def fromXML(self, node):
"""
Load corfunc states from a file
:param node: node of an XML document to read from (optional)
"""
if node.get('version') and node.get('version') == '1.0':
# Parse filename
entry = get_content('ns:filename', node)
if entry is not None:
self.file = entry.text.strip()
# Parse timestamp
entry = get_content('ns:timestamp', node)
if entry is not None and entry.get('epoch'):
try:
self.timestamp = (entry.get('epoch'))
except:
msg = ("CorfuncState.fromXML: Could not read timestamp",
"\n{}").format(sys.exc_value)
logger.error(msg)
# Parse current state
entry = get_content('ns:state', node)
if entry is not None:
for item in DEFAULT_STATE.iterkeys():
input_field = get_content("ns:{}".format(item), entry)
if input_field is not None:
try:
value = float(input_field.text.strip())
except:
value = None
self.set_saved_state(name=item, value=value)
# Parse is_extrapolated and is_transformed
entry = get_content('ns:is_extrapolated', node)
if entry is not None:
self.is_extrapolated = bool(int(entry.text.strip()))
entry = get_content('ns:is_transformed', node)
if entry is not None:
self.is_transformed = bool(int(entry.text.strip()))
entry = get_content('ns:transform_type', node)
self.transform_type = entry.text.strip()
# Parse outputs
entry = get_content('ns:output', node)
if entry is not None:
for item in output_list:
parameter = get_content("ns:{}".format(item[0]), entry)
if parameter is not None:
self.outputs[item[0]] = float(parameter.text.strip())
def fromXML(self, node):
"""
Load corfunc states from a file
:param node: node of an XML document to read from (optional)
"""
if node.get('version') and node.get('version') == '1.0':
# Parse filename
entry = get_content('ns:filename', node)
if entry is not None:
self.file = entry.text.strip()
# Parse timestamp
entry = get_content('ns:timestamp', node)
if entry is not None and entry.get('epoch'):
try:
self.timestamp = (entry.get('epoch'))
except:
msg = ("CorfuncState.fromXML: Could not read timestamp",
"\n{}").format(sys.exc_value)
logger.error(msg)
# Parse current state
entry = get_content('ns:state', node)
if entry is not None:
for item in DEFAULT_STATE.iterkeys():
input_field = get_content("ns:{}".format(item), entry)
if input_field is not None:
try:
value = float(input_field.text.strip())
except:
value = None
self.set_saved_state(name=item, value=value)
# Parse is_extrapolated and is_transformed
entry = get_content('ns:is_extrapolated', node)
if entry is not None:
self.is_extrapolated = bool(int(entry.text.strip()))
entry = get_content('ns:is_transformed', node)
if entry is not None:
self.is_transformed = bool(int(entry.text.strip()))
entry = get_content('ns:transform_type', node)
self.transform_type = entry.text.strip()
# Parse outputs
entry = get_content('ns:output', node)
if entry is not None:
for item in output_list:
parameter = get_content("ns:{}".format(item[0]), entry)
if parameter is not None:
self.outputs[item[0]] = float(parameter.text.strip())
def fromXML(self, file=None, node=None):
"""
Load a P(r) inversion state from a file
:param file: .prv file
:param node: node of a XML document to read from
"""
if file is not None:
msg = "InversionState no longer supports non-CanSAS"
msg += " format for P(r) files"
raise RuntimeError, msg
if node.get('version') and node.get('version') == '1.0':
# Get file name
entry = get_content('ns:filename', node)
if entry is not None:
self.file = entry.text.strip()
# Get time stamp
entry = get_content('ns:timestamp', node)
if entry is not None and entry.get('epoch'):
try:
self.timestamp = float(entry.get('epoch'))
except:
msg = "InversionState.fromXML: Could not read "
msg += "timestamp\n %s" % sys.exc_value
logger.error(msg)
# Parse inversion inputs
entry = get_content('ns:inputs', node)
if entry is not None:
for item in in_list:
input_field = get_content('ns:%s' % item[0], entry)
if input_field is not None:
try:
setattr(self, item[1], float(input_field.text.strip()))
except:
setattr(self, item[1], None)
input_field = get_content('ns:estimate_bck', entry)
if input_field is not None:
try:
self.estimate_bck = input_field.text.strip() == 'True'
except:
self.estimate_bck = False
# Parse inversion outputs
entry = get_content('ns:outputs', node)
if entry is not None:
# Output parameters (scalars)
for item in out_list:
input_field = get_content('ns:%s' % item[0], entry)
if input_field is not None:
try:
setattr(self, item[1], float(input_field.text.strip()))
except:
setattr(self, item[1], None)
# Look for coefficients
# Format is [value, value, value, value]
coeff = get_content('ns:coefficients', entry)
if coeff is not None:
# Remove brackets
c_values = coeff.text.strip().replace('[', '')
c_values = c_values.replace(']', '')
toks = c_values.split()
self.coefficients = []
for c in toks:
try:
self.coefficients.append(float(c))
except:
# Bad data, skip. We will count the number of
# coefficients at the very end and deal with
# inconsistencies then.
pass
# Sanity check
if not len(self.coefficients) == self.nfunc:
# Inconsistent number of coefficients.
# Don't keep the data.
err_msg = "InversionState.fromXML: inconsistant "
err_msg += "number of coefficients: "
err_msg += "%d %d" % (len(self.coefficients),
self.nfunc)
logger.error(err_msg)
self.coefficients = None
# Look for covariance matrix
# Format is [ [value, value], [value, value] ]
coeff = get_content('ns:covariance', entry)
if coeff is not None:
# Parse rows
rows = coeff.text.strip().split('[')
self.covariance = []
for row in rows:
row = row.strip()
if len(row) == 0: continue
# Remove end bracket
row = row.replace(']', '')
c_values = row.split()
cov_row = []
for c in c_values:
try:
cov_row.append(float(c))
except:
# Bad data, skip. We will count the number of
# coefficients at the very end and deal with
# inconsistencies then.
pass
# Sanity check: check the number of entries in the row
if len(cov_row) == self.nfunc:
self.covariance.append(cov_row)
# Sanity check: check the number of rows in the covariance
# matrix
if not len(self.covariance) == self.nfunc:
# Inconsistent dimensions of the covariance matrix.
# Don't keep the data.
err_msg = "InversionState.fromXML: "
err_msg += "inconsistant dimensions of the "
err_msg += " covariance matrix: "
err_msg += "%d %d" % (len(self.covariance), self.nfunc)
logger.error(err_msg)
self.covariance = None
def fromXML(self, file=None, node=None):
"""
Load invariant states from a file
: param file: .inv file
: param node: node of a XML document to read from
"""
if file is not None:
msg = "InvariantSate no longer supports non-CanSAS"
msg += " format for invariant files"
raise RuntimeError(msg)
if node.get('version')\
and node.get('version') == '1.0':
# Get file name
entry = get_content('ns:filename', node)
if entry is not None:
file_name = entry.text.strip()
# Get time stamp
entry = get_content('ns:timestamp', node)
if entry is not None and entry.get('epoch'):
try:
timestamp = (entry.get('epoch'))
except Exception as exc:
msg = "InvariantSate.fromXML: Could not read"
msg += " timestamp\n %s" % exc
logger.error(msg)
# Parse bookmarks
entry_bookmark = get_content('ns:bookmark', node)
for ind in range(1, len(entry_bookmark) + 1):
temp_state = {}
temp_bookmark = {}
entry = get_content('ns:mark_%s' % ind, entry_bookmark)
if entry is not None:
my_time = get_content('ns:time', entry)
val_time = str(my_time.text.strip())
date = get_content('ns:date', entry)
val_date = str(date.text.strip())
state_entry = get_content('ns:state', entry)
for item in DEFAULT_STATE:
input_field = get_content('ns:%s' % item, state_entry)
val = str(input_field.text.strip())
if input_field is not None:
temp_state[item] = val
comp_entry = get_content('ns:comp_state', entry)
for item in DEFAULT_STATE:
input_field = get_content('ns:%s' % item, comp_entry)
val = str(input_field.text.strip())
if input_field is not None:
temp_bookmark[item] = val
try:
self.bookmark_list[ind] = [
val_time, val_date, temp_state, temp_bookmark
]
except:
raise "missing components of bookmarks..."
# Parse histories
entry_history = get_content('ns:history', node)
for ind in range(0, len(entry_history)):
temp_state = {}
entry = get_content('ns:state_%s' % ind, entry_history)
if entry is not None:
for item in DEFAULT_STATE:
input_field = get_content('ns:%s' % item, entry)
if input_field.text is not None:
val = str(input_field.text.strip())
else:
val = ''
if input_field is not None:
temp_state[item] = val
self.state_list[str(ind)] = temp_state
# Parse current state (ie, saved_state)
entry = get_content('ns:state', node)
if entry is not None:
for item in DEFAULT_STATE:
input_field = get_content('ns:%s' % item, entry)
if input_field.text is not None:
val = str(input_field.text.strip())
else:
val = ''
if input_field is not None:
self.set_saved_state(name=item, value=val)
self.file = file_name
def fromXML(self, file=None, node=None):
"""
Load a P(r) inversion state from a file
:param file: .prv file
:param node: node of a XML document to read from
"""
if file is not None:
msg = "InversionState no longer supports non-CanSAS"
msg += " format for P(r) files"
raise RuntimeError(msg)
if node.get('version') and node.get('version') == '1.0':
# Get file name
entry = get_content('ns:filename', node)
if entry is not None:
self.file = entry.text.strip()
# Get time stamp
entry = get_content('ns:timestamp', node)
if entry is not None and entry.get('epoch'):
try:
self.timestamp = float(entry.get('epoch'))
except Exception as exc:
msg = "InversionState.fromXML: Could not read "
msg += "timestamp\n %s" % exc
logger.error(msg)
# Parse inversion inputs
entry = get_content('ns:inputs', node)
if entry is not None:
for item in in_list:
input_field = get_content('ns:%s' % item[0], entry)
if input_field is not None:
try:
setattr(self, item[1], float(input_field.text.strip()))
except:
setattr(self, item[1], None)
input_field = get_content('ns:estimate_bck', entry)
if input_field is not None:
try:
self.estimate_bck = input_field.text.strip() == 'True'
except:
self.estimate_bck = False
# Parse inversion outputs
entry = get_content('ns:outputs', node)
if entry is not None:
# Output parameters (scalars)
for item in out_list:
input_field = get_content('ns:%s' % item[0], entry)
if input_field is not None:
try:
setattr(self, item[1], float(input_field.text.strip()))
except:
setattr(self, item[1], None)
# Look for coefficients
# Format is [value, value, value, value]
coeff = get_content('ns:coefficients', entry)
if coeff is not None:
# Remove brackets
c_values = coeff.text.strip().replace('[', '')
c_values = c_values.replace(']', '')
toks = c_values.split()
self.coefficients = []
for c in toks:
try:
self.coefficients.append(float(c))
except:
# Bad data, skip. We will count the number of
# coefficients at the very end and deal with
# inconsistencies then.
pass
# Sanity check
if not len(self.coefficients) == self.nfunc:
# Inconsistent number of coefficients.
# Don't keep the data.
err_msg = "InversionState.fromXML: inconsistant "
err_msg += "number of coefficients: "
err_msg += "%d %d" % (len(self.coefficients),
self.nfunc)
logger.error(err_msg)
self.coefficients = None
# Look for covariance matrix
# Format is [ [value, value], [value, value] ]
coeff = get_content('ns:covariance', entry)
if coeff is not None:
# Parse rows
rows = coeff.text.strip().split('[')
self.covariance = []
for row in rows:
row = row.strip()
if len(row) == 0: continue
# Remove end bracket
row = row.replace(']', '')
c_values = row.split()
cov_row = []
for c in c_values:
try:
cov_row.append(float(c))
except:
# Bad data, skip. We will count the number of
# coefficients at the very end and deal with
# inconsistencies then.
pass
# Sanity check: check the number of entries in the row
if len(cov_row) == self.nfunc:
self.covariance.append(cov_row)
# Sanity check: check the number of rows in the covariance
# matrix
if not len(self.covariance) == self.nfunc:
# Inconsistent dimensions of the covariance matrix.
# Don't keep the data.
err_msg = "InversionState.fromXML: "
err_msg += "inconsistant dimensions of the "
err_msg += " covariance matrix: "
err_msg += "%d %d" % (len(self.covariance), self.nfunc)
logger.error(err_msg)
self.covariance = None
def fromXML(self, file=None, node=None):
"""
Load invariant states from a file
: param file: .inv file
: param node: node of a XML document to read from
"""
if file is not None:
msg = "InvariantSate no longer supports non-CanSAS"
msg += " format for invariant files"
raise RuntimeError, msg
if node.get('version')\
and node.get('version') == '1.0':
# Get file name
entry = get_content('ns:filename', node)
if entry is not None:
file_name = entry.text.strip()
# Get time stamp
entry = get_content('ns:timestamp', node)
if entry is not None and entry.get('epoch'):
try:
timestamp = (entry.get('epoch'))
except:
msg = "InvariantSate.fromXML: Could not read"
msg += " timestamp\n %s" % sys.exc_value
logging.error(msg)
# Parse bookmarks
entry_bookmark = get_content('ns:bookmark', node)
for ind in range(1, len(entry_bookmark) + 1):
temp_state = {}
temp_bookmark = {}
entry = get_content('ns:mark_%s' % ind, entry_bookmark)
if entry is not None:
my_time = get_content('ns:time', entry)
val_time = str(my_time.text.strip())
date = get_content('ns:date', entry)
val_date = str(date.text.strip())
state_entry = get_content('ns:state', entry)
for item in DEFAULT_STATE:
input_field = get_content('ns:%s' % item, state_entry)
val = str(input_field.text.strip())
if input_field is not None:
temp_state[item] = val
comp_entry = get_content('ns:comp_state', entry)
for item in DEFAULT_STATE:
input_field = get_content('ns:%s' % item, comp_entry)
val = str(input_field.text.strip())
if input_field is not None:
temp_bookmark[item] = val
try:
self.bookmark_list[ind] = [val_time, val_date, temp_state, temp_bookmark]
except:
raise "missing components of bookmarks..."
# Parse histories
entry_history = get_content('ns:history', node)
for ind in range(0, len(entry_history)):
temp_state = {}
entry = get_content('ns:state_%s' % ind, entry_history)
if entry is not None:
for item in DEFAULT_STATE:
input_field = get_content('ns:%s' % item, entry)
val = str(input_field.text.strip())
if input_field is not None:
temp_state[item] = val
self.state_list[ind] = temp_state
# Parse current state (ie, saved_state)
entry = get_content('ns:state', node)
if entry is not None:
for item in DEFAULT_STATE:
input_field = get_content('ns:%s' % item, entry)
val = str(input_field.text.strip())
if input_field is not None:
self.set_saved_state(name=item, value=val)
self.file = file_name