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https://forgemia.inra.fr/theophile.terraz/acoused.git
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Aquascat Data Loader is updated with the Loader of Guillaume Froment (with Dexmes data). Save as and Open actions are added and connected to create_table_for_save_as.py and read_table_for_open.py. Data are saved in sqlite database. Four tables are created : File (acoustic_data (integer) and acoustic file), Measure (acoustic_data, frequencies, kt, nb_profiles, nb_cells and other measurement information), Settings (temperature, tmin, tmax, depth_min, depth_max) and BS_data (backscatter data with time, depth (list of 2D arrays) and BS_raw_data (list of 3D arrays)). 3D arrays are saved with binary (np.tobytes()) in one cell of table BS_data (BLOB type). They are then loaded with np.frombuffer() function.
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@@ -103,7 +103,11 @@ class AcousticDataLoader:
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# order="F")
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r = np.zeros((self._r.shape[1] * self._time.shape[1], self._freq.shape[0]))
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for i, _ in enumerate(self._freq):
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r[:, i] = np.repeat(self._r[i, :], self._time.shape[1])
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for j in range(self._time.shape[1]):
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r[j*self._r.shape[1]:(j+1)*self._r.shape[1], i] = self._r[i, :]
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# r[:, i] = np.repeat(self._r[i, :], self._time.shape[1])
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print(r.shape)
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return r
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@@ -0,0 +1,328 @@
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import numpy as np
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from PyQt5.QtWidgets import QFileDialog, QApplication
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import sqlite3
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import settings as stg
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from os import chdir
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import time
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class CreateTableForSaveAs():
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def __init__(self):
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self.create_AcousticFile = """CREATE TABLE File(
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ID INTEGER PRIMARY KEY AUTOINCREMENT,
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acoustic_data INTEGER,
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acoustic_file STRING)"""
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self.create_Measure = """ CREATE TABLE Measure(
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ID INTEGER PRIMARY KEY AUTOINCREMENT,
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acoustic_data INTEGER,
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frequency FLOAT,
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kt FLOAT,
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NbProfiles INTEGER,
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NbProfilesPerSeconds FLOAT,
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NbCells INTEGER,
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CellSize FLOAT,
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PulseLength FLOAT,
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NbPingsPerSeconds FLOAT,
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NbPingsAveragedPerProfile FLOAT,
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GainRx FLOAT,
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GainTx FLOAT)
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"""
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# for i in stg.acoustic_data:
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# exec("self.create_BSRawData_" + str(i) + " = '''CREATE TABLE BSRawData_" + str(i) +
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# "(ID INTEGER PRIMARY KEY AUTOINCREMENT, " +
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# "acoustic_data INTEGER, " +
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# " ".join(["time_" + str(int(f)) + " FLOAT," for f in stg.freq[i][:-1]]) +
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# ["time_" + str(int(stg.freq[i][-1]))][0] + " FLOAT" + ")''' ")
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# for i in stg.acoustic_data:
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# exec("self.create_BSRawData_" + str(i) + " = '''CREATE TABLE BSRawData_" + str(i) +
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# "(ID INTEGER PRIMARY KEY AUTOINCREMENT, " +
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# "acoustic_data INTEGER, " +
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# " ".join(["time_" + str(int(f)) + " FLOAT," for f in stg.freq[i]]) +
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# " ".join(["depth_" + str(int(f)) + " FLOAT," for f in stg.freq[i]]) +
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# " ".join(["BS_raw_data_" + str(int(f)) + " FLOAT," for f in stg.freq[i][:-1]]) +
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# ["BS_raw_data_" + str(int(stg.freq[i][-1]))][0] + " FLOAT" + ")''' ")
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self.create_BSRawData = '''CREATE TABLE BSRawData(
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ID INTEGER PRIMARY KEY AUTOINCREMENT,
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acoustic_data INTEGER,
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time BLOB,
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depth BLOB,
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BS_raw_data BLOB)'''
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self.create_Settings = '''CREATE TABLE Settings(
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ID INTEGER PRIMARY KEY AUTOINCREMENT,
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acoustic_data INTEGER,
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temperature FLOAT,
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time_min_ind INTEGER,
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time_min_val FLOAT,
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time_max_ind INTEGER,
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time_max_val FLOAT,
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depth_min_ind INTEGER,
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depth_min_val FLOAT,
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depth_max_ind INTEGER,
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depth_max_val FLOAT)'''
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self.open_file_dialog()
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start = time.time()
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self.create_table()
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print(f"end : {time.time() - start} sec")
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def open_file_dialog(self):
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options = QFileDialog.Options()
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name = QFileDialog.getSaveFileName(
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caption="Save As", directory="", filter="AcouSed Files (*.acd)", options=options)
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if name:
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stg.dirname_save_as = "/".join(name[0].split("/")[:-1]) + "/"
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stg.filename_save_as = name[0].split("/")[-1]
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chdir(stg.dirname_save_as)
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# file = open(stg.filename_save_as, 'w')
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# file.write(self.create_Measure)
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# file.close()
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def create_table(self):
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# Create a new database and open a database connection to allow sqlite3 to work with it.
