Add placeholder functions to xrd/io.py
This commit is contained in:
rasmusvt
parent
65a5497970
commit
5c977cc387
3 changed files with 315 additions and 6 deletions
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@ -3,6 +3,12 @@ import pandas as pd
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import numpy as np
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import os
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import zipfile
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import io
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import sys
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import glob
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import xml.etree.ElementTree as ET
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def get_image_array(path):
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@ -141,3 +147,312 @@ def view_integrator(calibrant):
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print("\nIntegrator: \n", ai)
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def brml_reader(file_name):
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"""
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From: https://github.com/aboulle/DxTools/blob/master/data_reader.py
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Extracts brml into a temporary unzip file, and parses all xml files.
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For every intensity value, saves all relevant motor coordinates and sensor values.
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All values are save in temporary SPEC-style tmp file.
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"""
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#*****************************************************************************************************
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# Unzip xml files
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#*****************************************************************************************************
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extract_path = os.path.join(os.getcwd(),"unzip")
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if sys.platform == "win32":
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print("Detected platform: Windows")
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os.system("RMDIR "+ extract_path +" /s /q")
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elif sys.platform == "darwin":
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print("Detected platform: MacOS")
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os.system("rm -rf "+ extract_path)
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elif sys.platform == "linux" or sys.platform == "linux2":
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print("Detected platform: Linux")
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os.system("rm -rf "+ extract_path)
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#Extract all RawData*.xml files and InstructionContainer the brml to temporary unzip file
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with zipfile.ZipFile(file_name,"r") as brml:
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for info in brml.infolist():
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if ("RawData" in info.filename) or ("InstructionContainer" in info.filename):
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#if ("RawData" in info.filename):
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brml.extract(info.filename, extract_path)
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#*****************************************************************************************************
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# For time counting, the number of days is initialized to 0.
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# Compatibility fixes with D8 advance and older Discover: offsets, chi and tx, ty are initialized to 0
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#*****************************************************************************************************
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# Initialize the number of days to 0
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n_day = 0.
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# Initialize all offsets to 0
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off_tth = off_om = off_phi = off_chi = off_tx = off_ty = 0
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# Set Chi, tx and ty to 0 for D8 advance (July 2017 Julia Stroh)
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chi = tx = ty = "0"
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#*****************************************************************************************************
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#Modification June 2017 (Duc Dinh)
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#In some RawData.xml files, wavelength and static motors are missing.
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#Find wl and static motors in MeasurementContainer.xml
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#*****************************************************************************************************
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data_path = os.path.join(extract_path, "*0","InstructionContainer.xml")
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for file in sorted(glob.glob(data_path)):
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tree = ET.parse(file)
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root = tree.getroot()
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for chain in root.findall("./ComparisonMethod/HrxrdAlignmentData"):
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wl = chain.find("WaveLength").attrib["Value"]
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for chain in root.findall("./ComparisonMethod/HrxrdAlignmentData/Data"):
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if chain.get("LogicName") == "TwoTheta":
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tth = chain.find("TheoreticalPosition").attrib["Value"]
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off_tth = chain.find("PositionOffset").attrib["Value"]
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tth = str(float(tth)-float(off_tth))
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if chain.get("LogicName") == "Theta":
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om = chain.find("TheoreticalPosition").attrib["Value"]
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off_om = chain.find("PositionOffset").attrib["Value"]
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om = str(float(om)-float(off_om))
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if chain.get("LogicName") == "Chi":
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chi = chain.find("TheoreticalPosition").attrib["Value"]
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off_chi = chain.find("PositionOffset").attrib["Value"]
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chi = str(float(chi)-float(off_chi))
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if chain.get("LogicName") == "Phi":
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phi = chain.find("TheoreticalPosition").attrib["Value"]
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off_phi = chain.find("PositionOffset").attrib["Value"]
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phi = str(float(phi)-float(off_phi))
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if chain.get("LogicName") == "X":
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tx = chain.find("TheoreticalPosition").attrib["Value"]
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off_tx = chain.find("PositionOffset").attrib["Value"]
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tx = str(float(tx)-float(off_tx))
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if chain.get("LogicName") == "Y":
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ty = chain.find("TheoreticalPosition").attrib["Value"]
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off_ty = chain.find("PositionOffset").attrib["Value"]
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ty = str(float(ty)-float(off_ty))
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os.remove(file)
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#Create ouput file
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outfile = open("tmp", "w", encoding='utf8') # Create output data file
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outfile.write("#temperature khi phi x y theta offset 2theta scanning motor intensity time\n")
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#*****************************************************************************************************
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# Finds scan type, wl, scanning motors and fixed motors values in RawData*.xml
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#*****************************************************************************************************
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data_path = os.path.join(extract_path, "*0","*.xml") #reading files in Experiment0 folder
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for file in sorted(glob.glob(data_path), key=file_nb):
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new_file = 0
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check_temperature = 0
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check_1Dmode = 0
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#parsing XML file
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tree = ET.parse(file)
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root = tree.getroot()
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#obtain scan type
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for chain in (root.findall("./DataRoutes/DataRoute/ScanInformation") or root.findall("./ScanInformation")):
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scan_type = chain.get("VisibleName")
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if ("PSD" in scan_type) or ("Psd" in scan_type):
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scan_type = "PSDFIXED"
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if ("Coupled" in scan_type) or ("coupled" in scan_type) or ("2Theta-Omega" in scan_type):
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scan_type = "COUPLED"
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if ("Rocking" in scan_type) or ("rocking" in scan_type):
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scan_type = "THETA"
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# Check if temperature is recorded
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for chain in (root.findall("./DataRoutes/DataRoute/DataViews/RawDataView/Recording") or root.findall("./DataViews/RawDataView/Recording")):
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if "Temperature" in chain.get("LogicName"):
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check_temperature = 1
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#Find wl in RawData.xml
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for chain in root.findall("./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1"):
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wl = chain.get("Value")
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# Find the fast-scanning axis
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for chain in (root.findall("./DataRoutes/DataRoute/ScanInformation/ScanAxes/ScanAxisInfo") or root.findall("./ScanInformation/ScanAxes/ScanAxisInfo")):
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if new_file == 0:
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if chain.get("AxisName") == "TwoTheta": #Added offset correction / June 2017. Only relevant if offset in InstructionContainer. 0 otherwise.
