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

pychemstation/control/table_controller.py

@@ -0,0 +1,75 @@
+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()

pychemstation/utils/__init__.py

@@ -1,2 +0,0 @@
-from .hplc_param_types import Command, RegisterFlag, TableOperation, PType, Param, HPLCMethodParams, Entry, \
-    SequenceEntry, SequenceTable, MethodTimetable, HPLCRunningStatus, HPLCAvailStatus, HPLCErrorStatus

{ag_hplc_macro/control → pychemstation/utils}/chromatogram.py

@@ -6,8 +6,8 @@ import time
 
 import numpy as np
 
+from .parsing import CHFile
 from ..analysis import AbstractSpectrum
-from ..utils.chemstation import CHFile
 
 # Chemstation data path
 DATA_DIR = r"C:\Chem32\1\Data"
@@ -20,6 +20,7 @@ ACQUISITION_PARAMETERS = "acq.txt"
 
 # format used in acquisition parameters
 TIME_FORMAT = "%Y-%m-%d-%H-%M-%S"
+SEQUENCE_TIME_FORMAT = "%Y-%m-%d %H"
 
 
 class AgilentHPLCChromatogram(AbstractSpectrum):

pychemstation/utils/constants.py

@@ -1,4 +1,4 @@
-from pychemstation.utils.hplc_param_types import Table
+from ..utils.table_types import Table
 
 # maximum command number
 MAX_CMD_NO = 255

hein_analytical_control/devices/Agilent/hplc_param_types.py → pychemstation/utils/macro.py

@@ -1,8 +1,5 @@
-from dataclasses import dataclass
 from enum import Enum
-from typing import Union, Any
-
-from ...generated import SolventElement, Signal
+from typing import Union
 
 
 # Commands sent to the Chemstation Macro
@@ -27,71 +24,10 @@ class Command(Enum):
     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
+    SWITCH_SEQUENCE_CMD = 'LoadSequence _SeqPath$, _SeqFile$'
+    SAVE_SEQUENCE_CMD = 'SaveSequence _SeqPath$, _SeqFile$'
+    GET_SEQUENCE_CMD = 'response$ = _SeqFile$'
+    RUN_SEQUENCE_CMD = 'RunSequence'
 
 
 class HPLCRunningStatus(Enum):

pychemstation/utils/method_types.py

@@ -0,0 +1,44 @@
+from dataclasses import dataclass
+from enum import Enum
+from typing import Union, Any, Optional
+
+from .table_types import RegisterFlag
+from ..generated import Signal, SolventElement
+
+
+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 TimeTableEntry:
+    start_time: float
+    organic_modifer: float
+    flow: float
+
+
+@dataclass
+class MethodTimetable:
+    first_row: HPLCMethodParams
+    subsequent_rows: list[TimeTableEntry]
+    dad_wavelengthes: Optional[list[Signal]] = None
+    organic_modifier: Optional[SolventElement] = None
+    modifier_a: Optional[SolventElement] = None

pychemstation/utils/sequence_types.py

@@ -0,0 +1,33 @@
+from dataclasses import dataclass
+from enum import Enum
+from typing import Optional
+
+
+class SampleType(Enum):
+    SAMPLE = 1
+    BLANK = 2
+    CONTROL = 3
+    CALIBRATION = 4
+
+
+class InjectionSource(Enum):
+    AS_METHOD = "AsMethod"
+    MANUAL = "Manual"
+    HIP_ALS = "HipAls"
+
+
+@dataclass
+class SequenceEntry:
+    vial_location: Optional[int] = None
+    method: Optional[str] = None
+    num_inj: Optional[int] = 1
+    inj_vol: Optional[int] = 2
+    inj_source: Optional[InjectionSource] = InjectionSource.HIP_ALS
+    sample_name: Optional[str] = None
+    sample_type: Optional[SampleType] = SampleType.SAMPLE
+
+
+@dataclass
+class SequenceTable:
+    name: str
+    rows: list[SequenceEntry]