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cnx = sqlite3.connect(stg.filename_save_as + '.acd')
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# Create database cursor to execute SQL statements and fetch results from SQL queries.
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cur = cnx.cursor()
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# --------------------------------------------------------------------------------------------------------------
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# --- Table File ---
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start_table_File = time.time()
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cur.execute("DROP TABLE if exists File")
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cur.execute(self.create_AcousticFile)
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for i in stg.acoustic_data:
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query0 = (f"INSERT into File(acoustic_data, acoustic_file)"
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f"VALUES({stg.acoustic_data[i]}, {str(stg.filename_BS_raw_data[i]).split('.')[0]})")
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cur.execute(query0)
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cnx.commit()
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print(f"table File : {time.time() - start_table_File} sec")
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# --------------------------------------------------------------------------------------------------------------
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# --- Table Measure ---
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start_table_Measure = time.time()
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# Drop Table if exists
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cur.execute("DROP TABLE if exists Measure")
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# Execute the CREATE TABLE statement
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cur.execute(self.create_Measure)
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# Fill the table Measure
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for i in stg.acoustic_data:
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for f, k, r, t in zip(stg.freq[i], stg.kt[i], stg.gain_rx[i], stg.gain_tx[i]):
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query = (f"INSERT into Measure(acoustic_data, frequency, kt, NbProfiles, NbProfilesPerSeconds, "
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f"NbCells, CellSize, PulseLength, NbPingsPerSeconds, "
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f"NbPingsAveragedPerProfile, GainRx, GainTx) "
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f"VALUES({i}, {f}, {k}, {stg.nb_profiles[i]}, {stg.nb_profiles_per_sec[i]}, "
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f"{stg.nb_cells[i]}, {stg.cell_size[i]}, {stg.pulse_length[i]}, {stg.nb_pings_per_sec[i]}, "
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f"{stg.nb_pings_averaged_per_profile[i]}, {r}, {t})")
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cur.execute(query)
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# Commit the transaction after executing INSERT.
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cnx.commit()
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print(f"table Measure : {time.time() - start_table_Measure} sec")
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# --------------------------------------------------------------------------------------------------------------
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# --- Table BSRawData_i ---
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start_table_BSRawData = time.time()
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cur.execute('DROP TABLE if exists BSRawData')
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# # Drop Table BSRawData_i if exists
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# for i in stg.acoustic_data:
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# exec("cur.execute('DROP TABLE if exists BSRawData_" + str(i) + "')")
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#
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# # Execute the CREATE TABLE BSRawData_i statement
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# for i in stg.acoustic_data:
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# exec("cur.execute(self.create_BSRawData_" + str(i) + ")")
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# Fill the table BSRawData_i
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# # --- Fill table BSRawData_i with acoustic data integer ---
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# for i in stg.acoustic_data:
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# for j in range(stg.time_reshape[i].shape[0]):
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# exec(f"query1 = ('''INSERT into BSRawData_" + str(i) + "(acoustic_data)" +
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# f" VALUES({i}) ''') ")
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#
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# exec("cur.execute(query1)")
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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# for i in stg.acoustic_data:
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# , depth, BS_raw_data
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cur.execute(self.create_BSRawData)
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# homer = np.array([1, 2, 3, 4, 5])
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# bart = np.array([6, 7, 8, 9, 10])
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# lisa = np.array([11, 12, 13, 14, 15])
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# marge = homer.tobytes()
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# print("to string : ", homer.tostring())
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# print("to bytes : ", homer.tobytes())
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# query2 = f''' INSERT into BSRawData(acoustic_data, time) VALUES({0}, {marge}) '''
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# cur.execute('''CREATE TABLE IF NOT EXISTS BSRawData(time BLOB)''')
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for i in stg.acoustic_data:
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# cur.execute(''' INSERT into BSRawData(acoustic_data, time, depth, BS_raw_data) VALUES(?, ?, ?, ?)''',
