Package qubx_single :: Module rates

Module rates

Provides a visual panel (qubx.faces.Face) to optimize single-molecule rate constants.

/* This file is part of QUB Express. */

/* QUB Express is free software; you can redistribute it and/or modify */ /* it under the terms of the GNU General Public License as published by */ /* the Free Software Foundation, either version 3 of the License, or */ /* (at your option) any later version. */

/* QUB Express is distributed in the hope that it will be useful, */ /* but WITHOUT ANY WARRANTY; without even the implied warranty of */ /* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the */ /* GNU General Public License for more details. */

/* You should have received a copy of the GNU General Public License, */ /* named LICENSE.txt, in the QUB Express program directory. If not, see */ /* <http://www.gnu.org/licenses/>. */

Version: 1.11.0

Classes

[hide private]

ModelPrep
Represents a model ready for computation.

DataPrep
Represents data ready for computation.

Workspace
Holds data, model, and results for one file.

MultiplexedSignals

RatesFace

Functions

[hide private]

cl_dimension(Ns)

source code

get_data_prep(segs, model_prep, wait=True, receiver=<__builtin__.function object>)

source code

inter_ll_from_subi_args(args)

source code

Variables

[hide private]

MAXITER = 300

LBL_TDEAD = 'Tdead (ms)'

OPT_SIMPLEX = 0

OPT_DFP = 1

QUBX_SINGLE_RATES_METHODS = ['MIL', 'MSL']

ALLOW_THREADS = 1

BUFSIZE = 8192

CLIP = 0

COPY_ROWS_ALL = 0

COPY_ROWS_CHECKED = 3

COPY_ROWS_CRITERIA = 2

COPY_ROWS_GROUP = 1

DATAFILE = 'msl_test.qsf'

DATASOURCE_FILE = 0

DATASOURCE_LIST = 2

DATASOURCE_SCREEN = 1

ERR_CALL = 3

ERR_DEFAULT = 521

ERR_IGNORE = 0

ERR_LOG = 5

ERR_PRINT = 4

ERR_RAISE = 2

ERR_WARN = 1

Eigen_Scipy_Ptr = Eigen_Scipy_Ptr

FACE_POP_INSIDE = 0

FACE_POP_MAXIMIZED = 3

FACE_POP_MINIMIZED = 2

FACE_POP_WINDOW = 1

FLOATING_POINT_SUPPORT = 1

FPE_DIVIDEBYZERO = 1

FPE_INVALID = 8

FPE_OVERFLOW = 2

FPE_UNDERFLOW = 4

False_ = False

HAVE_LIB = True

Inf = inf

Infinity = inf

MAXDIMS = 32

MAX_ULP_DIFF = 4

MAY_SHARE_BOUNDS = 0

MAY_SHARE_EXACT = -1

MIN_TOTAL_RATE = 1e-09

MODELFILE = 'msl_test.qmf'

MSL_ACCEL_NONE = 0

MSL_ACCEL_OPENCL = 2

MSL_ACCEL_OPENMP = 1

NAN = nan

NINF = -inf

NZERO = -0.0

NaN = nan

PINF = inf

PZERO = 0.0

RAISE = 2

SHIFT_DIVIDEBYZERO = 0

SHIFT_INVALID = 9

SHIFT_OVERFLOW = 3

SHIFT_UNDERFLOW = 6

STIM_TYPE_CONST = 0

STIM_TYPE_EXPR = 2

STIM_TYPE_SIGNAL = 1

ScalarType = (<type 'int'>, <type 'float'>, <type 'complex'>, ...

TDEAD = 0.1

True_ = True

UFUNC_BUFSIZE_DEFAULT = 8192

UFUNC_PYVALS_NAME = 'UFUNC_PYVALS'

WRAP = 1

__package__ = 'qubx_single'

absolute = <ufunc 'absolute'>

add = <ufunc 'add'>

arccos = <ufunc 'arccos'>

arccosh = <ufunc 'arccosh'>

arcsin = <ufunc 'arcsin'>

arcsinh = <ufunc 'arcsinh'>

arctan = <ufunc 'arctan'>

arctan2 = <ufunc 'arctan2'>

arctanh = <ufunc 'arctanh'>

bitwise_and = <ufunc 'bitwise_and'>

bitwise_not = <ufunc 'invert'>

bitwise_or = <ufunc 'bitwise_or'>

bitwise_xor = <ufunc 'bitwise_xor'>

c_ = <numpy.lib.index_tricks.CClass object>

cast = {<type 'numpy.bool_'>: <function <lambda> at 0x7fd1396e...

