274 lines
20 KiB
Python
274 lines
20 KiB
Python
# ============================================================================== #
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# settings .py - AcouSed #
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# Copyright (C) 2024 INRAE #
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# #
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# This program is free software: you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License as published by #
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# the Free Software Foundation, either version 3 of the License, or #
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# (at your option) any later version. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# #
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# You should have received a copy of the GNU General Public License #
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# along with this program. If not, see <https://www.gnu.org/licenses/>. #
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# by Brahim MOUDJED #
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# ============================================================================== #
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# -*- coding: utf-8 -*-
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""" this file includs global variables shared between tab """
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import numpy as np
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import pandas as pd
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import datetime
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# --- Save study ---
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acoustic_data = [] # Acoustic data number # List of integer
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dirname_save_as = "" # Path to save a study # String
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filename_save_as = "" # File name to save a study # String
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# --- load raw data ---
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dirname_open = "" # Path to open a study # String
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filename_open = "" # File name to open a study # String
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# =========================================================
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# --- ACOUSTIC DATA TAB ---
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# =========================================================
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# Variables names # Description # Type
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ABS_name = [] # Acoustic Backscatter System name : ["Aquascat 1000R", "UB-SediFlow"] # List of strings
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temperature = 0.00 # Temperature of measurements (One temperature for all measurements) # Float
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water_velocity = 0.00 # Speed of sound in water (One speed of sound for all measurements) # Float
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# --- Acoustic raw data ---
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path_BS_raw_data = [] # Paths of the acoustic data files # List of strings
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filename_BS_raw_data = [] # Files names of the acoustic data files # List of strings
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BS_raw_data = [] # Acoustic raw data measurements : 3D arrays (freq x depth x time) # List of arrays
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BS_raw_data_reshape = [] # Acoustic raw data measurements : 2D arrays (freq x (depth x time)) # List of arrays
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depth = [] # Distance from transducer : 2D array (freq x depth) # List of arrays
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depth_reshape = [] # Distance from transducer : 2D array (freq x (depth x time)) # List of arrays
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depth_2D = [] # Distance from transducer : 2D array (freq x depth) # List of arrays
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time = [] # Time of measurements : 2D array (freq x time) # List of arrays
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time_reshape = [] # Time of measurements : 2D array (freq x (depth x time)) # List of arrays
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# --- Measurement information ---
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date = [] # Date of measurements # List of dates
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hour = [] # Time of measurements # List of time
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distance_from_ABS_to_free_surface = [] # Set distance from ABS to free surface # List of floats
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freq = [] # Frequency of measurements : 1D array # List of arrays
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freq_text = [] # Frequency of measurements : list of string # List of lists
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kt_read = [] # Constant of calibration kt of the ABS read from acoustic file # List of list
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# for each frequency
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kt_corrected = [] # Constant of calibration kt of the ABS corrected # list of float
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# Sometimes, the read values of kt are wrong. Then, we define
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# default values for all frequency of the ABS.
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water_attenuation = [] # Sound attenuation in water for each frequency and for one temperature # List of lists
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nb_profiles = [] # Total number of profiles for each frequency = time length # List of lists
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nb_profiles_per_sec = [] # Profile rate (Hz) for each frequency # List of lists
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nb_cells = [] # Number of cells in profiles for each frequency # List of lists
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cell_size = [] # Cell size for each frequency (m) # List of lists
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pulse_length = [] # Pulse length (m) # List of lists
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nb_pings_per_sec = [] # Number of pings per seconds (Hz) # List of lists
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nb_pings_averaged_per_profile = [] # Profiles per average # List of lists
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gain_rx = [] # Rx gain # List of lists
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gain_tx = [] # Tx gain # List of lists
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DataFrame_acoustic = pd.DataFrame()
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# --- Modify raw data limits ---
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tmin = [] # Minimum boundary of time for each recording : (index, value) # List of tuples
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tmax = [] # Maximum boundary of time for each recording : (index, value) # List of tuples
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rmin = [] # Minimum boundary of depth for each recording : (index, value) # List of tuples
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rmax = [] # Maximum boundary of depth for each recording : (index, value) # List of tuples
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BS_cross_section = [] # BS data limited with tmin and tmax values # List of arrays
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depth_cross_section = [] # depth limited with rmin and rmax values # List of arrays
