add files

added files for SIMSEF tool. Bruker library and code referring to said library removed due to bruker restrictions

src/AcquisitionControl.py

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+import os
+import shutil
+
+from src.AcquisitionParameters import AcquisitionParameters
+from src.InstrumentController import InstrumentController
+
+
+class AcquisitionControl:
+    # controller: InstrumentController
+
+    def __init__(self):
+        self.controller = InstrumentController()
+
+    def runAcquisition(self, parameters: AcquisitionParameters):
+        if not os.path.exists(parameters.path):
+            os.mkdir(parameters.path)
+
+        # copy precursor file
+        shutil.copyfile(parameters.precursorList, "C:/BDalSystemData/timsTOF/maldi/maldi_tims_precursors.csv")
+
+        # if acqtype == 'accumulate':
+        #     controller.setAppendAcquisition(True)
+        # else:
+        #     controller.setAppendAcquisition(False)
+
+        if parameters.laserOffsetX is not None and parameters.laserOffsetY is not None:
+            self.controller.setLaserOffset(parameters.laserOffsetX, parameters.laserOffsetY)
+
+        self.controller.directory = parameters.path
+        self.controller.sampleName = parameters.name
+
+        if parameters.geometry is not None:
+            self.controller.maldiControl.selectGeometry(parameters.geometry)
+
+        if parameters.ceTable is not None and os.path.exists(parameters.ceTable):
+            self.controller.readAndSetCeTable(parameters.ceTable)
+
+        if parameters.isowdith is not None:
+            self.controller.overrideIsolationWidth(parameters.isowdith)
+
+        self.controller.moveToSpotAndWait(parameters.spot, parameters.xOffset, parameters.yOffset)
+        self.controller.singleSpotAcquisition()
+        if(os.path.isfile("C:/BDalSystemData/timsTOF/maldi/maldi_tims_precursors.csv")):
+            os.remove("C:/BDalSystemData/timsTOF/maldi/maldi_tims_precursors.csv")
+
+        # self.controller.snapshot()

src/AcquisitionParameters.py

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+import argparse
+
+
+class AcquisitionParameters:
+    # spot: str
+    # xOffset: int
+    # yOffset: int
+    # path: str
+    # name: str
+    # geometry: str
+    # laserOffsetX: int
+    # laserOffsetY: int
+    # acqtype: str
+    # ceTable: str
+
+    def __init__(self, args):
+        parser = argparse.ArgumentParser(description="timsTOF Maldi controller")
+
+        parser.add_argument('--spot', required=True, type=str, help="The spot on a 384 target plate to be measured")
+        parser.add_argument('--xoffset', required=True, type=int, help="The offset in x dimension")
+        parser.add_argument('--yoffset', required=True, type=int, help="The offset in y dimension")
+        parser.add_argument('--path', required=True, type=str, help="The parent directory to store the analysis in.")
+        parser.add_argument('--name', required=True, type=str, help="The name of the analysis.")
+        parser.add_argument('--acqtype', required=False, choices=['accumulate', 'single'],
+                            help="Specifies how the data shall be handled.\n"
+                                 "\"accumulate\" = add to current acquisition.\n" +
+                                 "\"single\" = store as single file (default).\n", default='single')
+        parser.add_argument('--cetable', required=False,
+                            help="Path to csv file with collision energy settings. Must contain columns \'mass\' (decimal), " +
+                                 "\'iso_width\' (decimal), \'ce\' (decimal), \'type\' (0=base or 1=fixed) ")
+        parser.add_argument('--geometry', required=False, type=str,
+                            help="Speficy a sample carrier geometry to select specific spots.")
+        parser.add_argument('--laseroffsetx', required=False, type=int, help="Specifies a laser offset in x dimension",
+                            default=None)
+        parser.add_argument('--laseroffsety', required=False, type=int, help="Specifies a laser offset in y dimension",
+                            default=None)
+        parser.add_argument('--precursorlist', required=True, type=str,
+                            help="Path to csv file containing the list of precursors for this spot")
+        parser.add_argument('--isolationwidth', required=False, type=float, default=None,
+                            help="Manually sets the isolation width in the MALDI mode. Overrides the isolation given in the CE table (if there is one).")
+
+        arguments = parser.parse_args(args)
+
+        # make a valid path so we can concatenate
+        if not arguments.path[len(arguments.path) - 1] == '/':
+            arguments.path = arguments.path + '/'
+
+        self.spot: str = arguments.spot
+        self.xOffset: int = arguments.xoffset
+        self.yOffset: int = arguments.yoffset
+        self.path: str = arguments.path
+        self.name: str = arguments.name
+        self.geometry: str = arguments.geometry
+        self.laserOffsetX: int = arguments.laseroffsetx
+        self.laserOffsetY: int = arguments.laseroffsety
+        self.acqtype: str = arguments.acqtype
+        self.ceTable = arguments.cetable
+        self.precursorList = arguments.precursorlist
+        self.isowdith = arguments.isolationwidth
+
+        # print(str(arguments))
+
+    def fromArgs(spot: str, path: str, name: str, precursorList: str, xOffset: int = 0, yOffset: int = 0,
+                 geometry: str = None, laserOffsetX: int = 0, laserOffsetY: int = 0, acqtype: str = "single",
+                 ceTable: str = None, isowidth: float = None):
+        # self.ceTable = ceTable
+        # self.laserOffsetY = laserOffsetY
+        # self.laserOffsetX = laserOffsetX
+        # self.yOffset = yOffset
+        # self.xOffset = xOffset
+        # self.spot = spot
+        # self.path = path
+        # self.geometry = geometry
+        # self.name = name
+        # self.acqtype = acqtype
+        return AcquisitionParameters(
+            ["--spot", spot, "--path", path, "--name", name, "--xoffset", xOffset, "--yoffset", yOffset, "--geometry",
+             geometry, "--laserOffsetX", laserOffsetX, "--laserOffsetY", laserOffsetY, "--acqtype", acqtype,
+             "--cetable", ceTable, "--precursorlist", precursorList, "--isolationwidth", isowidth])

