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tomo_ctrl_fxi.py
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tomo_ctrl_fxi.py
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import sys
import os
import re
import json
from PyQt5 import QtGui
from PyQt5.QtWidgets import (QMainWindow, QFileDialog, QRadioButton, QApplication,
QLineEdit, QWidget, QPushButton, QLabel, QGroupBox,
QVBoxLayout, QHBoxLayout, QGridLayout)
from PyQt5.QtGui import QIntValidator, QDoubleValidator
from PyQt5 import QtCore
from PyQt5.QtCore import pyqtSlot
from datetime import datetime
import numpy as np
import h5py
#from temp import tomo_test
global tomo
class App(QWidget):
def __init__(self):
super().__init__()
self.title = 'Tomo Control'
self.left = 400
self.top = 400
self.width = 800
self.height = 480
self.initUI()
self.scan_mode = '3D'
def initUI(self):
self.setWindowTitle(self.title)
self.setGeometry(self.left, self.top, self.width, self.height)
self.font1 = QtGui.QFont('Arial', 11, QtGui.QFont.Bold)
self.font2 = QtGui.QFont('Arial', 11, QtGui.QFont.Normal)
self.fpath = os.getcwd()
self.xeng = XEng.position * 1000 # convert from keV to eV
self.xeng_list = [float(self.xeng)]
# lb_empty = QLabel()
grid = QGridLayout()
gpbox1 = self.GP_prepare()
gpbox2 = self.GP_tomo_param()
self.pb_run = QPushButton('Start scan')
self.pb_run.setToolTip('Run tomo scan')
self.pb_run.setFont(self.font1)
self.pb_run.clicked.connect(run_scan)
self.pb_run.setFixedWidth(150)
grid.addWidget(gpbox1,0,1)
grid.addWidget(gpbox2,1,1)
layout = QVBoxLayout()
layout.addLayout(grid)
layout.addWidget(QLabel())
layout.addWidget(self.pb_run)
self.setLayout(layout)
# self.resize(640,200)
def GP_prepare(self):
lb_empty = QLabel()
gpbox = QGroupBox('Preparation')
gpbox.setFont(self.font1)
lb_pid = QLabel(self)
lb_pid.setText('Proposal ID:')
lb_pid.setFont(self.font2)
lb_or = QLabel(self)
lb_or.setText(' or ')
lb_or.setFont(self.font2)
self.tx_pid = QLineEdit(self) # proposal ID
self.tx_pid.setValidator(QIntValidator())
self.tx_pid.setFont(self.font2)
lb_pi = QLabel(self)
lb_pi.setText('PI name:')
lb_pi.setFont(self.font2)
self.tx_pi = QLineEdit(self) # PI name
self.tx_pi.setFont(self.font2)
self.pb_godir = QPushButton('Go to directory')
self.pb_godir.setToolTip('create directory if not exist')
self.pb_godir.setFont(self.font2)
self.pb_godir.clicked.connect(go_to_directory)
self.pb_godir.setFixedWidth(150)
self.pb_new = QPushButton('New user')
self.pb_new.setToolTip('create a new user')
self.pb_new.setFont(self.font2)
self.pb_new.clicked.connect(new_user)
self.pb_new.setFixedWidth(150)
lb_pa = QLabel()
lb_pa.setFont(self.font2)
lb_pa.setText('Current directory:')
self.lb_path = QLabel()
self.lb_path.setFont(self.font2)
self.lb_path.setText(self.fpath)
pb_conf = QPushButton('Load config file')
pb_conf.setFont(self.font2)
pb_conf.setFixedWidth(150)
pb_conf.clicked.connect(load_config_file)
self.lb_conf = QLabel()
self.lb_conf.setFont(self.font2)
# self.lb_conf.setText('No configuration file selected ... ')
# configure file info
lb_zd = QLabel()
lb_zd.setFont(self.font2)
lb_zd.setText('ZP Dia (um):')
lb_zd.setFixedWidth(100)
lb_zw = QLabel()
lb_zw.setFont(self.font2)
lb_zw.setText('ZP Width (nm):')
lb_zw.setFixedWidth(100)
lb_vlm = QLabel()
lb_vlm.setFont(self.font2)
lb_vlm.setText('VLM Mag.:')
lb_vlm.setFixedWidth(100)
