pychemstation 0.5.3.dev1__py3-none-any.whl → 0.5.5__py3-none-any.whl

pychemstation/control/__init__.py

@@ -1,5 +1,4 @@
 """
 .. include:: README.md
 """
-from .comm import CommunicationController
 from .hplc import HPLCController

pychemstation/control/comm.py

@@ -86,17 +86,18 @@ class CommunicationController:
 
     def set_status(self):
         """Updates current status of HPLC machine"""
-        self._most_recent_hplc_status = self.get_status()[0]
+        self._most_recent_hplc_status = self.get_status()
 
-    def check_if_running(self, data_path: str) -> bool:
+    def check_if_running(self) -> bool:
         """Checks if HPLC machine is in an available state, meaning a state that data is not being written.
 
         :return: whether the HPLC machine is in a safe state to retrieve data back."""
         self.set_status()
-        file_exists = os.path.exists(data_path)
         hplc_avail = isinstance(self._most_recent_hplc_status, HPLCAvailStatus)
-        done_writing_data = hplc_avail and file_exists
-        return done_writing_data
+        time.sleep(30)
+        self.set_status()
+        hplc_actually_avail = isinstance(self._most_recent_hplc_status, HPLCAvailStatus)
+        return hplc_avail and hplc_actually_avail
 
     def _send(self, cmd: str, cmd_no: int, num_attempts=5) -> None:
         """Low-level execution primitive. Sends a command string to HPLC.
@@ -170,6 +171,9 @@ class CommunicationController:
         cmd_to_send: str = cmd.value if isinstance(cmd, Command) else cmd
         self.cmd_no += 1
         self._send(cmd_to_send, self.cmd_no)
+        f = open("out.txt", "a")
+        f.write(cmd_to_send + "\n")
+        f.close()
 
     def receive(self) -> Result[Response, str]:
         """Returns messages received in reply file.

pychemstation/control/controllers/__init__.py

@@ -0,0 +1,4 @@
+from .method import MethodController
+from .sequence import SequenceController
+from .table_controller import TableController
+from .comm import CommunicationController

