def main():
print 'Building lookup tables.',
outfile = open(FILENAME,'w')
outfile.write('#include <avr/pgmspace.h>\n\n#define NUM_WAVE_ENTRIES {0}\nunsigned char wave_table[{0}] PROGMEM = \n{{\n'.format(N_ENTRIES))
np.set_string_function(arrayPrint,False)
# calculate
time = np.linspace(0,10*pi,N_ENTRIES)
wave_vals = np.zeros_like(time)
wave_vals = (np.exp(-time / T_CONST) + (0.05 * np.cos(time * 2) + .05) * np.exp(-time / T_CONST / 5)) * 200
if 1:
plt.plot(time, wave_vals)
plt.grid(True)
plt.show()
# Output to file
for row in range(0,N_ENTRIES):
outfile.write(str(int(max(0,wave_vals[row]))) + ',\n')
print '.',
outfile.write('};\n')
outfile.close()
print '\nLookup tables built'
pass
def __setitem__(self, key: Tuple[Union[int, slice], Union[int, slice],
Union[int, slice]], value: str):
"""Sets cell code and resets result cache
:param key: Cell key(s) that shall be set
:param value: Code for cell(s) to be set
"""
# Change numpy array repr function for grid cell results
numpy.set_string_function(lambda s: repr(s.tolist()))
# Prevent unchanged cells from being recalculated on cursor movement
repr_key = repr(key)
unchanged = (repr_key in self.result_cache and
value == self(key)) or \
((value is None or value == "") and
repr_key not in self.result_cache)
super().__setitem__(key, value)
if not unchanged:
# Reset result cache
self.result_cache = {}
def DisplaySkillScores(skillScores, skillScoreName):
"""
Display the skill score results in a neat manner.
Note, this function messes around with the formatting options
of printing numpy arrays. It does restore the settings back to
the numpy defaults, but if you had your own formatting specified
before calling this function, you will need to reset it.
"""
np.set_string_function(lambda x: '\n'.join(
[' '.join(["% 11.8f" % val for val in row]) for row in x]),
repr=True)
# Print the last eleven characters of each trackrun name for
# the column labels.
print(' '.join(
["%11.11s" % tracker[-11:] for tracker in skillScores.label[-1]]))
print(repr(skillScores.x))
print("-" * (11 * skillScores.shape[1] + 2 * (skillScores.shape[1] - 1)))
# Resetting back to how it was
np.set_string_function(None, repr=True)
def export_data_if_needed(df, props):
def get_prop(k):
return props[k] if k in props else None
def printer(arr):
return np.array_str(arr)
if _parse_optional_bool(get_prop("export_data")):
format = "csv"
folder = get_prop("image_export_folder") or os.getcwd()
filename = get_prop("image_export_filename") or _sanitize_filename(
chart.get_name())
filepath = os.path.join(folder,
filename) + "." + format #TODO make it better
print("exporting data to: '" + filepath + "' as " + format)
old_opts = np.get_printoptions()
np.set_printoptions(threshold=np.inf, linewidth=np.inf)
np.set_string_function(printer, False)
pd.set_option('display.max_columns', None)
pd.set_option('display.max_colwidth', None)
df.to_csv(filepath)
np.set_string_function(None, False)
np.set_printoptions(**old_opts)
def DisplaySkillScores(skillScores, skillScoreName) :
"""
Display the skill score results in a neat manner.
Note, this function messes around with the formatting options
of printing numpy arrays. It does restore the settings back to
the numpy defaults, but if you had your own formatting specified
before calling this function, you will need to reset it.
"""
np.set_string_function(
lambda x: '\n'.join([' '.join(["% 11.8f" % val for val in row])
for row in x]),
repr=True)
# Print the last eleven characters of each trackrun name for
# the column labels.
print ' '.join(["%11.11s" % tracker[-11:] for
tracker in skillScores.label[-1]])
print repr(skillScores.x)
print "-" * (11*skillScores.shape[1] + 2*(skillScores.shape[1] - 1))
# Resetting back to how it was
np.set_string_function(None, repr=True)
def process_Iqxy_data(file_content):
"""
Process the content of an I(qx,qy) file and return a string representation
of the data that we can ship to the client for plotting.
@param file_content: content of the data file
"""
fd = tempfile.NamedTemporaryFile()
fd.write(file_content)
fd.seek(0)
numpy.set_printoptions(threshold='nan', nanstr='0', infstr='0')
fd = h5py.File(fd.name, 'r')
g = fd['mantid_workspace_1']
y = g['workspace']['axis1']
x = g['workspace']['axis2']
values = g['workspace']['values']
z_max = numpy.amax(values)
numpy.set_string_function( lambda x: '['+','.join(map(lambda y:'['+','.join(map(lambda z: "%.4g" % z,y))+']',x))+']' )
data_str_2d = values[:].__repr__()
numpy.set_string_function( lambda x: '['+','.join(map(lambda z: "%.4g" % z,x))+']' )
y_str = y[:].__repr__()
x_str = x[:].__repr__()
return data_str_2d, x_str, y_str, 0.0, z_max
def main():
# set up and parse arguments
class MyFormatter(argparse.ArgumentDefaultsHelpFormatter,
argparse.MetavarTypeHelpFormatter):
pass
parser = argparse.ArgumentParser(
description='Calculate RONN disorder prediction.',
formatter_class=MyFormatter)
parser.add_argument('inputfile',
type=str,
default=sys.stdin,
help='File of protein coding sequences to predict on.')
parser.add_argument('--inputformat',
type=str,
default='fasta',
help='File format of [inputfile]. '
'Any Bio.SeqIO-readable supported')
args = parser.parse_args()
if (args.inputfile == '-'):
args.inputfile = sys.stdin
# print numpy entire array one by entry at a time
np.set_string_function(lambda x: "\n".join(map(str, x.tolist())), False)
np.set_printoptions(threshold=sys.maxsize)
for record in Bio.SeqIO.parse(args.inputfile, args.inputformat):
record.seq = record.seq.upper()
print(">" + record.id, calc_ronn(str(record.seq)), sep='\n')
return
def set_numpy_oneline_repr():
"""Change the default Numpy array ``__repr__`` to a
compact one. This is useful for keeping the log
clean when the job functions involve large Numpy
arrays as args.
"""
import numpy as np
EDGEITEMS = 3
def oneline_repr(a):
N = np.prod(a.shape)
if N == 0: # No numbers to show if the last dimension is zero
return f"array[{a.shape}]([])"
ind = np.unravel_index(range(min(EDGEITEMS, N)), a.shape)
afew = []
for x, val in zip(np.c_[ind], a[ind]):
for i, y in enumerate(x[::-1]):
if y != 0: break
else: i += 1
for j, y in enumerate(x[::-1]):
if y + 1 != a.shape[len(x) - j - 1]: break
else: j += 1
afew.append(f"{'['*i}{val}{']'*j}")
return f"array[{a.shape}]({', '.join(afew)}{'...' if N > EDGEITEMS else ''})"
np.set_string_function(oneline_repr, repr=True)
def simulation(self, N=50000):
import pandas
import scikits.statsmodels.tsa.api
np.set_string_function(None)
nSims = 1
logger.debug('\n\n--------- SIMULATION---------\n\n')
logger.debug('T = %d\n' % N)
cumTransMatrix = np.cumsum(self.T, 1)
varSim = np.zeros((N, self.vars))
shocks = np.zeros((N), dtype=int)
shocks[0] = 1
varSim[0, :] = self.S[shocks[0], :]
lastShock = 1
for t in range(1, N):
shockR = np.random.random_sample()
itemindex = np.where(shockR < cumTransMatrix[lastShock, :])
shock = itemindex[0][0]
shocks[t] = shock
for ixVar in range(self.vars):
varSim[t, ixVar] = self.S[shock, ixVar]
lastShock = shock
index = np.arange(N)
varSim = pandas.DataFrame(data=varSim,
index=index,
columns=map(str, range(self.vars)))
logger.debug(varSim)
logger.debug('\nUnconditional means(E)')
logger.debug(varSim.mean())
logger.debug('\nUnconditional std')
logger.debug(varSim.std())
logger.debug('\nUnconditional skewness')
logger.debug(varSim.skew())
try:
logger.debug('\nUnconditional correlation')
logger.debug(varSim.corr())
except:
pass
model = scikits.statsmodels.tsa.api.VAR(varSim)
# model = scikits.statsmodels.tsa.vector_ar.var_model.VAR(varSim)
results = model.fit(1)
Theta = results.params[1:, :]
logger.debug('\n Persistence')
logger.debug(Theta)
logger.debug('done with simulation')
return varSim, Theta
def repr_g(a):
(precision, linewidth, edgeitems) = est_options(a)
set_options(precision, linewidth, edgeitems)
np.set_string_function(None, repr=True)
str = a.__repr__()
np.set_string_function(repr_g, repr=True)
return str
def main_paste(args):
"""
Correlate particles properties from trajectory files.
