Paths of the acoustic data files                                          # List of strings
+filename_BS_raw_data = []       # Files names of the acoustic data files                                    # List of strings
+
+BS_raw_data = []                # Acoustic raw data measurements : 3D arrays (freq x depth x time)          # List of arrays
+BS_raw_data_reshape = []        # Acoustic raw data measurements : 2D arrays (freq x (depth x time))        # List of arrays
+
+depth = []                      # Distance from transducer : 2D array (freq x depth)                        # List of arrays
+depth_reshape = []              # Distance from transducer : 2D array (freq x (depth x time))               # List of arrays
+depth_2D = []                   # Distance from transducer : 2D array (freq x depth)                        # List of arrays
+
+time = []                       # Time of measurements : 2D array (freq x time)                             # List of arrays
+time_reshape = []               # Time of measurements : 2D array (freq x (depth x time))                   # List of arrays
+
+# --- Measurement information ---
+date = []                       # Date of measurements                                                      # List of dates
+hour = []                       # Time of measurements                                                      # List of time
+
+distance_from_ABS_to_free_surface = []   # Set distance from ABS to free surface                            # List of floats
+
+freq = []                       # Frequency of measurements : 1D array                                      # List of arrays
+freq_text = []                  # Frequency of measurements : list of string                                # List of lists
+
+kt_read = []                    # Constant of calibration kt of the ABS read from acoustic file             # List of list
+                                    # for each frequency
+kt_corrected = {}               # Constant of calibration kt of the ABS corrected                           # Dictionary
+                                    # Sometimes, the read values of kt are wrong. Then, we define
+                                    # default values for all frequency of the ABS.
+
+water_attenuation = []          # Sound attenuation in water for each frequency and for one temperature     # List of lists
+nb_profiles = []                # Total number of profiles for each frequency = time length                 # List of lists
+nb_profiles_per_sec = []        # Profile rate (Hz) for each frequency                                      # List of lists
+nb_cells = []                   # Number of cells in profiles for each frequency                            # List of lists
+cell_size = []                  # Cell size for each frequency (m)                                          # List of lists
+pulse_length = []               # Pulse length (m)                                                          # List of lists
+nb_pings_per_sec = []           # Number of pings per seconds (Hz)                                          # List of lists
+nb_pings_averaged_per_profile = [] # Profiles per average                                                   # List of lists
+gain_rx = []                    # Rx gain                                                                   # List of lists
+gain_tx = []                    # Tx gain                                                                   # List of lists
+
+DataFrame_acoustic = pd.DataFrame()
+
+# --- Modify raw data limits ---
+tmin = []                       # Minimum boundary of time for each recording : (index, value)              # List of tuples
+tmax = []                       # Maximum boundary of time for each recording : (index, value)              # List of tuples
+rmin = []                       # Minimum boundary of depth for each recording : (index, value)             # List of tuples
+rmax = []                       # Maximum boundary of depth for each recording : (index, value)             # List of tuples
+
+BS_cross_section = []           # BS data limited with tmin and tmax values                                 # List of arrays
+depth_cross_section = []        # depth limited with rmin and rmax values                                   # List of arrays
+time_cross_section = []         # time limited with rmin and rmax values                                    # List of arrays
+
+# --- Detect bottom ---
+BS_stream_bed = []              # BS data (raw or cross_section) with detected bottom :                     # List of arrays
+                                    # 3D array : (freq x depth x time)
+depth_bottom = []               # Depth value of th bottom : 1D array                                       # List of arrays
+val_bottom = []                 # Level of the BS signal on the bottom : 1D array                           # List of arrays
+ind_bottom = []                 # Index of bottom in depth array : list of int                              # List of lists
+freq_bottom_detection = []      # Frequency use to detect the bottom : (index, string)                      # List of tuple
+
+dept_bottom_detection_min = []  # Min value to detect bottom on the first vertical                          # List of float
+depth_bottom_detection_max = [] # Max value to detect bottom on the first vertical                          # List of float
+depth_bottom_detection_1st_int_area = [] # interval for searching area                                      # List of float
+
+# ----------------------------------------------------------------------------------------------------------------------
+# =========================================================
+#              --- SIGNAL PREPROCESSING TAB ---
+# =========================================================
+
+# Variables names               # Description                                                               # Type
 
 path_BS_noise_data = []
 filename_BS_noise_data = []
 BS_noise_raw_data = []            # BS noise raw data : BS signal listen
 BS_noise_averaged_data = []       # BS noise raw data averaged (array has the same shape than BS_raw_data shape)
 
+date_noise = []
+hour_noise = []
+
 noise_method = []
 noise_value = []
 SNR_filter_value = []
 Nb_cells_to_average_BS_signal = []
 data_preprocessed = []
 
-date = []
-date_noise = []
-hour = []
-hour_noise = []
-nb_profiles = []
-nb_profiles_per_sec = []
-nb_cells = []
-cell_size = []
-pulse_length = []
-nb_pings_per_sec = []
-nb_pings_averaged_per_profile = []
-kt_read = []
-kt_corrected = {}
-gain_rx = []
-gain_tx = []
+time_snr_reshape = np.array([])
+SNR_reshape = np.array([])      # snr is reshape to be included in table of values in acoustic data tab
 
