def load_trajectory_file(self, filename):
array_out = []
with open(str(filename)) as f:
for line in f:
array_out.append(int(line))
array_out = np.array(array_out)
self.energy_grid_loaded = -xray.encoder2energy(array_out, 0)
def load(self,
encoder_trace,
i0trace,
iflutrace,
irtrace='',
trigtrace='',
i0offset=0,
ifluoffset=0,
iroffset=0,
angleoffset=0):
self.encoder_file = encoder_trace
self.i0_file = i0trace
self.it_file = iflutrace
self.ir_file = irtrace
self.trig_file = trigtrace
self.encoder = self.loadENCtrace(encoder_trace)
self.energy = np.copy(self.encoder)
#self.energy[:, 1] = xray.encoder2energy(self.encoder[:, 1], 0.041)
self.energy[:, 1] = xray.encoder2energy(self.encoder[:, 1],
-angleoffset)
self.i0 = self.loadADCtrace(i0trace)
self.i0[:, 1] = self.i0[:, 1] - i0offset
self.ir = self.loadADCtrace(irtrace)
self.ir[:, 1] = self.ir[:, 1] - iroffset
self.iflu = self.loadADCtrace(iflutrace)
self.iflu[:, 1] = self.iflu[:, 1] - ifluoffset
self.trigger = self.loadTRIGtrace(trigtrace)
self.it = np.copy(self.iflu)
def load(self,
encoder_trace,
i0trace,
ittrace,
irtrace='',
i0offset=0,
itoffset=0,
iroffset=0,
angleoffset=0):
self.encoder_file = encoder_trace
self.i0_file = i0trace
self.it_file = ittrace
self.ir_file = irtrace
self.encoder = self.loadENCtrace(encoder_trace)
self.energy = self.encoder
#self.energy[:, 1] = xray.encoder2energy(self.encoder[:, 1], 0.041)
self.energy[:, 1] = xray.encoder2energy(
self.encoder[:, 1], -angleoffset
) #-12400 / (2 * 3.1356 * np.sin((np.pi / 180) * ((self.encoder[:, 1]/360000) + 0)))
self.i0 = self.loadADCtrace(i0trace)
self.it = self.loadADCtrace(ittrace)
self.ir = self.loadADCtrace(irtrace)
self.i0[:, 1] = self.i0[:, 1] - i0offset
self.it[:, 1] = self.it[:, 1] - itoffset
self.ir[:, 1] = self.ir[:, 1] - iroffset
def load(self, uid):
#if self.db is None:
# raise Exception('The databroker was not passed as argument to the parser. This feature is disabled.')
self.arrays = {}
self.interp_arrays = {}
self.uid = uid
has_encoder = False
for i in self.db[uid]['descriptors']:
if 'filename' in i['data_keys'][i['name']]:
name = i['name']
if name == 'pb9_enc1' or name == 'hhm_theta':
has_encoder = name
if 'devname' in i['data_keys'][i['name']]:
name = i['data_keys'][i['name']]['devname']
if name == 'hhm_theta':
has_encoder = name
if i['data_keys'][i['name']]['source'] == 'pizzabox-di-file':
data = self.loadTRIGtrace(i['data_keys'][i['name']]['filename'], '')
if i['data_keys'][i['name']]['source'] == 'pizzabox-adc-file':
data = self.loadADCtrace(i['data_keys'][i['name']]['filename'], '')
if i['name'] + ' offset' in self.db[uid]['start'] and type(data) == pd.core.frame.DataFrame:
data.iloc[:, 1] = data.iloc[:, 1] - self.db[uid]['start'][i['name'] + ' offset']
if i['data_keys'][i['name']]['source'] == 'pizzabox-enc-file':
data = self.loadENCtrace(i['data_keys'][i['name']]['filename'], '')
#if type(data) == np.ndarray:
self.arrays[name] = data
if has_encoder is not False:
energy = self.arrays.get(has_encoder).copy()
if 'angle_offset' in self.db[uid]['start']:
energy.iloc[:, 1] = xray.encoder2energy(energy.iloc[:, 1], self.pulses_per_deg, -float(self.db[uid]['start']['angle_offset']))
energy.columns = ['timestamp', 'energy']
del self.arrays[has_encoder]
self.arrays['energy'] = energy
def load_trajectory_file(self, filename, offset, is_energy):
array_out = []
with open(str(filename)) as f:
first = f.readline()
if first[0] != '#':
array_out.append(float(first))
for line in f:
array_out.append(float(line))
array_out = np.array(array_out)
if is_energy:
self.energy_grid_loaded = array_out
else:
self.energy_grid_loaded = -xray.encoder2energy(
array_out, self.hhm.pulses_per_deg, offset)
def loadDB(self, uid):