src/simsef_pewpew.py

@@ -0,0 +1,136 @@
+import subprocess
+import sys
+import time
+import argparse
+import os
+import shutil
+from datetime import datetime
+import sys
+from PyQt5.QtWidgets import QApplication, QWidget, QTextEdit, QPushButton, QVBoxLayout, QHBoxLayout, QFileDialog
+from PyQt5.QtGui import QPalette, QColor
+from PyQt5.QtCore import Qt
+
+# instrument specific imports
+from src.AcquisitionControl import AcquisitionControl
+from src.AcquisitionParameters import AcquisitionParameters
+
+def main():
+    app = QApplication(sys.argv)
+
+    # Create a QWidget object (a window)
+    window = QWidget()
+    window.setGeometry(100, 100, 300, 200)  # Set the position and size of the window
+    window.setWindowTitle('SIMSEF pewpew')  # Set the window title
+
+    # Create a QTextEdit object (a text area)
+    global text_area
+    text_area = QTextEdit()
+    text_area.setPlaceholderText('Please select a file')
+
+    # Create two QPushButton objects (buttons)
+    button1 = QPushButton('Select command file')
+    button2 = QPushButton('Run acquisition')
+
+    # Define a function to handle the button1 click event
+    def open_file_dialog():
+        file_dialog = QFileDialog()
+        file_dialog.setNameFilter("Text file (*.txt)")
+        file_path = file_dialog.getOpenFileName(window, 'Select command file')[0]
+        if file_path:
+            text_area.setText(file_path)
+
+    # Connect the button1 click event to the open_file_dialog function
+    button1.clicked.connect(open_file_dialog)
+
+    # Connect the button2 click event to the run_function function
+    button2.clicked.connect(run_function)
+
+    # Create a QVBoxLayout object to arrange the widgets vertically
+    layout = QVBoxLayout()
+    layout.addWidget(text_area)
+    layout.addWidget(button1)
+
+    # Create a QHBoxLayout object to arrange the buttons horizontally
+    button_layout = QHBoxLayout()
+    button_layout.addWidget(button1)
+    button_layout.addWidget(button2)
+    layout.addLayout(button_layout)
+
+    # Set the dark mode stylesheet
+    dark_palette = QPalette()
+    dark_palette.setColor(QPalette.Window, QColor(53, 53, 53))
+    dark_palette.setColor(QPalette.WindowText, Qt.white)
+    dark_palette.setColor(QPalette.Base, QColor(25, 25, 25))
+    dark_palette.setColor(QPalette.AlternateBase, QColor(53, 53, 53))
+    dark_palette.setColor(QPalette.ToolTipBase, Qt.white)
+    dark_palette.setColor(QPalette.ToolTipText, Qt.white)
+    dark_palette.setColor(QPalette.Text, Qt.white)
+    dark_palette.setColor(QPalette.Button, QColor(53, 53, 53))
+    dark_palette.setColor(QPalette.ButtonText, Qt.white)
+    dark_palette.setColor(QPalette.BrightText, Qt.red)
+    dark_palette.setColor(QPalette.Link, QColor(42, 130, 218))
+    dark_palette.setColor(QPalette.Highlight, QColor(42, 130, 218))
+    dark_palette.setColor(QPalette.HighlightedText, Qt.black)
+    app.setPalette(dark_palette)
+
+    # Apply the stylesheet to the widgets
+    style_sheet = """
+    QTextEdit {
+        background-color: #252525;
+        color: white;
+        border: 1px solid #444444;
+    }
+
+    QPushButton {
+        background-color: #333333;
+        color: white;
+        border: 1px solid #444444;
+    }
+
+    QPushButton:hover {
+        background-color: #444444;
+    }
+    """
+    window.setStyleSheet(style_sheet)
+
+    window.setLayout(layout)
+
+    window.show()  # Show the window
+
+    sys.exit(app.exec_())
+
+def run_function():
+
+    # Your code here
+    # text_area.append('Button 2 was clicked!')
+    # create Parameters
+    control = AcquisitionControl()
+
+    # parser = argparse.ArgumentParser()
+    # parser.add_argument('--commandfile', help='the path to command file', type=str, required=True)
+    # argtable = parser.parse_args()
+    commandFilePath = text_area.toPlainText()
+
+    with open(commandFilePath) as f:
+        lines = f.readlines()
+
+        measured = 0
+        starttime = datetime.now()
+        for line in lines:
+            line = line.strip()
+            args = line.split(" ")
+            parameters = AcquisitionParameters(args)
+            control.runAcquisition(parameters)
+
+            control.controller.waitUntilAcqFinished()
+
+            measured = measured + 1
+            elapsedTime = datetime.now() - starttime
+            text_area.append('Acquired MS/MS in spot ' + parameters.spot + ' ' + str(measured) + '/' + str(len(lines)))
+
+            remaining = (elapsedTime / measured) * (len(lines) - measured)
+            text_area.append('Time elapsed: ' + str(elapsedTime) + ' Remaining: ' + str(remaining))
+
+
+if __name__ == "__main__":
+    main()