 SNR_raw_data = []              # SNR is computed with BS_noise_averaged_data
 time_noise = []
 depth_noise = []
 
-# --- reshape raw data for table of values in Acoustic Data tab ---
-time_reshape = []
-time_snr_reshape = np.array([])
-depth_reshape = []
-BS_raw_data_reshape = []
-SNR_reshape = np.array([])      # snr is reshape to be included in table of values in acoustic data tab
-DataFrame_acoustic = pd.DataFrame()
-
-# --- Processed data in Acoustic Data Tab and used in Acoustic processing tab ---
-tmin = []                # minimum boundary of time (spin box tmin)
 tmin_snr = np.array([])
-tmax = []                 # maximum boundary of time (spin box tmin)
 tmax_snr = np.array([])
-rmin = []
-rmax = []
-BS_cross_section = []               # BS data limited with tmin and tmax values of spin box
 
-BS_stream_bed = []                  # BS_data_section = BS data in the section. Values NaN outside the bottom of the section are deleted
 # BS_noise_cross_section = []         # BS_noise_cross_section = BS_noise_data[:, :, tmin:tmax]  (former Noise_data)
 SNR_cross_section = []              # SNR_data = snr[:, :, tmin:tmax]
 SNR_stream_bed = []
-time_cross_section = []
 time_snr = []
-depth_cross_section = []
-depth_bottom = []
-val_bottom = []
-ind_bottom = []
-freq_bottom_detection = []
-depth_bottom_detection_1st_int_area = []
+time_average = np.array([])
+SNR_data_average = np.array([])             # SNR data computed with BS signal averaged (not with BS raw signal)
 
 # --- Processed data in Signal Processing Tab ---
-# BS_cross_section_SNR_filter = np.array([[[]]])      # BS data filtered with SNR values (remove point if SNR < value) - bottom is not detected
-# BS_cross_section_averaged = np.array([[[]]])        # BS data averaged - bottom is not detected
-# BS_cross_section_averaged_SNR = np.array([[[]]])        # BS data averaged and filtered with SNR - bottom is not detected
-
-# BS_stream_bed_SNR_filter = np.array([])             # BS data filtered with SNR values (remove point if SNR < value) - bottom is detected
-# BS_stream_bed_averaged = np.array([])               # BS data averaged - bottom is detected
-# BS_stream_bed_averaged_SNR = np.array([])               # BS data averaged and filtered with SNR - bottom is detected
-
 BS_raw_data_pre_process_SNR = []
 BS_raw_data_pre_process_average = []
 BS_raw_data_pre_process_SNR_average = []
@@ -99,16 +131,18 @@ BS_stream_bed_pre_process_SNR = []             # BS data filtered with SNR value
 BS_stream_bed_pre_process_average = []               # BS data averaged - bottom is detected
 BS_stream_bed_pre_process_SNR_average = []               # BS data averaged and filtered with SNR - bottom is detected
 
-time_average = np.array([])
-SNR_data_average = np.array([])             # SNR data computed with BS signal averaged (not with BS raw signal)
+# ----------------------------------------------------------------------------------------------------------------------
+# =========================================================
+#                  --- SAMPLE DATA TAB ---
+# =========================================================
 
-sediment_attenuation = []
+# Variables names               # Description                                                               # Type
 
-FCB = []
-depth_real = []
-lin_reg = []
+# --- Fine sediment Data ---
 
-# --- Sample Data ---
+
+
+# --- Sand sediment Data ---
 
 sample_fine = []
 
@@ -158,19 +192,18 @@ Ctot_sand_per_cent = []
 fine_sample_position = []
 sand_sample_position = []
 
-# --- Acoustic inversion method ---
 
-temperature = 0
-water_attenuation = []
-water_velocity = 0
+# ----------------------------------------------------------------------------------------------------------------------
+# =========================================================
+#              --- SEDIMENT CALIBRATION TAB ---
+# =========================================================
 
-# kt_corrected = np.array([])
-# kt_corrected_2D = np.array([])
-# kt_corrected_3D = np.array([])
+# Variables names               # Description                                                               # Type
 
-frequencies_to_compute_VBI = np.array([])
-VBI_cross_section = []
-# VBI_stream_bed = np.array([[[]]])
+sediment_attenuation = []
+FCB = []
+depth_real = []
+lin_reg = []
 
 # --- Sediment Calibration
 frequencies_for_calibration = []
@@ -192,6 +225,18 @@ J_cross_section = []
 
 frequency_for_inversion = tuple()
 
+
+# ----------------------------------------------------------------------------------------------------------------------
+# =========================================================
+#               --- ACOUSTIC INVERSION TAB ---
+# =========================================================
+
+# Variables names               # Description                                                               # Type
+
+frequencies_to_compute_VBI = np.array([])
+VBI_cross_section = []
+# VBI_stream_bed = np.array([[[]]])
+
 SSC_fine = []
 SSC_sand = []