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# (stg.acoustic_data[i], homer.tobytes(),
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# bart.tobytes(), lisa.tobytes()))
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cur.execute(''' INSERT into BSRawData(acoustic_data, time, depth, BS_raw_data, BS_cross_section)
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VALUES(?, ?, ?, ?)''',
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(stg.acoustic_data[i], stg.time[i].tobytes(),
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stg.depth[i].tobytes(), stg.BS_raw_data[i].tobytes()))
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# cur.execute(''' INSERT into BSRawData(time) VALUES(?)''', (marge,))
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# query2 = f''' INSERT into BSRawData(acoustic_data, time) VALUES({0}, {stg.time[0][0, :].tobytes()}) ''' # , {stg.depth[i].tobytes()}, {stg.BS_raw_data[i].tobytes()}
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# for j in range(stg.time_reshape[i].shape[0]):
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#
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# # print("query2 = ('''INSERT into BSRawData_" + str(i) + "(acoustic_data, " +
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# # ", ".join(["time_" + str(int(f)) for f in stg.freq[i]]) + ", " +
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# # ", ".join(["depth_" + str(int(f)) for f in stg.freq[i]]) + ")" +
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# # f" VALUES" + str(eval("0, " +
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# # ", ".join(["stg.time_reshape[" + str(i) + "][" + str(
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# # j) + ", " + str(k) + "]" for k, _ in
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# # enumerate(stg.freq[i])]) + ", " +
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# # ", ".join(["stg.depth_reshape[" + str(i) + "][" + str(j) + ", " + str(k) + "]" for k, _ in enumerate(stg.freq[i])]))) + " ''' )")
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#
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# exec("query2 = ('''INSERT into BSRawData_" + str(i) + "(acoustic_data, " +
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# ", ".join(["time_" + str(int(f)) for f in stg.freq[i]]) + ", " +
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# ", ".join(["depth_" + str(int(f)) for f in stg.freq[i]]) + ", " +
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# ", ".join(["BS_raw_data_" + str(int(f)) for f in stg.freq[i]]) + ")"
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# f" VALUES" + str(eval(str(i) + ", " +
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# ", ".join(["stg.time_reshape[" + str(i) + "][" + str(
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# j) + ", " + str(k) + "]" for k, _ in
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# enumerate(stg.freq[i])]) + ", " +
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# ", ".join(["stg.depth_reshape[" + str(i) + "][" + str(
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# j) + ", " + str(k) + "]" for k, _ in
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# enumerate(stg.freq[i])]) + ", " +
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# ", ".join(["stg.BS_raw_data_reshape[" + str(i) + "][" + str(
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# j) + ", " + str(k) + "]" for k, _ in
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# enumerate(stg.freq[i])]))) + " ''' )")
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# cur.execute(query2)
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# Commit the transaction after executing INSERT.
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cnx.commit()
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print(f"table BSRawData : {time.time() - start_table_BSRawData} sec")
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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# # --- Fill table BSRawData_i with data stg.time_reshape ---
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# for i in stg.acoustic_data:
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# for j in range(stg.time_reshape[i].shape[0]):
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#
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# # print("query2 = ('''INSERT into BSRawData_" + str(i) + "(acoustic_data, " +
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# # ", ".join(["time_" + str(int(f)) for f in stg.freq[i]]) + ")" +
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# # f" VALUES" + str(eval("0, " + ", ".join(["stg.time_reshape[" + str(i) + "][" + str(j) + ", " + str(k) + "]" for k, _ in enumerate(stg.freq[i])]))) + " ''' )")
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#
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# exec("query2 = ('''INSERT into BSRawData_" + str(i) + "(acoustic_data, " +
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# ", ".join(["time_" + str(int(f)) for f in stg.freq[i]]) + ")" +
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# f" VALUES" + str(eval("0, " + ", ".join(["stg.time_reshape[" + str(i) + "][" + str(j) + ", " + str(k) + "]" for k, _ in enumerate(stg.freq[i])]))) + " ''' )")
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#
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# exec("cur.execute(query2)")
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#
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# # Commit the transaction after executing INSERT.
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# cnx.commit()
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#
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# # --- Fill table BSRawData_i with data stg.depth_reshape ---
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# for i in stg.acoustic_data:
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# for f in stg.freq[i]:
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# exec("query3 = ('''ALTER TABLE BSRawData_" + str(i) +
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# " ADD " + ["depth_" + str(int(f)) + " FLOAT"][0] + " ''')")
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#
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# exec("cur.execute(query3)")
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#
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# # Commit the transaction after executing INSERT.
