tsp 1.7.3__py3-none-any.whl → 1.7.7__py3-none-any.whl

tsp/dataloggers/RBRXR420.py

@@ -1,308 +1,308 @@
-import sqlite3
-import pathlib
-import warnings
-import numpy as np
-import pandas as pd
-import datetime as dt
-try:
-    from pyrsktools import RSK
-except ModuleNotFoundError:
-    warnings.warn("Missing pyRSKtools library. .rsk files can not be imported.")
-from .AbstractReader import AbstractReader
-
-
-class RBRXR420(AbstractReader):
-
-    def read(self, file_path: str) -> "pd.DataFrame":
-        """
-
-        Parameters
-        ----------
-        file_path
-
-        Returns
-        -------
-
-        """
-        file_extention = pathlib.Path(file_path).suffix.lower()
-        if file_extention in [".dat", ".hex"]:
-            with open(file_path, "r") as f:
-                first_50 = [next(f) for i in range(50)]
-                for line_num in range(len(first_50)):
-                    if first_50[line_num].lower().startswith("logger start:"):
-                        header_length = line_num + 1
-                        break
-
-            with open(file_path, "r") as f:
-                header_lines = [next(f) for i in range(header_length)]
-                self._parse_meta(header_lines)
-
-                data_lines = f.readlines()
-                if file_extention == ".dat":
-                    line_num = 0
-                    for line_num in range(len(data_lines)):
-                        if data_lines[line_num] != "\n":
-                            split_line = data_lines[line_num].split()
-                        else:
-                            split_line = ["no data"]
-                        if split_line[0].lower() == "temp":
-                            break
-                    if line_num == len(data_lines) - 1:
-                        raise RuntimeError("No column names found")
-                    data_lines = data_lines[line_num:]
-                    first_line = data_lines[0].split()
-                    second_line = data_lines[1].split()
-
-                    if len(first_line) == len(second_line):
-                        self._read_standard_dat_format(data_lines[1:], False)
-                    elif len(first_line) + 2 == len(second_line):
-                        try:
-                            is_datetime = bool(dt.datetime.strptime(" ".join(second_line[:2]), "%Y/%m/%d %H:%M:%S"))
-                        except ValueError:
-                            is_datetime = False
-                        if is_datetime:
-                            self._read_standard_dat_format(data_lines[1:], True)
-                        else:
-                            raise RuntimeError("Error, expected date time with format %Y/%m/%d %H:%M:%S at start of"
-                                               "row.")
-                    else:
-                        raise RuntimeError("Error: Number of column names and number of columns do not match any"
-                                           "expected pattern.")
-
-                else:
-                    self._read_standard_hex_format(data_lines)
-        elif file_extention == ".xls":
-            self._read_standard_xls_format(file_path)
-        elif file_extention == ".xlsx":
-            self._read_standard_xlsx_format(file_path)
-        elif file_extention == ".rsk":
-            self._read_standard_rsk_format(file_path)
-        else:
-            raise IOError("Unrecognised file. File is not a .dat, .hex, .xls, .xlsx, or .rsk.")