Example:
--------
trj.py paste.py file1.xyz:radius file2.xyz.voronoi.xyz:volume
"""
from atooms import trajectory as trj
from atooms.core.utils import tipify
f1, attr1 = args.file_inp[0].split(':')
f2, attr2 = args.file_inp[1].split(':')
if args.inp is None:
fmt1, fmt2 = None, None
else:
fmt1, fmt2 = args.inp.split(',')
t1 = trj.Trajectory(f1, fmt=fmt1)
t2 = trj.Trajectory(f2, fmt=fmt2)
# Define slice.
# We interpret --first N --last N as a request of step N
if args.last == args.first and args.last is not None:
args.last += 1
sl1 = fractional_slice(args.first, args.last, args.skip, len(t1))
sl2 = fractional_slice(args.first, args.last, args.skip, len(t2))
# Here we could you a trajectory slice t[sl] but this will load
# everything in ram (getitem doesnt provide a generator). This
# will be fixed with python 3.
ts1 = trajectory.Sliced(t1, sl1)
ts2 = trajectory.Sliced(t2, sl2)
def array_fmt(arr):
"""Remove commas and [] from numpy array repr."""
# Passing a scalar will trigger an error (gotcha: even
# when casting numpy array to list, the elements remain of
# numpy type and this function gets called! (4% slowdown)
_fmt = '%g'
try:
return ' '.join([_fmt % x for x in arr])
except:
return _fmt % arr
# except:
# return numpy.array2string(arr, precision=self.precision, separator=',')[1:-1]
import numpy
numpy.set_string_function(array_fmt, repr=False)
for step, s1, s2 in trj.utils.paste(ts1, ts2):
try:
for i in range(len(s1.particle)):
print(getattr(s1.particle[i], attr1),
getattr(s2.particle[i], attr2))
except:
print(getattr(s1, attr1), getattr(s2, attr2))
def simulation(self, N = 50000):
import pandas
import scikits.statsmodels.tsa.api
np.set_string_function(None)
nSims = 1
logger.debug('\n\n--------- SIMULATION---------\n\n')
logger.debug('T = %d\n' % N)
cumTransMatrix = np.cumsum(self.T, 1)
varSim = np.zeros( (N, self.vars ) )
shocks = np.zeros( (N), dtype = int )
shocks[0] = 1
varSim[0, :] = self.S[shocks[0], :]
lastShock = 1
for t in range(1, N):
shockR = np.random.random_sample()
itemindex = np.where(shockR < cumTransMatrix[lastShock, :])
shock = itemindex[0][0]
shocks[t] = shock
for ixVar in range(self.vars):
varSim[t, ixVar] = self.S[shock, ixVar]
lastShock = shock
index = np.arange(N)
varSim = pandas.DataFrame(data = varSim, index = index, columns = map(str, range(self.vars)))
logger.debug(varSim)
logger.debug('\nUnconditional means(E)')
logger.debug(varSim.mean())
logger.debug('\nUnconditional std')
logger.debug(varSim.std())
logger.debug('\nUnconditional skewness')
logger.debug(varSim.skew())
try:
logger.debug('\nUnconditional correlation')
logger.debug(varSim.corr())
except:
pass
model = scikits.statsmodels.tsa.api.VAR(varSim)
# model = scikits.statsmodels.tsa.vector_ar.var_model.VAR(varSim)
results = model.fit(1)
Theta = results.params[1:,:]
logger.debug('\n Persistence')
logger.debug(Theta)
logger.debug('done with simulation')
return varSim, Theta
def _install():
import io
import numpy as np
from IPython import get_ipython
from IPython.core import magic
from highlighter import HighlightTextFormatter
ip = get_ipython()
ip.display_formatter.formatters[
'text/plain'] = HighlightTextFormatter(config=ip.config)
import ipython_autocd
ipython_autocd.register()
import lambda_filter
lambda_filter.register()
@magic.register_line_magic
def run_cython(args):
"""Run a Cython file using %%cython magic."""
args = magic.arg_split(args, posix=True)
filename = args.pop()
if '--force' not in args:
args.append('--force')
ip = get_ipython()
ip.extension_manager.load_extension('cython')
with io.open(filename, 'r', encoding='utf-8') as f:
ip.run_cell_magic('cython', ' '.join(args), f.read())
@magic.register_line_cell_magic
def create(line='', cell=None):
"""Start a plotinteract session from user namespace data."""
from plottools import create, dataobj
ip = get_ipython()
if not cell:
cell = line
line = ''
args = ip.ev('dict({})'.format(line))
objs = (eval('dataobj({})'.format(line),
ip.user_global_ns, dict(dataobj=dataobj))
for line in cell.splitlines())
create(*objs, **args)
def arraystr(a, max_line_width=None, precision=None, suppress_small=None):
"""Separate values with a comma in array2string."""
return np.array2string(a, max_line_width,
precision, suppress_small,
separator=', ', prefix="", style=str)\
.replace('..., ', '..., ' if PY3 else 'Ellipsis, ')
np.set_string_function(arraystr, repr=False)
if not PY3:
np.set_string_function(arraystr)
np.ma.masked_print_option.set_display("masked")
def _install():
import io
import numpy as np
from IPython import get_ipython
from IPython.core import magic
from highlighter import HighlightTextFormatter
ip = get_ipython()
ip.display_formatter.formatters['text/plain'] = HighlightTextFormatter(
config=ip.config)
import ipython_autocd
ipython_autocd.register()
import lambda_filter
lambda_filter.register()
@magic.register_line_magic
def run_cython(args):
"""Run a Cython file using %%cython magic."""
args = magic.arg_split(args, posix=True)
filename = args.pop()
if '--force' not in args:
args.append('--force')
ip = get_ipython()
ip.extension_manager.load_extension('cython')
with io.open(filename, 'r', encoding='utf-8') as f:
ip.run_cell_magic('cython', ' '.join(args), f.read())
@magic.register_line_cell_magic
def create(line='', cell=None):
"""Start a plotinteract session from user namespace data."""
from plottools import create, dataobj
ip = get_ipython()
if not cell:
cell = line
line = ''
args = ip.ev('dict({})'.format(line))
objs = (eval('dataobj({})'.format(line), ip.user_global_ns,
dict(dataobj=dataobj)) for line in cell.splitlines())
create(*objs, **args)
def arraystr(a, max_line_width=None, precision=None, suppress_small=None):
"""Separate values with a comma in array2string."""
return np.array2string(a, max_line_width,
precision, suppress_small,
separator=', ', prefix="", style=str)\
.replace('..., ', '..., ' if PY3 else 'Ellipsis, ')
np.set_string_function(arraystr, repr=False)
if not PY3:
np.set_string_function(arraystr)
np.ma.masked_print_option.set_display("masked")
def __str__(self):
np.set_string_function(format_array, repr=False)
s = '{'
for k in sorted(self.keys()):
v = self[k]
if v.ndim > 1:
v = v.ravel()
if s == '{':
s += '{}: {}'.format(k, v)
else:
s += ', {}: {}'.format(k, v)
s += '}'
np.set_string_function(None, repr=False)
return s
def __str__(self):
np.set_string_function(format_array, repr=False)
s = '{'
for k in sorted(self.keys()):
v = self[k]
if v.ndim > 1:
v = v.ravel()
if s == '{':
s += '{}: {}'.format(k, v)
else:
s += ', {}: {}'.format(k, v)
s += '}'
np.set_string_function(None, repr=False)
return s
def __str__(self):
def format_array(array):
def format_element(e):
if e > 1e15:
return '%(n).2e' % {'n': e}
elif e == np.floor(e):
return '%(n).0f' % {'n': e}
elif e - np.floor(e) > 0.01 or e < 1000:
return '%(n).2f' % {'n': e}
else:
return '%(n).2e' % {'n': e}
if array.ndim == 0:
return str(array.item())
elif len(array) == 0:
return ''
elif len(array) == 1:
if defaults.compact_print:
return '[' + format_element(array[0]) + ']'
else:
return '[{}]'.format(array[0])
s = '['
for ii in np.arange(len(array) - 1):
if defaults.compact_print:
s += format_element(array[ii]) + ', '
else:
s += '{}, '.format(array[ii])
if defaults.compact_print:
s += format_element(array[-1]) + ']'
else:
s += '{}]'.format(array[-1])
return s
np.set_string_function(format_array, repr=False)
if self.__keys is None:
self.__keys = sorted(self.keys())
s = '{'
for k in self.__keys:
v = self[k]
if v.ndim > 1:
v = v.ravel()
if s == '{':
s += '{}: {}'.format(k, v)
else:
s += ', {}: {}'.format(k, v)
s += '}'
np.set_string_function(None, repr=False)
return s
def set_ndarray_format() -> None:
"""ndarrayのstr()やrepr()でshapeが分かるようにする。"""
def format_ndarray(x):
try:
result = f"<ndarray shape={x.shape} dtype={x.dtype}"
if issubclass(x.dtype.type, numbers.Number):
result += f" min={x.min()}"
result += f" max={x.max()}"
result += f" mean={x.mean(dtype=np.float32)}"
s = np.array_str(x).replace("\n", "")
result += f" values={s}"
result += ">"
return result
except Exception:
return np.array_repr(x) # 念のため
np.set_string_function(format_ndarray, repr=False)
np.set_string_function(format_ndarray, repr=True)
def DisplayTableAnalysis(figTitles, plotLabels, tickLabels, meanSkills,
skills_ci_upper, skills_ci_lower):
np.set_string_function(lambda x: ' '.join(["% 8.4f" % val for val in x]),
repr=True)
for figIndex, title in enumerate(figTitles):
print("%50s" % title)
print(" " * 10, )
print(" ".join(["%9s"] * len(tickLabels)) % tuple(tickLabels))
print("-" * (11 + 10 * len(tickLabels)))
for plotIndex, label in enumerate(plotLabels):
print("%10s|" % label, )
print(repr(meanSkills[:, figIndex, plotIndex]))
# Restore the formatting state to the default
np.set_string_function(None, repr=True)
def html(self, css=None):
"""Create an HTML representation of the table
Parameters
----------
css : str
A string that may refer to a CSS or style parameter. This can be used for special
formatting of the table, e.g. striping. Default: No extra formatting.