pychemstation/control/controllers/comm.py

@@ -0,0 +1,206 @@
+"""
+Module to provide API for the communication with Agilent HPLC systems.
+
+HPLCController sends commands to Chemstation software via a command file.
+Answers are received via reply file. On the Chemstation side, a custom
+Macro monitors the command file, executes commands and writes to the reply file.
+Each command is given a number (cmd_no) to keep track of which commands have
+been processed.
+
+Authors: Alexander Hammer, Hessam Mehr, Lucy Hao
+"""
+
+import os
+import time
+
+from result import Result, Ok, Err
+
+from ...utils.macro import *
+
+
+class CommunicationController:
+    """
+    Class that communicates with Agilent using Macros
+    """
+
+    # maximum command number
+    MAX_CMD_NO = 255
+
+    def __init__(
+            self,
+            comm_dir: str,
+            cmd_file: str = "cmd",
+            reply_file: str = "reply",
+    ):
+        """
+        :param comm_dir:
+        :param cmd_file: Name of command file
+        :param reply_file: Name of reply file
+        """
+        if os.path.isdir(comm_dir):
+            self.cmd_file = os.path.join(comm_dir, cmd_file)
+            self.reply_file = os.path.join(comm_dir, reply_file)
+            self.cmd_no = 0
+        else:
+            raise FileNotFoundError(f"comm_dir: {comm_dir} not found.")
+        self._most_recent_hplc_status = None
+
+        # Create files for Chemstation to communicate with Python
+        open(self.cmd_file, "a").close()
+        open(self.reply_file, "a").close()
+
+        self.reset_cmd_counter()
+
+    def get_num_val(self, cmd: str) -> Union[int, float, Err]:
+        self.send(Command.GET_NUM_VAL_CMD.value.format(cmd=cmd))
+        res = self.receive()
+        if res.is_ok():
+            return res.ok_value.num_response
+        else:
+            raise RuntimeError("Failed to get number.")
+
+    def get_text_val(self, cmd: str) -> str:
+        self.send(Command.GET_TEXT_VAL_CMD.value.format(cmd=cmd))
+        res = self.receive()
+        if res.is_ok():
+            return res.ok_value.string_response
+        else:
+            raise RuntimeError("Failed to get string")
+
+    def get_status(self) -> Union[HPLCRunningStatus, HPLCAvailStatus, HPLCErrorStatus]:
+        """Get device status(es).
+
+        :return: list of ChemStation's current status
+        """
+        self.send(Command.GET_STATUS_CMD)
+        time.sleep(1)
+
+        try:
+            parsed_response = self.receive().value.string_response
+            self._most_recent_hplc_status = str_to_status(parsed_response)
+            return self._most_recent_hplc_status
+        except IOError:
+            return HPLCErrorStatus.NORESPONSE
+        except IndexError:
+            return HPLCErrorStatus.MALFORMED
+
+    def set_status(self):
+        """Updates current status of HPLC machine"""
+        self._most_recent_hplc_status = self.get_status()
+
+    def check_if_running(self) -> bool:
+        """Checks if HPLC machine is in an available state, meaning a state that data is not being written.
+
+        :return: whether the HPLC machine is in a safe state to retrieve data back."""
+        self.set_status()
+        hplc_avail = isinstance(self._most_recent_hplc_status, HPLCAvailStatus)
+        time.sleep(30)
+        self.set_status()
+        hplc_actually_avail = isinstance(self._most_recent_hplc_status, HPLCAvailStatus)
+        return hplc_avail and hplc_actually_avail
+
+    def _send(self, cmd: str, cmd_no: int, num_attempts=5) -> None:
+        """Low-level execution primitive. Sends a command string to HPLC.
+
+        :param cmd: string to be sent to HPLC
+        :param cmd_no: Command number
+        :param num_attempts: Number of attempts to send the command before raising exception.
+        :raises IOError: Could not write to command file.
+        """
+        err = None
+        for _ in range(num_attempts):
+            time.sleep(1)
+            try:
+                with open(self.cmd_file, "w", encoding="utf8") as cmd_file:
+                    cmd_file.write(f"{cmd_no} {cmd}")
+            except IOError as e:
+                err = e
+                continue
+            else:
+                return
+        else:
+            raise IOError(f"Failed to send command #{cmd_no}: {cmd}.") from err
+
+    def _receive(self, cmd_no: int, num_attempts=100) -> Result[str, str]:
+        """Low-level execution primitive. Recives a response from HPLC.
+
+        :param cmd_no: Command number
+        :param num_attempts: Number of retries to open reply file
+        :raises IOError: Could not read reply file.
+        :return: Potential ChemStation response
+        """
+        err = None
+        for _ in range(num_attempts):
+            time.sleep(1)
+
+            try:
+                with open(self.reply_file, "r", encoding="utf_16") as reply_file:
+                    response = reply_file.read()
+            except OSError as e:
+                err = e
+                continue
+
+            try:
+                first_line = response.splitlines()[0]
+                response_no = int(first_line.split()[0])
+            except IndexError as e:
+                err = e
+                continue
+
+            # check that response corresponds to sent command
+            if response_no == cmd_no:
+                return Ok(response)
+            else:
+                continue
+        else:
+            return Err(f"Failed to receive reply to command #{cmd_no} due to {err}.")
+
+    def sleepy_send(self, cmd: Union[Command, str]):
+        self.send("Sleep 0.1")
+        self.send(cmd)
+        self.send("Sleep 0.1")
+
+    def send(self, cmd: Union[Command, str]):
+        """Sends a command to Chemstation.
+
+        :param cmd: Command to be sent to HPLC
+        """
+        if self.cmd_no == self.MAX_CMD_NO:
+            self.reset_cmd_counter()
+
+        cmd_to_send: str = cmd.value if isinstance(cmd, Command) else cmd
+        self.cmd_no += 1
+        self._send(cmd_to_send, self.cmd_no)
+        f = open("out.txt", "a")
+        f.write(cmd_to_send + "\n")
+        f.close()
+
+    def receive(self) -> Result[Response, str]:
+        """Returns messages received in reply file.
+
+        :return: ChemStation response 
+        """
+        num_response_prefix = "Numerical Responses:"
+        str_response_prefix = "String Responses:"
+        possible_response = self._receive(self.cmd_no)
+        if Ok(possible_response):
+            lines = possible_response.value.splitlines()
+            for line in lines:
+                if str_response_prefix in line and num_response_prefix in line:
+                    string_responses_dirty, _, numerical_responses = line.partition(num_response_prefix)
+                    _, _, string_responses = string_responses_dirty.partition(str_response_prefix)
+                    return Ok(Response(string_response=string_responses.strip(),
+                                       num_response=float(numerical_responses.strip())))
+            return Err(f"Could not retrieve HPLC response")
+        else:
+            return Err(f"Could not establish response to HPLC: {possible_response}")
+
+    def reset_cmd_counter(self):
+        """Resets the command counter."""
+        self._send(Command.RESET_COUNTER_CMD.value, cmd_no=self.MAX_CMD_NO + 1)
+        self._receive(cmd_no=self.MAX_CMD_NO + 1)
+        self.cmd_no = 0
+
+    def stop_macro(self):
+        """Stops Macro execution. Connection will be lost."""
+        self.send(Command.STOP_MACRO_CMD)