-        return self.DATA
-
-    def _parse_meta(self, header_lines: list):
-        self.META["logger model"] = header_lines[0].split()[1]
-        self.META["logger SN"] = header_lines[0].split()[3]
-        sample_interval = dt.datetime.strptime(header_lines[5].split()[-1], "%H:%M:%S")
-        self.META["download date"] = dt.datetime.strptime(header_lines[1][14:31], "%y/%m/%d %H:%M:%S")
-        self.META["sample interval"] = dt.timedelta(hours=sample_interval.hour, minutes=sample_interval.minute,
-                                                    seconds=sample_interval.second)
-        self.META["logging start"] = dt.datetime.strptime(" ".join(header_lines[3].split()[-2:]),
-                                                          "%y/%m/%d %H:%M:%S")
-        line_7_info = header_lines[6].split(",")
-        self.META["num channels"] = int(line_7_info[0].split()[-1])
-        self.META["num samples"] = int(line_7_info[1].split()[-1])
-        formatting = header_lines[7].split("%")[1]
-        if formatting.endswith("\n"):
-            self.META["precision"] = int(formatting[-3])
-        else:
-            self.META["precision"] = int(formatting[-2])
-
-        self.META["calibration parameters"] = {}
-        calibration_start_line = 8
-        for i in range(self.META["num channels"]):
-            self.META["calibration parameters"][f"channel {i + 1}"] = {}
-            for j in range(4):
-                line_num = calibration_start_line + 4 * i + j
-                if header_lines[line_num].lower().startswith("calibration"):
-                    self.META["calibration parameters"][f"channel {i + 1}"][chr(ord("a") + j)]\
-                        = float(header_lines[line_num].split()[-1])
-                else:
-                    self.META["calibration parameters"][f"channel {i + 1}"][chr(ord("a") + j)] \
-                        = float(header_lines[line_num].split()[0])
-
-        self.META['raw'] = "".join(header_lines)
-        return
-
-    def _read_standard_dat_format(self, raw_data: list, time_stamps: bool = False):
-        """
-
-        Parameters
-        ----------
-        raw_data
-        line_numbers
-
-        Returns
-        -------
-
-        """
-        self.DATA = pd.DataFrame(columns=[f"channel {i + 1}" for i in range(self.META["num channels"])])
-        line_num = 0
-        for line in raw_data:
-            line_data = line.split()
-            if time_stamps:
-                self.DATA.loc[dt.datetime.strptime(" ".join(line_data[:2]), "%Y/%m/%d %H:%M:%S")] = line_data[2:]
-            else:
-                self.DATA.loc[self.META["logging start"] + self.META["sample interval"] * line_num] = line_data
-            line_num += 1
-        for col in self.DATA:
-            self.DATA[col] = pd.to_numeric(self.DATA[col], errors='coerce')
-        self.DATA.reset_index(inplace=True)
-        self.DATA.rename(columns={"index": "TIME"}, inplace=True)
-        return
-
-    def _read_standard_hex_format(self, raw_data: list):
-        """
-
-        Parameters
-        ----------
-        raw_data
-
-        Returns
-        -------
-
-        """
-        for line_num in range(len(raw_data)):
-            if raw_data[line_num].lower().startswith("number of bytes of data"):
-                hex_header_length = line_num + 2
-                break
-            elif raw_data[line_num].lower().startswith("number of bytes in header"):
-                header_bytes = int(raw_data[line_num].split()[-1])
-        num_hex_header_values = int(header_bytes / 3)
-        hex_vals = []
-        raw_data = raw_data[hex_header_length:]
-        for line_num in range(len(raw_data)):
-            line = raw_data[line_num]
-            line_hex_vals = [line[i: i + 6] for i in range(0, len(line), 6)][:-1]
-            for hex_val in line_hex_vals:
-                hex_vals.append(hex_val)
-        hex_vals = hex_vals[num_hex_header_values:]
-
-        self.DATA = pd.DataFrame(columns=[f"channel {i + 1}" for i in range(self.META["num channels"])])
-        line_num = 0
-        hex_num = 0
-        for line in range(self.META["num samples"]):
-            line_time = self.META["logging start"] + self.META["sample interval"] * line_num
-            time_hex_vals = hex_vals[hex_num: hex_num + 8]
-            line_vals = [int(h, 16) / int("FFFFFF", 16) for h in time_hex_vals]
-            line_temps = []
-            for channel in range(len(line_vals)):
-                val = line_vals[channel]
-                if val not in [0, 1]:
-                    a = self.META["calibration parameters"][f"channel {channel + 1}"]["a"]
-                    b = self.META["calibration parameters"][f"channel {channel + 1}"]["b"]
