def step_xia_scan(motor, filename, energy_grid,
integration_times=np.array([])):
"""
Example
-------
>>> TODO
"""
xia1_chan1_array = []
xia1_chan2_array = []
xia1_chan3_array = []
xia1_chan4_array = []
i0_array = []
if (len(integration_times)) == 0:
integration_times = np.ones(len(energy_grid)) * xia1.real_time.value
#energy_grid = np.arange(7112 - 50, 7112 + 50, 1)#get_xia_energy_grid(energy_start, e0, edge_start, edge_end, energy_end, preedge_spacing, xanes, exafsk)
pba1.adc7.filepath.put('')
pba1.adc7.enable_sel.put(0)
xia1.collect_mode.put(0)
while (xia1.collect_mode.value != 0):
ttime.sleep(.01)
for i in range(len(energy_grid)):
print("[{}/{}]".format(i + 1, len(energy_grid)))
if (xia1.real_time.value != integration_times[i]):
xia1.real_time.put(integration_times[i])
ttime.sleep(.005)
motor.move(xray.energy2encoder(energy_grid[i]) / 360000)
while (np.abs(motor.read()['hhm_theta']['value'] -
motor.read()['hhm_theta_user_setpoint']['value']) >
0.00001 or motor.moving == True):
ttime.sleep(.005)
xia1.erase_start.put(1)
ttime.sleep(.1)
while (xia1.acquiring.value):
ttime.sleep(.005)
ttime.sleep(.1)
i0_array.append([energy_grid[i], pba1.adc7.volt.value])
xia1_chan1_array.append(xia1.mca_array1.value)
xia1_chan2_array.append(xia1.mca_array2.value)
xia1_chan3_array.append(xia1.mca_array3.value)
xia1_chan4_array.append(xia1.mca_array4.value)
pba1.adc7.enable_sel.put(1)
np.savetxt('/GPFS/xf08id/xia_files/' + filename + '-i0',
np.array(i0_array))
np.savetxt('/GPFS/xf08id/xia_files/' + filename + '-1',
np.array(xia1_chan1_array))
np.savetxt('/GPFS/xf08id/xia_files/' + filename + '-2',
np.array(xia1_chan2_array))
np.savetxt('/GPFS/xf08id/xia_files/' + filename + '-3',
np.array(xia1_chan3_array))
np.savetxt('/GPFS/xf08id/xia_files/' + filename + '-4',
np.array(xia1_chan4_array))
def calibrate_offset(self):
ret = self.questionMessage(
'Confirmation', 'Are you sure you would like to calibrate it?')
if not ret:
print('[E0 Calibration] Aborted!')
return False
new_value = str(
self.hhm.angle_offset.value -
(xray.energy2encoder(float(self.edit_E0_2.text(
)), self.hhm.pulses_per_deg) - xray.energy2encoder(
float(self.edit_ECal.text()), self.hhm.pulses_per_deg)) /
self.hhm.pulses_per_deg)
if self.set_new_angle_offset(new_value):
return
print('[E0 Calibration] New value: {}\n[E0 Calibration] Completed!'.
format(new_value))
def calibrate_offset(self):
ret = question_message_box(
self, 'Confirmation',
'Are you sure you would like to calibrate it?')
if not ret:
print('[E0 Calibration] Aborted!')
return False
new_value = str(
self.hhm.angle_offset.value -
(xray.energy2encoder(float(self.edit_E0.text(
)), self.hhm.pulses_per_deg) - xray.energy2encoder(
float(self.edit_ECal.text()), self.hhm.pulses_per_deg)) /
self.hhm.pulses_per_deg)
if self.set_new_angle_offset(new_value):
return
print('[E0 Calibration] New value: {}\n[E0 Calibration] Completed!'.
