Module Hierarchy

• qubx: QUB Express - an interactive simulator of ion channel current
  • qubx.GTK: General-purpose UI components.
  • qubx.accept: Functions for parsing strings into various data types, ranging from string (a no-op) to a system of differential equations.
  • qubx.acquirefile
  • qubx.chop: Build selection lists.
  • qubx.crash_rep: Crash detection and reporting
  • qubx.cube: Components for the top level of the QUB Express or Fitness.
  • qubx.dataGTK: Specialized scope for qub data.
  • qubx.data_abf: Reads Axon binary data using ABFFIO.dll, if available.
  • qubx.data_acquire: Reads .acquire data files.
  • qubx.data_fit: Curve fitting tool acting on data window.
  • qubx.data_gpatch: Reads .gpatch data files.
  • qubx.data_ibw
  • qubx.data_panel: Components for the top level of the QUB Express or Fitness.
  • qubx.data_pulse: Reads Pulse and Patchmaster files.
  • qubx.data_tacidl: Reads idealized data from TacFit table of transitions, saved with extension .tacidl.
  • qubx.data_types: Data file structure and i/o.
  • qubx.date: Date/time conversion between module datetime, Delphi, and "HH:MM:SS".
  • qubx.express: Top level of the application QUB Express.
  • qubx.extract: Panel to chop, process and save extracts of data.
  • qubx.faces: Container widgets.
  • qubx.fast: Interface to the qubfast library.
    • qubx.fast.baseline: Compiled structure for linear baseline between nodes.
    • qubx.fast.clickmap: Compiled routines for sampled data.
    • qubx.fast.data: Compiled routines for sampled data.
    • qubx.fast.fast_utils: Common imports and data marshalling for qubfast/ctypes bridge.
    • qubx.fast.filter: Compiled routines for filtering.
    • qubx.fast.fit: Compiled routines for curve fitting.
    • qubx.fast.kalman: Kalman filter from qubfast/qub_kalman.
    • qubx.fast.kmeans: Compiled routines for sampled data.
    • qubx.fast.model: Compiled routines for graph theory and linear constraints.
    • qubx.fast.simulate: Compiled routines for HMM simulation.
  • qubx.fit: Curve Fitting.
  • qubx.fit_robot: Background thread to operate qubx.fit.
  • qubx.fit_robots: Background thread to operate qubx.fit.
  • qubx.fit_space: Widget to display and control qubx.fit_robot.
  • qubx.fitness: Top level of the application QUB Express.
  • qubx.global_namespace: Container for global namespace, used by qubx.pyenv.env; import and define names in qub-express/global_names.py
  • qubx.hill: Auto-fit of Hill equation.
  • qubx.hist: Histograms panel with amplitude histogram.
  • qubx.http_post
  • qubx.ideal: Interface to the qubidl module (in the qubfast library) for efficiently handling sequences of dwells.
  • qubx.ideal_tools: Panel to modify idealized data.
  • qubx.idealize: Provides a visual panel (qubx.faces.Face) to idealize single-molecule data.
  • qubx.kalman: Kalman filter panel for Data.
  • qubx.list_average: Panel with live average of selections in active List.
  • qubx.list_figure: Panel which generates high-quality figures of the selections in active List.
  • qubx.maths: Mathematical utilities.
  • qubx.model: Hidden Markov model and math.
  • qubx.modelGTK: Panel which shows an open qub model.
  • qubx.model_charts: Model visualizations and matrices.
  • qubx.model_constraints: System of linear constraints for constrained optimization.
  • qubx.model_link: "Modeling Tools" menu: "Link to this model online"
  • qubx.modeling_utils: QubX.Modeling.Utils panel; hosts a registry of generic model/data-based optimizers, and sub-panels which can use them.
  • qubx.models_panel: Components for the top level of the QUB Express.
  • qubx.notebook: Base classes and registry for notebook figure export.
  • qubx.notebookGTK: GUI components to control notebook export of figures.