-                    c = self.META["calibration parameters"][f"channel {channel + 1}"]["c"]
-                    d = self.META["calibration parameters"][f"channel {channel + 1}"]["d"]
-                    x = np.log((1 / val) - 1)
-                    temp = 1 / (a + b * x + c * x**2 + d * x**3) - 273.15
-                    line_temps.append(round(temp, self.META["precision"]))
-                else:
-                    line_temps.append(np.nan)
-            self.DATA.loc[line_time] = line_temps
-            line_num += 1
-            hex_num += 8
-        for col in self.DATA:
-            self.DATA[col] = pd.to_numeric(self.DATA[col], errors='coerce')
-        self.DATA.reset_index(inplace=True)
-        self.DATA.rename(columns={"index": "TIME"}, inplace=True)
-        return
-
-    def _read_standard_xls_format(self, file_path: str):
-        xls = pd.ExcelFile(file_path)
-        sheet = xls.sheet_names[0]
-        xls.close()
-        raw_data = pd.read_excel(file_path, sheet, header=None)
-        raw_meta = raw_data.iloc[:5].copy()
-        if raw_meta.iloc[0, 0] != "RBR data file":
-            raise IOError("Not a valid .xls file")
-        meta = {}
-        for i, r in raw_meta.iterrows():
-            for j in range(0, len(r) - 1, 2):
-                if not pd.isna(raw_meta.iloc[i, j]):
-                    meta[raw_meta.iloc[i, j]] = raw_meta.iloc[i, j + 1]
-        self.META["logger model"] = meta["Model:"]
-        self.META["logger SN"] = meta["Serial Number:"]
-        self.META["sample interval"] = dt.timedelta(seconds=int(meta["Logging sampling period (s):"]))
-        self.META["logging start"] = dt.datetime.strptime(meta["Logging start time:"], "%Y/%m/%d")
-
-        column_names = {}
-        for col in raw_data:
-            if col == 0:
-                col_name = "TIME"
-            else:
-                col_name = f"channel {col}"
-            column_names[col] = col_name
-        self.DATA = raw_data.iloc[6:].copy()
-        self.DATA.reset_index(drop=True, inplace=True)
-        self.DATA.rename(columns=column_names, inplace=True)
-        for col in self.DATA:
-            if col == "TIME":
-                self.DATA["TIME"] = pd.to_datetime(self.DATA["TIME"], format="%d/%m/%Y %H:%M:%S.%f")
-            else:
-                self.DATA[col] = pd.to_numeric(self.DATA[col], errors='coerce')
-        return
-
-    def _read_standard_xlsx_format(self, file_path: str):
-        meta_table = {"Instrument": pd.read_excel(file_path, sheet_name="Metadata", header=9, nrows=1),
-                      "Schedule": pd.read_excel(file_path, sheet_name="Metadata", header=24, nrows=1),
-                      "Sampling": pd.read_excel(file_path, sheet_name="Metadata", header=28, nrows=1)}
-        self.META["logger model"] = meta_table["Instrument"]["Model"].loc[0]
-        self.META["logger SN"] = meta_table["Instrument"]["Serial"].loc[0]
-        self.META["sample interval"] = dt.timedelta(seconds=int(meta_table["Sampling"]["Period"].loc[0]))
-        self.META["logging start"] = meta_table["Schedule"]["Start time"].loc[0]
-
-        self.DATA = pd.read_excel(file_path, sheet_name="Data", header=1)
-
-        column_names = {}
-        for col in self.DATA:
-            if col == "Time":
-                col_name = "TIME"
-            elif col == "Temperature":
-                col_name = "channel 1"
-            else:
-                col_name = f"channel {int(col.split('.')[-1]) + 1}"
-            column_names[col] = col_name
-        self.DATA.rename(columns=column_names, inplace=True)
-
-        for col in self.DATA:
-            if col == "TIME":
-                self.DATA["TIME"] = pd.to_datetime(self.DATA["TIME"], format="%Y-%m-%d %H:%M:%S.%f")
-            else:
-                self.DATA[col] = pd.to_numeric(self.DATA[col], errors='coerce')
-        return
-
-    def _read_standard_rsk_format(self, file_path: str):
-        raw_meta = {}
-        try:
-            with RSK(file_path) as rsk:
-                rsk.open()
-                rsk.readdata()
-                rsk_data = rsk.data
-                raw_meta["calibration"] = rsk.calibrations
-                raw_meta["instrument"] = rsk.instrument
-                raw_meta["schedule"] = rsk.scheduleInfo
-                raw_meta["parameter key"] = rsk.parameterKeys
-                raw_meta["epoch"] = rsk.epoch
-        except NameError:
-            raise ModuleNotFoundError("You must install pyRSKtools")
-        except sqlite3.OperationalError:
-            raise RuntimeError("An error occurred when opening the .rsk file. Try opening the .rsk file in the ruskin\n"
-                               " software then rerunning the code.")