pychemstation/utils/table_types.py

@@ -0,0 +1,60 @@
+from dataclasses import dataclass
+from enum import Enum
+
+
+class TableOperation(Enum):
+    def __str__(self):
+        return '%s' % self.value
+
+    DELETE_TABLE = 'DelTab {register}, "{table_name}"'
+    CREATE_TABLE = 'NewTab {register}, "{table_name}"'
+    NEW_ROW = 'InsTabRow {register}, "{table_name}"'
+    EDIT_ROW_VAL = 'SetTabVal "{register}", "{table_name}", {row}, "{col_name}", {val}'
+    EDIT_ROW_TEXT = 'SetTabText "{register}", "{table_name}", {row}, "{col_name}", "{val}"'
+    GET_ROW_VAL = 'TabVal ("{register}", "{table_name}", {row}, "{col_name}")'
+    GET_ROW_TEXT = 'TabText ("{register}", "{table_name}", {row}, "{col_name}")'
+    GET_OBJ_HDR_VAL = '{internal_val} = TabHdrVal({register}, "{table_name}", "{col_name}")'
+    GET_OBJ_HDR_TEXT = ''
+    UPDATE_OBJ_HDR_VAL = 'SetObjHdrVal {register}, {register_flag}, {val}'
+    UPDATE_OBJ_HDR_TEXT = 'SetObjHdrText {register}, {register_flag}, {val}'
+    NEW_COL_TEXT = 'NewColText {register}, "{table_name}", "{col_name}", "{val}"'
+    NEW_COL_VAL = 'NewColVal {register}, "{table_name}", "{col_name}", {val}'
+
+
+class RegisterFlag(Enum):
+    def __str__(self):
+        return '%s' % self.value
+
+    # for table
+    NUM_ROWS = "NumberOfRows"
+
+    # for Method
+    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"
+
+    # for Method Timetable
+    SOLVENT_COMPOSITION = "SolventComposition"
+
+    # for Sequence
+    VIAL_LOCATION = "Vial"
+    NAME = "SampleName"
+    METHOD = "Method"
+    INJ_VOL = "InjVolume"
+    INJ_SOR = "InjectionSource"
+    NUM_INJ = "InjVial"
+    SAMPLE_TYPE = "SampleType"
+    DATA_FILE = "DataFileName"
+
+
+@dataclass
+class Table:
+    register: str
+    name: str

{pychemstation-0.4.7.dev1.dist-info → pychemstation-0.4.7.dev2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.4.7.dev1
+Version: 0.4.7.dev2
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Home-page: https://gitlab.com/heingroup/pychemstation
 Author: Lucy Hao
@@ -15,8 +15,9 @@ Requires-Dist: seabreeze
 
 # Agilent HPLC Macro Control
 
-[![PyPI Downloads](https://img.shields.io/pypi/dm/hein-analytical-control.svg?label=PyPI%20downloads)](https://pypi.org/project/hein-analytical-control)
-[![PyPI Latest Release](https://img.shields.io/pypi/v/hein-analytical-control.svg)](https://pypi.org/project/hein-analytical-control/)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/pychemstation)
+
+[![PyPI Latest Release](https://img.shields.io/pypi/v/pychemstation.svg)](https://pypi.org/project/pychemstation/)
 