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off_scan = float(off_tth)
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elif chain.get("AxisName") == "Theta":
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off_scan = float(off_om)
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else:
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off_scan = 0
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step = chain.find("Increment").text
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start = chain.find("Start").text
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stop = chain.find("Stop").text
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ref = chain.find("Reference").text
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start = str(float(ref)+float(start)-off_scan) #Added offset correction / June 2017.
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#start = str(float(ref)+float(start))
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new_file += 1
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# Find scanning motors
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for chain in (root.findall("./DataRoutes/DataRoute/ScanInformation/ScanAxes/ScanAxisInfo") or root.findall("./ScanInformation/ScanAxes/ScanAxisInfo")):
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if chain.get("AxisName") == "TwoTheta":
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tth = chain.find("Start").text
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ref = chain.find("Reference").text
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tth = str(float(ref)+float(tth)-float(off_tth)) #Added offset correction / June 2017.
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#tth = str(float(ref)+float(tth))
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if chain.get("AxisName") == "Theta":
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om = chain.find("Start").text
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ref = chain.find("Reference").text
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om = str(float(ref)+float(om)-float(off_om)) #Added offset correction / June 2017.
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#om = str(float(ref)+float(om))
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if chain.get("AxisName") == "Chi":
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chi = chain.find("Start").text
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ref = chain.find("Reference").text
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chi = str(float(ref)+float(chi)-float(off_chi)) #Added offset correction / June 2017.
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#chi = str(float(ref)+float(chi))
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if chain.get("AxisName") == "Phi":
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phi = chain.find("Start").text
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ref = chain.find("Reference").text
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phi = str(float(ref)+float(phi)-float(off_phi)) #Added offset correction / June 2017.
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#phi = str(float(ref)+float(phi))
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if chain.get("AxisName") == "X":
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tx = chain.find("Start").text
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ref = chain.find("Reference").text
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tx = str(float(ref)+float(tx)-float(off_tx)) #Added offset correction / June 2017.
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#tx = str(float(ref)+float(tx))
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if chain.get("AxisName") == "Y":
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ty = chain.find("Start").text
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ref = chain.find("Reference").text
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ty = str(float(ref)+float(ty)-float(off_ty)) #Added offset correction / June 2017.
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#ty = str(float(ref)+float(ty))
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# Find static motors
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for chain in root.findall("./FixedInformation/Drives/InfoData"):
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if chain.get("LogicName") == "TwoTheta":
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tth = chain.find("Position").attrib["Value"]
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tth = str(float(tth)-float(off_tth)) #Added offset correction / June 2017.
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if chain.get("LogicName") == "Theta":
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om = chain.find("Position").attrib["Value"]
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om = str(float(om)-float(off_om)) #Added offset correction / June 2017.
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if chain.get("LogicName") == "Chi":
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chi = chain.find("Position").attrib["Value"]
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chi = str(float(chi)-float(off_chi)) #Added offset correction / June 2017.
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if chain.get("LogicName") == "Phi":
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phi = chain.find("Position").attrib["Value"]
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phi = str(float(phi)-float(off_phi)) #Added offset correction / June 2017.
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if chain.get("LogicName") == "X":
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tx = chain.find("Position").attrib["Value"]
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tx = str(float(tx)-float(off_tx)) #Added offset correction / June 2017.
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if chain.get("LogicName") == "Y":
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ty = chain.find("Position").attrib["Value"]
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ty = str(float(ty)-float(off_ty)) #Added offset correction / June 2017.
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offset = str(float(om) - float(tth)/2.)