-        self.DATA = pd.DataFrame(rsk_data)
-
-        self.META["logger model"] = raw_meta["instrument"].model
-        self.META["logger SN"] = raw_meta["instrument"].serialID
-        self.META["sample interval"] = dt.timedelta(seconds=raw_meta["schedule"].samplingPeriod/1000)
-        self.META["logging start"] = raw_meta["epoch"].startTime
-        self.META["utc offset"] = [int(float(element.value) * 3600) for element in raw_meta["parameter key"]
-                                   if element.key == "OFFSET_FROM_UTC"][0]
-        self.META["calibration parameters"] = {}
-        for cal in raw_meta["calibration"]:
-            self.META["calibration parameters"][f"channel {cal.channelOrder}"] = {}
-            self.META["calibration parameters"][f"channel {cal.channelOrder}"]["a"] = cal.c[0]
-            self.META["calibration parameters"][f"channel {cal.channelOrder}"]["b"] = cal.c[1]
-            self.META["calibration parameters"][f"channel {cal.channelOrder}"]["c"] = cal.c[2]
-            self.META["calibration parameters"][f"channel {cal.channelOrder}"]["d"] = cal.c[3]
-
-        column_names = {}
-        for col in self.DATA:
-            if col == "timestamp":
-                col_name = "TIME"
-            elif col == "temperature":
-                col_name = "channel 1"
-            else:
-                col_name = f"channel {int(col[-1]) + 1}"
-            column_names[col] = col_name
-        self.DATA.rename(columns=column_names, inplace=True)
-        return
+import sqlite3
+import pathlib
+import warnings
+import numpy as np
+import pandas as pd
+import datetime as dt
+try:
+    from pyrsktools import RSK
+except ModuleNotFoundError:
+    warnings.warn("Missing pyRSKtools library. .rsk files can not be imported.")
+from .AbstractReader import AbstractReader
+
+
+class RBRXR420(AbstractReader):
+
+    def read(self, file_path: str) -> "pd.DataFrame":
+        """
+
+        Parameters
+        ----------
+        file_path
+
+        Returns
+        -------
+
+        """
+        file_extention = pathlib.Path(file_path).suffix.lower()
+        if file_extention in [".dat", ".hex"]:
+            with open(file_path, "r") as f:
+                first_50 = [next(f) for i in range(50)]
+                for line_num in range(len(first_50)):
+                    if first_50[line_num].lower().startswith("logger start:"):
+                        header_length = line_num + 1
+                        break
+
+            with open(file_path, "r") as f:
+                header_lines = [next(f) for i in range(header_length)]
+                self._parse_meta(header_lines)
+
+                data_lines = f.readlines()
+                if file_extention == ".dat":
+                    line_num = 0
+                    for line_num in range(len(data_lines)):
+                        if data_lines[line_num] != "\n":
+                            split_line = data_lines[line_num].split()
+                        else:
+                            split_line = ["no data"]
+                        if split_line[0].lower() == "temp":
+                            break
+                    if line_num == len(data_lines) - 1:
+                        raise RuntimeError("No column names found")
+                    data_lines = data_lines[line_num:]
+                    first_line = data_lines[0].split()
+                    second_line = data_lines[1].split()
+
+                    if len(first_line) == len(second_line):
+                        self._read_standard_dat_format(data_lines[1:], False)
+                    elif len(first_line) + 2 == len(second_line):
+                        try:
+                            is_datetime = bool(dt.datetime.strptime(" ".join(second_line[:2]), "%Y/%m/%d %H:%M:%S"))
+                        except ValueError:
+                            is_datetime = False
+                        if is_datetime:
+                            self._read_standard_dat_format(data_lines[1:], True)
+                        else:
+                            raise RuntimeError("Error, expected date time with format %Y/%m/%d %H:%M:%S at start of"
+                                               "row.")
+                    else:
+                        raise RuntimeError("Error: Number of column names and number of columns do not match any"
+                                           "expected pattern.")
