def _build_configs(self):
"""Build the :attr:`configs` dictionary"""
# Assumptions:
# 1. only one NI_XYZ drive was ever built, so there will always
# be only one configuration
# - naming configuration 'config01'
# 2. there's only one dataset ever created 'Run time list'
# 3. there can be multiple motion lists defined
# - each sub-group is a configuration for a different
# motion list
# - the name of the sub-group is the name of the motion list
#
# initialize configuration
cname = 'config01'
self.configs[cname] = {}
# check there are existing motion lists
if len(self.subgroup_names) == 0:
warn(self.info['group path'] +
': no defining motion list groups exist')
# get dataset
try:
dset = self.group[self.construct_dataset_name()]
except KeyError:
why = ("Dataset '" + self.construct_dataset_name() + "' not found")
raise HDFMappingError(self.info['group path'], why=why)
# ---- define general config values ----
self.configs[cname].update({
'Note':
"The 'r', 'theta', and 'phi' fields in the "
"NI_XYZ data set are suppose to represent "
"spherical coordinates of the probe tip with "
"respect to the pivot point of the probe drive, "
"but the current calculation and population of the"
"fields is inaccurate. For user reference, the "
"distance between the probe drive pivot point and"
"LaPD axis is (Lpp =) 58.771 cm.",
'Lpp':
58.771 * u.cm,
})
# ---- define motion list values ----
self.configs[cname]['motion lists'] = {}
# get sub-group names (i.e. ml names)
_ml_names = []
for name in self.group:
if isinstance(self.group[name], h5py.Group):
_ml_names.append(name)
# a motion list group must have the attributes
# Nx, Ny, Nz, dx, dy, dz, x0, y0, z0
names_to_remove = []
for name in _ml_names:
if all(attr not in self.group[name].attrs
for attr in ('Nx', 'Ny', 'Nz', 'dx', 'dy', 'dz', 'x0', 'y0',
'z0')):
names_to_remove.append(name)
if bool(names_to_remove):
for name in names_to_remove:
_ml_names.remove(name)
# warn if no motion lists exist
if not bool(_ml_names):
why = 'NI_XYZ has no identifiable motion lists'
warn(why)
# gather ML config values
pairs = [
('Nx', 'Nx'),
('Ny', 'Ny'),
('Nz', 'Nz'),
('dx', 'dx'),
('dy', 'dy'),
('dz', 'dz'),
('fan_XYZ', 'fan_XYZ'),
('max_ydrive_steps', 'max_ydrive_steps'),
('min_ydrive_steps', 'min_ydrive_steps'),
('max_zdrive_steps', 'max_zdrive_steps'),
('min_zdrive_steps', 'min_zdrive_steps'),
('x0', 'x0'),
('y0', 'y0'),
('z0', 'z0'),
('port', 'z_port'),
]
for name in _ml_names:
# initialize ML dictionary
self.configs[cname]['motion lists'][name] = {}
# add ML values
for pair in pairs:
try:
# get attribute value
val = self.group[name].attrs[pair[1]]
# condition value
if np.issubdtype(type(val), np.bytes_):
# - val is a np.bytes_ string
val = val.decode('utf-8')
if pair[1] == 'fan_XYZ':
# convert to boolean
if val == 'TRUE':
val = True
else:
val = False
# assign val to configs
self.configs[cname]['motion lists'][name][pair[0]] \
= val
except KeyError:
self.configs[cname]['motion lists'][name][pair[0]] \
= None
why = "Motion List attribute '" + pair[1] \
+ "' not found for ML group '" + name + "'"
warn(why)
# ---- define 'dset paths' ----
self.configs[cname]['dset paths'] = (dset.name, )
# ---- define 'shotnum' ----
# check dset for 'Shot number' field
if 'Shot number' not in dset.dtype.names:
why = "Dataset '" + dset.name \
+ "' is missing 'Shot number' field"
raise HDFMappingError(self.info['group path'], why=why)
# initialize
self.configs[cname]['shotnum'] = {
'dset paths': self.configs[cname]['dset paths'],
'dset field': ('Shot number', ),
'shape': dset.dtype['Shot number'].shape,
'dtype': np.int32,
}
# ---- define 'state values' ----
self._configs[cname]['state values'] = {
'xyz': {
'dset paths': self._configs[cname]['dset paths'],
'dset field': ('x', 'y', 'z'),
'shape': (3, ),
'dtype': np.float64
},
}
# check dset for 'x', 'y' and 'z' fields
fx = 'x' not in dset.dtype.names
fy = 'y' not in dset.dtype.names
fz = 'z' not in dset.dtype.names
if fx and fy and fz:
why = "Dataset '" + dset.name \
+ "' missing fields 'x', 'y' and 'z'"
raise HDFMappingError(self.info['group path'], why=why)
elif fx or fy or fz:
mlist = [('x', fx), ('y', fy), ('z', fz)]
missf = ', '.join([val for val, bol in mlist if bol])
why = " Dataset '" + dset.name \
+ "' missing field '" + missf + "'"
warn(why)
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# look for required datasets
for dset_name in [
'Magnet power supply currents', 'Magnetic field profile',
'Magnetic field summary'
]:
if dset_name not in self.group:
why = "dataset '" + dset_name + "' not found"
raise HDFMappingError(self.info['group path'], why=why)
# initialize general info values
pairs = [('calib tag', 'Calibration tag'),
('z', 'Profile z locations')]
for pair in pairs:
try:
val = self.group.attrs[pair[1]]
if isinstance(val, (list, tuple, np.ndarray)):
self._configs[pair[0]] = val
else:
self._configs[pair[0]] = [val]
except KeyError:
self._configs[pair[0]] = []
warn("Attribute '" + pair[1] +
"' not found for MSI diagnostic '" + self.device_name +
"', continuing with mapping")
# initialize 'shape'
# - this is used by HDFReadMSI
self._configs['shape'] = ()
# initialize 'shotnum'
self._configs['shotnum'] = {
'dset paths': (),
'dset field': ('Shot number', ),
'shape': (),
'dtype': np.int32,
}
# initialize 'signals'
# - there are two signal fields
# 1. 'magnet ps current'
# 2. 'magnetic field'
#
self._configs['signals'] = {
'magnet ps current': {
'dset paths': (),
'dset field': (),
'shape': (),
'dtype': np.float32,
},
'magnetic field': {
'dset paths': (),
'dset field': (),
'shape': (),
'dtype': np.float32,
}
}
# initialize 'meta'
self._configs['meta'] = {
'shape': (),
'timestamp': {
'dset paths': (),
'dset field': ('Timestamp', ),
'shape': (),
'dtype': np.float64,
},
'data valid': {
'dset paths': (),
'dset field': ('Data valid', ),
'shape': (),
'dtype': np.int8,
},
'peak magnetic field': {
'dset paths': (),
'dset field': ('Peak magnetic field', ),
'shape': (),
'dtype': np.float32,
},
}
# ---- update configs related to 'Magnetic field summary' ----
# - dependent configs are:
# 1. 'shotnum'
# 2. all of 'meta'
#
dset_name = 'Magnetic field summary'
dset = self.group[dset_name]
# define 'shape'
expected_fields = [
'Shot number', 'Timestamp', 'Data valid', 'Peak magnetic field'
]
if dset.ndim == 1 and \
all(field in dset.dtype.names
for field in expected_fields):
self._configs['shape'] = dset.shape
else:
why = "'/Magnetic field summary' does not match expected " \
"shape"
raise HDFMappingError(self.info['group path'], why=why)
# update 'shotnum'
self._configs['shotnum']['dset paths'] = (dset.name, )
self._configs['shotnum']['shape'] = \
dset.dtype['Shot number'].shape
# update 'meta/timestamp'
self._configs['meta']['timestamp']['dset paths'] = (dset.name, )
self._configs['meta']['timestamp']['shape'] = \
dset.dtype['Timestamp'].shape
# update 'meta/data valid'
self._configs['meta']['data valid']['dset paths'] = (dset.name, )
self._configs['meta']['data valid']['shape'] = \
dset.dtype['Data valid'].shape
# update 'meta/peak magnetic field'
self._configs['meta']['peak magnetic field']['dset paths'] = \
(dset.name,)
self._configs['meta']['peak magnetic field']['shape'] = \
dset.dtype['Peak magnetic field'].shape
# update configs related to 'Magnet power supply currents' ----
# - dependent configs are:
# 1. 'signals/magnet ps current'
#
dset_name = 'Magnet power supply currents'
dset = self.group[dset_name]
self._configs['signals']['magnet ps current']['dset paths'] = \
(dset.name,)
# check 'shape'
_build_success = True
if dset.dtype.names is not None:
# dataset has fields (it should not have fields)
_build_success = False
elif dset.ndim == 2:
if dset.shape[0] == self._configs['shape'][0]:
self._configs['signals']['magnet ps current']['shape'] = (
dset.shape[1], )
else:
_build_success = False
else:
_build_success = False
if not _build_success:
why = "'/Magnet power supply currents' does not match " \
"expected shape"
raise HDFMappingError(self.info['group path'], why=why)
# update configs related to 'Magnetic field profile' ----
# - dependent configs are:
# 1. 'signals/magnetic field'
#
dset_name = 'Magnetic field profile'
dset = self.group[dset_name]
self._configs['signals']['magnetic field']['dset paths'] = \
(dset.name,)
# check 'shape'
_build_success = True
if dset.dtype.names is not None:
# dataset has fields (it should not have fields)
_build_success = False
elif dset.ndim == 2:
if dset.shape[0] == self._configs['shape'][0]:
self._configs['signals']['magnetic field']['shape'] = (
dset.shape[1], )
else:
_build_success = False
else:
_build_success = False
if not _build_success:
why = "'/Magnetic field profile' does not match expected " \
"shape"
raise HDFMappingError(self.info['group path'], why=why)
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# What should be in configs
# 1. num. of interferometers
# 2. start times for each interferometers
# 3. dt for each interferometer
# 4. n_bar_L for each interferometer
# 5. z location for each interferometer
# 6. 'shotnum' field
# - contains mapping of HDF5 file quantity to np
# a. shape
# b. dtype
# 7. 'signals' field
# - another dict where keys are the fields to be added to
# the np.array
# 8. 'meta' field
#
# initialize general info values
# - pairs[0:2] are found in the main group's attributes
# - pairs[2] corresponds to the sub-group names
# - pairs[3:] are found in the main group's attributes (as an
# array) and in the sub-group attributes (elements of the
# main group's array)...I'm choosing to populate via the
# sub-group attributes to ensure one-to-one correspondence
# when extracting data with the HDFReadMSI class
#
pairs = [('n interferometer', 'Interferometer count'),