cbrt = <ufunc 'cbrt'>

cdll = <ctypes.LibraryLoader object>

ceil = <ufunc 'ceil'>

conj = <ufunc 'conjugate'>

conjugate = <ufunc 'conjugate'>

copysign = <ufunc 'copysign'>

cos = <ufunc 'cos'>

cosh = <ufunc 'cosh'>

dbl_to_lng = <functools.partial object>

deg2rad = <ufunc 'deg2rad'>

degrees = <ufunc 'degrees'>

divide = <ufunc 'divide'>

e = 2.71828182846

equal = <ufunc 'equal'>

euler_gamma = 0.577215664902

exp = <ufunc 'exp'>

exp2 = <ufunc 'exp2'>

expm1 = <ufunc 'expm1'>

fabs = <ufunc 'fabs'>

floor = <ufunc 'floor'>

floor_divide = <ufunc 'floor_divide'>

flt_to_int = <functools.partial object>

fmax = <ufunc 'fmax'>

fmin = <ufunc 'fmin'>

fmod = <ufunc 'fmod'>

frexp = <ufunc 'frexp'>

greater = <ufunc 'greater'>

greater_equal = <ufunc 'greater_equal'>

hypot = <ufunc 'hypot'>

index_exp = <numpy.lib.index_tricks.IndexExpression object>

inf = inf

infty = inf

int_to_flt = <functools.partial object>

invert = <ufunc 'invert'>

isfinite = <ufunc 'isfinite'>

isinf = <ufunc 'isinf'>

isnan = <ufunc 'isnan'>

ldexp = <ufunc 'ldexp'>

left_shift = <ufunc 'left_shift'>

less = <ufunc 'less'>

less_equal = <ufunc 'less_equal'>

little_endian = True

lng_to_dbl = <functools.partial object>

log = <ufunc 'log'>

log10 = <ufunc 'log10'>

log1p = <ufunc 'log1p'>

log2 = <ufunc 'log2'>

logaddexp = <ufunc 'logaddexp'>

logaddexp2 = <ufunc 'logaddexp2'>

logical_and = <ufunc 'logical_and'>

logical_not = <ufunc 'logical_not'>

logical_or = <ufunc 'logical_or'>

logical_xor = <ufunc 'logical_xor'>

maxill = <CDLL 'libmaxill.so', handle 60ec7c0 at 7fd11c7f7750>

maximum = <ufunc 'maximum'>

mgrid = <numpy.lib.index_tricks.nd_grid object>

minimum = <ufunc 'minimum'>

mod = <ufunc 'remainder'>

modf = <ufunc 'modf'>

multiply = <ufunc 'multiply'>

nan = nan

nbytes = {<type 'numpy.bool_'>: 1, <type 'numpy.timedelta64'>:...

negative = <ufunc 'negative'>

newaxis = None
hash(x)

nextafter = <ufunc 'nextafter'>

not_equal = <ufunc 'not_equal'>

ogrid = <numpy.lib.index_tricks.nd_grid object>

pi = 3.14159265359

power = <ufunc 'power'>

pybuf = ctypes.pythonapi.PyBuffer_FromReadWriteMemory

pyobj_asreadbuf = ctypes.pythonapi.PyObject_AsReadBuffer

qubfast = <CDLL 'libqubfast.so', handle 2c23810 at 7fd12ac5d110>

r_ = <numpy.lib.index_tricks.RClass object>

rad2deg = <ufunc 'rad2deg'>

radians = <ufunc 'radians'>

rdbk = 'Expired.'

rdbreak = 'supporting'

rdname = 'qubfast.txt'

reciprocal = <ufunc 'reciprocal'>

remainder = <ufunc 'remainder'>

right_shift = <ufunc 'right_shift'>

rint = <ufunc 'rint'>

s_ = <numpy.lib.index_tricks.IndexExpression object>

sctypeDict = {0: <type 'numpy.bool_'>, 1: <type 'numpy.int8'>,...

sctypeNA = {'?': 'Bool', 'B': 'UInt8', 'Bool': <type 'numpy.bo...

sctypes = {'complex': [<type 'numpy.complex64'>, <type 'numpy....

sign = <ufunc 'sign'>

signbit = <ufunc 'signbit'>

sin = <ufunc 'sin'>

sinh = <ufunc 'sinh'>

spacing = <ufunc 'spacing'>

sqrt = <ufunc 'sqrt'>

square = <ufunc 'square'>

subtract = <ufunc 'subtract'>

tan = <ufunc 'tan'>

tanh = <ufunc 'tanh'>

true_divide = <ufunc 'true_divide'>

trunc = <ufunc 'trunc'>

typeDict = {0: <type 'numpy.bool_'>, 1: <type 'numpy.int8'>, 2...

typeNA = {'?': 'Bool', 'B': 'UInt8', 'Bool': <type 'numpy.bool...

typecodes = {'All': '?bhilqpBHILQPefdgFDGSUVOMm', 'AllFloat': ...