+
+                else:
+                    self._read_standard_hex_format(data_lines)
+        elif file_extention == ".xls":
+            self._read_standard_xls_format(file_path)
+        elif file_extention == ".xlsx":
+            self._read_standard_xlsx_format(file_path)
+        elif file_extention == ".rsk":
+            self._read_standard_rsk_format(file_path)
+        else:
+            raise IOError("Unrecognised file. File is not a .dat, .hex, .xls, .xlsx, or .rsk.")
+        return self.DATA
+
+    def _parse_meta(self, header_lines: list):
+        self.META["logger model"] = header_lines[0].split()[1]
+        self.META["logger SN"] = header_lines[0].split()[3]
+        sample_interval = dt.datetime.strptime(header_lines[5].split()[-1], "%H:%M:%S")
+        self.META["download date"] = dt.datetime.strptime(header_lines[1][14:31], "%y/%m/%d %H:%M:%S")
+        self.META["sample interval"] = dt.timedelta(hours=sample_interval.hour, minutes=sample_interval.minute,
+                                                    seconds=sample_interval.second)
+        self.META["logging start"] = dt.datetime.strptime(" ".join(header_lines[3].split()[-2:]),
+                                                          "%y/%m/%d %H:%M:%S")
+        line_7_info = header_lines[6].split(",")
+        self.META["num channels"] = int(line_7_info[0].split()[-1])
+        self.META["num samples"] = int(line_7_info[1].split()[-1])
+        formatting = header_lines[7].split("%")[1]
+        if formatting.endswith("\n"):
+            self.META["precision"] = int(formatting[-3])
+        else:
+            self.META["precision"] = int(formatting[-2])
+
+        self.META["calibration parameters"] = {}
+        calibration_start_line = 8
+        for i in range(self.META["num channels"]):
+            self.META["calibration parameters"][f"channel {i + 1}"] = {}
+            for j in range(4):
+                line_num = calibration_start_line + 4 * i + j
+                if header_lines[line_num].lower().startswith("calibration"):
+                    self.META["calibration parameters"][f"channel {i + 1}"][chr(ord("a") + j)]\
+                        = float(header_lines[line_num].split()[-1])
+                else:
+                    self.META["calibration parameters"][f"channel {i + 1}"][chr(ord("a") + j)] \
+                        = float(header_lines[line_num].split()[0])
+
+        self.META['raw'] = "".join(header_lines)
+        return
+
+    def _read_standard_dat_format(self, raw_data: list, time_stamps: bool = False):
+        """
+
+        Parameters
+        ----------
+        raw_data
+        line_numbers
+
+        Returns
+        -------
+
+        """
+        self.DATA = pd.DataFrame(columns=[f"channel {i + 1}" for i in range(self.META["num channels"])])
+        line_num = 0
+        for line in raw_data:
+            line_data = line.split()
+            if time_stamps:
+                self.DATA.loc[dt.datetime.strptime(" ".join(line_data[:2]), "%Y/%m/%d %H:%M:%S")] = line_data[2:]
+            else:
+                self.DATA.loc[self.META["logging start"] + self.META["sample interval"] * line_num] = line_data
+            line_num += 1
+        for col in self.DATA:
+            self.DATA[col] = pd.to_numeric(self.DATA[col], errors='coerce')
+        self.DATA.reset_index(inplace=True)
+        self.DATA.rename(columns={"index": "TIME"}, inplace=True)
+        return
+
+    def _read_standard_hex_format(self, raw_data: list):
+        """
+
+        Parameters
+        ----------
+        raw_data
+
+        Returns
+        -------
+
+        """
+        for line_num in range(len(raw_data)):
+            if raw_data[line_num].lower().startswith("number of bytes of data"):
+                hex_header_length = line_num + 2
+                break
+            elif raw_data[line_num].lower().startswith("number of bytes in header"):
+                header_bytes = int(raw_data[line_num].split()[-1])
+        num_hex_header_values = int(header_bytes / 3)
+        hex_vals = []
+        raw_data = raw_data[hex_header_length:]
