Steady-state inactivation (h∞) curve from a two-pulse VC protocol#366
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Adds an INACTIVATION_PROTOCOL ("Inactivation") voltage-clamp protocol whose
per-sweep holding voltage is the conditioning prepulse (swept via the existing
min/max/step range) and whose step amplitude is a fixed test_pulse_voltage.
Built from ordinary step_voltage arrays so the standard I-V analysis can later
extract the test-pulse peak current per sweep.
- patch_sim/constants.py: INACTIVATION_PROTOCOL, STEADY_STATE_INACTIVATION
preset-name constant, "Inactivation" added to VOLTAGE_PROTOCOLS.
- build_voltage_protocol: new test_pulse_voltage param + "Inactivation" branch
(rejects a missing prepulse range — inherently multi-sweep).
- ProtocolState: vc_test_pulse_voltage field + setter, passed through
_build_protocols; can_run_continuous now excludes the Inactivation protocol.
- protocol_panel: param-form schema entry so the new type renders in the UI.
Refs #184
New patch_sim/analysis/inactivation.py: InactivationPoint, InactivationAnalysisResult, and compute_inactivation, which takes an IVAnalysisResult whose stimulus window is the fixed test pulse of a two-pulse protocol and returns normalized availability h∞(V) = I_peak(V) / I_peak_max per conditioning prepulse, plus a decreasing-Boltzmann fit h∞(V) = 1 / (1 + exp((V - v_half) / k)). Reuses gv_curve.boltzmann (via a _decreasing_boltzmann wrapper) and gv_curve.BoltzmannFit so the activation and inactivation analyses share one Boltzmann implementation, per #184. Re-exports compute_inactivation, InactivationAnalysisResult, InactivationPoint and the INACTIVATION_PROTOCOL constant from patch_sim / patch_sim.analysis. Refs #184
A two-pulse VC preset: 150 ms conditioning prepulse from -120 to -20 mV in 10 mV steps, then a 15 ms fixed test pulse to 0 mV. Auto-surfaces in the UI preset dropdown via PROTOCOL_PRESET_NAMES. Refs #184
…V panel Wires compute_inactivation through the simulation pipeline and renders it: - _analysis_format._compute_inactivation_data: serialise an InactivationAnalysisResult (h∞ points + decreasing-Boltzmann fit, with a pre-computed dense fit curve) for AnalysisState. - _sweep_executor: when the protocol is "Inactivation", run the h∞ analysis off the same IVAnalysisResult and skip g-V / τ-V (the swept command voltage is the conditioning prepulse, not the test voltage); new _SimResult.inactivation_data field. - simulation._do_apply_simulation: copy inactivation_data to AnalysisState. - AnalysisState: inactivation_data field, clear_results entry, has_inactivation_data / inactivation_figure rx.vars. - plotting/inactivation.build_inactivation_figure: h∞ scatter + dashed decreasing-Boltzmann line + V₁/₂ / k annotation. - metrics/fi_gv_panel: _inactivation_plot() shown below the I-V curve in the I-V Analysis tab when h∞ data is available. Refs #184
…refix) ProtocolState._apply_protocol_preset setattr's preset-dict keys onto the state, and build_protocol_from_preset forwards the same dict to build_voltage_protocol — so the field name must match the builder parameter test_pulse_voltage. Like holding_voltage it has no current-clamp twin, so the vc_ disambiguation prefix isn't needed. Without this, loading the Steady-State Inactivation preset raised SetUndefinedStateVarError. Refs #184
- tests/unit/test_inactivation.py: compute_inactivation normalization, sorting, unit-range clamping, Boltzmann parameter recovery, monotonicity, and edge cases (empty / single point / all-non-negative peaks). - tests/unit/test_protocol_builders.py: build_voltage_protocol "Inactivation" shape, per-sweep prepulse/test-pulse levels, the range/step/min>max validation errors, and the Steady-State Inactivation preset. - tests/integration/test_inactivation_simulation.py: end-to-end squid HH run → analyze_iv → compute_inactivation; h∞ in [0, 1], monotone-decreasing, Boltzmann V½ ≈ -60 mV, k > 0. - tests/ui/test_plotting.py: build_inactivation_figure traces, fit/annotation, and axis titles. - tests/ui/test_state.py: clear_results also clears inactivation_data. - tests/e2e/test_voltage_clamp_flow.py: the Steady-State Inactivation preset produces multi-sweep, populates inactivation_data, and skips g-V / τ-V. Refs #184
…30 ms The 5 ms post-test window crammed the test-pulse current transient against the right edge of the trace. Widen it to 30 ms so the transient (and its decay) sit clear of the edge.
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Summary
Inactivationvoltage-clamp protocol type (INACTIVATION_PROTOCOL): a two-pulse protocol where each sweep holds at a different conditioning prepulse voltage (swept via the existing min/max/step range) and then steps to a fixedtest_pulse_voltage. Built from ordinarystep_voltagearrays soanalyze_ivextracts the test-pulse peak inward current per sweep over the[pre, pre+stim]window.patch_sim/analysis/inactivation.py—compute_inactivation(iv_result)derives normalized availabilityh∞(V) = I_peak(V) / I_peak_maxper prepulse and fits a decreasing Boltzmannh∞(V) = 1 / (1 + exp((V − V_half) / k)), reportingV_halfandk. Reusesgv_curve.boltzmann(via a_decreasing_boltzmannwrapper) andgv_curve.BoltzmannFit, sharing the Boltzmann implementation with the activation g-V curve (Compute and plot normalised conductance vs. voltage (g-V curve) #177).Steady-State Inactivationprotocol preset: 150 ms conditioning prepulse from −120 to −20 mV in 10 mV steps, 15 ms fixed test pulse to 0 mV.I-V Analysispanel now shows an h∞ vs. prepulse-voltage scatter with a dashed Boltzmann fit and aV₁/₂ = … mV, k = … mVannotation below the I-V curve when the Inactivation protocol is run. For that protocol the g-V / τ-V plots are skipped (their x-axis would be the prepulse voltage, not the test voltage); the I-V plot remains as the un-normalized inactivation curve.protocol_panelrenders Prepulse min/max/step + Test pulse fields, and continuous mode is disabled for this inherently-multi-sweep protocol.compute_inactivation, thebuild_voltage_protocolInactivation branch), integration (squid HH end-to-end: h∞ in [0, 1], monotone-decreasing, Boltzmann V½ ≈ −60 mV), UI plotting +clear_results, and e2e (preset populatesinactivation_data, skips g-V / τ-V).Test plan
V₁/₂ = … mV, k = … mVannotation; the g-V and τ-V plots are absent.Closes #184