Variables Details

[hide private]

ScalarType

Value:

(<type 'int'>,
 <type 'float'>,
 <type 'complex'>,
 <type 'long'>,
 <type 'bool'>,
 <type 'str'>,
 <type 'unicode'>,
 <type 'buffer'>,
...

cast

Value:

{<type 'numpy.bool_'>: <function <lambda> at 0x7fd1396ed758>, <type 'n
umpy.timedelta64'>: <function <lambda> at 0x7fd1396ed7d0>, <type 'nump
y.float16'>: <function <lambda> at 0x7fd1396ed848>, <type 'numpy.uint8
'>: <function <lambda> at 0x7fd1396ed8c0>, <type 'numpy.int8'>: <funct
ion <lambda> at 0x7fd1396ed938>, <type 'numpy.object_'>: <function <la
mbda> at 0x7fd1396ed9b0>, <type 'numpy.datetime64'>: <function <lambda
> at 0x7fd1396eda28>, <type 'numpy.uint64'>: <function <lambda> at 0x7
fd1396edaa0>, <type 'numpy.int64'>: <function <lambda> at 0x7fd1396edb
...

nbytes

Value:

{<type 'numpy.bool_'>: 1, <type 'numpy.timedelta64'>: 8, <type 'numpy.
float16'>: 2, <type 'numpy.uint8'>: 1, <type 'numpy.int8'>: 1, <type '
numpy.object_'>: 8, <type 'numpy.datetime64'>: 8, <type 'numpy.uint64'
>: 8, <type 'numpy.int64'>: 8, <type 'numpy.void'>: 0, <type 'numpy.co
mplex256'>: 32, <type 'numpy.float128'>: 16, <type 'numpy.uint64'>: 8,
 <type 'numpy.int64'>: 8, <type 'numpy.unicode_'>: 0, <type 'numpy.com
plex128'>: 16, <type 'numpy.float64'>: 8, <type 'numpy.uint32'>: 4, <t
ype 'numpy.int32'>: 4, <type 'numpy.string_'>: 0, <type 'numpy.complex
...

sctypeDict

Value:

{0: <type 'numpy.bool_'>,
 1: <type 'numpy.int8'>,
 2: <type 'numpy.uint8'>,
 3: <type 'numpy.int16'>,
 4: <type 'numpy.uint16'>,
 5: <type 'numpy.int32'>,
 6: <type 'numpy.uint32'>,
 7: <type 'numpy.int64'>,
...

sctypeNA

Value:

{'?': 'Bool',
 'B': 'UInt8',
 'Bool': <type 'numpy.bool_'>,
 'Complex128': <type 'numpy.complex256'>,
 'Complex32': <type 'numpy.complex64'>,
 'Complex64': <type 'numpy.complex128'>,
 'D': 'Complex64',
 'Datetime64': <type 'numpy.datetime64'>,
...

sctypes

Value:

{'complex': [<type 'numpy.complex64'>,
             <type 'numpy.complex128'>,
             <type 'numpy.complex256'>],
 'float': [<type 'numpy.float16'>,
           <type 'numpy.float32'>,
           <type 'numpy.float64'>,
           <type 'numpy.float128'>],
 'int': [<type 'numpy.int8'>, <type 'numpy.int16'>, <type 'numpy.int32
...

typeDict

Value:

{0: <type 'numpy.bool_'>,
 1: <type 'numpy.int8'>,
 2: <type 'numpy.uint8'>,
 3: <type 'numpy.int16'>,
 4: <type 'numpy.uint16'>,
 5: <type 'numpy.int32'>,
 6: <type 'numpy.uint32'>,
 7: <type 'numpy.int64'>,
...

typeNA

Value:

{'?': 'Bool',
 'B': 'UInt8',
 'Bool': <type 'numpy.bool_'>,
 'Complex128': <type 'numpy.complex256'>,
 'Complex32': <type 'numpy.complex64'>,
 'Complex64': <type 'numpy.complex128'>,
 'D': 'Complex64',
 'Datetime64': <type 'numpy.datetime64'>,
...

typecodes

Value:

{'All': '?bhilqpBHILQPefdgFDGSUVOMm',
 'AllFloat': 'efdgFDG',
 'AllInteger': 'bBhHiIlLqQpP',
 'Character': 'c',
 'Complex': 'FDG',
 'Datetime': 'Mm',
 'Float': 'efdg',
 'Integer': 'bhilqp',
...