lb_mag = QLabel()
lb_mag.setFont(self.font2)
lb_mag.setText('GLB Mag.:')
lb_mag.setFixedWidth(100)
lb_elow = QLabel()
lb_elow.setFont(self.font2)
lb_elow.setText('Low limit (ev).:')
lb_elow.setFixedWidth(100)
lb_ehigh = QLabel()
lb_ehigh.setFont(self.font2)
lb_ehigh.setText('High limit (ev).:')
lb_ehigh.setFixedWidth(100)
self.tx_zd = QLineEdit(self)
self.tx_zd.setValidator(QIntValidator())
self.tx_zd.setDisabled(True)
self.tx_zw = QLineEdit(self)
self.tx_zw.setValidator(QIntValidator())
self.tx_zw.setDisabled(True)
self.tx_vlm = QLineEdit(self)
self.tx_vlm.setValidator(QIntValidator())
self.tx_vlm.setDisabled(True)
self.tx_mag = QLineEdit(self)
self.tx_mag.setValidator(QIntValidator())
self.tx_mag.setDisabled(True)
self.tx_elow = QLineEdit(self)
self.tx_elow.setValidator(QDoubleValidator())
self.tx_elow.setDisabled(True)
self.tx_ehigh = QLineEdit(self)
self.tx_ehigh.setValidator(QDoubleValidator())
self.tx_ehigh.setDisabled(True)
self.load_config_default()
hbox1 = QHBoxLayout()
hbox1.addWidget(lb_pid)
hbox1.addWidget(self.tx_pid)
hbox1.addWidget(lb_pi)
hbox1.addWidget(self.tx_pi)
hbox2 = QHBoxLayout()
hbox2.addWidget(self.pb_new)
hbox2.addWidget(lb_or)
hbox2.addWidget(self.pb_godir)
hbox2.addWidget(lb_pa)
hbox2.addWidget(self.lb_path)
hbox2.setAlignment(QtCore.Qt.AlignLeft)
hbox3 = QHBoxLayout()
hbox3.addWidget(pb_conf)
hbox3.addWidget(self.lb_conf)
hbox3.setAlignment(QtCore.Qt.AlignLeft)
hbox4 = QHBoxLayout()
hbox4.addWidget(lb_zd)
hbox4.addWidget(self.tx_zd)
hbox4.addWidget(lb_zw)
hbox4.addWidget(self.tx_zw)
hbox4.addWidget(lb_mag)
hbox4.addWidget(self.tx_mag)
hbox5 = QHBoxLayout()
hbox5.addWidget(lb_vlm)
hbox5.addWidget(self.tx_vlm)
hbox5.addWidget(lb_elow)
hbox5.addWidget(self.tx_elow)
hbox5.addWidget(lb_ehigh)
hbox5.addWidget(self.tx_ehigh)
vbox = QVBoxLayout()
vbox.addLayout(hbox1)
vbox.addLayout(hbox2)
vbox.addWidget(lb_empty)
vbox.addLayout(hbox3)
vbox.addLayout(hbox4)
vbox.addLayout(hbox5)
gpbox.setLayout(vbox)
return gpbox
def GP_tomo_param(self):
gpbox = QGroupBox('Tomo parameters')
gpbox.setFont(self.font1)
lb_empty = QLabel()
lb_eng = QLabel()
lb_eng.setFont(self.font2)
lb_eng.setText('X-ray Energy:')
lb_eng.setFixedWidth(150)
# X-ray energy related
self.tx_eng = QLineEdit(self)
self.tx_eng.setFont(self.font2)
self.tx_eng.setText('[{:5.2f}]'.format(self.xeng))
# self.tx_eng.setValidator(QDoubleValidator())
self.pb_eng = QPushButton('Gen. Energ. list')
self.pb_eng.setToolTip('Energy is in unit of eV')
self.pb_eng.setFont(self.font2)
self.pb_eng.setFixedWidth(150)
self.pb_eng.clicked.connect(gen_eng_list)
self.pb_goeng = QPushButton('Goto 1st energy')
self.pb_goeng.setFont(self.font2)
self.pb_goeng.setFixedWidth(150)
self.pb_goeng.clicked.connect(go_to_energy)
self.lb_c_eng = QLabel()
self.lb_c_eng.setFont(self.font1)
self.lb_c_eng.setText('Current Energy: {0:5.2f} ({1} - {2} eV)'.format(self.xeng, (self.tx_elow.text()), (self.tx_ehigh.text())))
self.lb_c_eng.setFixedWidth(400)
lb_nt = QLabel()
lb_nt.setFont(self.font2)
lb_nt.setText('e.g., single/multiple energy: [8000,8100,8200]; with 1eV interval: [8000:1:8500]; combination: [8000, 8100];[8032:1:8060]')
lb_eng_list = QLabel()
lb_eng_list.setFont(self.font1)
lb_eng_list.setText('Energy list:')
self.lb_eng_list2 = QLabel()
self.lb_eng_list2.setFont(self.font2)
self.lb_eng_list2.setText('No energy entered...')
