# ============================================================================== # # read_table_for_open.py - AcouSed # # Copyright (C) 2024 INRAE # # # # This program is free software: you can redistribute it and/or modify # # it under the terms of the GNU General Public License as published by # # the Free Software Foundation, either version 3 of the License, or # # (at your option) any later version. # # # # This program is distributed in the hope that it will be useful, # # but WITHOUT ANY WARRANTY; without even the implied warranty of # # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # GNU General Public License for more details. # # # # You should have received a copy of the GNU General Public License # # along with this program. If not, see . # # by Brahim MOUDJED # # ============================================================================== # # -*- coding: utf-8 -*- import os import sys import sqlite3 import logging import numpy as np from PyQt5.QtWidgets import QFileDialog, QApplication, QWidget, QTabWidget import settings as stg from settings import BS_raw_data, acoustic_data from View.acoustic_data_tab import AcousticDataTab logger = logging.getLogger("acoused") class ReadTableForOpen: def __init__(self): self.opened = False self.open_file_dialog() def open_file_dialog(self): name, _ = QFileDialog.getOpenFileName( caption="Open Acoused file", directory="", filter="Acoused file (*.acd)", options=QFileDialog.DontUseNativeDialog ) if name != "": stg.dirname_open = os.path.dirname(name) stg.filename_open = os.path.basename(name) try: os.chdir(stg.dirname_open) except OSError as e: logger.warning(f"chdir: {str(e)}") self.read_table() self.opened = True def execute(self, query): return self._cur.execute(query).fetchall() def read_table(self): stg.read_table_trigger = 1 logger.debug(f"Open '{stg.filename_open}'") cnx = sqlite3.connect(stg.filename_open) self._cur = cnx.cursor() self.read_table_acoustic_file() self.read_table_measure() self.read_table_BS_raw_data() self.read_table_settings() self.read_table_sediment_file() self.read_table_table_sediment_data() logger.debug(f"Reading '{stg.filename_open}' done") self._cur.close() cnx.close() logger.debug(f"'{stg.filename_open}' closed") def read_table_acoustic_file(self): query0 = f'''SELECT acoustic_data FROM AcousticFile''' data0 = self.execute(query0) logger.debug(f"data0: {data0}") stg.acoustic_data = [x[0] for x in data0] logger.debug(f"stg.acoustic_data: {stg.acoustic_data}") for k in range(len(stg.acoustic_data)): query = f''' SELECT acoustic_data, acoustic_file, ABS_name, path_BS_noise_data, filename_BS_noise_data, noise_method, noise_value, data_preprocessed FROM AcousticFile WHERE (acoustic_data = {k}) ''' data = self.execute(query) print("data acoustic file", data) stg.filename_BS_raw_data.append( [str(y[1]) + '.aqa' for y in data][0] ) stg.ABS_name.append([z[2] for z in data][0]) stg.path_BS_noise_data.append([z[3] for z in data][0]) stg.filename_BS_noise_data.append([z[4] for z in data][0]) stg.noise_method.append([z[5] for z in data][0]) stg.noise_value.append([z[6] for z in data][0]) stg.data_preprocessed.append([z[7] for z in data][0]) logger.debug("data acoustic