pychemstation 0.5.2__py3-none-any.whl → 0.5.3.dev1__py3-none-any.whl

pychemstation/control/method.py

@@ -1,232 +0,0 @@
-import os
-import time
-
-from xsdata.formats.dataclass.parsers import XmlParser
-
-from ..control.table_controller import TableController, HPLCController
-from ..generated import DadMethod, PumpMethod
-from ..utils.chromatogram import TIME_FORMAT
-from ..utils.constants import METHOD_TIMETABLE
-from ..utils.macro import Command
-from ..utils.method_types import MethodTimetable, HPLCMethodParams, Param, PType, TimeTableEntry
-from ..utils.table_types import RegisterFlag, TableOperation
-
-
-class MethodController(TableController):
-    """
-    Class containing method related logic
-    """
-
-    def __init__(self, controller: HPLCController, src: str):
-        super().__init__(controller, src)
-
-    def is_loaded(self, method_name: str):
-        """Checks if a given method is already loaded into Chemstation. Method name does not need the ".M" extension.
-
-        :param method_name: a Chemstation method
-        :return: True if method is already loaded
-        """
-        self.send(Command.GET_METHOD_CMD)
-        parsed_response = self.receive().splitlines()[1].split()[1:][0]
-        return method_name in parsed_response
-
-    def switch(self, method_name: str):
-        """Allows the user to switch between pre-programmed methods. No need to append '.M'
-        to the end of the method name. For example. for the method named 'General-Poroshell.M',
-        only 'General-Poroshell' is needed.
-
-        :param method_name: any available method in Chemstation method directory
-        :raise IndexError: Response did not have expected format. Try again.
-        :raise AssertionError: The desired method is not selected. Try again.
-        """
-        self.send(Command.SWITCH_METHOD_CMD.value.format(method_dir=self.src,
-                                                         method_name=method_name))
-
-        time.sleep(2)
-        self.send(Command.GET_METHOD_CMD)
-        time.sleep(2)
-
-        # check that method switched
-        for _ in range(10):
-            try:
-                parsed_response = self.receive().splitlines()[1].split()[1:][0]
-                break
-            except IndexError:
-                continue
-
-        assert parsed_response == f"{method_name}.M", "Switching Methods failed."
-
-    def run(self, experiment_name: str):
-        """This is the preferred method to trigger a run.
-        Starts the currently selected method, storing data
-        under the <data_dir>/<experiment_name>.D folder.
-        The <experiment_name> will be appended with a timestamp in the '%Y-%m-%d-%H-%M' format.
-        Device must be ready.
-
-        :param experiment_name: Name of the experiment
-        """
-        timestamp = time.strftime(TIME_FORMAT)
-
-        self.send(Command.RUN_METHOD_CMD.value.format(data_dir=self.src,
-                                                      experiment_name=experiment_name,
-                                                      timestamp=timestamp))
-
-        folder_name = f"{experiment_name}_{timestamp}.D"
-        self.controller.data_files.append(os.path.join(self.src, folder_name))
-
-    def load(self, method_name: str):
-        """Retrieve method details of an existing method. Don't need to append ".M" to the end. This assumes the
-        organic modifier is in Channel B and that Channel A contains the aq layer. Additionally, assumes
-         only two solvents are being used.