Returns
-------
string
HTML <table> representation.
"""
if css:
tablestr = '<h3>%s</h3>\n<table %s><thead><tr>' % (
self.description, css)
else:
tablestr = '<h3>%s</h3>\n<table><thead><tr>' % self.description
for h in self.columns:
tablestr = tablestr + '<th>%s</th>' % h
tablestr = tablestr + '</tr>\n'
for u in self.units:
tablestr = tablestr + '<th>[%s]</th>' % u
tablestr = tablestr + '</tr></thead>\n<tbody>'
np.set_string_function(None)
np.set_printoptions(
threshold=None,
nanstr='NaN',
infstr='Inf',
formatter={
'float': '<td>{:.3E}</td>'.format,
#'str_kind' : '<td>{}</td>'.format
'str_kind': lambda x: self._formatcell(x)
})
for row in self.data:
#strip beginning and ending [,] from string.
rowstr = str(row)[1:-1]
tablestr = tablestr + '<tr>' + rowstr + '</tr>\n'
tablestr = tablestr + '</tbody></table>\n'
np.set_printoptions(formatter=None)
return tablestr
def test_set_string_function(self):
a = np.array([1])
np.set_string_function(lambda x: "FOO", repr=True)
assert_equal(repr(a), "FOO")
np.set_string_function(None, repr=True)
assert_equal(repr(a), "array([1])")
np.set_string_function(lambda x: "FOO", repr=False)
assert_equal(str(a), "FOO")
np.set_string_function(None, repr=False)
assert_equal(str(a), "[1]")
def html(self,css=None) :
"""Create an HTML representation of the table
Parameters
----------
css : str
A string that may refer to a CSS or style parameter. This can be used for special
formatting of the table, e.g. striping. Default: No extra formatting.
Returns
-------
string
HTML <table> representation.
"""
if css:
tablestr = '<h3>%s</h3>\n<table %s><thead><tr>' % (self.description,css)
else:
tablestr = '<h3>%s</h3>\n<table><thead><tr>' % self.description
for h in self.columns:
tablestr = tablestr + '<th>%s</th>' % h
tablestr = tablestr + '</tr>\n'
for u in self.units:
tablestr = tablestr + '<th>[%s]</th>' % u
tablestr = tablestr + '</tr></thead>\n<tbody>'
np.set_string_function(None)
np.set_printoptions(
threshold = None,
nanstr = 'NaN',
infstr = 'Inf',
formatter={'float' : '<td>{:.3E}</td>'.format,
#'str_kind' : '<td>{}</td>'.format
'str_kind' : lambda x: self._formatcell(x)
})
for row in self.data:
#strip beginning and ending [,] from string.
rowstr = str(row)[1:-1]
tablestr = tablestr + '<tr>'+rowstr+'</tr>\n'
tablestr = tablestr + '</tbody></table>\n'
np.set_printoptions(formatter=None)
return tablestr
def debug(func):
np.set_string_function(lambda arr: '<array>')
@wraps(func)
def new_func(*args, **kwargs):
if get_debug_flag():
# noinspection PyShadowingNames
logger = logging.getLogger()
str_args = ', '.join([repr(a) for a in args])
str_kwargs = ', '.join([f"{k}={v}" for k, v in kwargs.items()])
logger.debug(
f"Calling {func.__name__}({str_args}{', ' if str_kwargs else ''}{str_kwargs})"
)
out = func(*args, **kwargs)
logger.debug(f"Finished {func.__name__} -> {out}")
return out
else:
return func(*args, **kwargs)
return new_func
def DisplayTableAnalysis(figTitles, plotLabels, tickLabels,
meanSkills, skills_ci_upper, skills_ci_lower) :
np.set_string_function(
lambda x: ' '.join(["% 8.4f" % val for val in x]),
repr=True)
for figIndex, title in enumerate(figTitles) :
print "%50s" % title
print " " * 10,
print " ".join(["%9s"] * len(tickLabels)) % tuple(tickLabels)
print "-" * (11 + 10 * len(tickLabels))
for plotIndex, label in enumerate(plotLabels) :
print ("%10s|" % label),
print repr(meanSkills[:, figIndex, plotIndex])
# Restore the formatting state to the default
np.set_string_function(None, repr=True)
def __setitem__(self, key, value):
"""Sets cell code and resets result cache"""
# Change numpy array repr function for grid cell results
numpy.set_string_function(lambda s: repr(s.tolist()))
# Prevent unchanged cells from being recalculated on cursor movement
repr_key = repr(key)
unchanged = (repr_key in self.result_cache and
value == self(key)) or \
((value is None or value == "") and
repr_key not in self.result_cache)
super().__setitem__(key, value)
if not unchanged:
# Reset result cache
self.result_cache = {}
def _setup_format(self):
# %g allows to format both float and int but it's 2x slower.
# This switch is for performance
if self._fields_float:
_fmt = '%.' + str(self.precision) + 'f'
else:
_fmt = '%g'
def array_fmt(arr):
"""Remove commas and [] from numpy array repr."""
# Passing a scalar will trigger an error (gotcha: even
# when casting numpy array to list, the elements remain of
# numpy type and this function gets called! (4% slowdown)
try:
return ' '.join([_fmt % x for x in arr])
except:
return _fmt % arr
# Note: numpy.array2string is MUCH slower
numpy.set_string_function(array_fmt, repr=False)
def format_exc_info(info: ExcInfo,
as_html: bool,
color='Neutral') -> str:
# avoids printing the array data
# some discussion related to obtaining the current string function
# can be found here, https://github.com/numpy/numpy/issues/11266
np.set_string_function(
lambda arr: f'{type(arr)} {arr.shape} {arr.dtype}')
vbtb = IPython.core.ultratb.VerboseTB(color_scheme=color)
if as_html:
ansi_string = vbtb.text(*info).replace(" ", " ")
html = "".join(ansi2html(ansi_string))
html = html.replace("\n", "<br>")
html = (
"<span style='font-family: monaco,courier,monospace;'>" +
html + "</span>")
tb_text = html
else:
tb_text = vbtb.text(*info)
# resets to default behavior
np.set_string_function(None)
return tb_text
def format_exc_info(info: ExcInfo, as_html: bool, color=None) -> str:
# avoids printing the array data
np.set_string_function(
lambda arr: f'{type(arr)} {arr.shape} {arr.dtype}')
if as_html:
html = "\n".join(cgitb_chain(info[1]))
# cgitb has a lot of hardcoded colors that don't work for us
# remove bgcolor, and let theme handle it
html = re.sub('bgcolor="#.*"', '', html)
# remove superfluous whitespace
html = html.replace('<br>\n', '\n')
# but retain it around the <small> bits
html = re.sub(r'(<tr><td><small.*</tr>)', '<br>\\1<br>', html)
# weird 2-part syntax is a workaround for hard-to-grep text.
html = html.replace(
"<p>A problem occurred in a Python script. "
"Here is the sequence of",
"",
)
html = html.replace(
"function calls leading up to the error, "
"in the order they occurred.</p>",
"<br>",
)
# remove hardcoded fonts
html = html.replace('face="helvetica, arial"', "")
html = (
"<span style='font-family: monaco,courier,monospace;'>" +
html + "</span>")
tb_text = html
else:
# if we don't need HTML, just use traceback
tb_text = ''.join(traceback.format_exception(*info))
# resets to default behavior
np.set_string_function(None)
return tb_text
DIM_NETHER = -1
DIM_END = 1
_zeros = {}
def string_func(array):
numpy.set_string_function(None)
string = repr(array)
string = string[:-1] + ", shape=%s)" % (array.shape,)
numpy.set_string_function(string_func)
return string
numpy.set_string_function(string_func)
class EntityListProxy(collections.MutableSequence):
"""
A proxy for the Entities and TileEntities lists of a WorldEditorChunk. Accessing an element returns an EntityRef
or TileEntityRef wrapping the element of the underlying NBT compound, with a reference to the WorldEditorChunk.
