Package qubx :: Module modelGTK

Module modelGTK

Panel which shows an open qub model.

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/>.

Classes

[hide private]

QubModelView
Displays and edits one qubx.model.QubModel.

QubModelDefaultTool
Basic mouse interaction for QubModelView.

QubModelConnectTool
Mouse interaction and overlay while drawing a connection between states.

QubModelColorTool
Mouse interaction and overlay while picking a state's color.

QubModelScaleTool
Mouse interaction and overlay while picking a rate to complete a Scale constraint.

QubModelLoopTool
Mouse interaction and overlay while picking rates around a loop.

GrabTool
As qubx.dataGTK.QubDataView.tool, lets user highlight data to initialize class Amp/Std/Cond/CondStd.

QubModelCopyDialog
Modal window with settings for 'copy model image'.

IeqFvAboutBox

ModelMerge_Dialog

ModelNbPicturePrefs

Functions

[hide private]

distance(x1, y1, x2, y2)
Returns the Euclidean distance between (x1, y1) and (x2, y2).

source code

default_static(x)
Returns a function f; every time you call f() it returns x.

source code

can_regrab(model)

source code

pt_in_rect(x, y, r)
Returns True if the point (x, y) is within the rect r=(x0, y0, w, h).

source code

FitIeqFv(II, SS, DV, CC, GG, GS, I0, S0)
Finds the baseline current and per-class conductance which best fit current/voltage measurements.

source code

ModelMerge(item=None, count_paths=None, merged_name=None)

source code

CopyModelTree(item)

source code

PasteModelTree(item)

source code

PasteNewModel(item)

source code

iterstim(**stim)

source code

iter_stim_Pe(modelview, **stim)

source code

iter_Pe_of_state(modelview, state, **stim)

source code

iter_Pe_of_class(modelview, cls, **stim)

source code

calc_Pe_of_stim(modelview, stim, idx, out_name='Peq', calc=<__builtin__.function object>)
Calculates equilibrium probability at various combinations of stimulus. source code

find_ec50(modelview, stim_name, idx, calc=<__builtin__.function object>)

source code

Variables

[hide private]

Tools = <qubx.util_types.ToolRegistry object>

COLOR_STATE_BORDER = ('modelGTK.state.border', (0, 0, 0, 1))

COLOR_STATE_LABEL = ('modelGTK.state.label', (1, 1, 1, 1))

COLOR_RATE = ('modelGTK.rate', (0, 0, 0, 1))

COLOR_EFFECTIVE_RATE = ('modelGTK.rate.effective', (0.5, 0, 0....

COLOR_BG = ('modelGTK.bg', (1, 1, 0.75, 1))

COLOR_CHANCOUNT = ('modelGTK.channelCount', (1, 1, 1, 1))

COLOR_BUTTON = ('modelGTK.button', (0, 0, 0, 0.85))

COLOR_BUTTON_TEXT = ('modelGTK.button.text', (0.1, 1, 0.1, 0.9))

COLOR_BUTTON_GRAY = ('modelGTK.button.gray', (1, 1, 1, 0.4))

COLOR_BUTTON_HOVER = ('modelGTK.button.hover', (1, 0.9, 0.9, 1))

COLOR_QUESTION_BORDER = ('modelGTK.button.border', (1, 0, 0, 1))

CLICK_SLOP = 2

MENU_TIMEOUT = 360

MENU_STRAYDIUS = 2

IGNORE_MENU_RELEASE = 5

TheCopyDialog = <QubModelCopyDialog object at 0x7fd1219bd460 (...

TheIeqFvAboutBox = <IeqFvAboutBox object at 0x7fd1219bd6e0 (Gt...