+        for line_num in range(len(raw_data)):
+            line = raw_data[line_num]
+            line_hex_vals = [line[i: i + 6] for i in range(0, len(line), 6)][:-1]
+            for hex_val in line_hex_vals:
+                hex_vals.append(hex_val)
+        hex_vals = hex_vals[num_hex_header_values:]
+
+        self.DATA = pd.DataFrame(columns=[f"channel {i + 1}" for i in range(self.META["num channels"])])
+        line_num = 0
+        hex_num = 0
+        for line in range(self.META["num samples"]):
+            line_time = self.META["logging start"] + self.META["sample interval"] * line_num
+            time_hex_vals = hex_vals[hex_num: hex_num + 8]
+            line_vals = [int(h, 16) / int("FFFFFF", 16) for h in time_hex_vals]
+            line_temps = []
+            for channel in range(len(line_vals)):
+                val = line_vals[channel]
+                if val not in [0, 1]:
+                    a = self.META["calibration parameters"][f"channel {channel + 1}"]["a"]
+                    b = self.META["calibration parameters"][f"channel {channel + 1}"]["b"]
+                    c = self.META["calibration parameters"][f"channel {channel + 1}"]["c"]
+                    d = self.META["calibration parameters"][f"channel {channel + 1}"]["d"]
+                    x = np.log((1 / val) - 1)
+                    temp = 1 / (a + b * x + c * x**2 + d * x**3) - 273.15
+                    line_temps.append(round(temp, self.META["precision"]))
+                else:
+                    line_temps.append(np.nan)
+            self.DATA.loc[line_time] = line_temps
+            line_num += 1
+            hex_num += 8
+        for col in self.DATA:
+            self.DATA[col] = pd.to_numeric(self.DATA[col], errors='coerce')
+        self.DATA.reset_index(inplace=True)
+        self.DATA.rename(columns={"index": "TIME"}, inplace=True)
+        return
+
+    def _read_standard_xls_format(self, file_path: str):
+        xls = pd.ExcelFile(file_path)
+        sheet = xls.sheet_names[0]
+        xls.close()
+        raw_data = pd.read_excel(file_path, sheet, header=None)
+        raw_meta = raw_data.iloc[:5].copy()
+        if raw_meta.iloc[0, 0] != "RBR data file":
+            raise IOError("Not a valid .xls file")
+        meta = {}
+        for i, r in raw_meta.iterrows():
+            for j in range(0, len(r) - 1, 2):
+                if not pd.isna(raw_meta.iloc[i, j]):
+                    meta[raw_meta.iloc[i, j]] = raw_meta.iloc[i, j + 1]
+        self.META["logger model"] = meta["Model:"]
+        self.META["logger SN"] = meta["Serial Number:"]
+        self.META["sample interval"] = dt.timedelta(seconds=int(meta["Logging sampling period (s):"]))
+        self.META["logging start"] = dt.datetime.strptime(meta["Logging start time:"], "%Y/%m/%d")
+
+        column_names = {}
+        for col in raw_data:
+            if col == 0:
+                col_name = "TIME"
+            else:
+                col_name = f"channel {col}"
+            column_names[col] = col_name
+        self.DATA = raw_data.iloc[6:].copy()
+        self.DATA.reset_index(drop=True, inplace=True)
+        self.DATA.rename(columns=column_names, inplace=True)
+        for col in self.DATA:
+            if col == "TIME":
+                self.DATA["TIME"] = pd.to_datetime(self.DATA["TIME"], format="%d/%m/%Y %H:%M:%S.%f")
+            else:
+                self.DATA[col] = pd.to_numeric(self.DATA[col], errors='coerce')
+        return
+
+    def _read_standard_xlsx_format(self, file_path: str):
+        meta_table = {"Instrument": pd.read_excel(file_path, sheet_name="Metadata", header=9, nrows=1),
+                      "Schedule": pd.read_excel(file_path, sheet_name="Metadata", header=24, nrows=1),
+                      "Sampling": pd.read_excel(file_path, sheet_name="Metadata", header=28, nrows=1)}
+        self.META["logger model"] = meta_table["Instrument"]["Model"].loc[0]
+        self.META["logger SN"] = meta_table["Instrument"]["Serial"].loc[0]
+        self.META["sample interval"] = dt.timedelta(seconds=int(meta_table["Sampling"]["Period"].loc[0]))