These Refs cannot be created at load time as they hold a reference to the chunk, preventing the chunk from being
unloaded when its refcount reaches zero.
"""
chunk = weakrefprop()
def __init__(self, chunk, attrName, refClass):
self.attrName = attrName
def main():
parser = OptionParser()
#parser.add_option("-s",metavar="FILE",help="Reference Structure file",default="topol.tpr")
parser.add_option("-n",metavar="FILE",help="Index file")
parser.add_option("-f",metavar="FILE",help="Trajectory with coordinates, velocies, and forces")
parser.add_option("-x",metavar="FILE",help="Trajectory with coordinates")
parser.add_option("-v",metavar="FILE",help="Trajectory with velocities")
parser.add_option("-k",metavar="FILE",help="Trajectory with forces")
parser.add_option("-o",metavar="FILE",help="Output",default="corr.dat")
parser.add_option("-r",metavar="FILE",help="Output",default="rot.dat")
(options, args) = parser.parse_args()
#open files
#sf = tpxfile(options.s)
#read index
if options.n:
isize,idx,iname = rd_index(options.n,1)
print("Using group %s with %s atoms"%(iname[0],isize[0]))
idx=idx[0]
if not options.f and not(options.x and options.v and options.k):
print("Requires either one trajectory containing all input (-f) or three (-x, -v, -f)")
sys.exit(1);
if options.f and (options.x or options.v or options.k):
print("-f cannot be used with x,v, or k")
sys.exit(1);
if options.f:
tf = gmxfile(options.f,flags=TRX_NEED_X|TRX_NEED_V|TRX_NEED_F)
natoms = tf.natoms
else:
xf = gmxfile(options.x,flags=TRX_NEED_X)
vf = gmxfile(options.v,flags=TRX_NEED_X) #DCD doesn't have V/F so we expect all 3 files have X field
kf = gmxfile(options.k,flags=TRX_NEED_X)
print("Warning: NAMD units are expected for input files!")
natoms = xf.natoms
tf = izip(xf,vf,kf)
if natoms!=vf.natoms or natoms!=kf.natoms:
print("Number of atoms doesn't match between files!")
sys.exit(1);
if (natoms%3!=0):
print("This program only supports water. Number of atoms has to be multiple of 3.");
sys.exit(1);
temp_v=[]
temp_x=[]
temp_f=[]
trn_v=N.empty((nP,natoms/3,3,3),dtype=N_real)
trn_x=N.empty((nP,natoms/3,3,3),dtype=N_real)
for i,frm in enumerate(tf):
if not options.f:
frm_t = frm
class frm: #convert tuple into attributes
x = frm_t[0].x
v = frm_t[1].x*20.45482706
f = frm_t[2].x*(100/4.184)
if options.n:
frm_x = frm.x[idx]
frm_v = frm.v[idx]
frm_f = frm.f[idx]
else:
frm_x = frm.x
frm_v = frm.v
frm_f = frm.f
frm_v=frm_v.reshape(-1,3,3)
frm_x=frm_x.reshape(-1,3,3)
frm_f=frm_f.reshape(-1,3,3)
temp_v += [frm_v.copy()]
temp_x += [frm_x.copy()]
temp_f += [frm_f.copy()]
temp_v = temp_v[-3:]
temp_x = temp_x[-3:]
temp_f = temp_f[-3:]
if i%ds!=2: continue #assumes ds>=3,
if __debug__:
a=temp_x[1]
b=temp_x[0]+temp_v[1]*dt
#print(temp_v[1]*dt)
#print(temp_x[0])
#idx=N.abs(a-b).max(axis=1).max(axis=1)>.0005
#print(a.shape,temp_v[1].shape)
#print(idx)
#print(a[idx])
#print(b[idx])
N.testing.assert_almost_equal(a,b,decimal=2,verbose=True) #low accuracy dominated by pressure coupling
i=i//ds
trn_v[i] = .5*(temp_v[1]+temp_v[2])-dt/16/mass*(temp_f[2]-temp_f[0])
#trn_v[i] = .5*(temp_v[1]+temp_v[2])
##trn_v2 = 2*(trn_v[1:-1]+trn_v[2:])-3/2/dt*(trn_x[2:]-trn_x[:-2])
trn_x[i] = temp_x[1]
if i==nP-1: break
if __debug__:
a=(temp_v[0]+temp_v[1])/2#trn_v2[n]
b=trn_v[i]
#idx=N.abs((a-b))>.4+.2*N.abs(a+b) #.6 .4 old values: for 2fs: a few,, 1fs: none
idx=N.abs((a-b))>.6+.4*N.abs(a+b) #.6 .4 old values: for 2fs: a few,, 1fs: none
idx2=N.abs((a-b))<.1+.05*N.abs(a+b) #.1 .05 : 75% - 1fs: 91%
assert(N.sum(idx)/N.prod(idx2.shape)<1/400)
#assert(N.sum(idx2)/N.prod(idx2.shape)>.9)
assert(N.sum(idx2)/N.prod(idx2.shape)>.70)
assert(i==nP-1)
N.set_string_function(N.array_repr,False)
x=trn_x[0][0] #1st frame, 1st molecule
x=x-N.sum(x*mass,axis=0)/N.sum(mass)
I=inertia_tensor(x,mass)
I,evec=LA.eigh(I)
print()
print("I",I)
ic = N.array(N.dot(x,evec),dtype=N_real) #initial water coordinates (oriented according to I); orientation x: H1->H2, y: O->(H1+H2)/2, z: perpendicular to plane
print(trn_x.shape,trn_v.shape)
trn_w=N.empty((len(trn_v),natoms/3,3),dtype=N_real)
#COM
trn_x -= N.sum(trn_x*mass,axis=2).reshape(nP,natoms/3,1,3)/N.sum(mass) #reshape doesn't change shape but reinserts the summed axis
trn_v_com = trn_v - N.sum(trn_v*mass,axis=2).reshape(nP,natoms/3,1,3)/N.sum(mass)
for n in range(len(trn_v)):
trn_w[n] = compute_omega(trn_x[n], trn_v_com[n], ic, I, mass.reshape(3))
#trn_w[n] = compute_omega_py(trn_x[n], trn_v_com[n], ic, I, mass)
trn_w=trn_w[:nP]
corr = N.apply_along_axis(lambda a: scipy.signal.fftconvolve(a,a[::-1],'same'),axis=0,arr=trn_w)
corr = corr[len(corr)/2:] #remove negative lag
corr=norm_corr(corr)
rf=file(options.r,"w")
map(lambda x:print(x,file=rf),corr)
#if len(trn_v)%2==1: #remove last if uneven number of trn-data points
#
trn_v=trn_v[:nP] #TODO: make configurable, switch here for trn/rot
print(trn_v.shape)
if bCom:
#trn_v = trn_v.reshape((-1,natoms/3,3,3)) #group as waters
trn_v = N.mean(trn_v*mass, axis=2) #average over waters, now shape is: frame, mol, coor
print(trn_v.shape)
corr = N.apply_along_axis(lambda a: scipy.signal.fftconvolve(a,a[::-1],'same'),axis=0,arr=trn_v)
#corr = N.apply_along_axis(lambda a: N.correlate(a,a,'same'),axis=0,arr=trn_v) #slower identical alternative
print(corr.shape)
corr = corr[len(corr)/2:] #remove negative lag
if bCom:
if not bNormalize:
corr/=N.sum(mass) #we multiplied trn with mass and because correlation is trn*trn the correlation was mass^2
else:
corr = corr.reshape(-1,natoms/3,3,3) #frames, molecule, atoms, xyz; so that we can multiply with mass
print(corr.shape)
corr *= mass
corr=norm_corr(corr)
print(corr.shape)
of=file(options.o,"w")
map(lambda x:print(x,file=of),corr)
import Sofa
from SofaPython import Quaternion as quat
import numpy as np
np.set_string_function( lambda x: ' '.join( map(str, x)), repr = False )
import path
import tool
# rigid body operations
def id():
res = np.zeros(7)
res[-1] = 1
return res
def inv(x):
res = np.zeros(7)
res[3:] = quat.conj(x[3:])
res[:3] = -quat.rotate(res[3:], x[:3])
return res
def prod(x, y):
print x.inv()
res = np.zeros(7)
res[:3] = x[:3] + quat.rotate(x[3:], y[:3])
res[3:] = quat.prod(x[3:], y[3:])
fh.setFormatter(
logging.Formatter(
'%(asctime)s %(filename)s [line:%(lineno)d] %(levelname)s %(message)s'
))
logging.root.addHandler(fh)
if os.environ.get('log', '0') == '1':
