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

hein_analytical_control/devices/OceanOptics/oceanoptics.py

@@ -1,115 +0,0 @@
-"""Base module for interfacing with OceanOptics Spectrometers
-
-.. moduleauthor:: Artem Leonov, Graham Keenan
-"""
-import time
-import logging
-import numpy as np
-import seabreeze
-from seabreeze.pyseabreeze import SeaBreezeDevice
-
-seabreeze.use("cseabreeze")
-import seabreeze.spectrometers as sb
-
-# Spectrometer Types:
-SPECS = {"UV": "2192", "RAMAN": "QE-PRO", "IR": "NIRQUEST"}
-
-
-class UnsupportedSpectrometer(Exception):
-    """Exception for unsupported spectrometer types"""
-
-
-class NoSpectrometerDetected(Exception):
-    """Exception for when no spectrometer is detected"""
-
-
-def _get_spectrometer(spec_type: str) -> SeaBreezeDevice:
-    """Gets the Spectrometer from Seabreeze that matches given type
-
-    Arguments:
-        spec_type {str} -- Type of spectrometer to look for
-
-    Raises:
-        UnsupportedSpectrometer -- If the spec_type is not present
-
-    Returns:
-        str -- Name of the spectrometer
-    """
-
-    devices = sb.list_devices()
-
-    if not devices:
-        raise NoSpectrometerDetected("Are the spectrometers plugged in?")
-    if spec_type in SPECS.keys():
-        for dev in devices:
-            if SPECS[spec_type] in str(dev):
-                return dev
-    raise UnsupportedSpectrometer("Spectrometer {} unsupported!".format(spec_type))
-
-
-class OceanOpticsSpectrometer:
-    """Base class for interfacing with OceanOptics Spectrometers"""
-
-    def __init__(self, spec_type, name=None):
-        """
-        Args:
-            spec_type (str): The type of spectrometer, e.g. 'IR', 'raman', etc.
-            name (str, optional): Device name for easier access
-        """
-        self.integration_time = 0.01  # in seconds
-        self.__spec = _get_spectrometer(spec_type)
-        self._spectrometer = sb.Spectrometer(self.__spec)
-        self.name = name
-        self._delay = 0.01
-
-        self.logger = logging.getLogger("oceanoptics.spectrometer")
-        self.logger.setLevel(logging.INFO)
-        # Removing default handlers
-        self.logger.handlers = []
-        ch = logging.StreamHandler()
-        ch.setLevel(logging.INFO)
-        console_formatter = logging.Formatter(
-            "%(asctime)s ; %(module)s ; %(name)s ; %(message)s"
-        )
-        ch.setFormatter(console_formatter)
-        self.logger.addHandler(ch)
-        self.set_integration_time(self.integration_time)
-
-    def set_integration_time(self, integration_time):
-        """Sets the integration time for the spectrometer
-
-        Args:
-            integration_time (float): Desired integration time in seconds!
-        """
-
-        self._spectrometer.open()
-        self.integration_time = integration_time
-        integration_time *= 1000 * 1000  # converting to microseconds
-        self.logger.debug(
-            "Setting the integration time to %s microseconds", integration_time
-        )
-        self._spectrometer.integration_time_micros(integration_time)
-        self._spectrometer.close()
-
-    def scan(self, n=3):
-        """Reads the spectrometer and returns the spectrum
-
-        Args:
-            n (int, opitonal): Number of 'scans'
-
-        Returns:
-            (Tuple): Tuple containing spectrum wavelengths and intensities as numpy arrays
-                Example: (array(wavelengths), array(intensities))
-        """
-
-        i_mean = []
-        self.logger.debug("Scanning")
-        self._spectrometer.open()
-        for i in range(n):
-            wavelengths, intensities = self._spectrometer.spectrum()
-            i_mean.append(intensities)
-            time.sleep(self._delay)
-
-        intensities = np.mean(i_mean, axis=0)
-        self._spectrometer.close()
-        return (wavelengths, intensities)

