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conversion from python2 to python3 language #15

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Jul 28, 2024
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conversion from python2 to python3 language #15

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4064168
conversion from python2 to python3 language
stevenhua0320 Jul 28, 2024
19fd41f
[pre-commit.ci] auto fixes from pre-commit hooks
pre-commit-ci[bot] Jul 28, 2024
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797 changes: 484 additions & 313 deletions diffpy/srmise/applications/extract.py
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435 changes: 267 additions & 168 deletions diffpy/srmise/applications/plot.py
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143 changes: 85 additions & 58 deletions diffpy/srmise/basefunction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,12 +17,14 @@
import sys

import numpy as np
from fontTools.unicode import Unicode

from diffpy.srmise.modelparts import ModelPart, ModelParts
from diffpy.srmise.srmiseerrors import *

logger = logging.getLogger("diffpy.srmise")


class BaseFunction(object):
"""Base class for mathematical functions which model numeric sequences.

Expand Down Expand Up @@ -61,7 +63,15 @@ class BaseFunction(object):
transform_parameters()
"""

def __init__(self, parameterdict, parformats, default_formats, metadict, base=None, Cache=None):
def __init__(
self,
parameterdict,
parformats,
default_formats,
metadict,
base=None,
Cache=None,
):
"""Set parameterdict defined by subclass

Parameters
Expand Down Expand Up @@ -90,29 +100,37 @@ def __init__(self, parameterdict, parformats, default_formats, metadict, base=No
# arbitrary types, parameters are indexed by these keys as well as
# integer indices. Restricting keys to strings keeps things sane.
for p in self.parameterdict.keys():
if type(p) not in (str, unicode):
if type(p) not in (str, Unicode):
emsg = "Argument parameterdict's keys must be strings."
raise ValueError(emsg)
vals = self.parameterdict.values()
vals.sort()
if vals != range(self.npars):
emsg = "Argument parameterdict's values must uniquely specify "+\
"the index of each parameter defined by its keys."
emsg = (
"Argument parameterdict's values must uniquely specify "
+ "the index of each parameter defined by its keys."
)
raise ValueError(emsg)

self.parformats = parformats

# Check validity of default_formats
self.default_formats = default_formats
if not ("default_input" in self.default_formats and
"default_output" in self.default_formats):
emsg = "Argument default_formats must specify 'default_input' "+\
"and 'default_output' as keys."
if not (
"default_input" in self.default_formats
and "default_output" in self.default_formats
):
emsg = (
"Argument default_formats must specify 'default_input' "
+ "and 'default_output' as keys."
)
raise ValueError(emsg)
for f in self.default_formats.values():
if not f in self.parformats:
emsg = "Keys of argument default_formats must map to a "+\
"value within argument parformats."
emsg = (
"Keys of argument default_formats must map to a "
+ "value within argument parformats."
)
raise ValueError()

# Set metadictionary
Expand All @@ -126,12 +144,11 @@ def __init__(self, parameterdict, parformats, default_formats, metadict, base=No
# of PeakFunction.
# Object to cache: (basefunctioninstance, tuple of parameters)
if Cache is not None:
#self.value = Cache(self.value, "value")
#self.jacobian = Cache(self.jacobian, "jacobian")
# self.value = Cache(self.value, "value")
# self.jacobian = Cache(self.jacobian, "jacobian")
pass
return


#### "Virtual" class methods ####

def actualize(self, *args, **kwds):
Expand Down Expand Up @@ -164,7 +181,6 @@ def _valueraw(self, *args, **kwds):
emsg = "_valueraw must() be implemented in a BaseFunction subclass."
raise NotImplementedError(emsg)


#### Class methods ####

def jacobian(self, p, r, rng=None):
Expand All @@ -179,8 +195,10 @@ def jacobian(self, p, r, rng=None):
previously calculated values instead.
"""
if self is not p._owner:
emsg = "Argument 'p' must be evaluated by the BaseFunction "+\
"subclass which owns it."
emsg = (
"Argument 'p' must be evaluated by the BaseFunction "
+ "subclass which owns it."
)
raise ValueError(emsg)

# normally r will be a sequence, but also allow single numeric values
Expand All @@ -192,7 +210,7 @@ def jacobian(self, p, r, rng=None):
output = [None for j in jac]
for idx in range(len(output)):
if jac[idx] is not None:
output[idx] = r * 0.
output[idx] = r * 0.0
output[idx][rng] = jac[idx]
return output
except TypeError:
Expand All @@ -201,10 +219,10 @@ def jacobian(self, p, r, rng=None):
def transform_derivatives(self, pars, in_format=None, out_format=None):
"""Return gradient matrix for pars converted from in_format to out_format.