logging.root.setLevel(logging.DEBUG)
# set_stream_logger(logging.DEBUG)
set_stream_logger(logging.INFO)
set_file_logger(log_level=logging.DEBUG)
## ndarray will be pretty
np.set_string_function(lambda arr: f'{arr.shape} {arr.dtype} '
f'{arr.__str__()} '
f'dtype:{arr.dtype} shape:{arr.shape}',
repr=True)
logging.info('import lz')
## print(ndarray) will be pretty (and pycharm dbg)
# np.set_string_function(lambda arr: f'{arr.shape} {arr.dtype} \n'
# f'{arr.__repr__()} \n'
# f'dtype:{arr.dtype} shape:{arr.shape}', repr=False)
# old_np_repr = np.ndarray.__repr__
# np.ndarray.__repr__ = lambda arr: (f'{arr.shape} {arr.dtype} \n'
# f'{old_np_repr(arr)} \n'
# f'dtype:{arr.dtype} shape:{arr.shape}')
if self.orig_handlers is not None:
for sig, orig in zip(self.sigs, self.orig_handlers):
signal.signal(sig, orig)
self.orig_handlers = None
def df2md(df1):
import tabulate
return tabulate.tabulate(df1, headers="keys", tablefmt="pipe")
def np_print(arr):
return '{} \n dtype:{} shape:{}'.format(arr, arr.dtype, arr.shape)
np.set_string_function(np_print)
def set_stream_logger(log_level=logging.DEBUG):
sh = colorlog.StreamHandler()
sh.setLevel(log_level)
sh.setFormatter(
colorlog.ColoredFormatter(
' %(asctime)s %(filename)s [line:%(lineno)d] %(log_color)s%(levelname)s%(reset)s %(message)s'))
logging.root.addHandler(sh)
def set_file_logger(work_dir=None, log_level=logging.DEBUG):
work_dir = work_dir or os.getcwd()
fh = logging.FileHandler(os.path.join(work_dir, 'log.txt'))
fh.setLevel(log_level)
def genMarkov(markovFilePath, verb = 'INFO', nSimulation = int(5.e+4)):
logger.setStreamVerb(verb = verb)
logger.info('')
#os.system('cat ' + markovFilePath)
logger.debug('markovFilePath is %s' % markovFilePath)
# Read paramter file
beta = float(getParameter(markovFilePath, 'beta', 'bar-separated'))
muG = float(getParameter(markovFilePath, 'muG', 'bar-separated'))
sigmaG = float(getParameter(markovFilePath, 'sigmaG', 'bar-separated'))
p = float(getParameter(markovFilePath, 'p', 'bar-separated'))
dy = float(getParameter(markovFilePath, 'dy', 'bar-separated'))
nAgent = int(getParameter(markovFilePath, 'nAgent', 'bar-separated'))
theta = float(getParameter(markovFilePath, 'theta', 'bar-separated'))
periodsPerYear = int(getParameter(markovFilePath, 'periodsPerYear', 'bar-separated'))
# Output read parameters
logger.debug('')
logger.debug('read the following yearly parameters: ')
logger.debug('beta = %s' % beta)
logger.debug('muG = %s' % muG)
logger.debug('sigmaG = %s' % sigmaG)
logger.debug('p = %s' % p)
logger.debug('dy = %s' % dy)
logger.debug('nAgent = %s' % nAgent)
logger.debug('theta = %s' % theta)
logger.debug('periodsPerYear = %s' % periodsPerYear)
# perform consitency check on paramters:
assert periodsPerYear >= 1
assert beta >= 0.8 and beta <= 1.0
assert sigmaG >= 0.
assert muG <= 1.0
# computing scaled parameters
muG_sc = (1. + muG) ** (1./ periodsPerYear)
sigmaG_sc = sigmaG / np.sqrt(periodsPerYear)
beta_sc = beta ** (1./ periodsPerYear)
# scaled parameters:
logger.info('')
logger.info('computed the following scaled 1/%s parameters: ' % periodsPerYear)
logger.info('beta_sc = %s' % beta_sc)
logger.info('muG_sc = %s' % (muG_sc - 1.))
logger.info('sigmaG_sc = %s' % sigmaG_sc)
logger.info('')
# Build trans matrix
TransMatrix = np.array([[p, 1.-p], [1.-p, p]])
ShockMatrix = np.array([[ muG_sc - sigmaG_sc], [muG_sc + sigmaG_sc]])
mkov = MkovM(ShockMatrix, TransMatrix)
logger.debug(ShockMatrix)
logger.debug(TransMatrix)
#mkov.simulation()
logger.debug(mkov)
if nAgent > 1:
# Add unemployment shocks
#TransMatrixUnem = np.triu(np.ones( (nAgent, nAgent)), 1 ) * ( ( 1. - p) / ( nAgent - 1.) ) + np.tril(np.ones( (nAgent, nAgent)), -1 ) * ( ( 1. - p) / ( nAgent - 1.) ) + np.eye(nAgent) * p
ShockMatrixUnem = np.triu(np.ones( (nAgent, nAgent)), 1 ) * dy / ( nAgent - 1 ) + np.tril(np.ones( (nAgent, nAgent)), -1 ) * dy / (nAgent - 1 ) + np.eye(nAgent) * ( -dy )
# Print unemployment shock matrix
logger.info('ShockMatrixUnem \n %s' % ShockMatrixUnem)
# Combine aggregate uncertainty with idiosyncratic unemployment uncertainty
fullShockMatrix = np.hstack( ( np.repeat(ShockMatrix, nAgent, axis = 0), np.tile(ShockMatrixUnem, (2, 1))) )
#fullTransMatrix = np.kron(TransMatrix, TransMatrixUnem)
# ugly ugly ugly
fullShockMatrix = fullShockMatrix[:nAgent + 1]
fullShockMatrix[nAgent][ShockMatrix.shape[1]:] = np.zeros( (1, nAgent) )
# more ugly ugly ugly
pers = TransMatrix[0,0]
fullTransMatrix = np.vstack( (np.hstack( ( np.eye(nAgent) * pers, np.ones( (nAgent, 1) ) * (1.-pers) ) ), np.append(((1.-pers)/ nAgent) *np.ones(nAgent), pers) ) )
else:
fullShockMatrix = ShockMatrix
fullTransMatrix = TransMatrix
np.set_printoptions(precision = 7, linewidth = 300)
logger.info('fullShock\n %s' % fullShockMatrix )
logger.info('fullTrans\n %s' % fullTransMatrix )
###################
# Compute PD
# nD_t+1 = nYbar_t+1 - n(1-theta)E_tYbar_t+1
# divide through with Ybar_t+1
# nd_t+1 = n - n(1-theta) E_t[g_t+1]/ g_t+1
g = fullShockMatrix[:, 0]
Etg = np.dot(fullTransMatrix, g)
PD = 1. - ( 1. - theta ) * np.reshape(Etg, (len(Etg), 1)) / g
PB = np.reshape(Etg, (len(Etg), 1)) / g
##################
try:
np.savetxt(os.path.join(os.getcwd(), 'output', 'shockMatrix.in'), fullShockMatrix, fmt = '%15.10f')
np.savetxt(os.path.join(os.getcwd(), 'output', 'transMatrix.in'), fullTransMatrix, fmt = '%15.10f')
np.savetxt(os.path.join(os.getcwd(), 'output', 'p_a.in'), PD, fmt = '%15.10f')
np.savetxt(os.path.join(os.getcwd(), 'output', 'p_b.in'), PB, fmt = '%15.10f')
except IOError:
logger.critical('cannot write to output/.')
logger.info('')
#Estimate moments for full markov chain.
fullMChain = MkovM(fullShockMatrix, fullTransMatrix)
varSim, Theta = fullMChain.simulation(nSimulation)
# rename columns
varSim = varSim.rename(columns = {'0': 'agIncGrowth'})
for agent in range(1, nAgent):
varSim = varSim.rename(columns = {str(agent): 'dy_agent' + str(agent)})
qPers = Theta[1, 1]
yearlyStockSeries = pandas.DataFrame(varSim[::4])
model = scikits.statsmodels.tsa.api.VAR(yearlyStockSeries)
results = model.fit(1)
Theta = results.params[1:,:]
aPers = Theta[1, 1]
logger.info('quarterly pers %s, annual pers %s, diagnol pers %s' % (qPers, aPers, TransMatrix[0, 0]) )
np.set_string_function(None)
varSim['simInc'] = float(nAgent)
varSim['incGrIndAg0'] = float(1.)