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#*****************************************************************************************************
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# This section computes scanning time, scanning angular range and scanning speed
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# in order to convert 2th values to time values (July 2017, Julia Stroh)
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#*****************************************************************************************************
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for chain in (root.findall("./TimeStampStarted")):
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d_start = ((chain.text).split("T")[0]).split("-")[2]
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t_start = ((chain.text).split("T")[1]).split("+")[0]
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h_start, min_start, sec_start = t_start.split(":")
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t_start = float(h_start)*3600 + float(min_start)*60 + float(sec_start)
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if file_nb(file)==0:
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abs_start = t_start
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for chain in (root.findall("./TimeStampFinished")):
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d_stop = ((chain.text).split("T")[0]).split("-")[2]
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t_stop = ((chain.text).split("T")[1]).split("+")[0]
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h_stop, min_stop, sec_stop = t_stop.split(":")
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t_stop = float(h_stop)*3600 + float(min_stop)*60 + float(sec_stop)
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# Check if detector is in 1D mode
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for chain in (root.findall("./DataRoutes/DataRoute/ScanInformation") or root.findall("./ScanInformation")):
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if chain.find("TimePerStep").text != chain.find("TimePerStepEffective").text:
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check_1Dmode = 1
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# Check if day changed between start and stop and correct accordingly
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if d_stop != d_start:
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t_stop += 24*3600.
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total_scan_time = t_stop - t_start
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#scanning range
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dth_scan = float(stop)-float(start)
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#psd range
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dth_psd = 0
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for chain in root.findall("./FixedInformation/Detectors/InfoData/AngularOpening"):
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dth_psd = chain.get("Value")
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total_dth = float(dth_psd)*check_1Dmode+float(dth_scan)
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scan_speed = total_dth / total_scan_time
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#*****************************************************************************************************
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# Finds intensity values. If temperature is recorded, also fin temperature values.
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# The intensity data is formatted differently in PSDfixed mode and when temperature is recorded
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#*****************************************************************************************************
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if "PSDFIXED" in scan_type:
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if check_temperature == 0:
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for chain in (root.findall("./DataRoutes/DataRoute") or root.findall("./")):
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intensity = (chain.find("Datum").text).split(',')
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for chain in (root.findall("./DataRoutes/DataRoute/DataViews/RawDataView/Recording") or root.findall("./DataViews/RawDataView/Recording")):
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if chain.get("LogicName") == "Counter1D":
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n_channels = int(chain.find("Size/X").text)
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line_count = 0
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int_shift = len(intensity) - n_channels
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for i in range(n_channels): #the intensity values are shifted to the right by int_shift
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if i == 0:
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scanning = float(start)
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else:
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scanning += float(step)
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line_count += 1
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t_2th = (t_start+n_day*24*3600 - abs_start)+((float(dth_psd)*check_1Dmode + scanning - float(start)) / scan_speed)
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outfile.write("25" + " " + (chi) + " " + (phi)
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+ " " + (tx) + " " + (ty) + " " + (om)
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+ " " + (offset) + " " + (tth) + " " + str(scanning)
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+ " " + intensity[i+int_shift] +" " + str(t_2th) +'\n')
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else:
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return implementation_warning, 0, 0
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#if "COUPLED" in scan_type:
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# to do check in brml that all scans (except psd fixed) share the same data structure (wrt temperature)
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else:
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if check_temperature == 0:
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line_count = 0
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for chain in (root.findall("./DataRoutes/DataRoute/Datum") or root.findall("./Datum")):
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if line_count == 0:
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scanning = float(start)
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else:
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scanning += float(step)
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line_count += 1
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intensity = (chain.text).split(',')[-1]
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#compute time corresponding to scanning angle (July 2017)
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t_2th = (t_start+n_day*24*3600 - abs_start)+((float(dth_psd)*check_1Dmode + scanning - float(start)) / scan_speed)
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outfile.write("25" + " " + (chi) + " " + (phi)
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+ " " + (tx) + " " + (ty) + " " + (om)
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+ " " + (offset) + " " + (tth) + " " + str(round(scanning, 4))
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+ " " + intensity + " " + str(t_2th) +'\n')
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else:
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line_count = 0
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for chain in (root.findall("./DataRoutes/DataRoute/Datum") or root.findall("./Datum")):
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if line_count == 0:
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scanning = float(start)
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else:
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scanning += float(step)
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line_count += 1
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t_2th = (t_start+n_day*24*3600 - abs_start)+((float(dth_psd)*check_1Dmode + scanning - float(start)) / scan_speed)
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intensity = (chain.text).split(',')[-2]
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temperature = (chain.text).split(',')[-1]
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outfile.write(temperature + " " + (chi) + " " + (phi)
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+ " " + (tx) + " " + (ty) + " " + (om)
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+ " " + (offset) + " " + (tth) + " " + str(round(scanning, 4))
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+ " " + intensity + " " + str(t_2th) +'\n')
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if d_stop != d_start:
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n_day+=1
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outfile.close()
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if sys.platform == "win32":
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os.system("RMDIR "+ extract_path +" /s /q")
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elif sys.platform == "darwin":
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os.system("rm -rf "+ extract_path)
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elif sys.platform == "linux" or sys.platform == "linux2":
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os.system("rm -rf "+ extract_path)
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return scan_type, line_count, wl
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