pychemstation 0.4.7.dev1__py3-none-any.whl → 0.4.7.dev2__py3-none-any.whl

hein-analytical-control/devices/Agilent/chromatogram.py

@@ -1,129 +0,0 @@
-"""Module for HPLC chromatogram data loading and manipulating"""
-
-import os
-import logging
-import time
-
-import numpy as np
-
-from .chemstation import CHFile
-
-from ...analysis import AbstractSpectrum
-
-# Chemstation data path
-DATA_DIR = r"C:\Chem32\1\Data"
-
-
-# standard filenames for spectral data
-CHANNELS = {"A": "01", "B": "02", "C": "03", "D": "04"}
-
-ACQUISITION_PARAMETERS = "acq.txt"
-
-# format used in acquisition parameters
-TIME_FORMAT = "%Y-%m-%d-%H-%M-%S"
-
-
-class AgilentHPLCChromatogram(AbstractSpectrum):
-    """Class for HPLC spectrum (chromatogram) loading and handling."""
-
-    AXIS_MAPPING = {"x": "min", "y": "mAu"}
-
-    INTERNAL_PROPERTIES = {
-        "baseline",
-        "parameters",
-        "data_path",
-    }
-
-    # set of properties to be saved
-    PUBLIC_PROPERTIES = {
-        "x",
-        "y",
-        "peaks",
-        "timestamp",
-    }
-
-    def __init__(self, path=None, autosaving=False):
-
-        if path is not None:
-            os.makedirs(path, exist_ok=True)
-            self.path = path
-        else:
-            self.path = os.path.join(".", "hplc_data")
-            os.makedirs(self.path, exist_ok=True)
-
-        self.logger = logging.getLogger("AgilentHPLCChromatogram")
-
-        super().__init__(path=path, autosaving=autosaving)
-
-    def load_spectrum(self, data_path, channel="A"):
-        """Loads the spectra from the given folder.
-
-        Args:
-            data_path (str): Path where HPLC data has been saved.
-        """
-
-        # to avoid dropping parameters when called in parent class
-        if self.x is not None:
-            if self.autosaving:
-                self.save_data(filename=f"{data_path}_{channel}")
-                self._dump()
-
-        # get raw data
-        x, y = self.extract_rawdata(data_path, channel)
-
-        # get timestamp
-        tstr = data_path.split(".")[0].split("_")[-1]
-        timestamp = time.mktime(time.strptime(tstr, TIME_FORMAT))
-
-        # loading all data
-        super().load_spectrum(x, y, timestamp)
-
-    ### PUBLIC METHODS TO LOAD RAW DATA ###
-
-    def extract_rawdata(self, experiment_dir: str, channel: str):
-        """
-        Reads raw data from Chemstation .CH files.
-
-        Args:
-            experiment_dir: .D directory with the .CH files
-
-        Returns:
-            np.array(times), np.array(values)   Raw chromatogram data
-        """
-        filename = os.path.join(experiment_dir, f"DAD1{channel}")
-        npz_file = filename + ".npz"
-
-        if os.path.exists(npz_file):
-            # already processed
-            data = np.load(npz_file)
-            return data["times"], data["values"]
-        else:
-            self.logger.debug("NPZ file not found. First time loading data.")
-            ch_file = filename + ".ch"
-            data = CHFile(ch_file)
-            np.savez_compressed(npz_file, times=data.times, values=data.values)
-            return np.array(data.times), np.array(data.values)
-
-    def extract_peakarea(self, experiment_dir: str):
-        """
-        Reads processed data from Chemstation report files.
-
-        Args:
-            experiment_dir: .D directory with the report files
-        """
-        # filename = os.path.join(experiment_dir, f"REPORT{CHANNELS[channel]}.csv")
-        # TODO parse file properly
-        # data = np.genfromtxt(filename, delimiter=',')
-        # return data
-        pass
-
-    def default_processing(self):
-        """
-        Processes the chromatogram in place.
-        """
-        # trim first 5 min and last 3 min of run
-        self.trim(5, 25)
-        # parameters found to work best for chromatogram data
-        self.correct_baseline(lmbd=1e5, p=0.0001, n_iter=10)
-        # get all peaks in processed chromatogram
-        self.find_peaks()