-
-        :param method_name: name of method to load details of
-        :raises FileNotFoundError: Method does not exist
-        :return: method details
-        """
-        method_folder = f"{method_name}.M"
-        method_path = os.path.join(self.src, method_folder, "AgilentPumpDriver1.RapidControl.MethodXML.xml")
-        dad_path = os.path.join(self.src, method_folder, "Agilent1200erDadDriver1.RapidControl.MethodXML.xml")
-
-        if os.path.exists(os.path.join(self.src, f"{method_name}.M")):
-            parser = XmlParser()
-            method = parser.parse(method_path, PumpMethod)
-            dad = parser.parse(dad_path, DadMethod)
-
-            organic_modifier = None
-            aq_modifier = None
-
-            if len(method.solvent_composition.solvent_element) == 2:
-                for solvent in method.solvent_composition.solvent_element:
-                    if solvent.channel == "Channel_A":
-                        aq_modifier = solvent
-                    elif solvent.channel == "Channel_B":
-                        organic_modifier = solvent
-
-            return MethodTimetable(
-                first_row=HPLCMethodParams(
-                    organic_modifier=Param(val=organic_modifier.percentage,
-                                           chemstation_key=RegisterFlag.SOLVENT_B_COMPOSITION,
-                                           ptype=PType.NUM),
-                    flow=Param(val=method.flow,
-                               chemstation_key=RegisterFlag.FLOW,
-                               ptype=PType.NUM),
-                    maximum_run_time=Param(val=method.stop_time,
-                                           chemstation_key=RegisterFlag.MAX_TIME,
-                                           ptype=PType.NUM),
-                    temperature=Param(val=None,
-                                      chemstation_key=[RegisterFlag.COLUMN_OVEN_TEMP1,
-                                                       RegisterFlag.COLUMN_OVEN_TEMP2],
-                                      ptype=PType.NUM),
-                    inj_vol=Param(val=None,
-                                  chemstation_key=None,
-                                  ptype=PType.NUM),
-                    equ_time=Param(val=None,
-                                   chemstation_key=None,
-                                   ptype=PType.NUM)),
-                subsequent_rows=[
-                    TimeTableEntry(
-                        start_time=tte.time,
-                        organic_modifer=tte.percent_b,
-                        flow=method.flow
-                    ) for tte in method.timetable.timetable_entry
-                ],
-                dad_wavelengthes=dad.signals.signal,
-                organic_modifier=organic_modifier,
-                modifier_a=aq_modifier
-            )
-        else:
-            raise FileNotFoundError
-
-    def edit(self, updated_method: MethodTimetable):
-        """Updated the currently loaded method in ChemStation with provided values.
-
-        :param updated_method: the method with updated values, to be sent to Chemstation to modify the currently loaded method.
-        """
-        initial_organic_modifier: Param = updated_method.first_row.organic_modifier
-        max_time: Param = updated_method.first_row.maximum_run_time
-        temp: Param = updated_method.first_row.temperature
-        injvol: Param = updated_method.first_row.inj_vol
-        equalib_time: Param = updated_method.first_row.equ_time
-        flow: Param = updated_method.first_row.flow
-
-        # Method settings required for all runs
-        self.send(TableOperation.DELETE_TABLE.value.format(register=METHOD_TIMETABLE.register,
-                                                           table_name=METHOD_TIMETABLE.name, ))
-        self._update_param(initial_organic_modifier)
-        self._update_param(flow)
-        self._update_param(Param(val="Set",
-                                 chemstation_key=RegisterFlag.STOPTIME_MODE,
-                                 ptype=PType.STR))
-        self._update_param(max_time)
-        self._update_param(Param(val="Off",
-                                 chemstation_key=RegisterFlag.POSTIME_MODE,
-                                 ptype=PType.STR))
-
-        self.send("DownloadRCMethod PMP1")
-
-        self._update_method_timetable(updated_method.subsequent_rows)
-
-    def _update_method_timetable(self, timetable_rows: list[TimeTableEntry]):
-        self.sleepy_send('Local Rows')
-        self._get_table_rows(METHOD_TIMETABLE)
-