('calib tag', 'Calibration tag'),
('interferometer name', None), ('t0', 'Start time'),
('dt', 'Timestep'), ('n_bar_L', 'n_bar_L'),
('z', 'z location')]
self._configs['interferometer name'] = []
self._configs['t0'] = []
self._configs['dt'] = []
self._configs['n_bar_L'] = []
self._configs['z'] = []
for pair in pairs[0:2]:
try:
val = self.group.attrs[pair[1]]
if isinstance(val, (list, tuple, np.ndarray)):
self._configs[pair[0]] = val
else:
self._configs[pair[0]] = [val]
except KeyError:
self._configs[pair[0]] = []
warn("Attribute '" + pair[1] +
"' not found for MSI diagnostic '" + self.device_name +
"', continuing with mapping")
# more handling of general info value 'n interferometer'
pair = pairs[0]
check_n_inter = True
if len(self._configs[pair[0]]) != 1:
check_n_inter = False
warn("Attribute '" + pair[1] + "' for MSI diagnostic '" +
self.device_name +
"' not an integer, continuing with mapping")
elif not isinstance(self._configs[pair[0]][0], (int, np.integer)):
check_n_inter = False
warn("Attribute '" + pair[1] + "' for MSI diagnostic '" +
self.device_name +
"' not an integer, continuing with mapping")
# initialize 'shape'
# - this is used by HDFReadMSI
self._configs['shape'] = ()
# initialize 'shotnum'
self._configs['shotnum'] = {
'dset paths': [],
'dset field': ('Shot number', ),
'shape': [],
'dtype': np.int32,
}
# initialize 'signals'
# - there is only one signal field named 'signal'
self._configs['signals'] = {
'signal': {
'dset paths': [],
'dset field': (),
'shape': [],
'dtype': np.float32,
}
}
# initialize 'meta'
self._configs['meta'] = {
'timestamp': {
'dset paths': [],
'dset field': ('Timestamp', ),
'shape': [],
'dtype': np.float64
},
'data valid': {
'dset paths': [],
'dset field': ('Data valid', ),
'shape': [],
'dtype': np.int8
},
'peak density': {
'dset paths': [],
'dset field': ('Peak density', ),
'shape': [],
'dtype': np.float32
},
}
self._configs['meta']['shape'] = () if not check_n_inter \
else (int(self._configs['n interferometer'][0]),)
# populate self.configs from each interferometer group
# - all the population is done in this for-loop to ensure all
# lists are one-to-one
#
n_inter_count = 0
sn_size = 0
sig_size = 0
for name in self.group:
if isinstance(self.group[name], h5py.Group) \
and 'Interferometer' in name:
# count the number of interferometers
n_inter_count += 1
# ensure required datasets are present
for dset_name in [
'Interferometer summary list', 'Interferometer trace'
]:
if dset_name not in self.group[name]:
why = ("dataset '" + dset_name + "' not found " +
"for 'Interferometer/" + name + "'")
raise HDFMappingError(self.info['group path'], why=why)
# populate general info values
self._configs['interferometer name'].append(name)
for pair in pairs[3::]:
try:
self._configs[pair[0]].append(
self.group[name].attrs[pair[1]])
except KeyError:
self._configs[pair[0]].append(None)
warn("Attribute '" + pair[1] +
"' not found for MSI diagnostic '" +
self.device_name + '/' + name +
"', continuing with mapping")
# define values to ensure dataset sizes are consistent
# sn_size = number of shot numbers
# sig_size = number of samples in interferometer trace
# - the way the np.array will be constructed
# requires all interferometer signals to
# have the same sample size
# - define sn_size and ensure it's consistent among all
# datasets
# - define sig_size and ensure it's consistent among all
# datasets
#
# - Enforcement of the these dimensions is done when
# mapping each dataset below
#
if n_inter_count == 1:
# define sn_size
dset_name = name + '/Interferometer summary list'
dset = self.group[dset_name]
if dset.ndim == 1:
sn_size = self.group[dset_name].shape[0]
else:
why = "'/Interferometer summary list' " \
"does not match expected shape"
raise HDFMappingError(self.info['group path'], why=why)
# define sig_size
dset_name = name + '/Interferometer trace'
dset = self.group[dset_name]
shape = self.group[dset_name].shape
if dset.dtype.names is not None:
# dataset has fields (it should not have fields)
why = "can not handle a 'signal' dataset" \
+ "(" + dset_name + ") with fields"
raise HDFMappingError(self.info['group path'], why=why)
elif dset.ndim == 2:
if dset.shape[0] == sn_size:
sig_size = shape[1]
else:
why = "'Interferometer trace' and " \
"'Interferometer summary list' do " \
"not have same number of rows " \
"(shot numbers)"
raise HDFMappingError(self.info['group path'],
why=why)
else:
why = "'/Interferometer race' does not" \
" match expected shape"
raise HDFMappingError(self.info['group path'], why=why)
# define 'shape'
self._configs['shape'] = (sn_size, )
# -- update configs related to ----
# -- 'Interferometer summary list' ----
# - dependent configs are:
# 1. 'shotnum'
# 2. all of 'meta'
#
dset_name = name + '/Interferometer summary list'
dset = self.group[dset_name]
path = dset.name
# check 'shape'
expected_fields = [
'Shot number', 'Timestamp', 'Data valid', 'Peak density'
]
if dset.shape != (sn_size, ):
# shape is not consistent among all datasets
why = "'/Interferometer summary list' shape " \
"is not consistent across all " \
"interferometers"
raise HDFMappingError(self.info['group path'], why=why)
elif not all(field in dset.dtype.names
for field in expected_fields):
# required fields are not present
why = "'/Interferometer summary list' does " \
"NOT have required fields"
raise HDFMappingError(self.info['group path'], why=why)
# update 'shotnum'
self._configs['shotnum']['dset paths'].append(path)
self._configs['shotnum']['shape'].append(
dset.dtype['Shot number'].shape)
# update 'meta/timestamp'
self._configs['meta']['timestamp']['dset paths'].append(
dset.name)
self._configs['meta']['timestamp']['shape'].append(
dset.dtype['Timestamp'].shape)
# update 'meta/data valid'
self._configs['meta']['data valid']['dset paths'].append(
dset.name)
self._configs['meta']['data valid']['shape'].append(
dset.dtype['Data valid'].shape)
# update 'meta/peak density'
self._configs['meta']['peak density']['dset paths'].append(
dset.name)
self._configs['meta']['peak density']['shape'].append(
dset.dtype['Peak density'].shape)
# -- update configs related to ----
# -- 'Interferometer trace' ----
# - dependent configs are:
# 1. 'signals/signal'
#
dset_name = name + '/Interferometer trace'
dset = self.group[dset_name]
# check 'shape'
if dset.shape != (sn_size, sig_size):
# shape is not consistent among all datasets
why = "'/Interferometer trace' shape is" \
"not consistent across all " \
"interferometers"
raise HDFMappingError(self.info['group path'], why=why)
elif dset.dtype.names is not None:
# dataset has fields (it should not have fields)
why = "'/Interferometer trace' shape does" \
"not match expected shape "
raise HDFMappingError(self.info['group path'], why=why)
# update 'signals/signal' values
self._configs['signals']['signal']['dset paths'].append(
dset.name)
# -- Post Populate Checks ----
# check 'shotnum'
# 1. convert 'dset paths' from list to tuple
# 2. convert 'shape' to a single tuple of shape
self._configs['shotnum']['dset paths'] = \
tuple(self._configs['shotnum']['dset paths'])
sn_shapes = self._configs['shotnum']['shape']
self._configs['shotnum']['shape'] = sn_shapes[0]
# check 'signals' and 'meta'
# 1. convert 'dset paths' from list to tuple
# 2. every dataset has the same 'shape'
for subfield in ('signals', 'meta'):
subconfigs = self._configs[subfield]
for field, config in subconfigs.items():
# define shape
if check_n_inter:
# 'n interferometer' was found in the HDF5 file
shape = (int(self._configs['n interferometer'][0]),
sig_size)
else:
# 'n interferometer' was NOT found, rely on count
shape = (n_inter_count, sig_size)
# update ['meta']['shape']
if field == 'shape' and subfield == 'meta':
self._configs[subfield][field] = (shape[0], )
continue
# convert ['dset paths'] to tuple
self._configs[subfield][field]['dset paths'] = \
tuple(config['dset paths'])
# ensure all fields have the same shape
if subfield == 'signals':
self._configs[subfield][field]['shape'] = shape
else:
shapes = self._configs[subfield][field]['shape']
if all(shape == shapes[0] for shape in shapes):
self._configs[subfield][field]['shape'] = \
shapes[0]
else:
why = ("dataset shape for field '" + field +
"' is not consistent for all " +
"interferometers")
raise HDFMappingError(self.info['group path'], why=why)
# ensure the number of found interferometers is equal to the
# diagnostics 'Interferometer count'
#
if check_n_inter:
if n_inter_count != self._configs['n interferometer'][0]:
why = 'num. of found interferometers did not ' \
'match the expected num. of interferometers'
raise HDFMappingError(self.info['group path'], why=why)
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# check there are configurations to map
if len(self.subgroup_names) == 0:
why = "has no mappable configurations"
raise HDFMappingError(self._info["group path"], why=why)
# build configuration dictionaries
# - assume every sub-group represents a unique configuration
# to the control device
# - the name of each sub-group is used as the configuration
# name
# - assume all configurations are active (i.e. used)
#
for name in self.subgroup_names:
# get configuration group
cong = self.group[name]
# get dataset
try:
dset = self.group[self.construct_dataset_name()]
except KeyError:
why = (
f"Dataset '{self.construct_dataset_name()}' not found for "
f"configuration group '{name}'"