format(new_value))
message_box(
'Reload trajectory',
'Switch to Trajectory tab and re-load and re-initialize the trajectory'
)
def step_xia_scan(motor, filename, energy_grid, integration_times = np.array([])):
"""
Example
-------
>>> TODO
"""
xia1_chan1_array = []
xia1_chan2_array = []
xia1_chan3_array = []
xia1_chan4_array = []
i0_array = []
if(len(integration_times)) == 0:
integration_times = np.ones(len(energy_grid)) * xia1.real_time.value
#energy_grid = np.arange(7112 - 50, 7112 + 50, 1)#get_xia_energy_grid(energy_start, e0, edge_start, edge_end, energy_end, preedge_spacing, xanes, exafsk)
pba1.adc7.filepath.put('')
pba1.adc7.enable_sel.put(0)
xia1.collect_mode.put(0)
while(xia1.collect_mode.value != 0):
ttime.sleep(.01)
for i in range(len(energy_grid)):
print("[{}/{}]".format(i + 1, len(energy_grid)))
if(xia1.real_time.value != integration_times[i]):
xia1.real_time.put(integration_times[i])
ttime.sleep(.005)
motor.move(xray.energy2encoder(energy_grid[i])/360000)
while(np.abs(motor.read()['hhm_theta']['value'] - motor.read()['hhm_theta_user_setpoint']['value']) > 0.00001 or motor.moving == True):
ttime.sleep(.005)
xia1.erase_start.put(1)
ttime.sleep(.1)
while(xia1.acquiring.value):
ttime.sleep(.005)
ttime.sleep(.1)
i0_array.append([energy_grid[i], pba1.adc7.volt.value])
xia1_chan1_array.append(xia1.mca_array1.value)
xia1_chan2_array.append(xia1.mca_array2.value)
xia1_chan3_array.append(xia1.mca_array3.value)
xia1_chan4_array.append(xia1.mca_array4.value)
pba1.adc7.enable_sel.put(1)
np.savetxt('/GPFS/xf08id/xia_files/' + filename + '-i0', np.array(i0_array))
np.savetxt('/GPFS/xf08id/xia_files/' + filename + '-1', np.array(xia1_chan1_array))
np.savetxt('/GPFS/xf08id/xia_files/' + filename + '-2', np.array(xia1_chan2_array))
np.savetxt('/GPFS/xf08id/xia_files/' + filename + '-3', np.array(xia1_chan3_array))
np.savetxt('/GPFS/xf08id/xia_files/' + filename + '-4', np.array(xia1_chan4_array))
def e2encoder(self, offset):
self.encoder_grid = -xray.energy2encoder(self.energy_grid, offset)
def load(self,
orig_file_name,
new_file_path,
is_energy,
offset,
new_file_name='hhm.txt'):
ip = self.hhm.ip
orig_file_path = self.hhm.traj_filepath
print('[Load Trajectory] Starting...')
traj_fn = orig_file_name
# Check if new_file_path is between the possible values
if int(new_file_path) > 9 or int(new_file_path) < 1:
print(
"[Load Trajectory] Path '{}' not possible. Please use a value in the range 1 <= new_file_path <= 9."
.format(new_file_path))
return False
# Get number of lines in file
file_size = self.file_len(orig_file_path + orig_file_name)
print(
'[Load Trajectory] Number of lines in file: {}'.format(file_size))
# Get min and max of trajectory in eV
if orig_file_path[-1] != '/':
fp += '/'
traj = pd.read_table('{}{}'.format(orig_file_path, orig_file_name),
header=None,
comment='#')
name = orig_file_name
header = self.read_header('{}{}'.format(orig_file_path,
orig_file_name))
if is_energy:
min_energy = int(np.round(traj).min())
max_energy = int(np.round(traj).max())
enc = np.int64(
np.round(
xray.energy2encoder(-traj, self.hhm.pulses_per_deg,
-offset)))
orig_file_name = '.energy_traj_aux.txt'
np.savetxt('{}{}'.format(orig_file_path, orig_file_name),
enc,
fmt='%d',
header=header,
comments='')
else:
min_energy = int(
xray.encoder2energy((-traj, self.hhm.pulses_per_deg).min()))
max_energy = int(
xray.encoder2energy((-traj, self.hhm.pulses_per_deg).max()))
print('[Load Trajectory] Min energy: {}'.format(min_energy))
print('[Load Trajectory] Max energy: {}'.format(max_energy))
# Create ftp connection with default credential
ftp = FTP(ip)
ftp.login()
s = pxssh.pxssh()
ssh_login = s.login(ip, 'root', 'deltatau')
if ssh_login:
# Check if the directory exists in /usrflash/lut/. If it does not, create it.
if str(new_file_path) != '':
ftp.cwd('/usrflash/')
dir_list = ftp.nlst()
dir_exists = 0
for dir_name in dir_list:
if dir_name == 'lut':
dir_exists = 1
if not dir_exists:
print('[Load Trajectory] mkdir: /usrflash/lut')
ftp.mkd('/usrflash/lut')
s.sendline('chown ftp:root /var/ftp/usrflash/lut')
s.sendline('chmod a+wrx /var/ftp/usrflash/lut')
ftp.cwd('/usrflash/lut/')
dir_list = ftp.nlst()
dir_exists = 0
for dir_name in dir_list:
if dir_name == str(new_file_path):
dir_exists = 1
if not dir_exists:
print('[Load Trajectory] mkdir: /usrflash/lut/{}'.format(
new_file_path))
ftp.mkd('/usrflash/lut/{}'.format(new_file_path))
s.sendline(
'chown ftp:root /var/ftp/usrflash/lut/{}'.format(
new_file_path))
s.sendline('chmod a+wrx /var/ftp/usrflash/lut/{}'.format(
new_file_path))
s.sendline(
'chown ftp:root /var/ftp/usrflash/lut/{}/hhm.txt'.format(
new_file_path))
s.sendline('chmod 777 /var/ftp/usrflash/lut/{}/hhm.txt'.format(
new_file_path))
ftp_file_path = '/var/ftp/usrflash/lut/{}/{}'.format(
new_file_path, new_file_name)
# Open file and transfer to the power pmac
f = open(orig_file_path + str(orig_file_name), 'rb')
if (f.readable()):
line = f.readline().decode('utf-8')
if line[0] == '#':
element = line[line.find('element:') +
9:line.find(',')].lstrip()
edge_value = line[line.find('edge:') + 6:line.
find(',', line.find('edge:'))].lstrip()
e0_value = line[line.find('E0:') + 4:].lstrip()
curr_hhm_traj = getattr(self.hhm,
'traj{}'.format(new_file_path))
curr_hhm_traj.filename.put(traj_fn)
curr_hhm_traj.elem.put(element)
curr_hhm_traj.edge.put(edge_value)
curr_hhm_traj.e0.put(e0_value)
else:
curr_hhm_traj = getattr(self.hhm,
'traj{}'.format(new_file_path))
curr_hhm_traj.filename.put(traj_fn)
curr_hhm_traj.elem.put('')
curr_hhm_traj.edge.put('')
curr_hhm_traj.e0.put('')
f.close()
f = open(orig_file_path + str(orig_file_name), 'rb')
result = ftp.storbinary(
'STOR ' + '/usrflash/lut/' + str(new_file_path) + '/' +
new_file_name, f)
if (result == '226 File receive OK.'):
print('[Load Trajectory] File sent OK')
s.sendline(
'chown ftp:root /var/ftp/usrflash/lut/{}/{}'.format(
new_file_path, new_file_name))
s.sendline(
'chmod a+wrx /var/ftp/usrflash/lut/{}/{}'.format(
new_file_path, new_file_name))
s.sendline(
'echo "{}\n{}\n{}\n{}" > /var/ftp/usrflash/lut/{}/hhm-size.txt'
.format(file_size, name, min_energy, max_energy,
new_file_path))
ttime.sleep(0.01)
ftp.close()
print('[Load Trajectory] Permissions OK')
f.close()
s.logout()
s.pid = None
print('[Load Trajectory] Completed!')
else:
print(
'[Load Trajectory] Fail! Not able to ssh into the controller...'
)
def e2encoder(self, offset):
self.encoder_grid = -xray.energy2encoder(
self.energy_grid, self.hhm.pulses_per_deg, offset)