self.lb_eng_list2.setFixedWidth(600)
lb_md = QLabel()
lb_md.setFont(self.font1)
lb_md.setText('Scan mode:')
self.rd_md_2d = QRadioButton('2D')
self.rd_md_2d.toggled.connect(self.check_scan_mode)
self.rd_md_3d = QRadioButton('3D')
self.rd_md_3d.setChecked(True)
hbox1 = QHBoxLayout()
hbox1.addWidget(lb_eng)
hbox1.addWidget(self.tx_eng)
hbox1.addWidget(self.pb_eng)
hbox1.addWidget(self.pb_goeng)
hbox2 = QHBoxLayout()
hbox2.addWidget(lb_eng_list)
hbox2.addWidget(self.lb_eng_list2)
hbox2.setAlignment(QtCore.Qt.AlignLeft)
# hbox2.addStretch(1)
vbox = QVBoxLayout()
vbox.addWidget(self.lb_c_eng)
vbox.addLayout(hbox1)
vbox.addWidget(lb_nt)
# vbox.addWidget(lb_empty)
vbox.addLayout(hbox2)
vbox.addWidget(lb_empty)
# other control parameters
# Angle infor
lb_as = QLabel()
lb_as.setFont(self.font2)
lb_as.setText('Angle start:')
lb_as.setFixedWidth(130)
self.tx_as = QLineEdit(self)
self.tx_as.setText('0')
self.tx_as.setFont(self.font2)
self.tx_as.setValidator(QDoubleValidator())
self.tx_as.setFixedWidth(130)
lb_ae = QLabel()
lb_ae.setFont(self.font2)
lb_ae.setText('Angle end:')
lb_ae.setFixedWidth(130)
self.tx_ae =QLineEdit(self)
self.tx_ae.setText('180')
self.tx_ae.setFont(self.font2)
self.tx_ae.setValidator(QDoubleValidator())
self.tx_ae.setFixedWidth(130)
lb_ai = QLabel()
lb_ai.setFont(self.font2)
lb_ai.setText('Angle interval:')
lb_ai.setFixedWidth(130)
self.tx_ai =QLineEdit(self)
self.tx_ai.setText('1')
self.tx_ai.setFont(self.font2)
self.tx_ai.setValidator(QDoubleValidator())
self.tx_ai.setFixedWidth(130)
hbox3 = QHBoxLayout()
hbox3.addWidget(lb_as)
hbox3.addWidget(self.tx_as)
hbox3.addWidget(lb_ae)
hbox3.addWidget(self.tx_ae)
hbox3.addWidget(lb_ai)
hbox3.addWidget(self.tx_ai)
hbox3.setAlignment(QtCore.Qt.AlignLeft)
# others
lb_t = QLabel()
lb_t.setFont(self.font2)
lb_t.setText('Exposure time (s):')
lb_t.setFixedWidth(130)
lb_bkg = QLabel()
lb_bkg.setFont(self.font2)
lb_bkg.setText('# Bkg image:')
lb_bkg.setFixedWidth(130)
lb_dk = QLabel()
lb_dk.setFont(self.font2)
lb_dk.setText('# dark image:')
lb_dk.setFixedWidth(130)
self.tx_t = QLineEdit(self)
self.tx_t.setFont(self.font2)
self.tx_t.setValidator(QDoubleValidator())
self.tx_t.setText('0.1')
self.tx_t.setFixedWidth(130)
self.tx_bkg = QLineEdit(self)
self.tx_bkg.setFont(self.font2)
self.tx_bkg.setValidator(QIntValidator())
self.tx_bkg.setText('1')
self.tx_bkg.setFixedWidth(130)
self.tx_dk = QLineEdit(self)
self.tx_dk.setFont(self.font2)
self.tx_dk.setValidator(QIntValidator())
self.tx_dk.setText('1')
self.tx_dk.setFixedWidth(130)
lb_splx = QLabel()
lb_splx.setFont(self.font2)
lb_splx.setText('Sample out (x/um):')
lb_splx.setFixedWidth(130)
self.tx_splx = QLineEdit(self)