pychemstation/control/controllers/method.py

@@ -0,0 +1,274 @@
+import os
+import time
+from typing import Optional
+
+from xsdata.formats.dataclass.parsers import XmlParser
+
+from ...control.controllers.table_controller import TableController
+from ...control.controllers.comm import CommunicationController
+from ...generated import PumpMethod, DadMethod, SolventElement
+from ...utils.chromatogram import TIME_FORMAT, AgilentChannelChromatogramData
+from ...utils.macro import Command
+from ...utils.method_types import PType, TimeTableEntry, Param, MethodTimetable, HPLCMethodParams
+from ...utils.table_types import RegisterFlag, TableOperation, Table
+
+
+class MethodController(TableController):
+    """
+    Class containing method related logic
+    """
+
+    def __init__(self, controller: CommunicationController, src: str, data_dir: str, table: Table):
+        super().__init__(controller, src, data_dir, table)
+
+    def get_method_params(self) -> HPLCMethodParams:
+        return HPLCMethodParams(organic_modifier=self.controller.get_num_val(
+            cmd=TableOperation.GET_OBJ_HDR_VAL.value.format(
+                register=self.table.register,
+                register_flag=RegisterFlag.SOLVENT_B_COMPOSITION
+            )
+        ),
+            flow=self.controller.get_num_val(
+                cmd=TableOperation.GET_OBJ_HDR_VAL.value.format(
+                    register=self.table.register,
+                    register_flag=RegisterFlag.FLOW
+                )
+            ),
+            maximum_run_time=self.controller.get_num_val(
+                cmd=TableOperation.GET_OBJ_HDR_VAL.value.format(
+                    register=self.table.register,
+                    register_flag=RegisterFlag.MAX_TIME
+                )
+            ),
+        )
+
+    def get_row(self, row: int) -> TimeTableEntry:
+        return TimeTableEntry(start_time=self.get_num(row, RegisterFlag.TIME),
+                              organic_modifer=self.get_num(row, RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION),
+                              flow=None)
+
+    def load(self) -> MethodTimetable:
+        rows = self.get_num_rows()
+        if rows.is_ok():
+            timetable_rows = [self.get_row(r + 1) for r in range(int(rows.ok_value.num_response))]
+            return MethodTimetable(
+                first_row=self.get_method_params(),
+                subsequent_rows=timetable_rows)
+        else:
+            raise RuntimeError(rows.err_value)
+
+    def current_method(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()
+        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)
+        res = self.receive()
+        if res.is_ok():
+            parsed_response = res.ok_value.string_response
+            assert parsed_response == f"{method_name}.M", "Switching Methods failed."
+
+    def load_from_disk(self, method_name: str) -> MethodTimetable:
+        """
+        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: Optional[SolventElement] = None
+            aq_modifier: Optional[SolventElement] = 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=organic_modifier.percentage,
+                    flow=method.flow,
+                    maximum_run_time=method.stop_time,
+                    temperature=-1),
+                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, save: bool):
+        """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 = Param(val=updated_method.first_row.organic_modifier,
+                                                chemstation_key=RegisterFlag.SOLVENT_B_COMPOSITION,
+                                                ptype=PType.NUM)
+        max_time: Param = Param(val=updated_method.first_row.maximum_run_time,
+                                chemstation_key=RegisterFlag.MAX_TIME,
+                                ptype=PType.NUM)
+        flow: Param = Param(val=updated_method.first_row.flow,
+                            chemstation_key=RegisterFlag.FLOW,
+                            ptype=PType.NUM)
+
+        # Method settings required for all runs
+        self.delete_table()
+        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)
+
+        if save:
+            self.send(Command.SAVE_METHOD_CMD.value.format(
+                commit_msg=f"saved method at {str(time.time())}"
+            ))
+
+    def _update_method_timetable(self, timetable_rows: list[TimeTableEntry]):
+        self.sleepy_send('Local Rows')
+        self.get_num_rows()
+
+        self.sleepy_send('DelTab RCPMP1Method[1], "Timetable"')
+        res = self.get_num_rows()
+        while not res.is_err():
+            self.sleepy_send('DelTab RCPMP1Method[1], "Timetable"')
+            res = self.get_num_rows()
+
+        self.sleepy_send('NewTab RCPMP1Method[1], "Timetable"')
+        self.get_num_rows()
+
+        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_num_rows()
+
+                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_num_rows()
+
+    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 = self.table.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 method run. A dialog window will pop up and manual intervention may be required.\
+        """
+        self.send(Command.STOP_METHOD_CMD)
+
+    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.data_dir,
+                                                      experiment_name=experiment_name,
+                                                      timestamp=timestamp))
+
+        if self.check_hplc_is_running():
+            folder_name = f"{experiment_name}_{timestamp}.D"
+            self.data_files.append(os.path.join(self.data_dir, folder_name))
+
+        run_completed = self.check_hplc_done_running()
+
+        if not run_completed.is_ok():
+            raise RuntimeError("Run did not complete as expected")
+
+    def retrieve_recent_data_files(self) -> str:
+        return self.data_files[-1]
+
+    def get_data(self) -> AgilentChannelChromatogramData:
+        self.get_spectrum(self.data_files[-1])
+        return AgilentChannelChromatogramData(**self.spectra)