  • qubx.notebook_qtiplot: Notebook plugin to send figures to QtiPlot
  • qubx.notebook_scidavis: plugin to send figures to SciDAVis
  • qubx.optimize: Globally available pluggable optimizer framework.
  • qubx.optimizeGTK: GUI configuration for globally available pluggable optimizers.
  • qubx.pyenv: Support for user scripting, including
  • qubx.pyenvGTK: GUI support for user scripting.
  • qubx.remote_ctl: Gives outside processes access to the Python interpreter.
  • qubx.scope: 2d data display with oscilloscope-inspired controls.
  • qubx.script_seq: GUI support for user scripting.
  • qubx.select_charts: Charts and stats
  • qubx.settings: Preferences and presets management.
  • qubx.settingsGTK: pygtk GUI for qubx.settings.
  • qubx.simulate: Panel to control and orchestrate simulation and protocols.
  • qubx.simulation_protocol: Simulation protocol waveforms, same as QuB/PythonScripts/AcquisitionProtocol.
  • qubx.singleInstance: Passes command-line args from duplicate processes to the primary one.
  • qubx.sock: Network base classes.
  • qubx.sorted_collection: Sequence sorted by a key function.
  • qubx.spectrum
  • qubx.splash_main: Components for the top level of the QUB Express or Fitness.
  • qubx.stimulus: Panel to idealize stimulus signal(s).
  • qubx.table: Classes to represent tabular information.
  • qubx.tableGTK: GTK components for qubx.table.
  • qubx.table_panel: Components for the top level of the QUB Express or Fitness.
  • qubx.table_tree: Storage and retrieval of qubx.table info into qubx.tree format.
  • qubx.task: Thread management and multiprocessing.
  • qubx.tifffile: Read and write image data from and to TIFF files.
  • qubx.toolspace: Widget with switchable mouse controllers (Tools) and transparent overlays and layers.
  • qubx.tree: Classes for reading and writing all QuB binary files.
  • qubx.treeGTK: pygtk support for qubtree: clipboard and visual editing.
  • qubx.tree_native: Wrapper for qubtree shared library (gui mainly uses numpy variant from qubx.tree); this is the 'native' flavor, unless you have the obsolete _qubtree extension library.
  • qubx.trials: Components for the managing and visualizing qubx.trialset.TrialSets.
  • qubx.trialset: A trialset is a qubx.table.SimpleTable with one stored model per row.
  • qubx.ulp_diff
  • qubx.undo: Unlimited undo/redo.
  • qubx.util_panels: Components for the top level of the QUB Express or Fitness.
  • qubx.util_types: General-purpose types and utilities.
  • qubx.vcheck_client: Check over network for updates, invoked by qubx.cube.Cube (main window aka QubX) shortly after startup, and daily thereafter.
  • qubx.workflow: GUI support for user scripting.
  • qubx.xmlt: XML tools; so far just conversion between object attributes and xml.
• qubx_about_plug
  • qubx_about_plug.qubx_about_testing
  • qubx_about_plug.qubx_plugin: Base classes for QUB Express plugins, and sample implementations.
• qubx_testing
  • qubx_testing.calcserv
  • qubx_testing.i_over_var
  • qubx_testing.qubx_plugin: Base classes for QUB Express plugins, and sample implementations.
  • qubx_testing.stim_peq
• qubx_idl_mdl
  • qubx_idl_mdl.idealizer
• qubx_macro_r
  • qubx_macro_r.qubx_plugin: Base classes for QUB Express plugins, and sample implementations.
  • qubx_macro_r.rates: Provides a visual panel (qubx.faces.Face) to optimize rate constants from ensemble measurement.
• qubx_mac
  • qubx_mac.qubx_plugin: Base classes for QUB Express plugins, and sample implementations.
  • qubx_mac.rates: Provides a visual panel (qubx.faces.Face) to optimize rate constants from ensemble measurement.
• qubx_single
  • qubx_single.dur_hist
  • qubx_single.idealize: Provides a visual panel (qubx.faces.Face) to idealize single-molecule data.
  • qubx_single.rates: Provides a visual panel (qubx.faces.Face) to optimize single-molecule rate constants.