sartoriuslogger/sartorius_logger/__init__.py

""" Sartorius Logger

Make time series measurements with a Sartorius sartoriusb.
"""

__version__ = "0.0.1"

import pandas
import sartoriusb
import time
import sys

from collections import namedtuple
from datetime import datetime
from tqdm import tqdm

from .datalogger import DataLogger, NullLogger
from .parsers import parse_cli_arguments, parse_gui_arguments

try:
    from gooey import Gooey
except ImportError:

    def Gooey(*args, **kargs):
        msg = "The graphilcal user interface must be installed separately"
        raise NotImplementedError(msg)


SCALE_INFO_LABELS = {
    sartoriusb.CMD_INFO_TYPE: "Scale Model",
    sartoriusb.CMD_INFO_SNR: "Scale Serial Number",
    sartoriusb.CMD_INFO_VERSION_SCALE: "Software Version of Scale",
    sartoriusb.CMD_INFO_VERSION_CONTROL_UNIT: "Software Version of Control Unit",  # noqa: E501
}

MEASUREMENT_KEYS = [
    "nr",
    "time",
    "mode",
    "value",
    "unit",
    "stable",
    "message",
]


Result = namedtuple("Result", ["info", "scale", "data", "log_file"])


def get_scale_info(conn):
    """ returns the available scale information """
    data = {}

    for command, label in SCALE_INFO_LABELS.items():
        raw_data_lines = conn.get(command)
        if raw_data_lines:
            raw_data = raw_data_lines[0]
            raw_data = raw_data.strip()
            parts = raw_data.split(maxsplit=1)
            info = parts[1] if len(parts) > 1 else ""
        else:
            # propably a timeout of the serial connection
            info = ""
        data[label] = info

    return data


def _measure_and_log(nr, conn, logger):
    """ performs and logs one measurement

    :params nr: number of measurement
    :params conn: connection to the scale
    :params log: data logger instance
    :returns: dict for measurement point
    """
    measurement = conn.measure()
    data_list = [nr, datetime.now()] + list(measurement)
    logger.add_list(data_list)

    data_dict = dict(zip(MEASUREMENT_KEYS, data_list))

    # for the pandas data frame the value should be transformed into a float
    try:
        data_dict["value"] = float(data_dict["value"])
    except (ValueError, TypeError):
        pass

    return data_dict


def no_progress_bar(iterator):
    """" a stub function for not displaying a progress bar """
    return iterator


def gooey_progress_factory(settings):
    """" progress information, tailored to Gooey """
    total = settings.measurements
    print(
        (
            f"measuring every "
            f"{settings.interval.value}{settings.interval.unit} "
            f"for {settings.duration.value}{settings.duration.unit}"
        )
    )

    def gui_progress(iterator):
        for i in iterator:
            print(f"measurement {i} of {total}")
            yield i
            sys.stdout.flush()
        print(f"measurement {total} of {total}")
        sys.stdout.flush()

    return gui_progress


def _get_log_file_path(settings):
    """ constructs the path to the log file """

    now = datetime.now()
    log_file_name = now.strftime("%Y-%m-%d %H-%M-%S") + ".txt"
    return settings.directory / log_file_name


def _log_measurement_info(logger, settings):
    """ logs all measurement info """
    measurement_info = {
        "Measurements": settings.measurements,
        "Duration": f"{settings.duration.value}{settings.duration.unit}",
        "Interval": f"{settings.interval.value}{settings.interval.unit}",
        "Com-Port": settings.port,
    }
    logger.add_section("Measurement Settings", measurement_info.items())
    return measurement_info


def _log_scale_info(logger, conn):
    """ logs common scale info """
    scale_info = get_scale_info(conn)
    logger.add_section("Scale Info", scale_info.items())
    return scale_info


def measure_series(settings, progress_bar=no_progress_bar, data_logger=None):
    """ serial measurements

    will return the data as pandas data frames in a "Result" named tuple

    :params settings: parser.Settings named tuple
    :params progress_bar: progress bar function to use
    :params data_logger: class of the data logger to use
    :returns: named tuple "Result"
    """
    data_logger = data_logger or NullLogger()

    data_collection = []

    with data_logger as logger:
        measurement_info = _log_measurement_info(logger, settings)

        with sartoriusb.SartoriusUsb(settings.port) as conn:
            scale_info = _log_scale_info(logger, conn)

            # add column headers
            headers = [item.capitalize() for item in MEASUREMENT_KEYS]
            logger.add_section(
                "Measured Data", [headers], append_empty_line=False
            )

            for i in progress_bar(range(1, settings.measurements)):
                data = _measure_and_log(i, conn, logger)
                data_collection.append(data)
                time.sleep(settings.interval.seconds)

            data = _measure_and_log(settings.measurements, conn, logger)
            data_collection.append(data)

    data_df = pandas.DataFrame(data_collection).set_index("time")
    info_df = pandas.DataFrame(measurement_info.items()).set_index(0)
    scale_df = pandas.DataFrame(scale_info.items()).set_index(0)

    return Result(info_df, scale_df, data_df, data_logger.path)


def export_as_excel(measurement_result):
    """ saves the collected data as an Excel file """
    excel_path = measurement_result.log_file.with_suffix(".xlsx")
    with pandas.ExcelWriter(excel_path) as writer:
        measurement_result.data.to_excel(writer, sheet_name="Measurements")
        measurement_result.info.to_excel(writer, sheet_name="Settings")
        measurement_result.scale.to_excel(writer, sheet_name="Scale")


def cli():
    settings = parse_cli_arguments()
    log_file_path = _get_log_file_path(settings)
    result = measure_series(
        settings, progress_bar=tqdm, data_logger=DataLogger(log_file_path)
    )
    export_as_excel(result)


@Gooey(
    program_name="SartoriusLogger",
    progress_regex=r"^measurement (?P<current>\d+) of (?P<total>\d+)",
    progress_expr="current / total * 100",
)
def gui():
    settings = parse_gui_arguments()
    log_file_path = _get_log_file_path(settings)
    gpb = gooey_progress_factory(settings)
    result = measure_series(
        settings, progress_bar=gpb, data_logger=DataLogger(log_file_path)
    )
    export_as_excel(result)