 Unofficial Python package to control Agilent Chemstation; we are not affiliated with Agilent.
 Check out the [docs](https://hein-analytical-control-5e6e85.gitlab.io/) for usage instructions. This project is under
@@ -58,7 +59,7 @@ HPLCTalk_Run
 ## Example Usage
 
 ```python
-from pychemstation.control import HPLCController
+from pychemstation.control import HPLCController, MethodController, SequenceController
 import pandas as pd
 
 # these paths will be unique to your Chemstation setup
@@ -67,17 +68,17 @@ DATA_DIR = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
 DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\hplc-method-optimization\\tests"
 
 hplc_controller = HPLCController(data_dir=DATA_DIR,
-                                 comm_dir=DEFAULT_COMMAND_PATH,
-                                 method_dir=DEFAULT_METHOD_DIR)
+                                 comm_dir=DEFAULT_COMMAND_PATH)
+method_controller = MethodController(controller=hplc_controller,
+                                     src=DEFAULT_METHOD_DIR)
 
 hplc_controller.preprun()
-hplc_controller.switch_method(method_name="General-Poroshell")
-hplc_controller.run_method(experiment_name="Run 10")
-data_ready = hplc_controller.check_hplc_ready_with_data()
+method_controller.switch(method_name="General-Poroshell")
+method_controller.run(experiment_name="Run 10")
+data_ready = method_controller.data_ready()
 
 if data_ready:
-    hplc_controller.get_spectrum()
-    chrom = hplc_controller.spectra["A"]
+    chrom = method_controller.get_data()
     # afterwards, save, analyze or plot the data!
     values = {"x": chrom.x, "y": chrom.y}
     chromatogram_data = pd.DataFrame.from_dict(values)
@@ -92,7 +93,7 @@ put the file in the `user.mac` file and then list the function you want to use.
 ## Developing
 
 If you would like to contribute to this project, check out
-our [GitLab](https://gitlab.com/heingroup/hein-analytical-control)!
+our [GitLab](https://gitlab.com/heingroup/device-api/pychemstation)!
 
 ## Authors and Acknowledgements
 

pychemstation-0.4.7.dev2.dist-info/RECORD

@@ -0,0 +1,30 @@
+pychemstation/__init__.py,sha256=SpTl-Tg1B1HTyjNOE-8ue-N2wGnXN_2zl7RFUSxlkiM,33
+pychemstation/analysis/__init__.py,sha256=EWoU47iyn9xGS-b44zK9eq50bSjOV4AC5dvt420YMI4,44
+pychemstation/analysis/base_spectrum.py,sha256=FBvwzLtF9mdqW7f8ETY9G4cpfJ-SzbiSkZq9EtXcSXo,17045
+pychemstation/analysis/spec_utils.py,sha256=8NZMV0dtfxZLARjWzM5ks0tgEYQv_SKUiZzba2IoKgw,10505
+pychemstation/analysis/utils.py,sha256=ISupAOb_yqA4_DZRK9v18UL-XjUQccAicIJKb1VMnGg,2055
+pychemstation/control/__init__.py,sha256=Azsalc8Pz1PuygH7CoTzRV8xQOSfET6zd72AMAB7irE,142
+pychemstation/control/chromatogram.py,sha256=c4_RGconn4vYU9wyS0WX-GB5FlwnBf_sfVLh_GpeehE,3716
+pychemstation/control/comm.py,sha256=iuzeFLZ_BhNVJwyNJjDiUuaoQBQpFFc0rHiRk0qOgnk,9976
+pychemstation/control/hplc.py,sha256=GvEL2zxz0_V47E_JrP4ePTUc8FahDDT3PYmd7ASbobA,29746
+pychemstation/control/method.py,sha256=h9KcccDtqx0hQT7JaUc1TWCB8d21t0McOuzeBsEsh4c,10977
+pychemstation/control/sequence.py,sha256=ewc7l44VAtv3wHV2QgOILu5Ny3gmubHuEeHJN9N6OjQ,7511
+pychemstation/control/table_controller.py,sha256=83i1J2CvIrJ3NtAB_E46qhUe8MvXo1_GnDPmuiq-vSA,2957
+pychemstation/generated/__init__.py,sha256=GAoZFAYbPVEJDkcOw3e1rgOqd7TCW0HyKNPM8OMehMg,1005
+pychemstation/generated/dad_method.py,sha256=0W8Z5WDtF5jpIcudMqb7XrkTnR2EGg_QOCsHRFQ0rmM,8402
+pychemstation/generated/pump_method.py,sha256=sUhE2Oo00nzVcoONtq3EMWsN4wLSryXbG8f3EeViWKg,12174
+pychemstation/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pychemstation/utils/chemstation.py,sha256=bnFIsZZwFy9NKzVUf517yN-ogzQbm0hp_aho3KUD6Is,9317
+pychemstation/utils/chromatogram.py,sha256=X-D-FdMwHPugrqAtp5vfPPbD_aU3gor3G6WjQzvEuSk,3742
+pychemstation/utils/constants.py,sha256=jLY-NixemSofukzSXJhAIU4aO2IJmBRAhAcq5066mFI,249
+pychemstation/utils/hplc_param_types.py,sha256=xvmsbYQp3iiS1-0-9eUy--5zk_wE1bkrlHEHSm0UC18,5206
+pychemstation/utils/macro.py,sha256=y_ynL_A-FqK3v4-StTmmbUd741vWhjm6kmduVi5IUfE,2212
+pychemstation/utils/method_types.py,sha256=PSVbKq1IHL4QJNSEl0Szaymfvm3sfXy1rqjT2W_qbN0,911
+pychemstation/utils/parsing.py,sha256=bnFIsZZwFy9NKzVUf517yN-ogzQbm0hp_aho3KUD6Is,9317
+pychemstation/utils/sequence_types.py,sha256=sin3X37EQb52CAGY2MOzY4Us9tdLg7FScTGMBWAF5Fs,689
+pychemstation/utils/table_types.py,sha256=BBCRoz1R6zPV1i2u2Tdku7WwIp6EDv1rUuZVPVNgO1A,2090
+pychemstation-0.4.7.dev2.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
+pychemstation-0.4.7.dev2.dist-info/METADATA,sha256=QuJvRtOpyJboxO9qPJFi_VbuUw4JP2UTczqXWRz2iW0,3929
+pychemstation-0.4.7.dev2.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+pychemstation-0.4.7.dev2.dist-info/top_level.txt,sha256=ONCqQRPu9Z4_k7TOvj64NVTmO8CqMg_PITePUzYchdY,14
+pychemstation-0.4.7.dev2.dist-info/RECORD,,

ag_hplc_macro/__init__.py

@@ -1,3 +0,0 @@
-"""
-.. include:: ../README.md
-"""

ag_hplc_macro/analysis/__init__.py

@@ -1 +0,0 @@
-from .base_spectrum import AbstractSpectrum