self.tx_splx.setFont(self.font2)
self.tx_splx.setValidator(QDoubleValidator())
self.tx_splx.setFixedWidth(130)
lb_note = QLabel()
lb_note.setFont(self.font2)
lb_note.setText('Additional Note:')
lb_note.setFixedWidth(130)
self.tx_note = QLineEdit(self)
self.tx_note.setFont(self.font2)
# lb_sply = QLabel()
# lb_sply.setFont(self.font2)
# lb_sply.setText('y (um):')
# lb_sply.setFixedWidth(80)
# lb_splz = QLabel()
# lb_splz.setFont(self.font2)
# lb_splz.setText('z (um):')
# lb_splz.setFixedWidth(80)
# self.tx_sply = QLineEdit(self)
# self.tx_sply.setFont(self.font2)
# self.tx_sply.setValidator(QDoubleValidator())
# self.tx_splz = QLineEdit(self)
# self.tx_splz.setFont(self.font2)
# self.tx_splz.setValidator(QDoubleValidator())
hbox4 = QHBoxLayout()
hbox4.addWidget(lb_t)
hbox4.addWidget(self.tx_t)
hbox4.addWidget(lb_bkg)
hbox4.addWidget(self.tx_bkg)
hbox4.addWidget(lb_dk)
hbox4.addWidget(self.tx_dk)
hbox4.setAlignment(QtCore.Qt.AlignLeft)
hbox5 = QHBoxLayout()
hbox5.addWidget(lb_splx)
hbox5.addWidget(self.tx_splx)
# hbox5.addWidget(lb_sply)
# hbox5.addWidget(self.tx_sply)
# hbox5.addWidget(lb_splz)
# hbox5.addWidget(self.tx_splz)
# hbox5.addWidget(lb_note)
# hbox5.addWidget(self.tx_note)
hbox5.setAlignment(QtCore.Qt.AlignLeft)
hbox_note = QHBoxLayout()
hbox_note.addWidget(lb_note)
hbox_note.addWidget(self.tx_note)
hbox_note.setAlignment(QtCore.Qt.AlignLeft)
hbox_md = QHBoxLayout()
hbox_md.addWidget(lb_md)
hbox_md.addWidget(self.rd_md_2d)
hbox_md.addWidget(self.rd_md_3d)
hbox_md.setAlignment(QtCore.Qt.AlignLeft)
vbox.addLayout(hbox_md)
vbox.addLayout(hbox3)
vbox.addLayout(hbox4)
# vbox.addWidget(lb_empty)
vbox.addLayout(hbox5)
vbox.addLayout(hbox_note)
gpbox.setLayout(vbox)
return gpbox
@pyqtSlot()
def on_click(self):
print(self.title)
def load_config_default(self):
fn_pre = '/home/xf18id/.ipython/profile_collection/startup/tomo_ctrl/'
fn_f = 'zp_D100_30_vlm10_gMag650_(7000_8000).json'
fn = fn_pre + fn_f
self.lb_conf.setText('{} loaded'.format(fn_f))
with open(fn) as f:
conf = json.load(f)
self.tx_zd.setText(str(conf['ZONE_DIAMETER']))
self.tx_zd.setStyleSheet('color: rgb(80, 80, 80);')
self.tx_zw.setText(str(conf['OUT_ZONE_WIDTH']))
self.tx_zw.setStyleSheet('color: rgb(80, 80, 80);')
self.tx_mag.setText(str(conf['GLOBAL_MAG']))
self.tx_mag.setStyleSheet('color: rgb(80, 80, 80);')
self.tx_vlm.setText(str(conf['GLOBAL_VLM_MAG']))
self.tx_vlm.setStyleSheet('color: rgb(80, 80, 80);')
self.tx_elow.setText(str(conf['Eng_L']))
self.tx_elow.setStyleSheet('color: rgb(80, 80, 80);')
self.tx_ehigh.setText(str(conf['Eng_H']))
self.tx_ehigh.setStyleSheet('color: rgb(80, 80, 80);')
f.close()
def check_scan_mode(self):
if self.rd_md_2d.isChecked() == True:
self.tx_as.setDisabled(True)
self.tx_ae.setDisabled(True)
self.tx_ai.setDisabled(True)
self.scan_mode = '2D'
else:
self.tx_as.setEnabled(True)
self.tx_ae.setEnabled(True)
self.tx_ai.setEnabled(True)
self.scan_mode = '3D'
def new_user():
now = datetime.now()
year = np.str(now.year)
if now.month >= 1 and now.month <=4: qut = 'Q1'
elif now.month >= 5 and now.month <=8: qut = 'Q2'
else: qut = 'Q3'
PI_name = str(tomo.tx_pi.text())
PI_name = PI_name.replace(' ', '_').upper()
proposal_id = str(tomo.tx_pid.text())
if len(PI_name) == 0 or len(proposal_id) == 0:
tomo.lb_path.setText('Please input proposal ID and PI name')
return 0
pre = '/NSLS2/xf18id1/users/' + year + qut + '/' # need modify
fn = pre + PI_name + '_Proposal_' + proposal_id
try: os.makedirs(fn)
except Exception:
print('(user, proposal) existed\nEntering folder: {}'.format(os.getcwd()))
os.chdir(fn)
pass
os.chdir(fn)
tomo.lb_path.setText(fn)
def go_to_directory():
fn = str(QFileDialog.getExistingDirectory(tomo, "Select Directory"))
tomo.lb_path.setText(fn)
print('go_to_directory: {}'.format(fn))
print('{}'.format(tomo.tx_pid.text()))
def go_to_energy():
print('go_to_energy')
RE(go_eng(float(tomo.xeng)))
print('{}'.format(tomo.xeng))
tomo.lb_c_eng.setText('Current Energy: {:5.2f} eV'.format(XEng.position * 1000))
def load_config_file():
options = QFileDialog.Option()
options |= QFileDialog.DontUseNativeDialog
fn_conf, _ = QFileDialog.getOpenFileName(tomo, "QFileDialog.getOpenFileName()", "", "json files (*.json)", options=options)
if fn_conf:
print(fn_conf)
fn_relative = fn_conf.split('/')[-1]
tomo.lb_conf.setText('{} loaded'.format(fn_relative))
with open(fn_conf) as f:
conf = json.load(f)
tomo.tx_zd.setText(str(conf['ZONE_DIAMETER']))
tomo.tx_zd.setStyleSheet('color: rgb(80, 80, 80);')
tomo.tx_zw.setText(str(conf['OUT_ZONE_WIDTH']))
tomo.tx_zw.setStyleSheet('color: rgb(80, 80, 80);')
tomo.tx_mag.setText(str(conf['GLOBAL_MAG']))
tomo.tx_mag.setStyleSheet('color: rgb(80, 80, 80);')
tomo.tx_vlm.setText(str(conf['GLOBAL_VLM_MAG']))
tomo.tx_vlm.setStyleSheet('color: rgb(80, 80, 80);')
tomo.tx_elow.setText(str(conf['Eng_L']))
tomo.tx_elow.setStyleSheet('color: rgb(80, 80, 80);')
tomo.tx_ehigh.setText(str(conf['Eng_H']))
tomo.tx_ehigh.setStyleSheet('color: rgb(80, 80, 80);')
f.close()
def gen_eng_list():
txt = str(tomo.tx_eng.text())
txt = txt.replace(' ','')
if len(txt) == 0 or txt[0] != '[':
invalid_flag = 1
else:
txt = txt.split(';')
invalid_flag = 0
eng_list = []
for i in range(len(txt)):
tmp = txt[i]
if tmp[0] != '[' or tmp[-1] != ']':
invalid_flag = 1
print('{}'.format(i))
continue
num_l = len([a.start() for a in re.finditer('(?=\[)', tmp)])