)
raise HDFMappingError(self._info["group path"], why=why)
# initialize _configs
self._configs[name] = {}
# ---- define general info values ----
pairs = [
("IP address", "IP address"),
("generator device", "Generator type"),
("GPIB address", "GPIB address"),
("initial state", "Initial state"),
("command list", "Waveform command list"),
]
for pair in pairs:
try:
# get attribute value
val = cong.attrs[pair[1]]
# condition value
if pair[0] == "command list":
# - val gets returned as a np.bytes_ string
# - split line returns
# - remove trailing/leading whitespace
#
val = _bytes_to_str(val).splitlines()
val = tuple([cls.strip() for cls in val])
elif pair[0] in ("IP address", "generator device", "initial state"):
# - val is a np.bytes_ string
#
val = _bytes_to_str(val)
else:
# no conditioning is needed
# 'GPIB address' val is np.uint32
pass
# assign val to _configs
self._configs[name][pair[0]] = val
except KeyError:
self._configs[name][pair[0]] = None
warn_str = (
f"Attribute '{pair[1]}' not found in control device '"
f"{self.device_name}' configuration group '{name}'"
)
if pair[0] != "command list":
warn_str += ", continuing with mapping"
warn(warn_str)
else:
why = (
f"Attribute '{pair[1]}' not found for configuration "
f"group '{name}'"
)
raise HDFMappingError(self._info["group path"], why=why)
# ---- define 'dset paths' ----
self._configs[name]["dset paths"] = (dset.name,)
# ---- define 'shotnum' ----
# initialize
self._configs[name]["shotnum"] = {
"dset paths": self._configs[name]["dset paths"],
"dset field": ("Shot number",),
"shape": dset.dtype["Shot number"].shape,
"dtype": np.int32,
}
# ---- define 'state values' ----
# catch and suppress warnings only for initialization
with warnings.catch_warnings():
warnings.simplefilter("ignore")
try:
sv_state = self._construct_state_values_dict(
name, self._default_re_patterns
)
except KeyError:
sv_state = {}
# initialize
self._configs[name]["state values"] = (
sv_state if bool(sv_state) else self._default_state_values_dict(name)
)
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# look for required datasets
for dset_name in [
"Magnet power supply currents",
"Magnetic field profile",
"Magnetic field summary",
]:
if dset_name not in self.group:
why = f"dataset '{dset_name}' not found"
raise HDFMappingError(self.info["group path"], why=why)
# initialize general info values
pairs = [("calib tag", "Calibration tag"), ("z", "Profile z locations")]
for pair in pairs:
try:
val = self.group.attrs[pair[1]]
if isinstance(val, (list, tuple, np.ndarray)):
self._configs[pair[0]] = val
else:
self._configs[pair[0]] = [val]
except KeyError:
self._configs[pair[0]] = []
warn(
f"Attribute '{pair[1]}' not found for MSI diagnostic "
f"'{self.device_name}', continuing with mapping"
)
# initialize 'shape'
# - this is used by HDFReadMSI
self._configs["shape"] = ()
# initialize 'shotnum'
self._configs["shotnum"] = {
"dset paths": (),
"dset field": ("Shot number",),
"shape": (),
"dtype": np.int32,
}
# initialize 'signals'
# - there are two signal fields
# 1. 'magnet ps current'
# 2. 'magnetic field'
#
self._configs["signals"] = {
"magnet ps current": {
"dset paths": (),
"dset field": (),
"shape": (),
"dtype": np.float32,
},
"magnetic field": {
"dset paths": (),
"dset field": (),
"shape": (),
"dtype": np.float32,
},
}
# initialize 'meta'
self._configs["meta"] = {
"shape": (),
"timestamp": {
"dset paths": (),
"dset field": ("Timestamp",),
"shape": (),
"dtype": np.float64,
},
"data valid": {
"dset paths": (),
"dset field": ("Data valid",),
"shape": (),
"dtype": np.int8,
},
"peak magnetic field": {
"dset paths": (),
"dset field": ("Peak magnetic field",),
"shape": (),
"dtype": np.float32,
},
}
# ---- update configs related to 'Magnetic field summary' ----
# - dependent configs are:
# 1. 'shotnum'
# 2. all of 'meta'
#
dset_name = "Magnetic field summary"
dset = self.group[dset_name]
# define 'shape'
expected_fields = [
"Shot number",
"Timestamp",
"Data valid",
"Peak magnetic field",
]
if dset.ndim == 1 and all(field in dset.dtype.names for field in expected_fields):
self._configs["shape"] = dset.shape
else:
why = "'/Magnetic field summary' does not match expected shape"
raise HDFMappingError(self.info["group path"], why=why)
# update 'shotnum'
self._configs["shotnum"]["dset paths"] = (dset.name,)
self._configs["shotnum"]["shape"] = dset.dtype["Shot number"].shape
# update 'meta/timestamp'
self._configs["meta"]["timestamp"]["dset paths"] = (dset.name,)
self._configs["meta"]["timestamp"]["shape"] = dset.dtype["Timestamp"].shape
# update 'meta/data valid'
self._configs["meta"]["data valid"]["dset paths"] = (dset.name,)
self._configs["meta"]["data valid"]["shape"] = dset.dtype["Data valid"].shape
# update 'meta/peak magnetic field'
self._configs["meta"]["peak magnetic field"]["dset paths"] = (dset.name,)
self._configs["meta"]["peak magnetic field"]["shape"] = dset.dtype[
"Peak magnetic field"
].shape
# update configs related to 'Magnet power supply currents' ----
# - dependent configs are:
# 1. 'signals/magnet ps current'
#
dset_name = "Magnet power supply currents"
dset = self.group[dset_name]
self._configs["signals"]["magnet ps current"]["dset paths"] = (dset.name,)
# check 'shape'
_build_success = True
if dset.dtype.names is not None:
# dataset has fields (it should not have fields)
_build_success = False
elif dset.ndim == 2:
if dset.shape[0] == self._configs["shape"][0]:
self._configs["signals"]["magnet ps current"]["shape"] = (dset.shape[1],)
else:
_build_success = False
else:
_build_success = False
if not _build_success:
why = "'/Magnet power supply currents' does not match expected shape"
raise HDFMappingError(self.info["group path"], why=why)
# update configs related to 'Magnetic field profile' ----
# - dependent configs are:
# 1. 'signals/magnetic field'
#
dset_name = "Magnetic field profile"
dset = self.group[dset_name]
self._configs["signals"]["magnetic field"]["dset paths"] = (dset.name,)
# check 'shape'
_build_success = True
if dset.dtype.names is not None:
# dataset has fields (it should not have fields)
_build_success = False
elif dset.ndim == 2:
if dset.shape[0] == self._configs["shape"][0]:
self._configs["signals"]["magnetic field"]["shape"] = (dset.shape[1],)
else:
_build_success = False
else:
_build_success = False
if not _build_success:
why = "'/Magnetic field profile' does not match expected shape"
raise HDFMappingError(self.info["group path"], why=why)
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# What should be in configs
# 1. num. of interferometers
# 2. start times for each interferometers
# 3. dt for each interferometer
# 4. n_bar_L for each interferometer
# 5. z location for each interferometer
# 6. 'shotnum' field
# - contains mapping of HDF5 file quantity to np
# a. shape
# b. dtype
# 7. 'signals' field
# - another dict where keys are the fields to be added to
# the np.array
# 8. 'meta' field
#
# initialize general info values
# - pairs[0:2] are found in the main group's attributes
# - pairs[2] corresponds to the sub-group names
# - pairs[3:] are found in the main group's attributes (as an
# array) and in the sub-group attributes (elements of the
# main group's array)...I'm choosing to populate via the
# sub-group attributes to ensure one-to-one correspondence
# when extracting data with the HDFReadMSI class
#
pairs = [
("n interferometer", "Interferometer count"),
("calib tag", "Calibration tag"),
("interferometer name", None),
("t0", "Start time"),
("dt", "Timestep"),
("n_bar_L", "n_bar_L"),
("z", "z location"),
]
self._configs["interferometer name"] = []
self._configs["t0"] = []
self._configs["dt"] = []
self._configs["n_bar_L"] = []
self._configs["z"] = []
for pair in pairs[0:2]:
try:
val = self.group.attrs[pair[1]]
if isinstance(val, (list, tuple, np.ndarray)):
self._configs[pair[0]] = val
else:
self._configs[pair[0]] = [val]
except KeyError:
self._configs[pair[0]] = []
warn(f"Attribute '{pair[1]}' not found for MSI diagnostic "
f"'{self.device_name}', continuing with mapping")
# more handling of general info value 'n interferometer'
pair = pairs[0]
check_n_inter = True
if len(self._configs[pair[0]]) != 1:
check_n_inter = False
warn(
f"Attribute '{pair[1]}' for MSI diagnostic "
f"'{self.device_name}' not an integer, continuing with mapping"
)
elif not isinstance(self._configs[pair[0]][0], (int, np.integer)):
check_n_inter = False
warn(
f"Attribute '{pair[1]}' for MSI diagnostic "
f"'{self.device_name}' not an integer, continuing with mapping"
)
# initialize 'shape'
# - this is used by HDFReadMSI
self._configs["shape"] = ()
# initialize 'shotnum'
self._configs["shotnum"] = {
"dset paths": [],
"dset field": ("Shot number", ),
"shape": [],
"dtype": np.int32,
}
# initialize 'signals'
# - there is only one signal field named 'signal'
self._configs["signals"] = {
"signal": {
"dset paths": [],
"dset field": (),
"shape": [],
"dtype": np.float32,
}
}
# initialize 'meta'
self._configs["meta"] = {
"timestamp": {
"dset paths": [],
"dset field": ("Timestamp", ),
"shape": [],
"dtype": np.float64,
},
"data valid": {
"dset paths": [],
"dset field": ("Data valid", ),
"shape": [],
"dtype": np.int8,
},
"peak density": {
"dset paths": [],
"dset field": ("Peak density", ),
"shape": [],
"dtype": np.float32,
},
}
self._configs["meta"]["shape"] = (() if not check_n_inter else (int(
self._configs["n interferometer"][0]), ))
# populate self.configs from each interferometer group
# - all the population is done in this for-loop to ensure all
# lists are one-to-one
#
n_inter_count = 0