varSim['incShareAg0'] = ( 1. + varSim['dy_agent1'] ) / nAgent
for row in varSim.rows():
if row > 0:
varSim['simInc'][row] = varSim['simInc'][row-1] * varSim['agIncGrowth'][row]
varSim['incGrIndAg0'][row] = ( varSim['incShareAg0'][row] / varSim['incShareAg0'][row - 1] ) * varSim['agIncGrowth'][row]
varSim['simIndIncAg0'] = varSim['incShareAg0'] * varSim['simInc']
x = varSim.ix[:,['0','incShareAg0', 'incGrIndAg0']]
logger.info(x[:100])
## logger.info('VAR for growth, incshareAg0, incGrIndAg0')
## model = scikits.statsmodels.tsa.api.VAR(x)
## result = model.fit(1)
## logger.info(result.summary())
logger.info('incShareAg0')
incShareAg0 = x['incShareAg0']
logger.info(incShareAg0.describe())
logger.info('skewness %s' % scipy.stats.kurtosis(incShareAg0))
logger.info('kurtosis %s' % scipy.stats.skew(incShareAg0))
logger.info('\nincGrIndAg0')
incGrIndAg0 = x['incGrIndAg0']
logger.info(incGrIndAg0.describe())
logger.info('skewness %s' % scipy.stats.skew(incGrIndAg0))
logger.info('kurtosis %s' % (scipy.stats.kurtosis(incGrIndAg0)))
#scikits.statsmodels.tsa.ar_model.AR(np.asarray(varSim['simIndIncAg0']))
#varSim = varSim[:100]
#N = len(varSim)
#rng = pandas.DateRange('1/1/1900', periods = N, timeRule = 'Q@JAN')
#ts = pandas.Series(varSim['1'], index = rng)
return fullShockMatrix, fullTransMatrix, beta_sc, g, Etg, PD, PB, incGrIndAg0
sys.path.append(path2Src)
from pymods.markovChain.mcInterface import MkovM
from pymods.support.support import wrapLogger
from pymods.support.support import getParameter
from pymods.support.support import myArrayPrint
import numpy as np
import pandas
import scipy.optimize
from genMarkov import genMarkov
from numpy.core.umath_tests import inner1d
pprintFun = myArrayPrint(width = 12, prec = 7)
np.set_string_function(pprintFun, repr = False)
logger = wrapLogger(loggerName = 'lucasMainLog', streamVerb = 'DEBUG', logFile = None)
def lucasOneAgent(shockMatrix, transMatrix, beta, g, Etg, PD, PB, markovFilePath, deterministic = False):
'''
markovFilePath: path to parameters.in file
determistic: boolean indicating whether to compute special determistic or stochastic case.
One agent economy. Therefore we have:
C_t = Y_t
C_{t+1} = Y_{t+1}
In the normalied world:
c_t = 1
c_{t+1} = 1
'''
def genMarkov(markovFilePath, verb='INFO', nSimulation=int(5.e+4)):
logger.setStreamVerb(verb=verb)
logger.info('')
#os.system('cat ' + markovFilePath)
logger.debug('markovFilePath is %s' % markovFilePath)
# Read paramter file
beta = float(getParameter(markovFilePath, 'beta', 'bar-separated'))
muG = float(getParameter(markovFilePath, 'muG', 'bar-separated'))
sigmaG = float(getParameter(markovFilePath, 'sigmaG', 'bar-separated'))
p = float(getParameter(markovFilePath, 'p', 'bar-separated'))
dy = float(getParameter(markovFilePath, 'dy', 'bar-separated'))
nAgent = int(getParameter(markovFilePath, 'nAgent', 'bar-separated'))
theta = float(getParameter(markovFilePath, 'theta', 'bar-separated'))
periodsPerYear = int(
getParameter(markovFilePath, 'periodsPerYear', 'bar-separated'))
# Output read parameters
logger.debug('')
logger.debug('read the following yearly parameters: ')
logger.debug('beta = %s' % beta)
logger.debug('muG = %s' % muG)
logger.debug('sigmaG = %s' % sigmaG)
logger.debug('p = %s' % p)
logger.debug('dy = %s' % dy)
logger.debug('nAgent = %s' % nAgent)
logger.debug('theta = %s' % theta)
logger.debug('periodsPerYear = %s' % periodsPerYear)
# perform consitency check on paramters:
assert periodsPerYear >= 1
assert beta >= 0.8 and beta <= 1.0
assert sigmaG >= 0.
assert muG <= 1.0
# computing scaled parameters
muG_sc = (1. + muG)**(1. / periodsPerYear)
sigmaG_sc = sigmaG / np.sqrt(periodsPerYear)
beta_sc = beta**(1. / periodsPerYear)
# scaled parameters:
logger.info('')
logger.info('computed the following scaled 1/%s parameters: ' %
periodsPerYear)
logger.info('beta_sc = %s' % beta_sc)
logger.info('muG_sc = %s' % (muG_sc - 1.))
logger.info('sigmaG_sc = %s' % sigmaG_sc)
logger.info('')
# Build trans matrix
TransMatrix = np.array([[p, 1. - p], [1. - p, p]])
ShockMatrix = np.array([[muG_sc - sigmaG_sc], [muG_sc + sigmaG_sc]])
mkov = MkovM(ShockMatrix, TransMatrix)
logger.debug(ShockMatrix)
logger.debug(TransMatrix)
#mkov.simulation()
logger.debug(mkov)
if nAgent > 1:
# Add unemployment shocks
#TransMatrixUnem = np.triu(np.ones( (nAgent, nAgent)), 1 ) * ( ( 1. - p) / ( nAgent - 1.) ) + np.tril(np.ones( (nAgent, nAgent)), -1 ) * ( ( 1. - p) / ( nAgent - 1.) ) + np.eye(nAgent) * p
ShockMatrixUnem = np.triu(np.ones(
(nAgent, nAgent)
), 1) * dy / (nAgent - 1) + np.tril(np.ones(
(nAgent, nAgent)), -1) * dy / (nAgent - 1) + np.eye(nAgent) * (-dy)
# Print unemployment shock matrix
logger.info('ShockMatrixUnem \n %s' % ShockMatrixUnem)
# Combine aggregate uncertainty with idiosyncratic unemployment uncertainty
fullShockMatrix = np.hstack(
(np.repeat(ShockMatrix, nAgent,
axis=0), np.tile(ShockMatrixUnem, (2, 1))))
#fullTransMatrix = np.kron(TransMatrix, TransMatrixUnem)
# ugly ugly ugly
fullShockMatrix = fullShockMatrix[:nAgent + 1]
fullShockMatrix[nAgent][ShockMatrix.shape[1]:] = np.zeros((1, nAgent))
# more ugly ugly ugly
pers = TransMatrix[0, 0]
fullTransMatrix = np.vstack(
(np.hstack((np.eye(nAgent) * pers, np.ones(
(nAgent, 1)) * (1. - pers))),
np.append(((1. - pers) / nAgent) * np.ones(nAgent), pers)))
else:
fullShockMatrix = ShockMatrix
fullTransMatrix = TransMatrix
np.set_printoptions(precision=7, linewidth=300)
logger.info('fullShock\n %s' % fullShockMatrix)
logger.info('fullTrans\n %s' % fullTransMatrix)
###################
# Compute PD
# nD_t+1 = nYbar_t+1 - n(1-theta)E_tYbar_t+1
# divide through with Ybar_t+1
# nd_t+1 = n - n(1-theta) E_t[g_t+1]/ g_t+1
g = fullShockMatrix[:, 0]
Etg = np.dot(fullTransMatrix, g)
PD = 1. - (1. - theta) * np.reshape(Etg, (len(Etg), 1)) / g
PB = np.reshape(Etg, (len(Etg), 1)) / g
##################
try:
np.savetxt(os.path.join(os.getcwd(), 'output', 'shockMatrix.in'),
fullShockMatrix,
fmt='%15.10f')
np.savetxt(os.path.join(os.getcwd(), 'output', 'transMatrix.in'),
fullTransMatrix,
fmt='%15.10f')
np.savetxt(os.path.join(os.getcwd(), 'output', 'p_a.in'),
PD,
fmt='%15.10f')
np.savetxt(os.path.join(os.getcwd(), 'output', 'p_b.in'),
PB,
fmt='%15.10f')
except IOError:
logger.critical('cannot write to output/.')
logger.info('')
#Estimate moments for full markov chain.
fullMChain = MkovM(fullShockMatrix, fullTransMatrix)
varSim, Theta = fullMChain.simulation(nSimulation)
# rename columns
varSim = varSim.rename(columns={'0': 'agIncGrowth'})
for agent in range(1, nAgent):
varSim = varSim.rename(columns={str(agent): 'dy_agent' + str(agent)})
qPers = Theta[1, 1]
yearlyStockSeries = pandas.DataFrame(varSim[::4])
model = scikits.statsmodels.tsa.api.VAR(yearlyStockSeries)
results = model.fit(1)
Theta = results.params[1:, :]
aPers = Theta[1, 1]
logger.info('quarterly pers %s, annual pers %s, diagnol pers %s' %
(qPers, aPers, TransMatrix[0, 0]))
np.set_string_function(None)
varSim['simInc'] = float(nAgent)
varSim['incGrIndAg0'] = float(1.)