num_r = len([a.start() for a in re.finditer('(?=\])', tmp)])
if num_l != num_r:
invalid_flag = 2
continue
tmp = tmp.replace('[', '')
tmp = tmp.replace(']', '')
num_colon = len([a.start() for a in re.finditer('(?=:)', tmp)])
if num_colon == 2:
tmp_eng = tmp.split(':')
st = float(tmp_eng[0])
it = float(tmp_eng[1])
ed = float(tmp_eng[2]) + it
tmp_eng_list = list(np.arange(st, ed, it))
elif num_colon == 0:
tmp_eng = tmp.split(',')
tmp_eng_list = [float(t) for t in tmp_eng]
else:
invalid_flag = 3
continue
eng_list = eng_list + tmp_eng_list
eng_list = np.sort(np.unique(np.array(eng_list)))
if invalid_flag:
eng_list = [XEng.position * 1000]
tomo.xeng_list = eng_list
tomo.xeng = XEng.position * 1000
tomo.lb_eng_list2.setText('Invalid energy! Leave current X-ray energy unchanged ...')
tomo.lb_eng_list2.setStyleSheet('color: rgb(200, 0, 0);')
else:
tomo.xeng_list = [float(t) for t in eng_list]
tomo.xeng = tomo.xeng_list[0]
tomo.lb_eng_list2.setText(str(eng_list))
tomo.lb_eng_list2.setStyleSheet('color: rgb(0, 0, 0);')
# tomo.setFixedSize(tomo.layout.sizeHint())
def gen_json():
fn_conf = 'zp_D100_30_vlm10_gMag650_(7000_8000).json'
conf={'ZONE_DIAMETER': 100,
'OUT_ZONE_WIDTH': 30,
'GLOBAL_MAG': 650,
'GLOBAL_VLM_MAG': 10,
'Eng_L': 7000,
'Eng_H': 8000,
}
with open(fn_conf, 'w') as f:
json.dump(conf, f)
def run_scan():
cur_dir = tomo.lb_path.text() # current directory
start = float(tomo.tx_as.text()) if len(tomo.tx_as.text())>0 else None
stop = float(tomo.tx_ae.text()) if len(tomo.tx_ae.text())>0 else None
interval = float(tomo.tx_ai.text()) if len(tomo.tx_ai.text())>0 else None
if start==None or stop==None or interval==None:
start = 0
stop = 180
interval = 1
tomo.tx_as.setText(str(start))
tomo.tx_ae.setText(str(stop))
tomo.tx.ai.setText(str(interval))
num_angle = abs(stop-start)/interval + 1
exposure_t = float(tomo.tx_t.text()) if len(tomo.tx_t.text())>0 else 1 # default dwell time is 1sec
n_bkg = int(tomo.tx_bkg.text()) if len(tomo.tx_bkg.text())>0 else 10 # default # of backgroud-image is 10
n_dk = int(tomo.tx_dk.text()) if len(tomo.tx_dk.text())>0 else 10 # default # of dark-image is 10
out_pos_x = float(tomo.tx_splx.text()) if len(tomo.tx_splx.text())>0 else 1
eng_list = np.array(tomo.xeng_list)
note = tomo.tx_note.text()
scan_mode = tomo.scan_mode
print('{}'.format(eng_list))
check_eng_range(eng_list)
RE(mv(XEng, eng_list[0]/1000.0)) # move to the 1st energy in eng_list
if scan_mode == '2D':
print('start 2D scan (xanes) ...')
RE(xanes_scan(eng_list/1000.0, exposure_time=exposure_t, detectors=[detA1], bkg_num=n_bkg, out_pos=out_pos_x, md={'Note': note}))
h = db[-1]
load_scan(h, cur_dir)
else:
if len(eng_list) == 1:
print('start 3D scan (tomo) ...')
