Extract anatric config parsing
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from pyzebra.anatric import anatric
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from pyzebra.anatric import *
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from pyzebra.h5 import *
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from pyzebra.xtal import *
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import subprocess
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import xml.etree.ElementTree as ET
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def anatric(config_file):
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subprocess.run(["anatric", config_file], check=True)
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class AnatricConfig:
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def __init__(self, filename=None):
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if filename:
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self.load_from_file(filename)
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def load_from_file(self, filename):
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tree = ET.parse(filename)
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logfile_elem = tree.find("logfile")
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self.logfile = logfile_elem.attrib["file"]
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self.logfile_verbosity = logfile_elem.attrib["verbosity"]
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filelist_elem = tree.find("FileList")
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if filelist_elem is None:
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filelist_elem = tree.find("SinqFileList")
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self.filelist_type = "SINQ"
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else:
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self.filelist_type = "TRICS"
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self.filelist_format = filelist_elem.attrib["format"]
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self.filelist_datapath = filelist_elem.find("datapath").attrib["value"]
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range_vals = filelist_elem.find("range").attrib
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self.filelist_ranges = (int(range_vals["start"]), int(range_vals["end"]))
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crystal_elem = tree.find("crystal")
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self.crystal_sample = crystal_elem.find("Sample").attrib["name"]
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lambda_elem = crystal_elem.find("lambda")
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if lambda_elem is not None:
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self.crystal_lambda = lambda_elem.attrib["value"]
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else:
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self.crystal_lambda = None
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zeroOM_elem = crystal_elem.find("zeroOM")
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if zeroOM_elem is not None:
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self.crystal_zeroOM = zeroOM_elem.attrib["value"]
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else:
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self.crystal_zeroOM = None
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zeroSTT_elem = crystal_elem.find("zeroSTT")
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if zeroSTT_elem is not None:
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self.crystal_zeroSTT = zeroSTT_elem.attrib["value"]
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else:
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self.crystal_zeroSTT = None
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zeroCHI_elem = crystal_elem.find("zeroCHI")
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if zeroCHI_elem is not None:
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self.crystal_zeroCHI = zeroCHI_elem.attrib["value"]
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else:
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self.crystal_zeroCHI = None
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self.crystal_UB = crystal_elem.find("UB").text
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dataFactory_elem = tree.find("DataFactory")
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self.dist1 = dataFactory_elem.find("dist1").attrib["value"]
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reflectionPrinter_elem = tree.find("ReflectionPrinter")
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self.reflectionPrinter_format = reflectionPrinter_elem.attrib["format"]
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alg_elem = tree.find("Algorithm")
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self.algorithm = alg_elem.attrib["implementation"]
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if self.algorithm == "adaptivemaxcog":
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self.threshold = float(alg_elem.find("threshold").attrib["value"])
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self.shell = float(alg_elem.find("shell").attrib["value"])
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self.steepness = float(alg_elem.find("steepness").attrib["value"])
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self.duplicateDistance = float(alg_elem.find("duplicateDistance").attrib["value"])
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self.maxequal = float(alg_elem.find("maxequal").attrib["value"])
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# self.apd_window = float(alg_elem.find("window").attrib["value"])
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elif self.algorithm == "adaptivedynamic":
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# self.admi_window = float(alg_elem.find("window").attrib["value"])
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# self.border = float(alg_elem.find("border").attrib["value"])
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# self.minWindow = float(alg_elem.find("minWindow").attrib["value"])
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# self.reflectionFile = float(alg_elem.find("reflectionFile").attrib["value"])
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self.targetMonitor = float(alg_elem.find("targetMonitor").attrib["value"])
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self.smoothSize = float(alg_elem.find("smoothSize").attrib["value"])
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self.loop = float(alg_elem.find("loop").attrib["value"])
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self.minPeakCount = float(alg_elem.find("minPeakCount").attrib["value"])
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# self.displacementCurve = float(alg_elem.find("threshold").attrib["value"])
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else:
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raise ValueError("Unknown processing mode.")