ModelMerge_index = 0

ALLOW_THREADS = 1

BUFSIZE = 8192

CLIP = 0

ERR_CALL = 3

ERR_DEFAULT = 521

ERR_IGNORE = 0

ERR_LOG = 5

ERR_PRINT = 4

ERR_RAISE = 2

ERR_WARN = 1

FLOATING_POINT_SUPPORT = 1

FPE_DIVIDEBYZERO = 1

FPE_INVALID = 8

FPE_OVERFLOW = 2

FPE_UNDERFLOW = 4

False_ = False

Inf = inf

Infinity = inf

MAXDIMS = 32

MAY_SHARE_BOUNDS = 0

MAY_SHARE_EXACT = -1

MIN_TOTAL_RATE = 1e-09

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

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

True_ = True

UFUNC_BUFSIZE_DEFAULT = 8192

UFUNC_PYVALS_NAME = 'UFUNC_PYVALS'

WRAP = 1

__package__ = 'qubx'

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 = (1, 0, 1)

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

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

cbrt = <ufunc 'cbrt'>

conj = <ufunc 'conjugate'>

conjugate = <ufunc 'conjugate'>

deg2rad = <ufunc 'deg2rad'>

divide = <ufunc 'divide'>

e = 2.71828182846

equal = <ufunc 'equal'>

euler_gamma = 0.577215664902

exp2 = <ufunc 'exp2'>

floor_divide = <ufunc 'floor_divide'>

fmax = <ufunc 'fmax'>

fmin = <ufunc 'fmin'>

greater = <ufunc 'greater'>

greater_equal = <ufunc 'greater_equal'>

i = 19

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

inf = inf

infty = inf

invert = <ufunc 'invert'>

isfinite = <ufunc 'isfinite'>

left_shift = <ufunc 'left_shift'>

less = <ufunc 'less'>

less_equal = <ufunc 'less_equal'>

little_endian = True

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'>

maximum = <ufunc 'maximum'>

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

minimum = <ufunc 'minimum'>

mod = <ufunc 'remainder'>

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'>

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

rad2deg = <ufunc 'rad2deg'>

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'>

spacing = <ufunc 'spacing'>

square = <ufunc 'square'>

subtract = <ufunc 'subtract'>

true_divide = <ufunc 'true_divide'>

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

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

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

Function Details

[hide private]

FitIeqFv(II, SS, DV, CC, GG, GS, I0, S0)

source code

Finds the baseline current and per-class conductance which best fit current/voltage measurements.

Parameters:

II - list of current-mean measurements [pA]
SS - list of current-standard-deviation measurements [pA]
DV - list of (V - Vrev) measurements [Volts]
CC - list of the model class of each measurement
GG - list of starting values for conductance, per model class [pS]
GS - list of starting values for conductance standard deviation [pS]
I0 - mean baseline current [pA]
S0 - standard deviation of baseline current [pA]

Returns:

(GG, GS, I0, S0) after nonlinear least squares fitting

calc_Pe_of_stim(modelview, stim, idx, out_name=`'Peq'`, calc=<builtin.function object>)

source code

Calculates equilibrium probability at various combinations of stimulus.

Parameters:

modelview - e.g. QubX.Models.view
stim - dict(stim_name -> value or list of values); will evaluate the cartesian product of all values
idx - Index of class or state
calc - interpret idx as class (default), or as state with calc=iter_Pe_of_state

Returns:

list of dict, with entries for out_name and each stim_name, corresponding to cartesian product of all requested conditions

Variables Details

[hide private]

COLOR_EFFECTIVE_RATE

Value:

('modelGTK.rate.effective', (0.5, 0, 0.5, 1))

TheCopyDialog

Value:

<QubModelCopyDialog object at 0x7fd1219bd460 (GtkDialog at 0x2ff2360)>

TheIeqFvAboutBox

Value:

<IeqFvAboutBox object at 0x7fd1219bd6e0 (GtkWindow at 0x30d81a0)>

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',
...

Module modelGTK

FitIeqFv(II, SS, DV, CC, GG, GS, I0, S0)

calc_Pe_of_stim(modelview, stim, idx, out_name='Peq', calc=<__builtin__.function object>)

COLOR_EFFECTIVE_RATE

TheCopyDialog

TheIeqFvAboutBox

ScalarType

cast

nbytes

sctypeDict

sctypeNA

sctypes

typeDict

typeNA

typecodes

calc_Pe_of_stim(modelview, stim, idx, out_name=`'Peq'`, calc=<builtin.function object>)