RE(tomo_scan(start, stop, num_angle, exposure_time=exposure_t, detectors=[detA1], bkg_num=n_bkg, out_pos=out_pos_x, md={'Note': note}))
h = db[-1]
load_scan(h, cur_dir)
elif len(eng_list) > 1:
print('tomo scan at multiple energy ...')
for eng in eng_list:
RE(mv(XEng, eng/1000.))
RE(tomo_scan(start, stop, num_angle, exposure_time=exposure_t, detectors=[detA1], bkg_num=n_bkg, out_pos=out_pos_x, md={'Note': note}))
h = db[-1]
if eng == eng_list[0]:
folder_id = str(h.start['scan_id'])
tomo_dir = cur_dir + '/tomo_xanes_start_from_scan_' + folder_id
os.makedirs(tomo_dir)
load_scan(h, tomo_dir)
def load_scan(h, cur_dir='.'):
os.chdir(cur_dir)
scan_mode = h.start['plan_name']
if scan_mode == 'xanes_scan':
load_xanes_scan(h, cur_dir)
elif scan_mode == 'tomo_scan':
load_tomo_scan(h, cur_dir)
else:
print('scan not recognized')
def load_tomo_scan(h, cur_dir='.'):
os.chdir(cur_dir)
note = h.start['Note'] if h.start['Note'] else 'None'
det = h.start['detectors'][0] + '_image'
scan_id = str(h.start['scan_id'])
eng = '{:5.1f}'.format(h.start['x_ray_energy']*1000)
img = np.array(list(h.data(det)))
img = np.squeeze(img)
num_angles = int(h.start['num_angles'])
num_bkg = int(h.start['num_bkg_images'])
img_bkg = img[0:num_bkg]
img_tomo = img[num_bkg:]
img_bkg_avg = np.sum(img_bkg, 0)/num_bkg
fn = 'scan_' + scan_id + '_XEng_' + eng + 'eV_tomo.h5'
with h5py.File(fn, 'w') as f:
f.create_dataset('scan_type', data = 'tomo')
f.create_dataset('scan_id', data = scan_id)
f.create_dataset('num_of_angles', data = num_angles)
f.create_dataset('num_of_bkg_image', data = num_bkg)
f.create_dataset('img_tomo', data = img_tomo)
f.create_dataset('img_bkg_average', data = img_bkg_avg)
f.create_dataset('img_bkg_raw', data = img_bkg)
f.create_dataset('xray_energy', data = eng)
f.create_dataset('note', data = note)
def load_xanes_scan(h, cur_dir='./'):
os.chdir(cur_dir)
note = h.start['Note'] if h.start['Note'] else 'None'
det = h.start['detectors'][0] + '_image'
scan_id = str(h.start['scan_id'])
eng = np.array(list(h.data('XEng')))
img = np.array(list(h.data(det)))
img = np.squeeze(img)
num_eng = int(h.start['num_eng'])
num_bkg =int( h.start['num_bkg_images'])
img_xanes = img[0 : num_eng]
img_bkg_avg = np.zeros(img_xanes.shape)
img_bkg = img[num_eng:]
for i in range(num_eng):
img_bkg_avg[i] = np.sum(img_bkg[i*num_eng:(i+1)*num_eng+1],0)/num_bkg
fn = 'scan_' + scan_id + '_xanes.h5'
with h5py.File(fn, 'w') as f:
f.create_dataset('scan_type', data = 'xanes')
f.create_dataset('scan_id', data = scan_id)
f.create_dataset('num_of_energy', data = num_eng)
f.create_dataset('num_of_bkg_image', data = num_bkg)
f.create_dataset('img_xanes', data = img_xanes)
f.create_dataset('img_bkg_average', data = img_bkg_avg)
f.create_dataset('img_bkg_raw', data = img_bkg)
f.create_dataset('xray_energy', data = eng)
f.create_dataset('note', data = note)
f.close()
print('scan finished')
if __name__ == '__main__':
app = QApplication(sys.argv)
tomo = App()
tomo.show()
sys.exit(app.exec_())