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time_cross_section = [] # time limited with rmin and rmax values # List of arrays
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# --- Detect bottom ---
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BS_stream_bed = [] # BS data (raw or cross_section) with detected bottom : # List of arrays
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# 3D array : (freq x depth x time)
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depth_bottom = [] # Depth value of th bottom : 1D array # List of arrays
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val_bottom = [] # Level of the BS signal on the bottom : 1D array # List of arrays
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ind_bottom = [] # Index of bottom in depth array : list of int # List of lists
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freq_bottom_detection = [] # Frequency use to detect the bottom : (index, string) # List of tuple
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depth_bottom_detection_min = [] # Min value to detect bottom on the first vertical # List of float
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depth_bottom_detection_max = [] # Max value to detect bottom on the first vertical # List of float
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depth_bottom_detection_interval = [] # interval for searching area # List of float
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# ----------------------------------------------------------------------------------------------------------------------
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# =========================================================
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# --- SIGNAL PREPROCESSING TAB ---
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# =========================================================
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# Variables names # Description # Type
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path_BS_noise_data = [] # Paths of the acoustic noise data files # List of strings
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filename_BS_noise_data = [] # Files names of the acoustic noise data files # List of strings
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noise_method = [] # = 0 if noise is computed from a file # List of integer
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# = 1 if noise is computed from profile tail (value)
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noise_value = [] # Constant value get from profile tail # List of float
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BS_noise_raw_data = [] # Acoustic noise raw data measurements : 3D arrays # List of arrays
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# If a noise file is downloaded, shape is (freq x depth_noise x time_noise)
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# If noise is computed with value from profile tail, shape is the same than BS_raw_data or BS_cross_section or BS_stream_bed
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time_noise = [] # Time of noise data read from the noise file
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depth_noise = [] # Depth of noise data read from the noise file
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BS_noise_averaged_data = [] # BS_noise_raw_data is averaged and fit the shape of # List of arrays
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# BS_raw_data or BS_cross_section or BS_stream_bed
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BS_mean = [] # Average BS_raw_data or BS_cross_section or BS_stream_bed # List of arrays
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# to plot profile tail : 1D arrays
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SNR_filter_value = [] # Signal to Noise Ratio value use to delete point on BS signal # List of float
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Nb_cells_to_average_BS_signal = [] # Nb of cells used to average the BS signal # List of float
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data_preprocessed = [] # New name of preprocessed data # List of string
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SNR_raw_data = [] # SNR from BS_raw_data and BS_noise_averaged_data : 3D array # List of arrays
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SNR_cross_section = [] # SNR from BS_cross_section and BS_noise_averaged_data : 3D array # List of arrays
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SNR_stream_bed = [] # SNR from BS_stream_bed and BS_noise_averaged_data : 3D array # List of arrays
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# --- Processed data in Signal Processing Tab ---
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BS_raw_data_pre_process_SNR = [] # BS_raw_data preprocessed with SNR_filter_value # List of arrays
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# (remove point if SNR < SNR_filter_value) : 3D array
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BS_raw_data_pre_process_average = [] # BS_raw_data average with Nb_cells_to_average_BS_signal : 3D arrays # List of arrays
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BS_cross_section_pre_process_SNR = [] # BS_cross_section preprocessed with SNR_filter_value # List of arrays
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# (remove point if SNR < SNR_filter_value) : 3D array
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BS_cross_section_pre_process_average = [] # BS_cross_section averaged with Nb_cells_to_average_BS_signal : 3D arrays # List of arrays
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BS_stream_bed_pre_process_SNR = [] # BS_cross_section preprocessed with SNR_filter_value # List of arrays
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# (remove point if SNR < SNR_filter_value) : 3D array
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BS_stream_bed_pre_process_average = [] # BS_cross_section averaged with Nb_cells_to_average_BS_signal : 3D arrays # List of arrays
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# ----------------------------------------------------------------------------------------------------------------------
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# =========================================================
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# --- SAMPLE DATA TAB ---
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# =========================================================
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# Variables names # Description # Type
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# --- Fine sediment Data ---
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path_fine = "" # Path of the fine sediments data files # string
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filename_fine = "" # File name of the fine sediments data # string
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columns_fine = [] # Column names of the fine sediments data # Index list
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sample_fine = [] # Fine sediments sample [('Fn', n-1)] # List of tuples
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distance_from_bank_fine = [] # Distance from bank (m) of the fine sediments # List of float
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depth_fine = [] # Depth (m) of the fine sediments # List of float
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time_fine = [] # Collection time (sec) of the fine sediments # List of float
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radius_grain_fine = [] # Grain radius (m) of the fine sediments # 1D Array
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Ctot_fine = [] # Total concentration (g/L) of the fine sediments # List of float
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Ctot_fine_per_cent = [] # Total concentration (%) of the fine sediments # List of float