# if self.db is None:
# raise Exception('The databroker was not passed as argument to the parser. This feature is disabled.')
t1 = time.time()
self.arrays = {}
self.interp_arrays = {}
self.uid = uid
has_encoder = False
for i in self.db[uid]['descriptors']:
stream_name = i['name']
name = i['name']
if name == self.mono_name:
has_encoder = name
if 'devname' in i['data_keys'][i['name']]:
name = i['data_keys'][i['name']]['devname']
if name == self.mono_name:
has_encoder = name
if i['data_keys'][i['name']]['source'] == 'pizzabox-di-file':
print("loading data {}".format(stream_name))
data = self.loadTRIGtraceDB(uid, stream_name)
print("done")
if i['data_keys'][i['name']]['source'] == 'pizzabox-adc-file':
print("loading data {}".format(stream_name))
data = self.loadADCtraceDB(uid, stream_name)
print("done")
if i['name'] + ' offset' in self.db[uid]['start'] and type(
data) == pd.core.frame.DataFrame:
print("subtracting offset : {}".format(i['name']))
data.iloc[:, 1] = data.iloc[:, 1] - self.db[uid]['start'][
i['name'] + ' offset']
if i['data_keys'][i['name']]['source'] == 'pizzabox-enc-file':
print("loading data {}".format(stream_name))
data = self.loadENCtraceDB(uid, stream_name)
print("done")
# if type(data) == np.ndarray:
print("saving to {}".format(name))
self.arrays[name] = data
if has_encoder is not False:
energy = self.arrays.get(has_encoder).copy()
if 'angle_offset' in self.db[uid]['start']:
energy.iloc[:, 1] = xray.encoder2energy(
energy.iloc[:, 1], self.pulses_per_deg,
-float(self.db[uid]['start']['angle_offset']))
energy.columns = ['timestamp', 'energy']
del self.arrays[has_encoder]
self.arrays['energy'] = energy
t2 = time.time()
print(f"Data read took {t2-t1} sec")
def load(self, uid):
if self.db is None:
raise Exception(
'The databroker was not passed as argument to the parser')
self.arrays = {}
self.interp_arrays = {}
self.uid = uid
has_encoder = False
for i in self.db[uid]['descriptors']:
if 'filename' in i['data_keys'][i['name']]:
name = i['name']
if name == 'pb9_enc1' or name == 'hhm_theta':
has_encoder = name
if 'devname' in i['data_keys'][i['name']]:
name = i['data_keys'][i['name']]['devname']
if name == 'hhm_theta':
has_encoder = name
if i['data_keys'][i['name']]['source'] == 'pizzabox-di-file':
data = self.loadTRIGtrace(
i['data_keys'][i['name']]['filename'], '')
if i['data_keys'][i['name']]['source'] == 'pizzabox-adc-file':
data = self.loadADCtrace(
i['data_keys'][i['name']]['filename'], '')
if i['name'] + ' offset' in self.db[uid]['start']:
data[:,
1] = data[:,
1] - self.db[uid]['start'][i['name'] +
' offset']
if i['data_keys'][i['name']]['source'] == 'pizzabox-enc-file':
data = self.loadENCtrace(
i['data_keys'][i['name']]['filename'], '')
self.arrays[name] = data
if has_encoder is not False:
energy = np.copy(self.arrays.get(has_encoder))
if 'angle_offset' in self.db[uid]['start']:
energy[:, 1] = xray.encoder2energy(
energy[:, 1],
-float(self.db[uid]['start']['angle_offset']))
del self.arrays[has_encoder]
self.arrays['energy'] = energy
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 e2energy(self, offset):
self.energy_grid = -xray.encoder2energy(
self.encoder_grid, self.hhm.pulses_per_deg, offset)
def load(self,
orig_file_name,
new_file_path,
new_file_name='hhm.txt',
orig_file_path='/GPFS/xf08id/trajectory/',
ip='10.8.2.86'):
print('[Load Trajectory] Starting...')
# 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))
min_energy = int(xray.encoder2energy((-traj).min()))
max_energy = int(xray.encoder2energy((-traj).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))
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()):
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, orig_file_name, min_energy,
max_energy, new_file_path))
ttime.sleep(0.01)
ftp.close()
print('[Load Trajectory] Permissions OK')
s.logout()
s.pid = None
print('[Load Trajectory] Completed!')
else:
print(
'[Load Trajectory] Fail! Not able to ssh into the controller...'
)