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def export(self, filename):
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pass
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@ -1,5 +1,3 @@
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import xml.etree.ElementTree as ET
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from bokeh.layouts import column, row
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from bokeh.models import Button, Panel, RadioButtonGroup, Select, Spinner, TextAreaInput, TextInput
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@ -8,78 +6,45 @@ import pyzebra
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def create():
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def fileinput_callback(_attr, _old, new):
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tree = ET.parse(new)
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config = pyzebra.AnatricConfig(new)
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logfile_elem = tree.find("logfile")
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logfile_textinput.value = logfile_elem.attrib["file"]
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logfile_verbosity_select.value = logfile_elem.attrib["verbosity"]
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logfile_textinput.value = config.logfile
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logfile_verbosity_select.value = config.logfile_verbosity
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filelist_elem = tree.find("FileList")
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if filelist_elem is None:
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filelist_elem = tree.find("SinqFileList")
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filelist_type.value = "SINQ"
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else:
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filelist_type.value = "TRICS"
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filelist_type.value = config.filelist_type
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filelist_format_textinput.value = config.filelist_format
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filelist_datapath_textinput.value = config.filelist_datapath
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filelist_ranges_textareainput.value = str(config.filelist_ranges)
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filelist_format_textinput.value = filelist_elem.attrib["format"]
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filelist_datapath_textinput.value = filelist_elem.find("datapath").attrib["value"]
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range_vals = filelist_elem.find("range").attrib
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filelist_ranges_textareainput.value = str(
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(int(range_vals["start"]), int(range_vals["end"]))
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)
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crystal_sample_textinput.value = config.crystal_sample
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lambda_textinput.value = config.crystal_lambda
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zeroOM_textinput.value = config.crystal_zeroOM
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zeroSTT_textinput.value = config.crystal_zeroSTT
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zeroCHI_textinput.value = config.crystal_zeroCHI
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ub_textareainput.value = config.crystal_UB
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crystal_elem = tree.find("crystal")
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crystal_sample_textinput.value = crystal_elem.find("Sample").attrib["name"]
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dist1_textinput.value = config.dist1
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reflectionPrinter_format_select.value = config.reflectionPrinter_format
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lambda_elem = crystal_elem.find("lambda")
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if lambda_elem is not None:
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lambda_textinput.value = lambda_elem.attrib["value"]
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set_active_widgets(config.algorithm)
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if config.algorithm == "adaptivemaxcog":
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threshold_spinner.value = float(config.threshold)
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shell_spinner.value = float(config.shell)
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steepness_spinner.value = float(config.steepness)
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duplicateDistance_spinner.value = float(config.duplicateDistance)
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maxequal_spinner.value = float(config.maxequal)
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# apd_window_spinner.value = float(config.apd_window)
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zeroOM_elem = crystal_elem.find("zeroOM")
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if zeroOM_elem is not None:
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zeroOM_textinput.value = zeroOM_elem.attrib["value"]
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zeroSTT_elem = crystal_elem.find("zeroSTT")
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if zeroSTT_elem is not None:
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zeroSTT_textinput.value = zeroSTT_elem.attrib["value"]
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zeroCHI_elem = crystal_elem.find("zeroCHI")
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if zeroCHI_elem is not None:
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zeroCHI_textinput.value = zeroCHI_elem.attrib["value"]
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ub_textareainput.value = crystal_elem.find("UB").text
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dataFactory_elem = tree.find("DataFactory")
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dist1_textinput.value = dataFactory_elem.find("dist1").attrib["value"]
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reflectionPrinter_elem = tree.find("ReflectionPrinter")
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reflectionPrinter_format_select.value = reflectionPrinter_elem.attrib["format"]
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alg_elem = tree.find("Algorithm")
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if alg_elem.attrib["implementation"] == "adaptivemaxcog":
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set_active_widgets("adaptivemaxcog")
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threshold_spinner.value = float(alg_elem.find("threshold").attrib["value"])
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shell_spinner.value = float(alg_elem.find("shell").attrib["value"])
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steepness_spinner.value = float(alg_elem.find("steepness").attrib["value"])
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duplicateDistance_spinner.value = float(
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alg_elem.find("duplicateDistance").attrib["value"]
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)
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maxequal_spinner.value = float(alg_elem.find("maxequal").attrib["value"])
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# apd_window_spinner.value = float(alg_elem.find("window").attrib["value"])
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elif alg_elem.attrib["implementation"] == "adaptivedynamic":
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set_active_widgets("adaptivedynamic")
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# admi_window_spinner.value = float(alg_elem.find("window").attrib["value"])
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# .value = float(alg_elem.find("border").attrib["value"])
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# minWindow_spinner.value = float(alg_elem.find("minWindow").attrib["value"])
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# reflectionFile_spinner.value = float(alg_elem.find("reflectionFile").attrib["value"])
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targetMonitor_spinner.value = float(alg_elem.find("targetMonitor").attrib["value"])
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smoothSize_spinner.value = float(alg_elem.find("smoothSize").attrib["value"])
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loop_spinner.value = float(alg_elem.find("loop").attrib["value"])
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minPeakCount_spinner.value = float(alg_elem.find("minPeakCount").attrib["value"])
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# displacementCurve_spinner.value = float(alg_elem.find("threshold").attrib["value"])
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elif config.algorithm == "adaptivedynamic":
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# admi_window_spinner.value = float(config.admi_window)
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# border_spinner.value = float(config.border)
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# minWindow_spinner.value = float(config.minWindow)
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# reflectionFile_spinner.value = float(config.reflectionFile)
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targetMonitor_spinner.value = float(config.targetMonitor)
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smoothSize_spinner.value = float(config.smoothSize)
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loop_spinner.value = float(config.loop)
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minPeakCount_spinner.value = float(config.minPeakCount)
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# displacementCurve_spinner.value = float(config.displacementCurve)
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else:
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raise ValueError("Unknown processing mode.")
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