sn_size = 0
sig_size = 0
for name in self.group:
if isinstance(self.group[name],
h5py.Group) and "Interferometer" in name:
# count the number of interferometers
n_inter_count += 1
# ensure required datasets are present
for dset_name in [
"Interferometer summary list", "Interferometer trace"
]:
if dset_name not in self.group[name]:
why = (f"dataset '{dset_name}' not found for "
f"'Interferometer/{name}'")
raise HDFMappingError(self.info["group path"], why=why)
# populate general info values
self._configs["interferometer name"].append(name)
for pair in pairs[3::]:
try:
self._configs[pair[0]].append(
self.group[name].attrs[pair[1]])
except KeyError:
self._configs[pair[0]].append(None)
warn(
f"Attribute '{pair[1]}' not found for MSI diagnostic "
f"'{self.device_name}/{name}', continuing with mapping"
)
# define values to ensure dataset sizes are consistent
# sn_size = number of shot numbers
# sig_size = number of samples in interferometer trace
# - the way the np.array will be constructed
# requires all interferometer signals to
# have the same sample size
# - define sn_size and ensure it's consistent among all
# datasets
# - define sig_size and ensure it's consistent among all
# datasets
#
# - Enforcement of the these dimensions is done when
# mapping each dataset below
#
if n_inter_count == 1:
# define sn_size
dset_name = f"{name}/Interferometer summary list"
dset = self.group[dset_name]
if dset.ndim == 1:
sn_size = self.group[dset_name].shape[0]
else:
why = ("'/Interferometer summary list' "
"does not match expected shape")
raise HDFMappingError(self.info["group path"], why=why)
# define sig_size
dset_name = f"{name}/Interferometer trace"
dset = self.group[dset_name]
shape = self.group[dset_name].shape
if dset.dtype.names is not None:
# dataset has fields (it should not have fields)
why = (f"can not handle a 'signal' dataset "
f"({dset_name}) with fields")
raise HDFMappingError(self.info["group path"], why=why)
elif dset.ndim == 2:
if dset.shape[0] == sn_size:
sig_size = shape[1]
else:
why = ("'Interferometer trace' and "
"'Interferometer summary list' do "
"not have same number of rows "
"(shot numbers)")
raise HDFMappingError(self.info["group path"],
why=why)
else:
why = "'/Interferometer race' does not match expected shape"
raise HDFMappingError(self.info["group path"], why=why)
# define 'shape'
self._configs["shape"] = (sn_size, )
# -- update configs related to ----
# -- 'Interferometer summary list' ----
# - dependent configs are:
# 1. 'shotnum'
# 2. all of 'meta'
#
dset_name = f"{name}/Interferometer summary list"
dset = self.group[dset_name]
path = dset.name
# check 'shape'
expected_fields = [
"Shot number",
"Timestamp",
"Data valid",
"Peak density",
]
if dset.shape != (sn_size, ):
# shape is not consistent among all datasets
why = ("'/Interferometer summary list' shape "
"is not consistent across all "
"interferometers")
raise HDFMappingError(self.info["group path"], why=why)
elif not all(field in dset.dtype.names
for field in expected_fields):
# required fields are not present
why = "'/Interferometer summary list' does NOT have required fields"
raise HDFMappingError(self.info["group path"], why=why)
# update 'shotnum'
self._configs["shotnum"]["dset paths"].append(path)
self._configs["shotnum"]["shape"].append(
dset.dtype["Shot number"].shape)
# update 'meta/timestamp'
self._configs["meta"]["timestamp"]["dset paths"].append(
dset.name)
self._configs["meta"]["timestamp"]["shape"].append(
dset.dtype["Timestamp"].shape)
# update 'meta/data valid'
self._configs["meta"]["data valid"]["dset paths"].append(
dset.name)
self._configs["meta"]["data valid"]["shape"].append(
dset.dtype["Data valid"].shape)
# update 'meta/peak density'
self._configs["meta"]["peak density"]["dset paths"].append(
dset.name)
self._configs["meta"]["peak density"]["shape"].append(
dset.dtype["Peak density"].shape)
# -- update configs related to ----
# -- 'Interferometer trace' ----
# - dependent configs are:
# 1. 'signals/signal'
#
dset_name = f"{name}/Interferometer trace"
dset = self.group[dset_name]
# check 'shape'
if dset.shape != (sn_size, sig_size):
# shape is not consistent among all datasets
why = ("'/Interferometer trace' shape is"
"not consistent across all "
"interferometers")
raise HDFMappingError(self.info["group path"], why=why)
elif dset.dtype.names is not None:
# dataset has fields (it should not have fields)
why = "'/Interferometer trace' shape does not match expected shape "
raise HDFMappingError(self.info["group path"], why=why)
# update 'signals/signal' values
self._configs["signals"]["signal"]["dset paths"].append(
dset.name)
# -- Post Populate Checks ----
# check 'shotnum'
# 1. convert 'dset paths' from list to tuple
# 2. convert 'shape' to a single tuple of shape
self._configs["shotnum"]["dset paths"] = tuple(
self._configs["shotnum"]["dset paths"])
sn_shapes = self._configs["shotnum"]["shape"]
self._configs["shotnum"]["shape"] = sn_shapes[0]
# check 'signals' and 'meta'
# 1. convert 'dset paths' from list to tuple
# 2. every dataset has the same 'shape'
for subfield in ("signals", "meta"):
subconfigs = self._configs[subfield]
for field, config in subconfigs.items():
# define shape
if check_n_inter:
# 'n interferometer' was found in the HDF5 file
shape = (int(self._configs["n interferometer"][0]),
sig_size)
else:
# 'n interferometer' was NOT found, rely on count
shape = (n_inter_count, sig_size)
# update ['meta']['shape']
if field == "shape" and subfield == "meta":
self._configs[subfield][field] = (shape[0], )
continue
# convert ['dset paths'] to tuple
self._configs[subfield][field]["dset paths"] = tuple(
config["dset paths"])
# ensure all fields have the same shape
if subfield == "signals":
self._configs[subfield][field]["shape"] = shape
else:
shapes = self._configs[subfield][field]["shape"]
if all(shape == shapes[0] for shape in shapes):
self._configs[subfield][field]["shape"] = shapes[0]
else:
why = (
f"dataset shape for field '{field}' is not consistent "
f"for all interferometers")
raise HDFMappingError(self.info["group path"], why=why)
# ensure the number of found interferometers is equal to the
# diagnostics 'Interferometer count'
#
if check_n_inter:
if n_inter_count != self._configs["n interferometer"][0]:
why = ("num. of found interferometers did not "
"match the expected num. of interferometers")
raise HDFMappingError(self.info["group path"], why=why)
def _find_adc_connections(
self, adc_name: str, config_name: str
) -> Tuple[Tuple[int, Tuple[int, ...], Dict[str, Any]], ...]:
"""
Determines active connections on the adc.
:param adc_name: name of the analog-digital-converter
:param config_name: digitizer configuration name
:return:
Tuple of 3-element tuples where the 1st element of the
nested tuple represents a connected *board* number, the 2nd
element is a tuple of connected *channel* numbers for the
*board*, and the 3rd element is a dictionary of adc setup
values (*bit*, *clock rate*, etc.).
On determination of adc connections, the meta-info dict will
also be populated with:
.. csv-table::
:header: "Key", "Description"
:widths: 20, 60
"::
'clock rate'
", "
clock rate of the digitizer's analog-digital-converter
"
"::
'shot average (software)'
", "
number of shots intended to be averaged over
"
"::
'sample average (hardware)'
", "
number of data samples average together
"
"""
config_path = self.configs[config_name]["config group path"]
config_group = self.group.get(config_path)
active = self.configs[config_name]["active"]
# initialize conn
# conn = list of connections
#
conn = []
# define _helpers
if adc_name not in ("SIS 3302", "SIS 3305"): # pragma: no cover
# this should never happen
warn(f"Invalid adc name '{adc_name}'")
return ()
_helpers = {
"SIS 3302": {
"short": "3302",
"re": r"SIS crate 3302 configurations\[(?P<INDEX>\d+)\]",
},
"SIS 3305": {
"short": "3305",
"re": r"SIS crate 3305 configurations\[(?P<INDEX>\d+)\]",
},
}
# get slot numbers and configuration indices
slots = config_group.attrs["SIS crate slot numbers"] # type: np.ndarray
indices = config_group.attrs["SIS crate config indices"] # type: np.ndarray
# ensure slots and indices are 1D arrays of the same size
if slots.ndim != 1 or indices.ndim != 1:
raise HDFMappingError(
self.info["group path"],
"HDF5 structure unexpected...Defined slots and "
"configuration indices are not 1D arrays.",
)
elif slots.size != indices.size:
raise HDFMappingError(
self.info["group path"],
"HDF5 structure unexpected...Defined slots and "
"configuration indices are not the same size.",
)
# ensure defined slots are unique
if np.unique(slots).size != slots.size:
raise HDFMappingError(
self.info["group path"],
"HDF5 structure unexpected...defined slot numbers are not unique",
)
# Build tuple (slot, config index, board, adc)
# - build a tuple that pairs the adc name (adc), adc slot
# number (slot), configuration group index (index), and
# board number (brd)
#
adc_pairs = []
for slot, index in zip(slots, indices):
if slot != 3:
try:
brd, adc = self.slot_info[slot]
adc_pairs.append((slot, index, brd, adc))
except KeyError:
why = (
f"HDF5 structure unexpected...defined slot number {slot} "
f"is unexpected...not adding to `configs` mapping"
)
warn(why)
# Ensure the same configuration index is not assign to multiple
# slots for the same adc
for slot, index, brd, adc in adc_pairs:
for ss, ii, bb, aa in adc_pairs:
if ii == index and aa == adc and ss != slot:
why = (
"The same configuration index is assigned "
"to multiple slots of the same adc."
