Package qubx :: Module idealize

Module idealize

Provides a visual panel (qubx.faces.Face) to idealize single-molecule data.

/* 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/>. */

Classes

[hide private]

BaumWelchIdealizer

IdlFace
Hosts idealization methods, many from qubx_single_molecule plugin.

SKMIdealizer

Variables

[hide private]

ALLOW_THREADS = 1

BUFSIZE = 8192

CLIP = 0

COLOR = defaultdict(<function <lambda> at 0x7fd137b1e1b8>, {0:...

COLOR_CLEAR = ('toolspace.clear', (0, 0, 0, 0))

COLOR_MENU_FILE = ('faces.menu.file', (0, 1, 0, 1))

COLOR_MENU_TEXT = ('faces.menu.text', (0, 1, 0, 0.75))

COLOR_POPPED_BTN = ('faces.popped.btn', (0.7, 0, 0.1, 1))

COLOR_POPPED_TEXT = ('faces.popped.empty.text', (0.1, 0, 0, 1))

COLOR_TOOLTAB_BG = ('faces.tooltab.bg', (0, 0, 0, 1))

COLOR_TOOLTAB_CLOSE = ('faces.tooltoggle.close', (0.9, 0, 0, 1))

COLOR_TOOLTAB_CLOSE_HOVER = ('faces.tooltoggle.close.hover', (...

COLOR_TOOLTOGGLE_INFO = ('faces.tooltoggle.info', (1, 1, 1, 0....

COLOR_TOOLTOGGLE_MENU = ('faces.tooltoggle.menu', (0.2, 1, 0.2...

COPY_ROWS_ALL = 0

COPY_ROWS_CHECKED = 3

COPY_ROWS_CRITERIA = 2

COPY_ROWS_GROUP = 1

ColorInfo = defaultdict(<function <lambda> at 0x7fd123474500>,...

DATASOURCE_FILE = 0

DATASOURCE_LIST = 2

DATASOURCE_SCREEN = 1

DOWNSAMPLE_ALL_LOGCOUNT = 2.0

DOWNSAMPLE_LOGSLOPE = 3.0

ERR_CALL = 3

ERR_DEFAULT = 521

ERR_IGNORE = 0

ERR_LOG = 5

ERR_PRINT = 4

ERR_RAISE = 2

ERR_WARN = 1

FACE_POP_INSIDE = 0

FACE_POP_MAXIMIZED = 3

FACE_POP_MINIMIZED = 2

FACE_POP_WINDOW = 1

FILEMENU_WIDTH = 32

FLOATING_POINT_SUPPORT = 1

FPE_DIVIDEBYZERO = 1

FPE_INVALID = 8

FPE_OVERFLOW = 2

FPE_UNDERFLOW = 4

False_ = False

HARMLESS_KEYS = [65361, 65363, 65362, 65364, 65360, 65367, 65379]

Inf = inf

Infinity = inf

MAXDIMS = 32

MAX_BOOLS = 16

MAX_EVENTS_PER_WAIT = 20

MAX_FIELDS = 256

MAX_SAFENAME_LEN = 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

POS_DROPDOWN = 'dropdown'

PZERO = 0.0

RAISE = 2

RECENT_FILES_COUNT = 20

REQUEST_SHOW_AS_WINDOW = False

RESPONSE_NO_TO_ALL = 12345

Readers = {'.acquire': {'pattern': '*.acquire', 'create': <cla...

SAVEBUFLEN = 262144

SHIFT_DIVIDEBYZERO = 0

SHIFT_INVALID = 9

SHIFT_OVERFLOW = 3

SHIFT_UNDERFLOW = 6

STIM_LABELS = ('Constant', 'Signal', 'Expression')

STIM_TYPES = (0, 1, 2)

STIM_TYPE_CONST = 0

STIM_TYPE_EXPR = 2

STIM_TYPE_SIGNAL = 1

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

ShowDropped = False

TOOLTOGGLE_MENUHEIGHT_EM = 3.0

TOOLTOGGLE_NAME_EM = 16.0

TOOLTOGGLE_TABHEIGHT_EM = 10.0

TOOLTOGGLE_TAB_BORDER = 1.5

TOOLTOGGLE_WIDTH_EM = 2.0

Tasks = <qubx.task.TaskManager object>

True_ = True

UFUNC_BUFSIZE_DEFAULT = 8192

UFUNC_PYVALS_NAME = 'UFUNC_PYVALS'

UNSET_VALUE = 86738.82583

WRAP = 1

Writers = {'.csv': {'pattern': '*.csv', 'ext': '.csv', 'save':...