-        self.sleepy_send('DelTab RCPMP1Method[1], "Timetable"')
-        res = self._get_table_rows(METHOD_TIMETABLE)
-        while "ERROR" not in res:
-            self.sleepy_send('DelTab RCPMP1Method[1], "Timetable"')
-            res = self._get_table_rows(METHOD_TIMETABLE)
-
-        self.sleepy_send('NewTab RCPMP1Method[1], "Timetable"')
-        self._get_table_rows(METHOD_TIMETABLE)
-
-        for i, row in enumerate(timetable_rows):
-            if i == 0:
-                self.send('Sleep 1')
-                self.sleepy_send('InsTabRow RCPMP1Method[1], "Timetable"')
-                self.send('Sleep 1')
-
-                self.sleepy_send('NewColText RCPMP1Method[1], "Timetable", "Function", "SolventComposition"')
-                self.sleepy_send(f'NewColVal RCPMP1Method[1], "Timetable", "Time", {row.start_time}')
-                self.sleepy_send(
-                    f'NewColVal RCPMP1Method[1], "Timetable", "SolventCompositionPumpChannel2_Percentage", {row.organic_modifer}')
-
-                self.send('Sleep 1')
-                self.sleepy_send("DownloadRCMethod PMP1")
-                self.send('Sleep 1')
-            else:
-                self.sleepy_send('InsTabRow RCPMP1Method[1], "Timetable"')
-                self._get_table_rows(METHOD_TIMETABLE)
-
-                self.sleepy_send(
-                    f'SetTabText RCPMP1Method[1], "Timetable", Rows, "Function", "SolventComposition"')
-                self.sleepy_send(
-                    f'SetTabVal RCPMP1Method[1], "Timetable", Rows, "Time", {row.start_time}')
-                self.sleepy_send(
-                    f'SetTabVal RCPMP1Method[1], "Timetable", Rows, "SolventCompositionPumpChannel2_Percentage", {row.organic_modifer}')
-
-                self.send("Sleep 1")
-                self.sleepy_send("DownloadRCMethod PMP1")
-                self.send("Sleep 1")
-                self._get_table_rows(METHOD_TIMETABLE)
-
-    def _update_param(self, method_param: Param):
-        """Change a method parameter, changes what is visibly seen in Chemstation GUI. (changes the first row in the timetable)
-
-        :param method_param: a parameter to update for currently loaded method.
-        """
-        register = METHOD_TIMETABLE.register
-        setting_command = TableOperation.UPDATE_OBJ_HDR_VAL if method_param.ptype == PType.NUM else TableOperation.UPDATE_OBJ_HDR_TEXT
-        if isinstance(method_param.chemstation_key, list):
-            for register_flag in method_param.chemstation_key:
-                self.send(setting_command.value.format(register=register,
-                                                       register_flag=register_flag,
-                                                       val=method_param.val))
-        else:
-            self.send(setting_command.value.format(register=register,
-                                                   register_flag=method_param.chemstation_key,
-                                                   val=method_param.val))
-        time.sleep(2)
-
-    def stop(self):
-        """Stops the run. A dialog window will pop up and manual intervention may be required."""
-        self.send(Command.STOP_METHOD_CMD)

pychemstation/control/sequence.py

@@ -1,140 +0,0 @@
-import os
-import time
-
-from ..control.table_controller import TableController, HPLCController
-from ..utils.chromatogram import SEQUENCE_TIME_FORMAT
-from ..utils.constants import SEQUENCE_TABLE
-from ..utils.macro import Command
-from ..utils.sequence_types import SequenceTable, SequenceEntry
-from ..utils.table_types import RegisterFlag, TableOperation
-
-
-class SequenceController(TableController):
-    """
-    Class containing sequence related logic
-    """
-
-    def __init__(self, controller: HPLCController, src: str):
-        super().__init__(controller, src)
-
-    def switch(self, seq_name: str):
-        """Switch to the specified sequence. The sequence name does not need the '.S' extension.
-
-        :param seq_name: The name of the sequence file
-        """
-        self.send(f'_SeqFile$ = "{seq_name}.S"')
-        self.send(f'_SeqPath$ = "{self.src}"')
-        self.send(Command.SWITCH_SEQUENCE_CMD)
-        time.sleep(2)
-        self.send(Command.GET_SEQUENCE_CMD)
-        time.sleep(2)
-        # check that method switched
-        for _ in range(10):
-            try:
-                parsed_response = self.receive().splitlines()[1].split()[1:][0]
-                break
-            except IndexError:
-                continue
-
-        assert parsed_response == f"{seq_name}.S", "Switching sequence failed."