varSim['incShareAg0'] = (1. + varSim['dy_agent1']) / nAgent
for row in varSim.rows():
if row > 0:
varSim['simInc'][row] = varSim['simInc'][
row - 1] * varSim['agIncGrowth'][row]
varSim['incGrIndAg0'][row] = (
varSim['incShareAg0'][row] /
varSim['incShareAg0'][row - 1]) * varSim['agIncGrowth'][row]
varSim['simIndIncAg0'] = varSim['incShareAg0'] * varSim['simInc']
x = varSim.ix[:, ['0', 'incShareAg0', 'incGrIndAg0']]
logger.info(x[:100])
## logger.info('VAR for growth, incshareAg0, incGrIndAg0')
## model = scikits.statsmodels.tsa.api.VAR(x)
## result = model.fit(1)
## logger.info(result.summary())
logger.info('incShareAg0')
incShareAg0 = x['incShareAg0']
logger.info(incShareAg0.describe())
logger.info('skewness %s' % scipy.stats.kurtosis(incShareAg0))
logger.info('kurtosis %s' % scipy.stats.skew(incShareAg0))
logger.info('\nincGrIndAg0')
incGrIndAg0 = x['incGrIndAg0']
logger.info(incGrIndAg0.describe())
logger.info('skewness %s' % scipy.stats.skew(incGrIndAg0))
logger.info('kurtosis %s' % (scipy.stats.kurtosis(incGrIndAg0)))
#scikits.statsmodels.tsa.ar_model.AR(np.asarray(varSim['simIndIncAg0']))
#varSim = varSim[:100]
#N = len(varSim)
#rng = pandas.DateRange('1/1/1900', periods = N, timeRule = 'Q@JAN')
#ts = pandas.Series(varSim['1'], index = rng)
return fullShockMatrix, fullTransMatrix, beta_sc, g, Etg, PD, PB, incGrIndAg0
def string_func(array):
numpy.set_string_function(None)
string = repr(array)
string = string[:-1] + ", shape=%s)" % (array.shape, )
numpy.set_string_function(string_func)
return string
import os
import pathlib
import re
import subprocess
import warnings
os.environ['NO_AT_BRIDGE'] = '1' # Hide X org false warning.
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import numpy as np
import pandas as pd
np.set_string_function(lambda x: f'<np.array shape={x.shape} dtype={x.dtype}>')
Run = collections.namedtuple('Run', 'task method seed xs ys')
PALETTES = dict(
discrete=(
'#377eb8',
'#4daf4a',
'#984ea3',
'#e41a1c',
'#ff7f00',
'#a65628',
'#f781bf',
'#888888',
'#a6cee3',
'#b2df8a',
# Analyze with Rasch model. The shell gives a list of output datadicts.
data.rasch(
groups=
None, # [<None, {'row':int row of group labels}, ['key', {'group0':['i1', i2'],...}], ['index', {'group0':[0, 1],...}]> => identify groups]
anchors=
None, # [<None, {'Bank':<pickle file>, 'row_ents':[<None,'All',row entity list>], 'col_ents':[<None,'All',col entity list>]}> ]
runspecs=[
0.0001, 20
], # [<[stop_when_change, max_iteration]> => iteration stopping conditions ]
minvar=
0.001, # [<decimal> => minimum row/col variance allowed during iteration]
maxchange=10, # [<+num> => maximum change allowed per iteration]
)
# Row entity stats
np.set_string_function(None)
arr = data.row_ents_out.whole
print arr
sys.exit()
print '\nPerson Measures =\n', data.row_ents_out
sys.exit()
# Column entity stats
print '\nItem Measures =\n', data.col_ents_out
# Reliability
print '\nReliability =\n', data.reliability
# Export person measures to a text file using the export method.
def close(self):
self.trajectory.close()
# Restore numpy formatting defaults
numpy.set_string_function(None, False)
numpy.set_string_function(None, True)
import numpy as np
# noinspection PyUnusedLocal
def pprint(arr):
return 'HA! - What are you going to do now?'
np.set_string_function(pprint)
a = np.arange(10)
a
print
a
np.set_string_function(None)
a
x = np.arange(4)
np.set_string_function(lambda x_: 'random', repr=False)
x.__str__()
x.__repr__()
def set_array_layout():
numpy.set_printoptions(linewidth=300, suppress=True)
numpy.set_string_function(f=format_d2)
def __init__(self, *args, **kwargs):
super(AD, self).__init__(*args, **kwargs)
self.__dict__ = self
# ipshell = InteractiveShellEmbed()
# ipshell.magic('%load_ext autoreload')
# Add array shape to Numpy's repr
def my_array_repr(arr):
orig_str = array_repr(arr)
return orig_str + '\n\nShape: ' + str(arr.shape) + '\n\n\n'
np.set_string_function(my_array_repr)
def fromfile(filename):
return np.fromfile(filename, '>d')
def equal(ax=None):
ax = plt.gca() if ax is None else ax
ax.set_aspect('equal', 'box-forced')
def doc(fn):
oinfo = Inspector().info(fn)
url = sphinxify.rich_repr(oinfo)
try:
def get_dummy_data(request, job_id):
"""
Create a dummy job and plot data
@param request: request object
@param job_id: RemoteJob pk
"""
try:
remote_job = RemoteJob.objects.get(remote_id=job_id)
except:
eqsans = Instrument.objects.get(name='eqsans')
reduction = ReductionProcess(instrument=eqsans,
name='Dummy job',
owner=request.user,
data_file='/tmp/dummy.nxs')
reduction.save()
try:
transaction = Transaction.objects.get(trans_id=-1)
except:
transaction = Transaction(trans_id=-1,
owner=request.user,
directory='/tmp')
transaction.save()
remote_job = RemoteJob(reduction=reduction,
remote_id='-1',
transaction=transaction)
remote_job.save()
breadcrumbs = "<a href='%s'>home</a>" % reverse(settings.LANDING_VIEW)
breadcrumbs += " › <a href='%s'>eqsans reduction</a>" % reverse('eqsans.views.reduction_home')
breadcrumbs += " › <a href='%s'>jobs</a>" % reverse('eqsans.views.reduction_jobs')
breadcrumbs += " › dummy job"
template_values = {'remote_job': remote_job,
'parameters': remote_job.reduction.get_data_dict(),
'reduction_id': remote_job.reduction.id,
'breadcrumbs': breadcrumbs,
'back_url': request.path}
template_values = remote.view_util.fill_job_dictionary(request, job_id, **template_values)
template_values = users.view_util.fill_template_values(request, **template_values)
template_values = remote.view_util.fill_template_values(request, **template_values)
# Go through the files and find data to plot
f = os.path.join(os.path.split(__file__)[0],'..','plotting','data','4065_Iq.txt')
# Do we read this data already?
plot_object = remote_job.get_first_plot(filename='4065_Iq.txt', owner=request.user)
if plot_object is not None and plot_object.first_data_layout() is not None:
data_str = plot_object.first_data_layout().dataset.data
else:
# If we don't have data stored, read it from file
file_content = open(f,'r').read()
data_str = view_util.process_Iq_data(file_content)
plot_object = Plot1D.objects.create_plot(request.user,
data=data_str,
filename='4065_Iq.txt')
remote_job.plots.add(plot_object)
template_values['plot_1d'] = data_str
template_values['plot_object'] = plot_object
template_values['plot_1d_id'] = plot_object.id if plot_object is not None else None
# Now the 2D data
f = os.path.join(os.path.split(__file__)[0],'..','plotting','data','4065_Iqxy.nxs')
plot_object2d = remote_job.get_plot_2d(filename='4065_Iqxy.nxs', owner=request.user)
if plot_object2d is None:
numpy.set_printoptions(threshold='nan', nanstr='0', infstr='0')
fd = h5py.File(f, 'r')
g = fd['mantid_workspace_1']
y = g['workspace']['axis1']
x = g['workspace']['axis2']
values = g['workspace']['values']
z_max = numpy.amax(values)
numpy.set_string_function( lambda x: '['+','.join(map(lambda y:'['+','.join(map(lambda z: "%.4g" % z,y))+']',x))+']' )
data_str_2d = values[:].__repr__()
numpy.set_string_function( lambda x: '['+','.join(map(lambda z: "%.4g" % z,x))+']' )
y_str = y[:].__repr__()
x_str = x[:].__repr__()
plot_object2d = Plot2D.objects.create_plot(user=request.user, data=data_str_2d,
x_axis=x_str, y_axis=y_str,
z_min=0.0, z_max=z_max, filename='4065_Iqxy.nxs')
remote_job.plots2d.add(plot_object2d)
template_values['plot_2d'] = plot_object2d
return template_values
DIM_NETHER = -1
DIM_END = 1
_zeros = {}
def string_func(array):
numpy.set_string_function(None)
string = repr(array)
string = string[:-1] + ", shape=%s)" % (array.shape, )
numpy.set_string_function(string_func)
return string
numpy.set_string_function(string_func)
class WorldEditorChunk(object):
"""
This is a 16x16xH chunk in a format-independent world.