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D50_fine = [] # D50 diameter (um) of the fine sediments # List of float
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frac_vol_fine = [] # Volume fraction of the fine sediments # 2D Array
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frac_vol_fine_cumul = [] # Cumulated volume fraction (%) of the fine sediments # 2D Array
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# --- Sand sediment Data ---
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path_sand = "" # Path of the sand sediments data files # string
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filename_sand = "" # File name of the sand sediments data # string
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columns_sand = [] # Column names of the sand sediments data # Index list
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sample_sand = [] # Sand sediments sample [('Sn', n-1)] # List of tuples
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distance_from_bank_sand = [] # Distance from bank (m) of the sand sediments # List of float
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depth_sand = [] # Depth (m) of the sand sediments # List of float
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time_sand = [] # Collection time (sec) of the sand sediments # List of float
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radius_grain_sand = [] # Grain radius (m) of the sand sediments # 1D Array
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Ctot_sand = [] # Total concentration (g/L) of the sand sediments # List of float
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Ctot_sand_per_cent = [] # Total concentration (%) of the sand sediments # List of float
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D50_sand = [] # D50 diameter (um) of the sand sediments # List of float
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frac_vol_sand = [] # Volume fraction of the sand sediments # 2D Array
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frac_vol_sand_cumul = [] # Cumulated volume fraction (%) of the sand sediments # 2D Array
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# ----------------------------------------------------------------------------------------------------------------------
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# =========================================================
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# --- SEDIMENT CALIBRATION TAB ---
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# =========================================================
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# Variables names # Description # Type
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# --- Parameters choice for calibration ---
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calib_acoustic_data = -1
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calib_freq_1 = -1
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calib_freq_2 = -1
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calib_fine_profiles = []
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calib_sand_target = -1
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frequencies_for_calibration = [] # Frequencies chosen for calibration [(f1_val, f1_ind), (f2_val, f2_ind)] # List of 2 tuples
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frequency_for_inversion = tuple() # Frequency chosen for inversion (finv_val, finv_ind) # Tuple
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fine_sample_profile = [] # Fine samples choose for the profile in calibration [('Fn', n-1)] # List of tuples
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sand_sample_target = [] # Sand sample target for calibration [('Sn', n-1)] # List of 1 tuple
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sand_sample_target_indice = [] # position index (time, depth) of the Sand sample target for # List of 2 tuples
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# each calibration frequency
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# [(time_index_freq1, depth_index_freq1), (time_index_freq2, depth_index_freq2)]
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# --- Calibration computation ---
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range_lin_interp = np.array([]) # Point of the depth use to interpolate the fine sediment profile # 1D array
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M_profile_fine = np.array([]) # Interpolate concentration of fine sediments # 1D array
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path_calibration_file = "" # Path of the calibration file # string
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filename_calibration_file = "" # File name of the calibration file # string
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ks = [] # List [ks_freq1, ks_freq2] # List of floats
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sv = [] # List [sv_freq1, sv_freq2] # List of floats
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X_exponent = [] # List of one value [X_exponent] # List of one float
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alpha_s = [] # List [alphas_freq1, alphas_freq2] # List of floats
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zeta = [] # List [zeta_freq1, zeta_freq2] # List of floats
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kt2D = [] # List of kt2D, computed from kt_corrected or kt_read # List of 2D arrays
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kt3D = [] # List of kt3D, computed from kt2D # List of 3D arrays
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J_cross_section = [] # List of J_cross_section compute for all acoustic data recording # List of lists of 3D arrays
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# [[J_cross_section_freq1, J_cross_section_freq2], [], []]
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FCB = [] # 3D array
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depth_real = [] # 3D array
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lin_reg = [] # (lin_reg_compute.slope, lin_reg_compute.intercept) # Tuple
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# ----------------------------------------------------------------------------------------------------------------------
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# =========================================================
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# --- ACOUSTIC INVERSION TAB ---
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# =========================================================
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# Variables names # Description # Type
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VBI_cross_section = [] # Volume Backscattering Index # List of 2D array
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fine_sample_position = [] # Fine samples indexes position for time and depth [(time_index, depth_index)] # List of tuples
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sand_sample_position = [] # Sand samples indexes position for time and depth [(time_index, depth_index)] # List of tuples
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SSC_fine = [] # Suspended Sediment Concentration of the fine sediments # List of one 3D array
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SSC_sand = [] # Suspended Sediment Concentration of the sand sediments # List of one 3D array
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# =========================================================
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# --- ACOUSTIC NOTES TAB ---
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# =========================================================
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notes = ""
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