hein_analytical_control/devices/__init__.py

@@ -1,15 +0,0 @@
-"""
-.. include:: README.md
-"""
-
-# physical instruments
-from .Magritek.Spinsolve.spinsolve import SpinsolveNMR
-from .OceanOptics.Raman.raman_control import OceanOpticsRaman
-from .OceanOptics.UV.QEPro2192 import QEPro2192
-from .OceanOptics.IR.NIRQuest512 import NIRQuest512
-from .Agilent.hplc import HPLCController
-
-# classes for spectra processing
-from .OceanOptics.Raman.raman_spectrum import RamanSpectrum
-from .Magritek.Spinsolve.spectrum import SpinsolveNMRSpectrum
-from .Agilent.chromatogram import AgilentHPLCChromatogram

hein_analytical_control/generated/__init__.py

@@ -1,56 +0,0 @@
-from .pump_method import (
-    Channel1ExtendedSolventType,
-    Channel2ExtendedSolventType,
-    CompressA,
-    CompressB,
-    Definition,
-    PostTime,
-    PumpMethod,
-    SolventComposition,
-    SolventDescription,
-    SolventElement,
-    StopTime,
-    StrokeA,
-    Timetable,
-    TimetableEntry,
-)
-
-from .dad_method import (
-    AnalogOutput1,
-    AnalogOutput2,
-    DadMethod,
-    PostTime,
-    PrepareAutomation,
-    PrepareMode,
-    Signal,
-    Signals,
-    SpectraAcquisition,
-    StopTime,
-)
-
-__all__ = [
-    "Channel1ExtendedSolventType",
-    "Channel2ExtendedSolventType",
-    "CompressA",
-    "CompressB",
-    "Definition",
-    "PostTime",
-    "PumpMethod",
-    "SolventComposition",
-    "SolventDescription",
-    "SolventElement",
-    "StopTime",
-    "StrokeA",
-    "Timetable",
-    "TimetableEntry",
-    "AnalogOutput1",
-    "AnalogOutput2",
-    "DadMethod",
-    "PostTime",
-    "PrepareAutomation",
-    "PrepareMode",
-    "Signal",
-    "Signals",
-    "SpectraAcquisition",
-    "StopTime",
-]

