qubx.modeling

Module modeling_utils

QubX.Modeling.Utils panel; hosts a registry of generic model/data-based optimizers, and sub-panels which can use them.

Optimizer methods should be called from the gobject (gui) thread. To call from a qubx.task.Robot thread, use robot.gui_call_recv with wait=False.

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/>.

Functions

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task_exception_to_console(task, typ, val, tb)

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build_styled_model(optimizer, add_state, optimize=True, delta_ll=1.0, data_prep=None, task=None, should_quit=<__builtin__.function object>)
Builds up a model by, for all extant classes, repeatedly adding a state until LL improves by less than delta_ll.

source code

AngleOfStates(m, s1, s2)

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AddStarState(hub_index)

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AddChainState(cls)

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Connections(model)

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LeftmostState(model)

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ChainStateOrder(model)

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SubChain(model, cls)

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nauty_model_class(model)

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nauty_keep_model(nstate, code, max_conn, max_exit)

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nauty_setup_model(model, state_order, code, balance_loops, initial_k0, random_rates, random_from, random_to, decorate)

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nauty_connections(nstate, code)

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random_scaled(center, lo_mult, hi_mult)

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gen_perturbations(model, all_at_once, perturb_rates, perturb_channelCount, perturb_amp, perturb_std, perturb_cond, perturb_condstd, perturb_pct, trials)

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Variables

[hide private]

__package__ = 'qubx'

e = 2.71828182846

pi = 3.14159265359

rdbk = 'Expired.'

rdbreak = 'supporting'

rdname = 'qubfast.txt'

Function Details

[hide private]

build_styled_model(optimizer, add_state, optimize=True, delta_ll=1.0, data_prep=None, task=None, should_quit=<builtin.function object>)

source code

Builds up a model by, for all extant classes, repeatedly adding a state until LL improves by less than delta_ll. Can be called from non-gobject Task threads if you provide the qubx.task.Task.

Parameters:

optimizer - Optimizer
add_state - func(class_index) called on gobject thread, operates on QubX.Models.file
optimize - False to evaluate model LL as-is
data_prep - optional prepared data to override onscreen
task - qubx.task.Task if called from Task/robot thread