-
-    def run(self, sequence_table: SequenceTable):
-        """Starts the currently loaded sequence, storing data
-        under the <data_dir>/<sequence table name> folder.
-        The <sequence table name> will be appended with a timestamp in the "%Y %m %d %H %m %s" format.
-        Device must be ready.
-
-        :param sequence_table:
-        """
-        timestamp = time.strftime(SEQUENCE_TIME_FORMAT)
-        self.send(Command.RUN_SEQUENCE_CMD.value)
-        self.send(Command.RUN_SEQUENCE_CMD.value)
-        folder_name = f"{sequence_table.name} {timestamp}"
-        subdirs = [x[0] for x in os.walk(self.src)]
-        time.sleep(60)
-        potential_folders = sorted(list(filter(lambda d: folder_name in d, subdirs)))
-        self.controller.data_files.append(potential_folders[0])
-
-    def edit(self, sequence_table: SequenceTable):
-        """Updates the currently loaded sequence table with the provided table. This method will delete the existing sequence table and remake it.
-        If you would only like to edit a single row of a sequence table, use `edit_sequence_table_row` instead.
-
-        :param sequence_table:
-        """
-        self.send("Local Rows")
-        self.sleep(1)
-        self.delete_table(SEQUENCE_TABLE)
-        self.sleep(1)
-        self.new_table(SEQUENCE_TABLE)
-        self.sleep(1)
-        self._get_table_rows(SEQUENCE_TABLE)
-        for _ in sequence_table.rows:
-            self.add_table_row(SEQUENCE_TABLE)
-            self.sleep(1)
-            self.send(Command.SAVE_SEQUENCE_CMD)
-            self.sleep(1)
-        self._get_table_rows(SEQUENCE_TABLE)
-        self.send(Command.SWITCH_SEQUENCE_CMD)
-        for i, row in enumerate(sequence_table.rows):
-            self.edit(row=row, row_num=i + 0)
-            self.sleep(1)
-            self.send(Command.SAVE_SEQUENCE_CMD)
-            self.sleep(1)
-
-    def edit_row(self, row: SequenceEntry, row_num: int):
-        """Edits a row in the sequence table. Assumes the row already exists.
-
-        :param row: sequence row entry with updated information
-        :param row_num: the row to edit, based on -1-based indexing
-        """
-        if row.vial_location:
-            self.sleepy_send(TableOperation.EDIT_ROW_VAL.value.format(register=SEQUENCE_TABLE.register,
-                                                                      table_name=SEQUENCE_TABLE.name,
-                                                                      row=row_num,
-                                                                      col_name=RegisterFlag.VIAL_LOCATION,
-                                                                      val=row.vial_location))
-        if row.method:
-            self.sleepy_send(TableOperation.EDIT_ROW_TEXT.value.format(register=SEQUENCE_TABLE.register,
-                                                                       table_name=SEQUENCE_TABLE.name,
-                                                                       row=row_num,
-                                                                       col_name=RegisterFlag.METHOD,
-                                                                       val=row.method))
-
-        if row.num_inj:
-            self.sleepy_send(TableOperation.EDIT_ROW_VAL.value.format(register=SEQUENCE_TABLE.register,
-                                                                      table_name=SEQUENCE_TABLE.name,
-                                                                      row=row_num,
-                                                                      col_name=RegisterFlag.NUM_INJ,
-                                                                      val=row.num_inj))
-
-        if row.inj_vol:
-            self.sleepy_send(TableOperation.EDIT_ROW_TEXT.value.format(register=SEQUENCE_TABLE.register,
-                                                                       table_name=SEQUENCE_TABLE.name,
-                                                                       row=row_num,
-                                                                       col_name=RegisterFlag.INJ_VOL,
-                                                                       val=row.inj_vol))
-
-        if row.inj_source:
-            self.sleepy_send(TableOperation.EDIT_ROW_TEXT.value.format(register=SEQUENCE_TABLE.register,
-                                                                       table_name=SEQUENCE_TABLE.name,
-                                                                       row=row_num,
-                                                                       col_name=RegisterFlag.INJ_SOR,