hein-analytical-control/devices/Agilent/hplc_param_types.py

@@ -1,141 +0,0 @@
-from dataclasses import dataclass
-from enum import Enum
-from typing import Union, Any
-
-from ...generated import SolventElement, Signal
-
-
-# Commands sent to the Chemstation Macro
-# See https://www.agilent.com/cs/library/usermanuals/Public/MACROS.PDF
-class Command(Enum):
-    def __str__(self):
-        return '%s' % self.value
-
-    RESET_COUNTER_CMD = "last_cmd_no = 0"
-    GET_STATUS_CMD = "response$ = AcqStatus$"
-    SLEEP_CMD = "Sleep {seconds}"
-    STANDBY_CMD = "Standby"
-    STOP_MACRO_CMD = "Stop"
-    PREPRUN_CMD = "PrepRun"
-    LAMP_ON_CMD = "LampAll ON"
-    LAMP_OFF_CMD = "LampAll OFF"
-    PUMP_ON_CMD = "PumpAll ON"
-    PUMP_OFF_CMD = "PumpAll OFF"
-    GET_METHOD_CMD = "response$ = _MethFile$"
-    SWITCH_METHOD_CMD = 'LoadMethod "{method_dir}", "{method_name}.M"'
-    START_METHOD_CMD = "StartMethod"
-    RUN_METHOD_CMD = 'RunMethod "{data_dir}",, "{experiment_name}_{timestamp}"'
-    STOP_METHOD_CMD = "StopMethod"
-    UPDATE_METHOD_CMD = 'UpdateMethod'
-
-
-class RegisterFlag(Enum):
-    def __str__(self):
-        return '%s' % self.value
-
-    SOLVENT_A_COMPOSITION = "PumpChannel_CompositionPercentage"
-    SOLVENT_B_COMPOSITION = "PumpChannel2_CompositionPercentage"
-    SOLVENT_C_COMPOSITION = "PumpChannel3_CompositionPercentage"
-    SOLVENT_D_COMPOSITION = "PumpChannel4_CompositionPercentage"
-    FLOW = "Flow"
-    MAX_TIME = "StopTime_Time"
-    COLUMN_OVEN_TEMP1 = "TemperatureControl_Temperature"
-    COLUMN_OVEN_TEMP2 = "TemperatureControl2_Temperature"
-    STOPTIME_MODE = "StopTime_Mode"
-    POSTIME_MODE = "PostTime_Mode"
-
-
-class MethodTableOperation(Enum):
-    def __str__(self):
-        return '%s' % self.value
-
-    DELETE_TABLE = 'DelTab RCPMP1Method[1], "Timetable"'
-    CREATE_TABLE = 'NewTab RCPMP1Method[1], "Timetable"'
-    NEW_ROW = 'InsTabRow RCPMP1Method[1], "Timetable"'
-    NEW_COLUMN = ""
-    DOWNLOAD_TABLE = ""
-
-
-class PType(Enum):
-    STR = "str"
-    NUM = "num"
-
-
-@dataclass
-class Param:
-    ptype: PType
-    val: Union[float, int, str, Any]
-    chemstation_key: Union[RegisterFlag, list[RegisterFlag]]
-
-
-@dataclass
-class HPLCMethodParams:
-    organic_modifier: Param
-    flow: Param
-    temperature: Param
-    inj_vol: Param
-    equ_time: Param
-    maximum_run_time: Param
-
-
-@dataclass
-class Entry:
-    start_time: float
-    organic_modifer: float
-    flow: float
-
-
-@dataclass
-class MethodTimetable:
-    first_row: HPLCMethodParams
-    subsequent_rows: list[Entry]
-    dad_wavelengthes: list[Signal]
-    organic_modifier: SolventElement
-    modifier_a: SolventElement
-
-
-class HPLCRunningStatus(Enum):
-    @classmethod
-    def has_member_key(cls, key):
-        return key in cls.__members__
-
-    INJECTING = "INJECTING"
-    PREPARING = "PREPARING"
-    RUN = "RUN"
-    NOTREADY = "NOTREADY"
-    POSTRUN = "POSTRUN"
-    RAWDATA = "RAWDATA"
-    INITIALIZING = "INITIALIZING"
-    NOMODULE = "NOMODULE"
-
-
-class HPLCAvailStatus(Enum):
-    @classmethod
-    def has_member_key(cls, key):
-        return key in cls.__members__
-
-    PRERUN = "PRERUN"
-    OFFLINE = "OFFLINE"
-    STANDBY = "STANDBY"
-
-
-class HPLCErrorStatus(Enum):
-
-    @classmethod
-    def has_member_key(cls, key):
-        return key in cls.__members__
-
-    ERROR = "ERROR"
-    BREAK = "BREAK"
-    NORESPONSE = "NORESPONSE"
-    MALFORMED = "MALFORMED"
-
-
-def str_to_status(status: str) -> Union[HPLCAvailStatus, HPLCErrorStatus, HPLCRunningStatus]:
-    if HPLCErrorStatus.has_member_key(status):
-        return HPLCErrorStatus[status]
-    if HPLCRunningStatus.has_member_key(status):
-        return HPLCRunningStatus[status]
-    if HPLCAvailStatus.has_member_key(status):
-        return HPLCAvailStatus[status]
-    raise KeyError(status)