)
if active:
raise HDFMappingError(self.info["group path"], why=why)
else:
why += "...config not active so not adding to mapping"
warn(why)
return ()
# gather adc configuration groups
gnames = []
for name in config_group:
_match = re.fullmatch(_helpers[adc_name]["re"], name)
if bool(_match):
gnames.append((name, int(_match.group("INDEX"))))
# Determine connected (brd, ch) combinations
for name, config_index in gnames:
# find board number
brd = None
for slot, index, board, adc in adc_pairs:
if adc_name == adc and config_index == index:
brd = board
break
# ensure board number was found
if brd is None:
why = (
f"Board not found since group name determined "
f"`config_index` {config_index} not defined in top-level "
f"configuration group"
)
warn(why)
continue
# find connected channels
chs = []
if adc_name == "SIS 3302":
_patterns = (r"Enabled\s(?P<CH>\d+)",)
else:
# SIS 3305
_patterns = (
r"FPGA 1 Enabled\s(?P<CH>\d+)",
r"FPGA 2 Enabled\s(?P<CH>\d+)",
)
for key, val in config_group[name].attrs.items():
if "Enabled" in key and val == b"TRUE":
ch = None
for pat in _patterns:
_match = re.fullmatch(pat, key)
if bool(_match):
ch = int(_match.group("CH"))
if "FPGA 2" in pat:
ch += 4
break
if ch is not None:
chs.append(ch)
# ensure chs is not NULL
if len(chs) == 0:
why = (
f"HDF5 structure unexpected...'{config_name}/{name}' does "
f"not define any valid channel numbers...not adding to "
f"`configs` dict"
)
warn(why)
# skip adding to conn list
continue
# determine shot averaging
shot_ave = None
if "Shot averaging (software)" in config_group[name].attrs:
shot_ave = config_group[name].attrs["Shot averaging (software)"]
if shot_ave in (0, 1):
shot_ave = None
# determine sample averaging
sample_ave = None
if adc_name == "SIS 3305":
# the 'SIS 3305' adc does NOT support sample averaging
pass
else:
# SIS 3302
# - the HDF5 attribute is the power to 2
# - So, a hardware sample of 5 actually means the number
# of points sampled is 2^5
if "Sample averaging (hardware)" in config_group[name].attrs:
sample_ave = config_group[name].attrs["Sample averaging (hardware)"]
if sample_ave == 0:
sample_ave = None
else:
sample_ave = 2 ** sample_ave
# determine clock rate
if adc_name == "SIS 3305":
# has different clock rate modes
try:
cr_mode = config_group[name].attrs["Channel mode"]
cr_mode = int(cr_mode)
except (KeyError, ValueError):
why = (
f"HDF5 structure unexpected...'{config_name}/{name}' does "
f"not define a clock rate mode...setting to None in the "
f"`configs` dict"
)
warn(why)
cr_mode = -1
if cr_mode == 0:
cr = u.Quantity(1.25, unit="GHz")
elif cr_mode == 1:
cr = u.Quantity(2.5, unit="GHz")
elif cr_mode == 2:
cr = u.Quantity(5.0, unit="GHz")
else:
cr = None
else:
# 'SIS 3302' has one clock rate mode
cr = u.Quantity(100.0, unit="MHz")
# build subconn tuple with connected board, channels, and
# acquisition parameters
subconn = (
brd,
tuple(chs),
{
"clock rate": cr,
"shot average (software)": shot_ave,
"sample average (hardware)": sample_ave,
},
)
# add to all connections list
conn.append(subconn)
return tuple(conn)
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# look for required datasets
for dset_name in [
'Cathode-anode voltage', 'Discharge current',
'Discharge summary'
]:
if dset_name not in self.group:
why = "dataset '" + dset_name + "' not found "
raise HDFMappingError(self.info['group path'], why=why)
# initialize general info values
pairs = [('current conversion factor', 'Current conversion factor'),
('voltage conversion factor', 'Voltage conversion factor'),
('t0', 'Start time'), ('dt', 'Timestep')]
for pair in pairs:
try:
self._configs[pair[0]] = [self.group.attrs[pair[1]]]
except KeyError:
self._configs[pair[0]] = []
warn("Attribute '" + pair[1] +
"' not found for MSI diagnostic '" + self.device_name +
"', continuing with mapping")
# initialize 'shape'
# - this is used by HDFReadMSI
self._configs['shape'] = ()
# initialize 'shotnum'
self._configs['shotnum'] = {
'dset paths': (),
'dset field': ('Shot number', ),
'shape': (),
'dtype': np.int32,
}
# initialize 'signals'
# - there are two signal fields
# 1. 'voltage'
# 2. 'current'
#
self._configs['signals'] = {
'voltage': {
'dset paths': (),
'dset field': (),
'shape': (),
'dtype': np.float32,
},
'current': {
'dset paths': (),
'dset field': (),
'shape': (),
'dtype': np.float32,
}
}
# initialize 'meta'
self._configs['meta'] = {
'shape': (),
'timestamp': {
'dset paths': (),
'dset field': ('Timestamp', ),
'shape': (),
'dtype': np.float64,
},
'data valid': {
'dset paths': (),
'dset field': ('Data valid', ),
'shape': (),
'dtype': np.int8,
},
'pulse length': {
'dset paths': (),
'dset field': ('Pulse length', ),
'shape': (),
'dtype': np.float32,
},
'peak current': {
'dset paths': (),
'dset field': ('Peak current', ),
'shape': (),
'dtype': np.float32,
},
'bank voltage': {
'dset paths': (),
'dset field': ('Bank voltage', ),
'shape': (),
'dtype': np.float32,
},
}
# ---- update configs related to 'Discharge summary' ----
# - dependent configs are:
# 1. 'shape'
# 2. 'shotnum'
# 3. all of 'meta'
#
dset_name = 'Discharge summary'
dset = self.group[dset_name]
# define 'shape'
expected_fields = [
'Shot number', 'Timestamp', 'Data valid', 'Pulse length',
'Peak current', 'Bank voltage'
]
if dset.ndim == 1 and \
all(field in dset.dtype.names
for field in expected_fields):
self._configs['shape'] = dset.shape
else:
why = "'/Discharge summary' does not match expected shape"
raise HDFMappingError(self.info['group path'], why=why)
# update 'shotnum'
self._configs['shotnum']['dset paths'] = (dset.name, )
self._configs['shotnum']['shape'] = \
dset.dtype['Shot number'].shape
# update 'meta/timestamp'
self._configs['meta']['timestamp']['dset paths'] = (dset.name, )
self._configs['meta']['timestamp']['shape'] = \
dset.dtype['Timestamp'].shape
# update 'meta/data valid'
self._configs['meta']['data valid']['dset paths'] = (dset.name, )
self._configs['meta']['data valid']['shape'] = \
dset.dtype['Data valid'].shape
# update 'meta/pulse length'
self._configs['meta']['pulse length']['dset paths'] = \
(dset.name,)
self._configs['meta']['pulse length']['shape'] = \
dset.dtype['Pulse length'].shape
# update 'meta/peak current'
self._configs['meta']['peak current']['dset paths'] = \
(dset.name,)
self._configs['meta']['peak current']['shape'] = \
dset.dtype['Peak current'].shape
# update 'meta/bank voltage'
self._configs['meta']['bank voltage']['dset paths'] = \
(dset.name,)
self._configs['meta']['bank voltage']['shape'] = \
dset.dtype['Bank voltage'].shape
# ---- update configs related to 'Cathode-anode voltage' ----
# - dependent configs are:
# 1. 'signals/voltage'
#
dset_name = 'Cathode-anode voltage'
dset = self.group[dset_name]
self._configs['signals']['voltage']['dset paths'] = (dset.name, )
# check 'shape'
_build_success = True
if dset.dtype.names is not None:
# dataset has fields (it should not have fields)
_build_success = False
elif dset.ndim == 2:
if dset.shape[0] == self._configs['shape'][0]:
self._configs['signals']['voltage']['shape'] = \
(dset.shape[1],)
else:
_build_success = False
else:
_build_success = False
if not _build_success:
why = "'/Cathode-anode voltage' does not match expected " \
"shape"
raise HDFMappingError(self.info['group path'], why=why)
# update configs related to 'Discharge current' ----
# - dependent configs are:
# 1. 'signals/current'
#
dset_name = 'Discharge current'
dset = self.group[dset_name]
self._configs['signals']['current']['dset paths'] = (dset.name, )
# check 'shape'
_build_success = True
if dset.dtype.names is not None:
# dataset has fields (it should not have fields)
_build_success = False
elif dset.ndim == 2:
if dset.shape[0] == self._configs['shape'][0]:
self._configs['signals']['current']['shape'] = \
(dset.shape[1],)
else:
_build_success = False
else:
_build_success = False
if not _build_success:
why = "'/Discharge current' does not match expected shape"
raise HDFMappingError(self.info['group path'], why=why)
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# build order:
# 1. build a local motion list dictionary
# 2. build a local probe list dictionary
# 3. build configs dict
#
# TODO: HOW TO ADD MOTION LIST TO DICT
# - right now, the dataset has to be read which has the
# potential for creating long mapping times
# - this is probably best left to HDFReadControls
#
# build 'motion list' and 'probe list'
_motion_lists = {}
_probe_lists = {}
for name in self.subgroup_names:
ml_stuff = self._analyze_motionlist(name)
if bool(ml_stuff):
# build 'motion list'
_motion_lists[ml_stuff['name']] = \
ml_stuff['config']
else:
pl_stuff = self._analyze_probelist(name)
if bool(pl_stuff):
# build 'probe list'
_probe_lists[pl_stuff['name']] = pl_stuff['config']
# ensure a PL item (config group) is found
if len(_probe_lists) == 0:
why = 'has no mappable configurations (Probe List groups)'
raise HDFMappingError(self._info['group path'], why=why)
# build configuration dictionaries
# - the receptacle number is the config_name
# - each probe is one-to-one with receptacle number
#
for pname in _probe_lists:
# define configuration name
config_name = _probe_lists[pname]['receptacle']
# initialize _configs
self._configs[config_name] = {}
# ---- define general info values ----
# - this has to be done before getting the dataset since
# the _configs dist is used by construct_dataset_name()
#
# add motion list info
self._configs[config_name]['motion lists'] = \
_motion_lists
# add probe info
self._configs[config_name]['probe'] = _probe_lists[pname]
# add 'receptacle'
self._configs[config_name]['receptacle'] = \
self._configs[config_name]['probe']['receptacle']
# ---- get configuration dataset ----
try:
dset_name = self.construct_dataset_name(config_name)
dset = self.group[dset_name]
except (KeyError, ValueError):
# KeyError: the dataset was not found
# ValueError: the dataset name was not properly
# constructed
#
why = ("Dataset for configuration "
+ "'{}'".format(pname)
+ " could not be determined or found")
raise HDFMappingError(self._info['group path'], why=why)
# ---- define 'dset paths' ----
self._configs[config_name]['dset paths'] = (dset.name,)
# ---- define 'shotnum' ----
# initialize
self._configs[config_name]['shotnum'] = {
'dset paths': self._configs[config_name]['dset paths'],
'dset field': ('Shot number',),
'shape': dset.dtype['Shot number'].shape,
'dtype': np.int32,
}
# ---- define 'state values' ----
self._configs[config_name]['state values'] = {
'xyz': {
'dset paths':
self._configs[config_name]['dset paths'],
'dset field': ('x', 'y', 'z'),
'shape': (3,),
'dtype': np.float64
},
'ptip_rot_theta': {
'dset paths':
self._configs[config_name]['dset paths'],
'dset field': ('theta',),
'shape': (),
'dtype': np.float64
},
'ptip_rot_phi': {
'dset paths':
self._configs[config_name]['dset paths'],
'dset field': ('phi',),
'shape': (),
'dtype': np.float64
},
}
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# build order:
# 1. build a local motion list dictionary
# 2. build a local probe list dictionary
# 3. build configs dict
#
# TODO: HOW TO ADD MOTION LIST TO DICT
# - right now, the dataset has to be read which has the
# potential for creating long mapping times
# - this is probably best left to HDFReadControls
#
# build 'motion list' and 'probe list'
_motion_lists = {}
_probe_lists = {}
for name in self.subgroup_names:
ml_stuff = self._analyze_motionlist(name)
if bool(ml_stuff):
# build 'motion list'
_motion_lists[ml_stuff["name"]] = ml_stuff["config"]
else:
pl_stuff = self._analyze_probelist(name)
if bool(pl_stuff):
# build 'probe list'
_probe_lists[pl_stuff["probe-id"]] = pl_stuff["config"]
# ensure a PL item (config group) is found
if len(_probe_lists) == 0:
why = "has no mappable configurations (Probe List groups)"
raise HDFMappingError(self._info["group path"], why=why)
# build configuration dictionaries
# - the receptacle number is the config_name
# - each probe is one-to-one with receptacle number
#
for pname in _probe_lists:
# define configuration name
config_name = _probe_lists[pname]["receptacle"]
# initialize _configs
self._configs[config_name] = {}
# ---- define general info values ----
# - this has to be done before getting the dataset since
# the _configs dist is used by construct_dataset_name()
#
# add motion list info
self._configs[config_name]["motion lists"] = _motion_lists
# add probe info
self._configs[config_name]["probe"] = _probe_lists[pname]
# add 'receptacle'
self._configs[config_name]["receptacle"] = self._configs[
config_name]["probe"]["receptacle"]
# ---- get configuration dataset ----
try:
dset_name = self.construct_dataset_name(config_name)
dset = self.group[dset_name]
except (KeyError, ValueError):
# KeyError: the dataset was not found
# ValueError: the dataset name was not properly
# constructed
#
why = (f"Dataset for configuration '{pname}' could not be "
f"determined or found.")