Parameters
pars - Sequence of parameters
in_format - A format defined for this class
out_format - A format defined for this class
Parameters
pars - Sequence of parameters
in_format - A format defined for this class
out_format - A format defined for this class
"""
# Map unspecified formats to specific formats defined in default_formats
if in_format is None:
Expand All @@ -223,25 +241,29 @@ def transform_derivatives(self, pars, in_format=None, out_format=None):
out_format = self.default_formats["default_input"]

if not in_format in self.parformats:
raise ValueError("Argument 'in_format' must be one of %s." \
% self.parformats)
raise ValueError(
"Argument 'in_format' must be one of %s." % self.parformats
)
if not out_format in self.parformats:
raise ValueError("Argument 'out_format' must be one of %s." \
% self.parformats)
raise ValueError(
"Argument 'out_format' must be one of %s." % self.parformats
)
if in_format == out_format:
return np.identity(self.npars)
return self._transform_derivativesraw(pars, in_format=in_format, out_format=out_format)
return self._transform_derivativesraw(
pars, in_format=in_format, out_format=out_format
)

def transform_parameters(self, pars, in_format=None, out_format=None):
"""Return new sequence with pars converted from in_format to out_format.

Also restores parameters to a preferred range if it permits multiple
values that correspond to the same physical result.
Also restores parameters to a preferred range if it permits multiple
values that correspond to the same physical result.

Parameters
pars - Sequence of parameters
in_format - A format defined for this class
out_format - A format defined for this class
Parameters
pars - Sequence of parameters
in_format - A format defined for this class
out_format - A format defined for this class
"""
# Map unspecified formats to specific formats defined in default_formats
if in_format is None:
Expand All @@ -260,15 +282,18 @@ def transform_parameters(self, pars, in_format=None, out_format=None):
out_format = self.default_formats["default_input"]

if not in_format in self.parformats:
raise ValueError("Argument 'in_format' must be one of %s." \
% self.parformats)
raise ValueError(
"Argument 'in_format' must be one of %s." % self.parformats
)
if not out_format in self.parformats:
raise ValueError("Argument 'out_format' must be one of %s." \
% self.parformats)
#if in_format == out_format:
raise ValueError(
"Argument 'out_format' must be one of %s." % self.parformats
)
# if in_format == out_format:
# return pars
return self._transform_parametersraw(pars, in_format=in_format, out_format=out_format)

return self._transform_parametersraw(
pars, in_format=in_format, out_format=out_format
)

def value(self, p, r, rng=None):
"""Calculate value of ModelPart over r, possibly restricted by range.
Expand All @@ -282,16 +307,18 @@ def value(self, p, r, rng=None):
previously calculated values instead.
"""
if self is not p._owner:
emsg = "Argument 'p' must be evaluated by the BaseFunction "+\
"subclass which owns it."
emsg = (
"Argument 'p' must be evaluated by the BaseFunction "
+ "subclass which owns it."
)
raise ValueError(emsg)

# normally r will be a sequence, but also allow single numeric values
try:
if rng is None:
rng = slice(0, len(r))
rpart = r[rng]
output = r * 0.
output = r * 0.0
output[rng] = self._valueraw(p.pars, rpart)
return output
except TypeError:
Expand Down Expand Up @@ -338,17 +365,17 @@ def writestr(self, baselist):
raise ValueError("emsg")
lines = []
# Write function type
lines.append("function=%s" %repr(self.__class__.__name__))
lines.append("module=%s" %repr(self.getmodule()))
lines.append("function=%s" % repr(self.__class__.__name__))
lines.append("module=%s" % repr(self.getmodule()))
# Write base
if self.base is not None:
lines.append("base=%s" %repr(baselist.index(self.base)))
lines.append("base=%s" % repr(baselist.index(self.base)))
else:
lines.append("base=%s" %repr(None))
lines.append("base=%s" % repr(None))
# Write all other metadata
for k, (v, f) in self.metadict.iteritems():
lines.append("%s=%s" %(k, f(v)))
datastring = "\n".join(lines)+"\n"
lines.append("%s=%s" % (k, f(v)))
datastring = "\n".join(lines) + "\n"
return datastring

@staticmethod
Expand All @@ -367,19 +394,19 @@ def factory(functionstr, baselist):

# populate dictionary with parameter definition
# "key=value"->{"key":"value"}
data = re.split(r'(?:[\r\n]+|\A)(\S+)=', data)
data = re.split(r"(?:[\r\n]+|\A)(\S+)=", data)
ddict = {}
for i in range(len(data)/2):
ddict[data[2*i+1]] = data[2*i+2]
for i in range(len(data) / 2):
ddict[data[2 * i + 1]] = data[2 * i + 2]

# dictionary of parameters
pdict = {}
for (k, v) in ddict.items():
for k, v in ddict.items():
try:
pdict[k] = eval(v)
except Exception, e:
except Exception as e:
logger.exception(e)
emsg = ("Invalid parameter: %s=%s" %(k,v))
emsg = "Invalid parameter: %s=%s" % (k, v)
raise SrMiseDataFormatError(emsg)

function_name = pdict["function"]
Expand Down Expand Up @@ -438,9 +465,9 @@ def safefunction(f, fsafe):
return


#end of class BaseFunction
# end of class BaseFunction

if __name__ == '__main__':
if __name__ == "__main__":

from diffpy.srmise.peaks import GaussianOverR, TerminationRipples

Expand All @@ -451,7 +478,7 @@ def safefunction(f, fsafe):

pt = TerminationRipples(p, 20)
outstr2 = pt.writestr([p])
print outstr
print(outstr)

pt2 = BaseFunction.factory(outstr2, [p])
print type(pt2)
print(type(pt2))
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