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# cnx.commit()
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#
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# for i in stg.acoustic_data:
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# for k, f in enumerate(stg.freq[i]):
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# for j in range(stg.depth_reshape[i].shape[0]):
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# exec("query4 = '''UPDATE BSRawData_" + str(i) +
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# " SET " + ["depth_" + str(int(f))][0] + " = " +
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# str(eval("stg.depth_reshape[" + str(i) + "][" + str(j) + ", " + str(k) + "]")) +
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# " WHERE ID = " + str(j + 1) + " ''' ")
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#
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# exec("cur.execute(query4)")
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# # --- Fill table BSRawData_i with data stg.BS_raw_data_reshape ---
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# for i in stg.acoustic_data:
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# for f in stg.freq[i]:
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#
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# exec("query5 = ('''ALTER TABLE BSRawData_" + str(i) +
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# " ADD " + ["BS_raw_data_" + str(int(f)) + " FLOAT"][0] + " ''')")
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#
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# exec("cur.execute(query5)")
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#
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# # Commit the transaction after executing INSERT.
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# cnx.commit()
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#
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# for i in stg.acoustic_data:
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# for k, f in enumerate(stg.freq[i]):
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# for j in range(stg.BS_raw_data_reshape[i].shape[0]):
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#
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# exec("query6 = '''UPDATE BSRawData_" + str(i) +
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# " SET " + ["BS_raw_data_" + str(int(f))][0] + " = " +
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# str(eval("stg.BS_raw_data_reshape[" + str(i) + "][" + str(j) + ", " + str(k) + "]")) +
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# " WHERE ID = " + str(j+1) + " ''' ")
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#
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# exec("cur.execute(query6)")
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#
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# cnx.commit()
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# --------------------------------------------------------------------------------------------------------------
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# --- Table Settings ---
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start_table_Settings = time.time()
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cur.execute("DROP TABLE if exists Settings")
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cur.execute(self.create_Settings)
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print(stg.acoustic_data, stg.temperature, stg.rmin, stg.rmax, stg.tmin, stg.tmax)
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for i in stg.acoustic_data:
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query7 = (f'''INSERT into Settings(acoustic_data, temperature,
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time_min_ind, time_min_val, time_max_ind, time_max_val,
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depth_min_ind, depth_min_val, depth_max_ind, depth_max_val)
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VALUES({stg.acoustic_data[i]},
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{stg.temperature[i]},
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{stg.tmin[i][0]},
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{stg.tmin[i][1]},
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{stg.tmax[i][0]},
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{stg.tmax[i][1]},
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{stg.rmin[i][0]},
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{stg.rmin[i][1]},
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{stg.rmax[i][0]},
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{stg.rmax[i][1]})''')
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cur.execute(query7)
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cnx.commit()
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print(f"table Settings : {time.time() - start_table_Settings} sec")
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# Close database cursor
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cur.close()
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# Close database connection
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cnx.close()
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@@ -0,0 +1,157 @@
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import numpy as np
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from PyQt5.QtWidgets import QFileDialog, QApplication
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import sqlite3
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from os import path, chdir
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import settings as stg
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class ReadTableForOpen:
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def __init__(self):
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self.open_file_dialog()
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chdir(stg.dirname_open)
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self.sql_file_to_open = open(stg.filename_open)
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self.read_table()
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# self.reshape_variables()
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def open_file_dialog(self):
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name = QFileDialog.getOpenFileName(caption="Open Acoused file", directory="", filter="Acoused file (*.acd)")
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if name:
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stg.dirname_open = path.dirname(name[0])
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stg.filename_open = path.basename(name[0])
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def read_table(self):
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# connexion to File db
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cnx = sqlite3.connect(stg.filename_open)
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# Create database cursor to execute SQL statements and fetch results from SQL queries.
