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Add placeholder functions to xrd/io.py

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rasmusvt 2021-10-25 08:33:58 +02:00
parent 65a5497970
commit 5c977cc387
3 changed files with 315 additions and 6 deletions
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5
beamtime/halvorsen.txt
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@ -1,5 +0,0 @@
'''test'''
# changez
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5616521656

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