raise HDFMappingError(self._info["group path"], why=why)
# ---- define 'dset paths' ----
self._configs[config_name]["dset paths"] = (dset.name, )
# ---- define 'shotnum' ----
# initialize
self._configs[config_name]["shotnum"] = {
"dset paths": self._configs[config_name]["dset paths"],
"dset field": ("Shot number", ),
"shape": dset.dtype["Shot number"].shape,
"dtype": np.int32,
}
# ---- define 'state values' ----
self._configs[config_name]["state values"] = {
"xyz": {
"dset paths": self._configs[config_name]["dset paths"],
"dset field": ("x", "y", "z"),
"shape": (3, ),
"dtype": np.float64,
},
"ptip_rot_theta": {
"dset paths": self._configs[config_name]["dset paths"],
"dset field": ("theta", ),
"shape": (),
"dtype": np.float64,
},
"ptip_rot_phi": {
"dset paths": self._configs[config_name]["dset paths"],
"dset field": ("phi", ),
"shape": (),
"dtype": np.float64,
},
}
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# look for required datasets
for dset_name in ["Heater summary"]:
if dset_name not in self.group:
why = f"dataset '{dset_name}' not found"
raise HDFMappingError(self.info["group path"], why=why)
# initialize general info values
pairs = [("calib tag", "Calibration tag")]
for pair in pairs:
try:
self._configs[pair[0]] = [self.group.attrs[pair[1]]]
except KeyError:
self._configs[pair[0]] = []
warn(f"Attribute '{pair[1]}' not found for MSI diagnostic "
f"'{self.device_name}', continuing with mapping")
# initialize 'shape'
# - this is used by HDFReadMSI
self._configs["shape"] = ()
# initialize 'shotnum'
self._configs["shotnum"] = {
"dset paths": (),
"dset field": ("Shot number", ),
"shape": (),
"dtype": np.int32,
}
# initialize 'signals'
# - there are NO signal fields
#
self._configs["signals"] = {}
# initialize 'meta'
self._configs["meta"] = {
"shape": (),
"timestamp": {
"dset paths": (),
"dset field": ("Timestamp", ),
"shape": (),
"dtype": np.float64,
},
"data valid": {
"dset paths": (),
"dset field": ("Data valid", ),
"shape": (),
"dtype": np.int8,
},
"current": {
"dset paths": (),
"dset field": ("Heater current", ),
"shape": (),
"dtype": np.float32,
},
"voltage": {
"dset paths": (),
"dset field": ("Heater voltage", ),
"shape": (),
"dtype": np.float32,
},
"temperature": {
"dset paths": (),
"dset field": ("Heater temperature", ),
"shape": (),
"dtype": np.float32,
},
}
# ---- update configs related to 'Heater summary' ----
# - dependent configs are:
# 1. 'shape'
# 2. 'shotnum'
# 3. all of 'meta'
#
dset_name = "Heater summary"
dset = self.group[dset_name]
# define 'shape'
expected_fields = [
"Shot number",
"Timestamp",
"Data valid",
"Heater current",
"Heater voltage",
"Heater temperature",
]
if dset.ndim == 1 and all(field in dset.dtype.names
for field in expected_fields):
self._configs["shape"] = dset.shape
else:
why = "'/Heater summary' does not match expected shape"
raise HDFMappingError(self.info["group path"], why=why)
# update 'shotnum'
self._configs["shotnum"]["dset paths"] = (dset.name, )
self._configs["shotnum"]["shape"] = dset.dtype["Shot number"].shape
# update 'meta/timestamp'
self._configs["meta"]["timestamp"]["dset paths"] = (dset.name, )
self._configs["meta"]["timestamp"]["shape"] = dset.dtype[
"Timestamp"].shape
# update 'meta/data valid'
self._configs["meta"]["data valid"]["dset paths"] = (dset.name, )
self._configs["meta"]["data valid"]["shape"] = dset.dtype[
"Data valid"].shape
# update 'meta/current'
self._configs["meta"]["current"]["dset paths"] = (dset.name, )
self._configs["meta"]["current"]["shape"] = dset.dtype[
"Heater current"].shape
# update 'meta/voltage'
self._configs["meta"]["voltage"]["dset paths"] = (dset.name, )
self._configs["meta"]["voltage"]["shape"] = dset.dtype[
"Heater voltage"].shape
# update 'meta/current'
self._configs["meta"]["temperature"]["dset paths"] = (dset.name, )
self._configs["meta"]["temperature"]["shape"] = dset.dtype[
"Heater temperature"].shape
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# look for required datasets
for dset_name in ["Gas pressure summary", "RGA partial pressures"]:
if dset_name not in self.group:
why = f"dataset '{dset_name}' not found"
raise HDFMappingError(self.info["group path"], why=why)
# initialize general info values
pairs = [
("RGA AMUs", "RGA AMUs"),
("ion gauge calib tag", "Ion gauge calibration tag"),
("RGA calib tag", "RGA calibration tag"),
]
for pair in pairs:
try:
val = self.group.attrs[pair[1]]
if isinstance(val, (list, tuple, np.ndarray)):
self._configs[pair[0]] = val
else:
self._configs[pair[0]] = [val]
except KeyError:
self._configs[pair[0]] = []
warn(f"Attribute '{pair[1]}' not found for MSI diagnostic "
f"'{self.device_name}', continuing with mapping")
# initialize 'shape'
# - this is used by HDFReadMSI
self._configs["shape"] = ()
# initialize 'shotnum'
self._configs["shotnum"] = {
"dset paths": (),
"dset field": ("Shot number", ),
"shape": (),
"dtype": np.int32,
}
# initialize 'signals'
# - there is only one signal fields
# 1. 'partial pressures'
#
self._configs["signals"] = {
"partial pressures": {
"dset paths": (),
"dset field": (),
"shape": (),
"dtype": np.float32,
},
}
# initialize 'meta'
self._configs["meta"] = {
"shape": (),
"timestamp": {
"dset paths": (),
"dset field": ("Timestamp", ),
"shape": (),
"dtype": np.float64,
},
"data valid - ion gauge": {
"dset paths": (),
"dset field": ("Ion gauge data valid", ),
"shape": (),
"dtype": np.int8,
},
"data valid - RGA": {
"dset paths": [],
"dset field": ("RGA data valid", ),
"shape": (),
"dtype": np.int8,
},
"fill pressure": {
"dset paths": (),
"dset field": ("Fill pressure", ),
"shape": (),
"dtype": np.float32,
},
"peak AMU": {
"dset paths": (),
"dset field": ("Peak AMU", ),
"shape": (),
"dtype": np.float32,
},
}
# ---- update configs related to 'Gas pressure summary' ----
# - dependent configs are:
# 1. 'shape'
# 2. 'shotnum'
# 3. all of 'meta'
#
dset_name = "Gas pressure summary"
dset = self.group[dset_name]
# define 'shape'
expected_fields = [
"Shot number",
"Timestamp",
"Ion gauge data valid",
"RGA data valid",
"Fill pressure",
"Peak AMU",
]
if dset.ndim == 1 and all(field in dset.dtype.names
for field in expected_fields):
self._configs["shape"] = dset.shape
else:
why = "'/Gas pressure summary' does not match expected shape"
raise HDFMappingError(self.info["group path"], why=why)
# update 'shotnum'
self._configs["shotnum"]["dset paths"] = (dset.name, )
self._configs["shotnum"]["shape"] = dset.dtype["Shot number"].shape
# update 'meta/timestamp'
self._configs["meta"]["timestamp"]["dset paths"] = (dset.name, )
self._configs["meta"]["timestamp"]["shape"] = dset.dtype[
"Timestamp"].shape
# update 'meta/data valid - ion gauge'
self._configs["meta"]["data valid - ion gauge"]["dset paths"] = (
dset.name, )
self._configs["meta"]["data valid - ion gauge"]["shape"] = dset.dtype[
"Ion gauge data valid"].shape
# update 'meta/data valid - RGA'
self._configs["meta"]["data valid - RGA"]["dset paths"] = (dset.name, )
self._configs["meta"]["data valid - RGA"]["shape"] = dset.dtype[
"RGA data valid"].shape
# update 'meta/fill pressure'
self._configs["meta"]["fill pressure"]["dset paths"] = (dset.name, )
self._configs["meta"]["fill pressure"]["shape"] = dset.dtype[
"Fill pressure"].shape
# update 'meta/peak AMU'
self._configs["meta"]["peak AMU"]["dset paths"] = (dset.name, )
self._configs["meta"]["peak AMU"]["shape"] = dset.dtype[
"Peak AMU"].shape
# ---- update configs related to 'RGA partial pressures' ----
# - dependent configs are:
# 1. 'signals/partial pressures'
#
dset_name = "RGA partial pressures"
dset = self.group[dset_name]
self._configs["signals"]["partial pressures"]["dset paths"] = (
dset.name, )
# check 'shape'
_build_success = True
if dset.dtype.names is not None:
# dataset has fields (it should not have fields)
_build_success = False
elif dset.ndim == 2:
if dset.shape[0] == self._configs["shape"][0]:
self._configs["signals"]["partial pressures"]["shape"] = (
dset.shape[1], )
else:
_build_success = False
else:
_build_success = False
if not _build_success:
why = "'/RGA partial pressures' does not match expected shape"
raise HDFMappingError(self.info["group path"], why=why)
def _find_adc_connections(
self, adc_name: str, config_group: h5py.Group
) -> Tuple[Tuple[int, Tuple[int, ...], Dict[str, Any]], ...]:
"""
Determines active connections on the adc.