+        self.META["logging start"] = meta_table["Schedule"]["Start time"].loc[0]
+
+        self.DATA = pd.read_excel(file_path, sheet_name="Data", header=1)
+
+        column_names = {}
+        for col in self.DATA:
+            if col == "Time":
+                col_name = "TIME"
+            elif col == "Temperature":
+                col_name = "channel 1"
+            else:
+                col_name = f"channel {int(col.split('.')[-1]) + 1}"
+            column_names[col] = col_name
+        self.DATA.rename(columns=column_names, inplace=True)
+
+        for col in self.DATA:
+            if col == "TIME":
+                self.DATA["TIME"] = pd.to_datetime(self.DATA["TIME"], format="%Y-%m-%d %H:%M:%S.%f")
+            else:
+                self.DATA[col] = pd.to_numeric(self.DATA[col], errors='coerce')
+        return
+
+    def _read_standard_rsk_format(self, file_path: str):
+        raw_meta = {}
+        try:
+            with RSK(file_path) as rsk:
+                rsk.open()
+                rsk.readdata()
+                rsk_data = rsk.data
+                raw_meta["calibration"] = rsk.calibrations
+                raw_meta["instrument"] = rsk.instrument
+                raw_meta["schedule"] = rsk.scheduleInfo
+                raw_meta["parameter key"] = rsk.parameterKeys
+                raw_meta["epoch"] = rsk.epoch
+        except NameError:
+            raise ModuleNotFoundError("You must install pyRSKtools")
+        except sqlite3.OperationalError:
+            raise RuntimeError("An error occurred when opening the .rsk file. Try opening the .rsk file in the ruskin\n"
+                               " software then rerunning the code.")
+        self.DATA = pd.DataFrame(rsk_data)
+
+        self.META["logger model"] = raw_meta["instrument"].model
+        self.META["logger SN"] = raw_meta["instrument"].serialID
+        self.META["sample interval"] = dt.timedelta(seconds=raw_meta["schedule"].samplingPeriod/1000)
+        self.META["logging start"] = raw_meta["epoch"].startTime
+        self.META["utc offset"] = [int(float(element.value) * 3600) for element in raw_meta["parameter key"]
+                                   if element.key == "OFFSET_FROM_UTC"][0]
+        self.META["calibration parameters"] = {}
+        for cal in raw_meta["calibration"]:
+            self.META["calibration parameters"][f"channel {cal.channelOrder}"] = {}
+            self.META["calibration parameters"][f"channel {cal.channelOrder}"]["a"] = cal.c[0]
+            self.META["calibration parameters"][f"channel {cal.channelOrder}"]["b"] = cal.c[1]
+            self.META["calibration parameters"][f"channel {cal.channelOrder}"]["c"] = cal.c[2]
+            self.META["calibration parameters"][f"channel {cal.channelOrder}"]["d"] = cal.c[3]
+
+        column_names = {}
+        for col in self.DATA:
+            if col == "timestamp":
+                col_name = "TIME"
+            elif col == "temperature":
+                col_name = "channel 1"
+            else:
+                col_name = f"channel {int(col[-1]) + 1}"
+            column_names[col] = col_name
+        self.DATA.rename(columns=column_names, inplace=True)
+        return

tsp/dataloggers/__init__.py

@@ -1,15 +1,15 @@
-from .HOBO import HOBO, HOBOProperties
-from .FG2 import FG2
-from .GP5W import GP5W
-from .Geoprecision import detect_geoprecision_type
-from .logr import LogR
-
-HOBO.__module__ = __name__
-HOBOProperties.__module__ = __name__
-FG2.__module__ =__name__
-GP5W.__module__ = __name__
-LogR.__module__ = __name__
-
-__all__ = ['HOBO','HOBOProperties',
-           'FG2','GP5W', 'detect_geoprecision_type',
-           'LogR']
+from .HOBO import HOBO, HOBOProperties
+from .FG2 import FG2
+from .GP5W import GP5W
+from .Geoprecision import detect_geoprecision_type
+from .logr import LogR
+
+HOBO.__module__ = __name__
+HOBOProperties.__module__ = __name__
+FG2.__module__ =__name__
+GP5W.__module__ = __name__
+LogR.__module__ = __name__
+
+__all__ = ['HOBO','HOBOProperties',
+           'FG2','GP5W', 'detect_geoprecision_type',
+           'LogR']