hein_analytical_control/generated/dad_method.py

@@ -1,367 +0,0 @@
-from dataclasses import dataclass, field
-from typing import Optional
-
-
-@dataclass
-class AnalogOutput1:
-    analog_zero: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "AnalogZero",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    analog_att: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "AnalogAtt",
-            "type": "Element",
-            "required": True,
-        },
-    )
-
-
-@dataclass
-class AnalogOutput2:
-    analog_zero: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "AnalogZero",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    analog_att: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "AnalogAtt",
-            "type": "Element",
-            "required": True,
-        },
-    )
-
-
-@dataclass
-class PostTime:
-    post_time_mode: Optional[str] = field(
-        default=None,
-        metadata={
-            "name": "PostTimeMode",
-            "type": "Element",
-            "required": True,
-        },
-    )
-
-
-@dataclass
-class PrepareAutomation:
-    do_prep_run_balance: Optional[bool] = field(
-        default=None,
-        metadata={
-            "name": "DoPrepRunBalance",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    do_start_run_balance: Optional[bool] = field(
-        default=None,
-        metadata={
-            "name": "DoStartRunBalance",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    do_post_run_balance: Optional[bool] = field(
-        default=None,
-        metadata={
-            "name": "DoPostRunBalance",
-            "type": "Element",
-            "required": True,
-        },
-    )
-
-
-@dataclass
-class PrepareMode:
-    balance_mode: Optional[str] = field(
-        default=None,
-        metadata={
-            "name": "BalanceMode",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    headroom: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "Headroom",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    smpgain: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "SMPGain",
-            "type": "Element",
-            "required": True,
-        },
-    )
-
-
-@dataclass
-class Signal:
-    use_signal: Optional[bool] = field(
-        default=None,
-        metadata={
-            "name": "UseSignal",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    id: Optional[str] = field(
-        default=None,
-        metadata={
-            "name": "ID",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    wavelength: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "Wavelength",
-            "type": "Element",
-        },
-    )
-    bandwidth: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "Bandwidth",
-            "type": "Element",
-        },
-    )
-    use_reference: Optional[bool] = field(
-        default=None,
-        metadata={
-            "name": "UseReference",
-            "type": "Element",
-            "required": True,
-        },
-    )
-
-
-@dataclass
-class SpectraAcquisition:
-    spectra_range_from: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "SpectraRangeFrom",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    spectra_range_to: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "SpectraRangeTo",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    spectra_step: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "SpectraStep",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    spectra_acq_mode: Optional[str] = field(
-        default=None,
-        metadata={
-            "name": "SpectraAcqMode",
-            "type": "Element",
-            "required": True,
-        },
-    )
-
-
-@dataclass
-class StopTime:
-    stop_time_mode: Optional[str] = field(
-        default=None,
-        metadata={
-            "name": "StopTimeMode",
-            "type": "Element",
-            "required": True,
-        },
-    )
-
-
-@dataclass
-class Signals:
-    signal: list[Signal] = field(
-        default_factory=list,
-        metadata={
-            "name": "Signal",
-            "type": "Element",
-            "min_occurs": 1,
-        },
-    )
-
-
-@dataclass
-class DadMethod:
-    module_type: Optional[str] = field(
-        default=None,
-        metadata={
-            "name": "ModuleType",
-            "type": "Attribute",
-            "required": True,
-        },
-    )
-    schema_version: Optional[str] = field(
-        default=None,
-        metadata={
-            "name": "schemaVersion",
-            "type": "Attribute",
-            "required": True,
-        },
-    )
-    schema_si: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "schemaSI",
-            "type": "Attribute",
-            "required": True,
-        },
-    )
-    module_options: Optional[object] = field(
-        default=None,
-        metadata={
-            "name": "ModuleOptions",
-            "type": "Attribute",
-            "required": True,
-        },
-    )
-    configuration_xml: Optional[str] = field(
-        default=None,
-        metadata={
-            "name": "ConfigurationXml",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    timetable: Optional[object] = field(
-        default=None,
-        metadata={
-            "name": "Timetable",
-            "type": "Element",
-        },
-    )
-    stop_time: Optional[StopTime] = field(
-        default=None,
-        metadata={
-            "name": "StopTime",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    post_time: Optional[PostTime] = field(
-        default=None,
-        metadata={
-            "name": "PostTime",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    delay: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "Delay",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    analog_output1: Optional[AnalogOutput1] = field(
-        default=None,
-        metadata={
-            "name": "AnalogOutput1",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    analog_output2: Optional[AnalogOutput2] = field(
-        default=None,
-        metadata={
-            "name": "AnalogOutput2",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    signals: Optional[Signals] = field(
-        default=None,
-        metadata={
-            "name": "Signals",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    peakwidth: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "Peakwidth",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    slitwidth: Optional[int] = field(
-        default=None,
-        metadata={
-            "name": "Slitwidth",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    uvlamp_required: Optional[bool] = field(
-        default=None,
-        metadata={
-            "name": "UVLampRequired",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    vislamp_required: Optional[bool] = field(
-        default=None,
-        metadata={
-            "name": "VISLampRequired",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    prepare_mode: Optional[PrepareMode] = field(
-        default=None,
-        metadata={
-            "name": "PrepareMode",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    prepare_automation: Optional[PrepareAutomation] = field(
-        default=None,
-        metadata={
-            "name": "PrepareAutomation",
-            "type": "Element",
-            "required": True,
-        },
-    )
-    spectra_acquisition: Optional[SpectraAcquisition] = field(
-        default=None,
-        metadata={
-            "name": "SpectraAcquisition",
-            "type": "Element",
-            "required": True,
-        },
-    )