:param adc_name: name of the analog-digital-converter
:param config_group: HDF5 group object of the configuration
group
:return:
Tuple of 3-element tuples where the 1st element of the
nested tuple represents a connected *board* number, the 2nd
element is a tuple of connected *channel* numbers for the
*board*, and the 3rd element is a dictionary of adc setup
values (*bit*, *clock rate*, etc.).
"""
config_name = self._parse_config_name(
os.path.basename(config_group.name))
active = self.deduce_config_active_status(config_name)
# initialize conn, brd, and chs
# conn = list of connections
# brd = board number
# chs = list of connect channels of board brd
#
conn = []
# Determine connected (brd, ch) combinations
# scan thru board groups
for board in config_group:
# Is it a board group?
if not bool(re.fullmatch(r'Boards\[\d+\]', board)):
warn("'{}' does not match expected ".format(board) +
"board group name...not adding to mapping")
continue
# get board number
brd_group = config_group[board]
try:
brd = brd_group.attrs['Board']
except KeyError:
raise HDFMappingError(
self.info['group path'],
"board number attribute 'Board' missing")
# ensure brd is an int
if not isinstance(brd, (int, np.integer)):
warn("Board number is not an integer")
continue
elif brd < 0:
warn("Board number is less than 0.")
continue
# ensure there's no duplicate board numbers
if brd in [sconn[0] for sconn in conn]:
why = ("HDF5 structure unexpected..." +
"'{}'".format(config_group.name) +
" defines duplicate board numbers")
# error if active, else warn
if active:
raise HDFMappingError(self.info['group path'], why=why)
else:
warn(why)
# skip adding to conn list
continue
# scan thru channel groups
chs = []
for ch_key in brd_group:
# Is it a channel group?
if not bool(re.fullmatch(r'Channels\[\d+\]', ch_key)):
warn("'{}' does not match expected ".format(board) +
"channel group name...not adding to mapping")
continue
# get channel number
ch_group = brd_group[ch_key]
try:
ch = ch_group.attrs['Channel']
except KeyError:
raise HDFMappingError(
self.info['group path'],
"Channel number attribute 'Channel' missing")
# ensure ch is an int
if not isinstance(ch, (int, np.integer)):
warn("Channel number is not an integer")
continue
elif ch < 0:
warn("Channel number is less than 0.")
continue
# define list of channels
chs.append(ch)
# ensure connected channels are unique
if len(chs) != len(set(chs)):
why = ("HDF5 structure unexpected..." +
"'{}'".format(brd_group.name) +
" does not define a unique set of channel " +
"numbers...not adding to `configs` dict")
warn(why)
# skip adding to conn list
continue
# ensure chs is not NULL
if len(chs) == 0:
why = ("HDF5 structure unexpected..." +
"'{}'".format(brd_group.name) +
" does not define any valid channel " +
"numbers...not adding to `configs` dict")
warn(why)
# skip adding to conn list
continue
# build subconn tuple with connected board, channels, and
# acquisition parameters
subconn = (brd, tuple(chs), {
'bit': None,
'clock rate': (None, 'MHz')
})
# add to all connections list
conn.append(subconn)
return tuple(conn)
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# collect names of datasets and sub-groups
subgroup_names = []
dataset_names = []
for key in self.group.keys():
if isinstance(self.group[key], h5py.Dataset):
dataset_names.append(key)
if isinstance(self.group[key], h5py.Group):
subgroup_names.append(key)
# build self.configs
for name in subgroup_names:
# determine configuration name
config_name = self._parse_config_name(name)
# populate
if bool(config_name):
# initialize configuration name in the config dict
# - add 'config group path'
self._configs[config_name] = {
'config group path': self.group[name].name,
}
# determine if config is active
self._configs[config_name]['active'] = \
self.deduce_config_active_status(config_name)
# assign active adc's to the configuration
self._configs[config_name]['adc'] = \
self._find_active_adcs(self.group[name])
# define 'shotnum' entry
#
# Note:
# The original dataset shot number field was named
# 'Shot'. At some point (mid- to late- 00's) this
# field was renamed to 'Shot number'.
#
# When the header dataset is reviewed by
# `_adc_info_second_pass()` the field name will be
# changed when appropriate.
#
self._configs[config_name]['shotnum'] = {
'dset field': ('Shot', ),
'shape': (),
'dtype': np.uint32,
}
# initialize adc info
self._configs[config_name]['SIS 3301'] = \
self._adc_info_first_pass('SIS 3301',
self.group[name])
# update adc info with 'nshotnum' and 'nt'
# - `construct_dataset_name` needs adc info to be seeded
# - the following updates depend on
# construct_dataset_name
#
if self._configs[config_name]['active']:
self._configs[config_name]['SIS 3301'] = \
self._adc_info_second_pass(config_name,
'SIS 3301')
else:
for conn in self._configs[config_name]['SIS 3301']:
conn[2].update({
'nshotnum': -1,
'nt': -1,
})
# -- raise HDFMappingErrors ----
# no configurations found
if not bool(self._configs):
why = "there are no mappable configurations"
raise HDFMappingError(self.info['group path'], why=why)
# ensure there are active configs
if len(self.active_configs) == 0:
raise HDFMappingError(self.info['group path'],
"there are not active configurations")
# ensure active configs are not NULL
for config_name in self.active_configs:
config = self.configs[config_name]
if len(config['SIS 3301']) == 0:
raise HDFMappingError(
self.info['group path'],
"active configuration '{}'".format(config_name) +
" has no connected board and channels")
def _build_configs(self):
"""Build the :attr:`configs` dictionary"""
# Assumptions:
# 1. only one NI_XYZ drive was ever built, so there will always
# be only one configuration
# - naming configuration 'config01'
# 2. there's only one dataset ever created 'Run time list'
# 3. there can be multiple motion lists defined
# - each sub-group is a configuration for a different
# motion list
# - the name of the sub-group is the name of the motion list
#
# initialize configuration
cname = "config01"
self.configs[cname] = {}
# check there are existing motion lists
if len(self.subgroup_names) == 0:
warn(
f"{self.info['group path']}: no defining motion list groups exist"
)
# get dataset
try:
dset = self.group[self.construct_dataset_name()]
except KeyError:
why = f"Dataset '{self.construct_dataset_name()}' not found"
raise HDFMappingError(self.info["group path"], why=why)
# ---- define general config values ----
self.configs[cname].update({
"Note":
"The 'r', 'theta', and 'phi' fields in the "
"NI_XYZ data set are suppose to represent "
"spherical coordinates of the probe tip with "
"respect to the pivot point of the probe drive, "
"but the current calculation and population of the"
"fields is inaccurate. For user reference, the "
"distance between the probe drive pivot point and"
"LaPD axis is (Lpp =) 58.771 cm.",
"Lpp":
58.771 * u.cm,
})
# ---- define motion list values ----
self.configs[cname]["motion lists"] = {}
# get sub-group names (i.e. ml names)
_ml_names = []
for name in self.group:
if isinstance(self.group[name], h5py.Group):
_ml_names.append(name)
# a motion list group must have the attributes
# Nx, Ny, Nz, dx, dy, dz, x0, y0, z0
names_to_remove = []
for name in _ml_names:
if all(attr not in self.group[name].attrs
for attr in ("Nx", "Ny", "Nz", "dx", "dy", "dz", "x0", "y0",
"z0")):
names_to_remove.append(name)
if bool(names_to_remove):
for name in names_to_remove:
_ml_names.remove(name)
# warn if no motion lists exist
if not bool(_ml_names):
why = "NI_XYZ has no identifiable motion lists"
warn(why)
# gather ML config values
pairs = [
("Nx", "Nx"),
("Ny", "Ny"),
("Nz", "Nz"),
("dx", "dx"),
("dy", "dy"),
("dz", "dz"),
("fan_XYZ", "fan_XYZ"),
("max_ydrive_steps", "max_ydrive_steps"),
("min_ydrive_steps", "min_ydrive_steps"),
("max_zdrive_steps", "max_zdrive_steps"),
("min_zdrive_steps", "min_zdrive_steps"),
("x0", "x0"),
("y0", "y0"),
("z0", "z0"),
("port", "z_port"),
]
for name in _ml_names:
# initialize ML dictionary
self.configs[cname]["motion lists"][name] = {}
# add ML values
for pair in pairs:
try:
# get attribute value
val = self.group[name].attrs[pair[1]]
# condition value
if np.issubdtype(type(val), np.bytes_):
# - val is a np.bytes_ string
val = _bytes_to_str(val)
if pair[1] == "fan_XYZ":
# convert to boolean
if val == "TRUE":
val = True
else:
val = False
# assign val to configs
self.configs[cname]["motion lists"][name][pair[0]] = val
except KeyError:
self.configs[cname]["motion lists"][name][pair[0]] = None
why = (f"Motion List attribute '{pair[1]}' not found for "
f"ML group '{name}'")
warn(why)
# ---- define 'dset paths' ----
self.configs[cname]["dset paths"] = (dset.name, )
# ---- define 'shotnum' ----
# check dset for 'Shot number' field
if "Shot number" not in dset.dtype.names:
why = f"Dataset '{dset.name}' is missing 'Shot number' field"
raise HDFMappingError(self.info["group path"], why=why)
# initialize
self.configs[cname]["shotnum"] = {
"dset paths": self.configs[cname]["dset paths"],
"dset field": ("Shot number", ),
"shape": dset.dtype["Shot number"].shape,
"dtype": np.int32,
}
# ---- define 'state values' ----
self._configs[cname]["state values"] = {
"xyz": {
"dset paths": self._configs[cname]["dset paths"],
"dset field": ("x", "y", "z"),
"shape": (3, ),
"dtype": np.float64,
},
}
# check dset for 'x', 'y' and 'z' fields
fx = "x" not in dset.dtype.names
fy = "y" not in dset.dtype.names
fz = "z" not in dset.dtype.names
if fx and fy and fz:
why = f"Dataset '{dset.name}' missing fields 'x', 'y' and 'z'"
raise HDFMappingError(self.info["group path"], why=why)
elif fx or fy or fz:
mlist = [("x", fx), ("y", fy), ("z", fz)]
missf = ", ".join([val for val, bol in mlist if bol])
why = f" Dataset '{dset.name}' missing field '{missf}'"
warn(why)
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# collect names of datasets and sub-groups
subgroup_names = []
dataset_names = []
for key in self.group.keys():
if isinstance(self.group[key], h5py.Dataset):
dataset_names.append(key)
if isinstance(self.group[key], h5py.Group):
subgroup_names.append(key)
# build self.configs
for name in subgroup_names:
# determine configuration name
config_name = self._parse_config_name(name)
# populate
if bool(config_name):
# initialize configuration name in the config dict
# - add 'config group path'
self._configs[config_name] = {
"config group path": self.group[name].name,
}
# determine if config is active
self._configs[config_name]["active"] = self.deduce_config_active_status(
config_name
)
# assign active adc's to the configuration
self._configs[config_name]["adc"] = self._find_active_adcs(
self.group[name]
)
# define 'shotnum' entry
self._configs[config_name]["shotnum"] = {
"dset field": ("Shot number",),
"shape": (),
"dtype": np.uint32,
}
# initialize adc info
for adc in self._configs[config_name]["adc"]:
self._configs[config_name][adc] = self._adc_info_first_pass(
config_name, adc
)
# update adc info with 'nshotnum' and 'nt'
# - `construct_dataset_name` needs adc info to be seeded
# - the following updates depend on
# construct_dataset_name
#
for adc in self._configs[config_name]["adc"]:
if self._configs[config_name]["active"]:
self._configs[config_name][adc] = self._adc_info_second_pass(
config_name, adc
)
else:
for conn in self._configs[config_name][adc]:
conn[2].update(
{
"nshotnum": -1,
"nt": -1,
}
)
"""
for adc in self._configs[config_name]['adc']:
for conn in self._configs[config_name][adc]:
if self._configs[config_name]['active']:
nshotnum, nt = self._get_dset_shape(
config_name, adc, conn)
conn[2].update({
'nshotnum': nshotnum,
'nt': nt
})
else:
conn[2].update({
'nshotnum': None,
'nt': None
})
"""
# -- raise HDFMappingErrors ----
# no configurations found
if not bool(self._configs):
why = "there are no mappable configurations"
raise HDFMappingError(self.info["group path"], why=why)
# ensure there are active configs
if len(self.active_configs) == 0:
raise HDFMappingError(
self.info["group path"], "there are not active configurations"
)
# ensure active configs are not NULL
for config_name in self.active_configs: # pragma: no branch
config = self.configs[config_name]
if len(config["adc"]) == 0:
raise HDFMappingError(
self.info["group path"],
f"active configuration '{config_name}' has no active adc's",
)
adcs = list(config["adc"])
for adc in config["adc"]: # pragma: no branch
if len(config[adc]) == 0: # pragma: no branch
del config[adc]
adcs.remove(adc)
if len(adcs) == 0:
raise HDFMappingError(
self.info["group path"],
f"active configuration '{config_name}' has no mapped "
f"connections for any adc",
)
else:
config["adc"] = tuple(adcs)
def _build_configs(self):
"""Builds the :attr:`configs` dictionary."""
# check there are configurations to map
if len(self.subgroup_names) == 0:
why = 'has no mappable configurations'
raise HDFMappingError(self._info['group path'], why=why)
# build configuration dictionaries
# - assume every sub-group represents a unique configuration
# to the control device
# - the name of each sub-group is used as the configuration
# name
# - assume all configurations are active (i.e. used)
#
for name in self.subgroup_names:
# get configuration group
cong = self.group[name]
# get dataset
try:
dset = self.group[self.construct_dataset_name()]
except KeyError:
why = ("Dataset '" + self.construct_dataset_name() +
"' not found for configuration group '" + name + "'")
raise HDFMappingError(self._info['group path'], why=why)
# initialize _configs
self._configs[name] = {}
# ---- define general info values ----
pairs = [('IP address', 'IP address'),
('generator device', 'Generator type'),
('GPIB address', 'GPIB address'),
('initial state', 'Initial state'),
('command list', 'Waveform command list')]
for pair in pairs:
try:
# get attribute value
val = cong.attrs[pair[1]]
# condition value
if pair[0] == 'command list':
# - val gets returned as a np.bytes_ string
# - split line returns
# - remove trailing/leading whitespace
#
val = val.decode('utf-8').splitlines()
val = tuple([cls.strip() for cls in val])
elif pair[0] in ('IP address', 'generator device',
'initial state'):
# - val is a np.bytes_ string
#
val = val.decode('utf-8')
else:
# no conditioning is needed
# 'GPIB address' val is np.uint32
pass
# assign val to _configs
self._configs[name][pair[0]] = val
except KeyError:
self._configs[name][pair[0]] = None
warn_str = ("Attribute '" + pair[1] +
"' not found in control device '" +
self.device_name + "' configuration group '" +
name + "'")
if pair[0] != 'command list':
warn_str += ", continuing with mapping"
warn(warn_str)
else:
why = ("Attribute '" + pair[1] +
"' not found for configuration group '" + name +
"'")
raise HDFMappingError(self._info['group path'],
why=why)
# ---- define 'dset paths' ----
self._configs[name]['dset paths'] = (dset.name, )
# ---- define 'shotnum' ----
# initialize
self._configs[name]['shotnum'] = {
'dset paths': self._configs[name]['dset paths'],
'dset field': ('Shot number', ),
'shape': dset.dtype['Shot number'].shape,
'dtype': np.int32
}
# ---- define 'state values' ----
# catch and suppress warnings only for initialization
with warnings.catch_warnings():
warnings.simplefilter("ignore")
try:
sv_state = self._construct_state_values_dict(
name, self._default_re_patterns)
except KeyError:
sv_state = {}
# initialize
self._configs[name]['state values'] = sv_state \
if bool(sv_state) \
else self._default_state_values_dict(name)
def _build_configs(self):
"""Build the :attr:`configs` dictionary"""
# Assumptions:
# 1. only one NI_XZ drive was ever built, so there will always
# be only one configuration
# - naming configuration 'config01'
# 2. there's only one dataset ever created 'Run time list'
# 3. there can be multiple motion lists defined
# - each sub-group is a configuration for a different
# motion list
# - the name of the sub-group is the name of the motion list
#
# initialize configuration
cname = "config01"
self.configs[cname] = {}
# check there are existing motion lists
if len(self.subgroup_names) == 0:
warn(
f"{self.info['group path']}: no defining motion list groups exist"
)
# get dataset
try:
dset = self.group[self.construct_dataset_name()]
except KeyError:
why = f"Dataset '{self.construct_dataset_name()}' not found"
raise HDFMappingError(self.info["group path"], why=why)
# ---- define general config values ----
# none exist
# ---- define motion list values ----
self.configs[cname]["motion lists"] = {}
# get sub-group names (i.e. ml names)
_ml_names = []
for name in self.group:
if isinstance(self.group[name], h5py.Group):
_ml_names.append(name)
# a motion list group must have the attributes
# Nx, Nz, dx, dz, x0, z0
names_to_remove = []
for name in _ml_names:
if all(attr not in self.group[name].attrs
for attr in ("Nx", "Ny", "dx", "dz", "x0", "z0")):
names_to_remove.append(name)
if bool(names_to_remove):
for name in names_to_remove:
_ml_names.remove(name)
# warn if no motion lists exist
if not bool(_ml_names):
why = "NI_XZ has no identifiable motion lists"
warn(why)
# gather ML config values
pairs = [
("Nx", "Nx"),
("Nz", "Nz"),
("dx", "dx"),
("dz", "dz"),
("fan_XZ", "fan_XZ"),
("max_zdrive_steps", "max_zdrive_steps"),
("min_zdrive_steps", "min_zdrive_steps"),
("x0", "x0"),
("z0", "z0"),
("port", "z_port"),
]
for name in _ml_names:
# initialize ML dictionary
self.configs[cname]["motion lists"][name] = {}
# add ML values
for pair in pairs:
try:
# get attribute value
val = self.group[name].attrs[pair[1]]
# condition value
if np.issubdtype(type(val), np.bytes_):
# - val is a np.bytes_ string
val = _bytes_to_str(val)
if pair[1] == "fan_XZ":
# convert to boolean
if val == "TRUE":
val = True
else:
val = False
# assign val to configs
self.configs[cname]["motion lists"][name][pair[0]] = val
except KeyError:
self.configs[cname]["motion lists"][name][pair[0]] = None
why = (f"Motion List attribute '{pair[1]}' not found for "
f"ML group '{name}'")
warn(why)
# ---- define 'dset paths' ----
self.configs[cname]["dset paths"] = (dset.name, )
# ---- define 'shotnum' ----
# check dset for 'Shot number' field
if "Shot number" not in dset.dtype.names:
why = f"Dataset '{dset.name}' is missing 'Shot number' field"
raise HDFMappingError(self.info["group path"], why=why)
# initialize
self.configs[cname]["shotnum"] = {
"dset paths": self.configs[cname]["dset paths"],
"dset field": ("Shot number", ),
"shape": dset.dtype["Shot number"].shape,
"dtype": np.int32,
}
# ---- define 'state values' ----
self._configs[cname]["state values"] = {
"xyz": {
"dset paths": self._configs[cname]["dset paths"],
"dset field": ("x", "", "z"),
"shape": (3, ),
"dtype": np.float64,
},
}
# check dset for 'x' and 'z' fields
fx = "x" not in dset.dtype.names
fz = "z" not in dset.dtype.names
if fx and fz:
why = f"Dataset '{dset.name}' missing both field 'x' and 'z'"
raise HDFMappingError(self.info["group path"], why=why)
elif fx or fz:
missf = "x" if fx else "z"
why = f" Dataset '{dset.name}' missing field '{missf}'"
warn(why)