-                                                                       val=row.inj_source))
-
-        if row.sample_name:
-            self.sleepy_send(TableOperation.EDIT_ROW_TEXT.value.format(register=SEQUENCE_TABLE.register,
-                                                                       table_name=SEQUENCE_TABLE.name,
-                                                                       row=row_num,
-                                                                       col_name=RegisterFlag.NAME,
-                                                                       val=row.sample_name))
-            self.sleepy_send(TableOperation.EDIT_ROW_TEXT.value.format(register=SEQUENCE_TABLE.register,
-                                                                       table_name=SEQUENCE_TABLE.name,
-                                                                       row=row_num,
-                                                                       col_name=RegisterFlag.DATA_FILE,
-                                                                       val=row.sample_name))
-        if row.sample_type:
-            self.sleepy_send(TableOperation.EDIT_ROW_VAL.value.format(register=SEQUENCE_TABLE.register,
-                                                                      table_name=SEQUENCE_TABLE.name,
-                                                                      row=row_num,
-                                                                      col_name=RegisterFlag.SAMPLE_TYPE,
-                                                                      val=row.sample_type))

pychemstation/control/table_controller.py

@@ -1,75 +0,0 @@
-import os
-from typing import Union
-
-
-from .comm import HPLCController
-from ..utils.macro import Command
-from ..utils.table_types import Table, TableOperation, RegisterFlag
-
-
-class TableController:
-
-    def __init__(self, controller: HPLCController, src: str):
-        self.controller = controller
-        if os.path.isdir(src):
-            self.src: str = src
-        else:
-            raise FileNotFoundError(f"dir: {src} not found.")
-
-    def sleep(self, seconds: int):
-        self.controller.sleep(seconds)
-
-    def receive(self):
-        self.controller.receive()
-
-    def send(self, cmd: Union[Command, str]):
-        self.controller.send(cmd)
-
-    def sleepy_send(self, cmd: Union[Command, str]):
-        self.controller.sleepy_send(cmd)
-
-    def add_table_row(self, table: Table):
-        """Adds a row to the provided table for currently loaded method or sequence.
-         Import either the SEQUENCE_TABLE or METHOD_TIMETABLE from hein_analytical_control.constants.
-        You can also provide your own table.
-
-        :param table: the table to add a new row to
-        """
-        self.sleepy_send(TableOperation.NEW_ROW.value.format(register=table.register,
-                                                             table_name=table.name))
-
-    def delete_table(self, table: Table):
-        """Deletes the table for the current loaded method or sequence.
-         Import either the SEQUENCE_TABLE or METHOD_TIMETABLE from hein_analytical_control.constants.
-        You can also provide your own table.
-
-        :param table: the table to delete
-        """
-        self.sleepy_send(TableOperation.DELETE_TABLE.value.format(register=table.register,
-                                                                  table_name=table.name))
-
-    def new_table(self, table: Table):
-        """Creates the table for the currently loaded method or sequence. Import either the SEQUENCE_TABLE or
-        METHOD_TIMETABLE from hein_analytical_control.constants. You can also provide your own table.
-
-        :param table: the table to create
-        """
-        self.send(TableOperation.CREATE_TABLE.value.format(register=table.register,
-                                                           table_name=table.name))
-
-    def _get_table_rows(self, table: Table) -> str:
-        self.send(TableOperation.GET_OBJ_HDR_VAL.value.format(internal_val="Rows",
-                                                              register=table.register,
-                                                              table_name=table.name,
-                                                              col_name=RegisterFlag.NUM_ROWS, ))
-        res = self.controller.receive()
-        self.send("Sleep 1")
-        self.send('Print Rows')
-        return res
-
-    def get_data(self):
-        self.controller.get_spectrum()
-        return self.controller.spectra["A"]
-
-    def data_ready(self) -> bool:
-        return self.controller.check_hplc_ready_with_data()