file:") logger.debug(f"- {stg.filename_BS_raw_data}") logger.debug(f"- {stg.ABS_name}") logger.debug(f"- {stg.path_BS_noise_data}") logger.debug(f"- {stg.filename_BS_noise_data}") logger.debug(f"- {stg.noise_method}") logger.debug(f"- {stg.noise_value}") logger.debug(f"- {stg.data_preprocessed}") def read_table_measure(self): stg.date = [0]*len(stg.acoustic_data) stg.hour = [0]*len(stg.acoustic_data) for i in range(len(stg.acoustic_data)): query1 = f''' SELECT acoustic_data, Date, Hour, frequency, sound_attenuation, kt_read, kt_corrected, NbProfiles, NbProfilesPerSeconds, NbCells, CellSize, PulseLength, NbPingsPerSeconds, NbPingsAveragedPerProfile, GainRx, GainTx FROM Measure WHERE (acoustic_data = {i}) ''' data1 = self.execute(query1) logger.debug(f"data1 for {i}: {data1}") stg.date[i] = data1[0][1] stg.hour[i] = data1[0][2] stg.freq.append( np.array([x[3] for x in data1]) ) stg.freq_text.append( [str(x[3]*1e-6) + 'MHz' for x in data1] ) stg.water_attenuation.append( [x[4] for x in data1] ) stg.kt_read.append([x[5] for x in data1]) stg.kt_corrected = [x[6] for x in data1] stg.nb_profiles.append([x[7] for x in data1]) stg.nb_profiles_per_sec.append([x[8] for x in data1]) stg.nb_cells.append([x[9] for x in data1]) stg.cell_size.append([x[10] for x in data1]) stg.pulse_length.append([x[11] for x in data1]) stg.nb_pings_per_sec.append( [x[12] for x in data1] ) stg.nb_pings_averaged_per_profile.append( [x[13] for x in data1] ) stg.gain_rx.append([x[14] for x in data1]) stg.gain_tx.append([x[15] for x in data1]) logger.debug("measure:") logger.debug(f"- {stg.acoustic_data}") logger.debug(f"- {stg.freq}") logger.debug(f"- {stg.water_attenuation}") logger.debug(f"- {stg.kt_read}") logger.debug(f"- {stg.kt_corrected}") logger.debug(f"- {stg.nb_profiles}") logger.debug(f"- {stg.nb_profiles_per_sec}") logger.debug(f"- {stg.nb_cells}") logger.debug(f"- {stg.cell_size}") logger.debug(f"- {stg.pulse_length}") logger.debug(f"- {stg.nb_pings_per_sec}") logger.debug(f"- {stg.nb_pings_averaged_per_profile}") logger.debug(f"- {stg.gain_rx}") logger.debug(f"- {stg.gain_tx}") logger.debug(f"- {stg.date}") logger.debug(f"- {stg.hour}") def read_table_BS_raw_data(self): logger.debug(f"len stg.acoustic_data: {len(stg.acoustic_data)}") for i in range(len(stg.acoustic_data)): query = lambda values: f''' SELECT {", ".join(values)} FROM BSRawData WHERE (acoustic_data = {i}) ''' self.read_table_BS_raw_data_raw(query, i) self.read_table_BS_raw_data_cross_section(query, i) self.read_table_BS_raw_data_bed(query, i) self.read_table_BS_raw_data_noise(query, i) self.read_table_BS_raw_data_SNR(query, i) self.read_table_BS_raw_data_rest(query, i) self.read_table_BS_raw_data_mean(query, i) def read_table_BS_raw_data_raw(self, query, i): np_f64_parse = lambda d: np.frombuffer(d, dtype=np.float64) data = self.execute( query( [ "time", "depth", "BS_raw_data", "time_reshape", "depth_reshape", "BS_raw_data_reshape", ] ) )[0] it = iter(data) time = next(it) depth = next(it) BS_raw_data = next(it) time_reshape = next(it) depth_reshape = next(it) BS_raw_data_reshape = next(it) stg.time.append( np_f64_parse(time).reshape((stg.freq[i].shape[0], -1)) ) stg.depth.append(np_f64_parse(depth).reshape( (stg.freq[i].shape[0], -1) )) stg.BS_raw_data.append( np_f64_parse(BS_raw_data).reshape( ( stg.freq[i].shape[0], stg.depth[i].shape[1], stg.time[i].shape[1] ) ) ) stg.time_reshape.append( np_f64_parse(time_reshape).reshape( (-1, stg.freq[i].shape[0]) ) ) stg.depth_reshape.append( np_f64_parse(depth_reshape).reshape( (-1, stg.freq[i].shape[0]) ) ) stg.BS_raw_data_reshape.append( np_f64_parse(BS_raw_data_reshape).reshape( (-1, stg.freq[i].shape[0]) ) ) def read_table_BS_raw_data_cross_section(self, query, i): np_f64_parse = lambda d: np.frombuffer(d, dtype=np.float64) data = self.execute( query( [ "time_cross_section", "depth_cross_section", "BS_cross_section", ] ) )[0] it = iter(data) time = next(it) depth = next(it) BS = np_f64_parse(next(it)) if len(BS) == 0: stg.time_cross_section.append(np.array([])) stg.depth_cross_section.append(np.array([])) stg.BS_cross_section.append(np.array([])) else: stg.time_cross_section.append( np_f64_parse(time).reshape( (stg.freq[i].shape[0], -1) ) ) stg.depth_cross_section.append( np_f64_parse(depth).reshape( (stg.freq[i].shape[0], -1) ) ) stg.BS_cross_section.append( BS.reshape( ( stg.freq[i].shape[0], stg.depth_cross_section[i].shape[1], stg.time_cross_section[i].shape[1] ) ) ) def read_table_BS_raw_data_bed(self, query, i): np_f64_parse = lambda d: np.frombuffer(d, dtype=np.float64) data = self.execute( query( [ "BS_stream_bed", "depth_bottom", "val_bottom", "ind_bottom", ] ) )[0] it = iter(data) BS = np_f64_parse(next(it)) depth = np_f64_parse(next(it)) val = np_f64_parse(next(it)) ind = np_f64_parse(next(it)) if len(BS) == 0: stg.BS_stream_bed.append(np.array([])) else: stg.BS_stream_bed.append( BS.reshape( ( stg.freq[i].shape[0], stg.depth_cross_section[i].shape[1], stg.time_cross_section[i].shape[1] ) ) ) if len(depth) == 0: stg.depth_bottom.append(np.array([])) stg.val_bottom.append([]) stg.ind_bottom.append([]) else: stg.depth_bottom.append(depth) stg.val_bottom.append(val.tolist()) stg.ind_bottom.append(ind.tolist()) def read_table_BS_raw_data_noise(self, query, i): np_f64_parse = lambda d: np.frombuffer(d, dtype=np.float64) data = self.execute( query( [ "time_noise", "depth_noise", "BS_noise_raw_data", ] ) )[0] it = iter(data) time = next(it) depth = next(it) BS = np_f64_parse(next(it)) if len(BS) == 0: stg.time_noise.append(np.array([])) stg.depth_noise.append(np.array([])) stg.BS_noise_raw_data.append(np.array([])) else: stg.time_noise.append( np_f64_parse(time).reshape( (stg.freq[i].shape[0], -1) ) ) stg.depth_noise.append( np_f64_parse(depth).reshape( (stg.freq[i].shape[0], -1) ) ) stg.BS_noise_raw_data.append( BS.reshape( ( stg.freq[i].shape[0], stg.depth_noise[i].shape[1], stg.time_noise[i].shape[1] ) ) ) def read_table_BS_raw_data_SNR(self, query, i): np_f64_parse = lambda d: np.frombuffer(d, dtype=np.float64) data = self.execute( query( [ "SNR_raw_data", "SNR_cross_section", "SNR_stream_bed", ] ) )[0] it = iter(data) SNR_vars = [ (stg.SNR_raw_data, stg.BS_raw_data), (stg.SNR_cross_section, stg.BS_cross_section), (stg.SNR_cross_section, stg.BS_stream_bed), ] for dest, resh in SNR_vars: SNR = np_f64_parse(next(it)) if len(SNR) == 0: dest.append(np.array([])) else: dest.append(SNR.reshape(resh[i].shape)) def read_table_BS_raw_data_rest(self, query, i): np_f64_parse = lambda d: np.frombuffer(d, dtype=np.float64) data = self.execute( query( [ "BS_raw_data_pre_process_SNR", "BS_raw_data_pre_process_average", "BS_cross_section_pre_process_SNR", "BS_cross_section_pre_process_average", "BS_stream_bed_pre_process_SNR", "BS_stream_bed_pre_process_average", ] ) )[0] BS_vars = [ (stg.BS_raw_data_pre_process_SNR, stg.BS_raw_data), (stg.BS_raw_data_pre_process_average, stg.BS_raw_data), (stg.BS_cross_section_pre_process_SNR, stg.BS_cross_section), (stg.BS_cross_section_pre_process_average, stg.BS_cross_section), (stg.BS_stream_bed_pre_process_SNR, stg.BS_stream_bed), (stg.BS_stream_bed_pre_process_average, stg.BS_stream_bed), ] it = iter(data) for dest, resh in BS_vars: BS = np_f64_parse(next(it)) if len(BS) == 0: dest.append(np.array([])) else: dest.append(BS.reshape(resh[i].shape)) def read_table_BS_raw_data_mean(self, query, i): np_f64_parse = lambda d: np.frombuffer(d, dtype=np.float64) data = self.execute( query(["BS_mean"]) )[0] BS = np_f64_parse(data[0]) if len(BS) == 0: stg.BS_mean.append(np.array([])) else: stg.BS_mean.append( BS.reshape( (stg.freq[i].shape[0], -1) ) ) def read_table_settings(self): for s in range(len(stg.acoustic_data)): query3 = f''' SELECT acoustic_data, temperature, tmin_index, tmin_value, tmax_index, tmax_value, rmin_index, rmin_value, rmax_index, rmax_value, freq_bottom_detection_index, freq_bottom_detection_value, SNR_filter_value, Nb_cells_to_average_BS_signal FROM Settings WHERE (acoustic_data = {s}) ''' data3 = self.execute(query3) stg.temperature = [x[1] for x in data3][0] stg.tmin.append([(x[2], x[3]) for x in data3]) stg.tmax.append([(x[4], x[5]) for x in data3]) stg.rmin.append([(x[6], x[7]) for x in data3]) stg.rmax.append([(x[8], x[9]) for x in data3]) stg.freq_bottom_detection.append([(x[10], x[11]) for x in data3]) stg.SNR_filter_value.append([x[12] for x in data3]) stg.Nb_cells_to_average_BS_signal.append([x[13] for x in data3]) def read_table_sediment_file(self): query = f''' SELECT path_fine, filename_fine, radius_grain_fine, path_sand, filename_sand, radius_grain_sand, time_column_label, distance_from_bank_column_label, depth_column_label, Ctot_fine_column_label, D50_fine_column_label, Ctot_sand_column_label, D50_sand_column_label FROM SedimentsFile ''' data = self.execute(query)[0] stg.path_fine = data[0] stg.filename_fine = data[1] stg.radius_grain_fine = np.array( np.frombuffer(data[2], dtype=np.float64) ) stg.path_sand = data[3] stg.filename_sand = data[4] stg.radius_grain_sand = np.array( np.frombuffer(data[5], dtype=np.float64) ) stg.columns_fine = ( [data[6], data[7], data[8], data[9], data[10]] + list(stg.radius_grain_fine) ) stg.columns_sand = ( [data[6], data[7], data[8], data[11], data[12]] + list(stg.radius_grain_sand) ) def read_table_table_sediment_data(self): query5 = f'''SELECT sample_fine_name, sample_fine_index, distance_from_bank_fine, depth_fine, time_fine, Ctot_fine, Ctot_fine_per_cent, D50_fine, frac_vol_fine, frac_vol_fine_cumul, sample_sand_name, sample_sand_index, distance_from_bank_sand, depth_sand, time_sand, Ctot_sand, Ctot_sand_per_cent, D50_sand, frac_vol_sand, frac_vol_sand_cumul from SedimentsData''' data5 = self.execute(query5) stg.frac_vol_fine = [] stg.frac_vol_fine_cumul = [] stg.frac_vol_sand = [] stg.frac_vol_sand_cumul = [] for f in range(len(data5)): stg.sample_fine.append((data5[f][0], data5[f][1])) stg.distance_from_bank_fine.append(data5[f][2]) stg.depth_fine.append(data5[f][3]) stg.time_fine.append(data5[f][4]) stg.Ctot_fine.append(data5[f][5]) stg.Ctot_fine_per_cent.append(data5[f][6]) stg.D50_fine.append(data5[f][7]) print("np.frombuffer(data4[f][8], dtype=np.float64) ", np.frombuffer(data5[f][8], dtype=np.float64)) stg.frac_vol_fine.append(np.frombuffer(data5[f][8], dtype=np.float64)) stg.frac_vol_fine_cumul.append(np.frombuffer(data5[f][9], dtype=np.float64)) stg.sample_sand.append((data5[f][10], data5[f][11])) stg.distance_from_bank_sand.append(data5[f][12]) stg.depth_sand.append(data5[f][13]) stg.time_sand.append(data5[f][14]) stg.Ctot_sand.append(data5[f][15]) stg.Ctot_sand_per_cent.append(data5[f][16]) stg.D50_sand.append(data5[f][17]) stg.frac_vol_sand.append(np.frombuffer(data5[f][18], dtype=np.float64)) stg.frac_vol_sand_cumul.append(np.frombuffer(data5[f][19], dtype=np.float64)) stg.frac_vol_fine = np.array(stg.frac_vol_fine) stg.frac_vol_fine_cumul = np.array(stg.frac_vol_fine_cumul) stg.frac_vol_sand = np.array(stg.frac_vol_sand) stg.frac_vol_sand_cumul = np.array(stg.frac_vol_sand_cumul) # print("data 4 : ", len(data4), data4) print('data 5 :') print(stg.Ctot_fine, stg.sample_sand) print(type(stg.frac_vol_fine_cumul), stg.frac_vol_fine_cumul) def fill_acoustic_data_tab(self): print("start fill acoustic data tab") # tab_adt = AcousticDataTab(self.master_widget) print("1 AcousticDataTab ", id(AcousticDataTab)) print("tab_adt.combobox_ABS_system_choice ", self.tab.combobox_ABS_system_choice) self.tab.combobox_ABS_system_choice.editTextChanged.connect(self.tab.ABS_system_choice) if stg.ABS_name[0] == "AQUAscat": self.tab.combobox_ABS_system_choice.setCurrentText(stg.ABS_name[0]) print("combobox_ABS_system_choice.setCurrentIndex(1)", self.tab.combobox_ABS_system_choice.itemText(1), self.tab.combobox_ABS_system_choice.itemText(2)) else: self.tab.combobox_ABS_system_choice.setCurrentText(stg.ABS_name[0]) self.tab.plot_backscattered_acoustic_signal_recording() # app = QApplication(sys.argv) # sys.exit(app.exec_()) def reshape_variables(self): for i in stg.acoustic_data: for f, _ in enumerate(stg.freq[i]): if f == 0: depth_temp = np.array([ stg.depth_reshape[i][np.where(stg.depth_reshape[i][:, f] == stg.depth_reshape[i][0, f])[0][0]: np.where(stg.depth_reshape[i][:, f] == stg.depth_reshape[i][0, f])[0][1], f] ]) time_temp = np.array([ stg.time_reshape[i][ np.where(stg.depth_reshape[i][:, f] == stg.depth_reshape[i][0, f])[0], f] ]) else: # print(np.where(stg.depth_reshape[i][:, f] == stg.depth_reshape[i][0, f])) depth_temp = np.insert(depth_temp, depth_temp.shape[0], stg.depth_reshape[i][np.where(stg.depth_reshape[i][:, f] == stg.depth_reshape[i][0, f])[0][0]: np.where(stg.depth_reshape[i][:, f] == stg.depth_reshape[i][0, f])[0][1], f], axis=0) time_temp = np.insert(time_temp, time_temp.shape[0], stg.time_reshape[i][ np.where(stg.depth_reshape[i][:, f] == stg.depth_reshape[i][0, f])[0], f], axis=0) stg.depth.append(depth_temp) stg.time.append(time_temp) stg.BS_raw_data.append(np.reshape(stg.BS_raw_data_reshape[i], (len(stg.freq[i]), stg.depth[i].shape[1], stg.time[i].shape[1])))