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cur = cnx.cursor()
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query = '''SELECT acoustic_data, acoustic_file FROM File'''
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data = cur.execute(query).fetchall()
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stg.acoustic_data, stg.filename_BS_raw_data = [x[0] for x in data], [y[1] for y in data]
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|
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for i in stg.acoustic_data:
|
||||
|
||||
query1 = f'''SELECT frequency, kt, NbProfiles, NbProfilesPerSeconds, "
|
||||
f"NbCells, CellSize, PulseLength, NbPingsPerSeconds, "
|
||||
f"NbPingsAveragedPerProfile, GainRx, GainTx
|
||||
FROM Measure WHERE (acoustic_data = {i})'''
|
||||
data1 = cur.execute(query1).fetchall()
|
||||
# print(data1)
|
||||
# print([x[0] for x in data1])
|
||||
stg.freq.append([x[0] for x in data1])
|
||||
stg.kt.append([x[1] for x in data1])
|
||||
stg.nb_profiles.append([x[2] for x in data1])
|
||||
stg.nb_profiles_per_sec.append([x[3] for x in data1])
|
||||
stg.nb_cells.append([x[4] for x in data1])
|
||||
stg.cell_size.append([x[5] for x in data1])
|
||||
stg.pulse_length.append([x[6] for x in data1])
|
||||
stg.nb_pings_per_sec.append([x[7] for x in data1])
|
||||
stg.nb_pings_averaged_per_profile.append([x[8] for x in data1])
|
||||
stg.gain_rx.append([x[9] for x in data1])
|
||||
stg.gain_tx.append([x[10] for x in data1])
|
||||
|
||||
# for f_ind, f_val in enumerate(stg.freq[i]):
|
||||
#
|
||||
# exec("query2 = '''SELECT time_" + str(int(f_val)) + ", depth_" + str(int(f_val)) + ", BS_raw_data_" + str(int(f_val)) +
|
||||
# " FROM BSRawData_" + str(int(i)) + " WHERE (acoustic_data = " + str(i) + ") ''' ")
|
||||
# exec("data2 = cur.execute(query2).fetchall()")
|
||||
# # print(eval("data2"))
|
||||
#
|
||||
# if f_ind == 0:
|
||||
# time_reshape_temp = np.array([[x[0] for x in eval("data2")]])
|
||||
# # print("1 time_reshape_temp.shape ", time_reshape_temp.shape)
|
||||
# depth_reshape_temp = np.array([[x[1] for x in eval("data2")]])
|
||||
# BS_raw_data_reshape_temp = np.array([[x[2] for x in eval("data2")]])
|
||||
# else:
|
||||
# time_reshape_temp = np.insert(time_reshape_temp, f_ind, [x[0] for x in eval("data2")], axis=0)
|
||||
# # print("2 time_reshape_temp.shape ", time_reshape_temp.shape)
|
||||
# depth_reshape_temp = np.insert(depth_reshape_temp, f_ind, [x[1] for x in eval("data2")], axis=0)
|
||||
# BS_raw_data_reshape_temp = np.insert(BS_raw_data_reshape_temp, f_ind, [x[1] for x in eval("data2")], axis=0)
|
||||
#
|
||||
# stg.time_reshape.append(time_reshape_temp.transpose())
|
||||
# # print(len(stg.time_reshape))
|
||||
# # print(stg.time_reshape[i].shape)
|
||||
# stg.depth_reshape.append(depth_reshape_temp.transpose())
|
||||
# stg.BS_raw_data_reshape.append(BS_raw_data_reshape_temp.transpose())
|
||||
|
||||
query2 = f'''SELECT acoustic_data, time, depth, BS_raw_data FROM BSRawData WHERE (acoustic_data = {i})'''
|
||||
|
||||
data2 = cur.execute(query2).fetchall()
|
||||
print("len(data2) ", len(data2[0]))
|
||||
# print("data2 : ", data2)
|
||||
# data2_retreived = np.frombuffer(data2[0][1], dtype=np.float64)
|
||||
# print("", data2_retreived)
|
||||
|
||||
stg.time.append(np.frombuffer(data2[0][1], dtype=np.float64).reshape((len(stg.freq[i]), -1)))
|
||||
print(stg.time[0].shape)
|
||||
print(stg.time)
|
||||
stg.depth.append(np.frombuffer(data2[0][2], dtype=np.float64).reshape(len(stg.freq[i]), -1))
|
||||
print(stg.depth[0].shape)
|
||||
print(stg.depth)
|
||||
stg.BS_raw_data.append(np.frombuffer(data2[0][3], dtype=np.float64))
|
||||
|
||||
# time_reshape_temp = np.insert(time_reshape_temp, time_reshape_temp.shape[0], [x[0] for x in eval("data2")], axis=0)
|
||||
# stg.depth_reshape.append([x[2] for x in data2])
|
||||
# stg.BS_raw_data_reshape.append([x[3] for x in data2])
|
||||
|
||||
# query = '''SELECT acoustic_file FROM File'''
|
||||
# cur.execute(query)
|
||||
# stg.acoustic_data = cur.fetchall()
|
||||
|
||||
# Close database cursor
|
||||
cur.close()
|
||||
|
||||
# Close database connection
|
||||
cnx.close()
|
||||
|
||||
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])))
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in new issue
Block a user