__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_ = <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'>

false = False

floor_divide = <ufunc 'floor_divide'>

fmax = <ufunc 'fmax'>

fmin = <ufunc 'fmin'>

greater = <ufunc 'greater'>

greater_equal = <ufunc 'greater_equal'>

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

inf = inf

infty = inf

invert = <ufunc 'invert'>

isfinite = <ufunc 'isfinite'>

keysyms = <gtk._lazyutils.LazyModule object>

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'>

name_float = 'a number'

name_int = 'an integer'

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 = True

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': ...

valid_identifier = re.compile(r'^[A-Za-z_][A-Za-z_0-9]*$')

Variables Details

[hide private]

COLOR

Value:

defaultdict(<function <lambda> at 0x7fd137b1e1b8>, {0: (0, 0, 0), 1: (
1, 0, 0), 2: (0, 0, 1), 3: (0, 1, 0), 4: (0, 1, 1), 5: (1, 1, 0), 6: (
1, 0, 1), 7: (0.5, 0.0, 0.0), 8: (0.525, 0.32025, 0.013125000000000012
), 9: (0.44550000000000006, 0.55, 0.027500000000000028), 10: (0.149499
99999999994, 0.575, 0.04312499999999997), 11: (0.059999999999999984, 0
.6, 0.2759999999999999), 12: (0.078125, 0.625, 0.625), 13: (0.09750000
000000002, 0.3185, 0.65), 14: (0.22949999999999962, 0.1181250000000000
4, 0.675), 15: (0.5879999999999999, 0.13999999999999996, 0.7), 16: (0.
...

COLOR_TOOLTAB_CLOSE_HOVER

Value:

('faces.tooltoggle.close.hover', (1, 0.2, 0.2, 1))

COLOR_TOOLTOGGLE_INFO

Value:

('faces.tooltoggle.info', (1, 1, 1, 0.76))

COLOR_TOOLTOGGLE_MENU

Value:

('faces.tooltoggle.menu', (0.2, 1, 0.2, 1))

ColorInfo

Value:

defaultdict(<function <lambda> at 0x7fd123474500>, {'qubx.cube.other.m
enu': {'label': 'Other panel menu'}, 'scope.signal.bg': {'label': 'Dat
a signal background'}, 'scope.mean.line': {'label': 'Data center line'
}, 'toolspace.layer.bg': {'label': 'Default layer background'}, 'list_
figure.fit': {'label': 'ListFigure fit curves'}, 'data_fit.button': {'
label': 'Data curvefit buttons'}, 'toolspace.focused': {'label': 'Pane
l border focused'}, 'modelGTK.state.label': {'label': 'Model state lab
el'}, 'scope.units.hover': {'label': 'Data units mouseover'}, 'dataGTK
...

Readers

Value:

{'.acquire': {'pattern': '*.acquire', 'create': <class 'qubx.data_acqu
ire.QubData_ACQ'>, 'ext': '.acquire', 'description': 'Acquire files'},
 '.csv': {'pattern': '*.csv', 'create': <function OpenTXT at 0x7fd1298
320c8>, 'ext': '.csv', 'description': 'Comma-separated files'},
 '.dat': {'pattern': '*.dat', 'create': <function QubData_PUL_Open at 
0x7fd121749b18>, 'ext': '.dat', 'description': 'DAT files'},
 '.dwt': {'pattern': '*.dwt', 'create': <function OpenDWT at 0x7fd1298
32140>, 'ext': '.dwt', 'description': 'QuB idealized data'},
...

ScalarType

Value:

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

Writers

Value:

{'.csv': {'pattern': '*.csv', 'ext': '.csv', 'save': <function Save at
 0x7fd12982e8c0>, 'description': 'Comma-separated ext files'},
 '.float32': {'pattern': '*.float32', 'ext': '.float32', 'save': <func
tion Save_Float32 at 0x7fd12982e6e0>, 'description': 'Raw binary (floa
t32)'},
 '.int16': {'pattern': '*.int16', 'ext': '.int16', 'save': <function S
ave_Int16 at 0x7fd12982e758>, 'description': 'Raw binary (int16)'},
 '.qdf': {'pattern': '*.qdf', 'ext': '.qdf', 'save': <function Save_QD
...

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',
...