The Blocks, Data, SkyLight, and BlockLight arrays are divided into
vertical sections of 16x16x16, accessed using the `getSection` method.
"""
def __init__(self, chunkData, editor):
self.worldEditor = editor
self.chunkData = chunkData
self.cx, self.cz = chunkData.cx, chunkData.cz
self.dimName = chunkData.dimName
self.dimension = editor.getDimension(self.dimName)
self.Entities = [
import Sofa
from SofaPython import Quaternion as quat
import numpy as np
np.set_string_function(lambda x: ' '.join(map(str, x)), repr=False)
import path
import tool
# rigid body operations
def id():
res = np.zeros(7)
res[-1] = 1
return res
def inv(x):
res = np.zeros(7)
res[3:] = quat.conj(x[3:])
res[:3] = -quat.rotate(res[3:], x[:3])
return res
def prod(x, y):
print x.inv()
res = np.zeros(7)
def string_func(array):
numpy.set_string_function(None)
string = repr(array)
string = string[:-1] + ", shape=%s)" % (array.shape,)
numpy.set_string_function(string_func)
return string
def main():
parser = OptionParser()
#parser.add_option("-s",metavar="FILE",help="Reference Structure file",default="topol.tpr")
parser.add_option("-n", metavar="FILE", help="Index file")
parser.add_option("-f",
metavar="FILE",
help="Trajectory with coordinates, velocies, and forces")
parser.add_option("-x", metavar="FILE", help="Trajectory with coordinates")
parser.add_option("-v", metavar="FILE", help="Trajectory with velocities")
parser.add_option("-k", metavar="FILE", help="Trajectory with forces")
parser.add_option("-o", metavar="FILE", help="Output", default="corr.dat")
parser.add_option("-r", metavar="FILE", help="Output", default="rot.dat")
(options, args) = parser.parse_args()
#open files
#sf = tpxfile(options.s)
#read index
if options.n:
isize, idx, iname = rd_index(options.n, 1)
print("Using group %s with %s atoms" % (iname[0], isize[0]))
idx = idx[0]
if not options.f and not (options.x and options.v and options.k):
print(
"Requires either one trajectory containing all input (-f) or three (-x, -v, -f)"
)
sys.exit(1)
if options.f and (options.x or options.v or options.k):
print("-f cannot be used with x,v, or k")
sys.exit(1)
if options.f:
tf = gmxfile(options.f, flags=TRX_NEED_X | TRX_NEED_V | TRX_NEED_F)
natoms = tf.natoms
else:
xf = gmxfile(options.x, flags=TRX_NEED_X)
vf = gmxfile(
options.v, flags=TRX_NEED_X
) #DCD doesn't have V/F so we expect all 3 files have X field
kf = gmxfile(options.k, flags=TRX_NEED_X)
print("Warning: NAMD units are expected for input files!")
natoms = xf.natoms
tf = izip(xf, vf, kf)
if natoms != vf.natoms or natoms != kf.natoms:
print("Number of atoms doesn't match between files!")
sys.exit(1)
if (natoms % 3 != 0):
print(
"This program only supports water. Number of atoms has to be multiple of 3."
)
sys.exit(1)
temp_v = []
temp_x = []
temp_f = []
trn_v = N.empty((nP, natoms / 3, 3, 3), dtype=N_real)
trn_x = N.empty((nP, natoms / 3, 3, 3), dtype=N_real)
for i, frm in enumerate(tf):
if not options.f:
frm_t = frm
class frm: #convert tuple into attributes
x = frm_t[0].x
v = frm_t[1].x * 20.45482706
f = frm_t[2].x * (100 / 4.184)
if options.n:
frm_x = frm.x[idx]
frm_v = frm.v[idx]
frm_f = frm.f[idx]
else:
frm_x = frm.x
frm_v = frm.v
frm_f = frm.f
frm_v = frm_v.reshape(-1, 3, 3)
frm_x = frm_x.reshape(-1, 3, 3)
frm_f = frm_f.reshape(-1, 3, 3)
temp_v += [frm_v.copy()]
temp_x += [frm_x.copy()]
temp_f += [frm_f.copy()]
temp_v = temp_v[-3:]
temp_x = temp_x[-3:]
temp_f = temp_f[-3:]
if i % ds != 2: continue #assumes ds>=3,
if __debug__:
a = temp_x[1]
b = temp_x[0] + temp_v[1] * dt
#print(temp_v[1]*dt)
#print(temp_x[0])
#idx=N.abs(a-b).max(axis=1).max(axis=1)>.0005
#print(a.shape,temp_v[1].shape)
#print(idx)
#print(a[idx])
#print(b[idx])
N.testing.assert_almost_equal(
a, b, decimal=2,
verbose=True) #low accuracy dominated by pressure coupling
i = i // ds
trn_v[i] = .5 * (temp_v[1] + temp_v[2]) - dt / 16 / mass * (temp_f[2] -
temp_f[0])
#trn_v[i] = .5*(temp_v[1]+temp_v[2])
##trn_v2 = 2*(trn_v[1:-1]+trn_v[2:])-3/2/dt*(trn_x[2:]-trn_x[:-2])
trn_x[i] = temp_x[1]
if i == nP - 1: break
if __debug__:
a = (temp_v[0] + temp_v[1]) / 2 #trn_v2[n]
b = trn_v[i]
#idx=N.abs((a-b))>.4+.2*N.abs(a+b) #.6 .4 old values: for 2fs: a few,, 1fs: none
idx = N.abs((a - b)) > .6 + .4 * N.abs(
a + b) #.6 .4 old values: for 2fs: a few,, 1fs: none
idx2 = N.abs(
(a - b)) < .1 + .05 * N.abs(a + b) #.1 .05 : 75% - 1fs: 91%
assert (N.sum(idx) / N.prod(idx2.shape) < 1 / 400)
#assert(N.sum(idx2)/N.prod(idx2.shape)>.9)
assert (N.sum(idx2) / N.prod(idx2.shape) > .70)
assert (i == nP - 1)
N.set_string_function(N.array_repr, False)
x = trn_x[0][0] #1st frame, 1st molecule
x = x - N.sum(x * mass, axis=0) / N.sum(mass)
I = inertia_tensor(x, mass)
I, evec = LA.eigh(I)
print()
print("I", I)
ic = N.array(
N.dot(x, evec), dtype=N_real
) #initial water coordinates (oriented according to I); orientation x: H1->H2, y: O->(H1+H2)/2, z: perpendicular to plane
print(trn_x.shape, trn_v.shape)
trn_w = N.empty((len(trn_v), natoms / 3, 3), dtype=N_real)
#COM
trn_x -= N.sum(trn_x * mass, axis=2).reshape(nP, natoms / 3, 1, 3) / N.sum(
mass) #reshape doesn't change shape but reinserts the summed axis
trn_v_com = trn_v - N.sum(trn_v * mass, axis=2).reshape(
nP, natoms / 3, 1, 3) / N.sum(mass)
for n in range(len(trn_v)):
trn_w[n] = compute_omega(trn_x[n], trn_v_com[n], ic, I,
mass.reshape(3))
#trn_w[n] = compute_omega_py(trn_x[n], trn_v_com[n], ic, I, mass)
trn_w = trn_w[:nP]
corr = N.apply_along_axis(
lambda a: scipy.signal.fftconvolve(a, a[::-1], 'same'),
axis=0,
arr=trn_w)
corr = corr[len(corr) / 2:] #remove negative lag
corr = norm_corr(corr)
rf = file(options.r, "w")
map(lambda x: print(x, file=rf), corr)
#if len(trn_v)%2==1: #remove last if uneven number of trn-data points
#
trn_v = trn_v[:nP] #TODO: make configurable, switch here for trn/rot
print(trn_v.shape)
if bCom:
#trn_v = trn_v.reshape((-1,natoms/3,3,3)) #group as waters
trn_v = N.mean(
trn_v * mass,
axis=2) #average over waters, now shape is: frame, mol, coor
print(trn_v.shape)
corr = N.apply_along_axis(
lambda a: scipy.signal.fftconvolve(a, a[::-1], 'same'),
axis=0,
arr=trn_v)
#corr = N.apply_along_axis(lambda a: N.correlate(a,a,'same'),axis=0,arr=trn_v) #slower identical alternative
print(corr.shape)
corr = corr[len(corr) / 2:] #remove negative lag
if bCom:
if not bNormalize:
corr /= N.sum(
mass
) #we multiplied trn with mass and because correlation is trn*trn the correlation was mass^2
else:
corr = corr.reshape(
-1, natoms / 3, 3, 3
) #frames, molecule, atoms, xyz; so that we can multiply with mass
print(corr.shape)
corr *= mass
corr = norm_corr(corr)
print(corr.shape)
of = file(options.o, "w")
map(lambda x: print(x, file=of), corr)
