Imaging>sensor.py change #68
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* initial structure / tests * put save_history in Device * basic scope functionality working * refactor so Opsin and Indicator are both LightDependentDevices * separate SynapseDevice and LightDependentDevice * refactor to light_receptor composition over inheritance * restructure light dependence * ODE convolution attempt 1 (failed) * conv to ODE attempt 2 * solve conv as ODE problem * start holo_stim, rename * finish GaussianEllipsoid * start noise notebook * finish imaging noise notebook * normalize equal photon flux spectra * refactor imaging * progress on 2p viz, all-optical tutorial * get all-optical mostly working * round images * make scope target viz points bigger * finalize all-optical tutorial * add scope SNR using heterogeneous expression * gitignore notebook figs * complete all-optical figure * add heterogeneous expression to all-optical tutorial * tweak scope viz * tweak all-optical fig * fix multi opto and LQR tutorials
* improve plot function * add Köhler illumination * fix numpy warning product->prod * add eNpHR3.0, 3-state Cl- pump model * update tklfp * give warning when action spectrum unspecified * remove old _tutorials.rst file * start newman15 validation notebook * clean up imports * support .-() in opsin names * remove sim from device repr * refactor IOProc to use preprocess_ctrl_signals * add light.color property * progress * add notebook results to .gitignore * tweak enphr3 * finish newman 15 validation notebook * tweak scope viz * bump to v0.13.0
* update doc deps, bump to v0.13.1 * fix overview nb execution test * try longer timeout * fix video viz tutorial, include in CI, use xdist on CI * increase overview doc timeout [skip ci]
* fix subgroup coords * add wslfp dep * start work on RWSLFPSignalFromSpikes * get RWSLFPFromSpikes working * clean up electrodes tutorial * rwslfp working * advanced LFP working * remove template_trace.ipynb * debugged RWSLFPFromPSCs * progress testing RWSLFP * finish RWSLFPFromSpikes test * finish RWSLFP tests * finish RWSLFP docs * add sphinx duration extension * add last LFP docstrings * update copyright date * bump to v0.14.0
* fix RWSLFPFromPSCs buffer issue * add style_plots_for_paper() * bump to v0.14.1 * add section headings to advanced_lfp.ipynb * fix RWSLFPFromPSCs buffer, add tests * use rounded sample times to avoid skips * add LFP comparison notebook
* fix Spiking.t_samp_ms * fix sample time test bug
…plab-gt#51) * use matplotlib legend_handles instead of deprecated legendHandles * update lock file
* progress on all_optical fig * improve action spectrum extrapolation * start Newman 15 with alternate opsins * update Overview doc * finish newman15 validation w/ alternate opsins * Update paper plot style * style_plots_for_paper docstring * change Jupyter to Python for linguist * change OGB-1 name * add warning to scope when sensor not injected * add showcase to docs * implement LIOP reset in _base_reset * add showcase doc to index * add _base_reset to sim.reset * fresh run through of all-optical-fig notebook * add README to notebooks, env info to all_optical_fig.ipynb * bump to v0.15.0 * remove images [skip ci]
* Update t_ms and interval_ms * updates t in other files * updated t * changed more _ms * added import * addes imports * fixed base.py and made changes to lfp - still failing 10 cases * Created jupyteer notebook for calculating ratios * added ratio into opsin library and added 2p action spectra into spectrum variables for all opsins * progress on all_optical fig * improve action spectrum extrapolation * start Newman 15 with alternate opsins * update Overview doc * finish newman15 validation w/ alternate opsins * Update paper plot style * style_plots_for_paper docstring * change Jupyter to Python for linguist * change OGB-1 name * add warning to scope when sensor not injected * add showcase to docs * implement LIOP reset in _base_reset * add showcase doc to index * add _base_reset to sim.reset * fresh run through of all-optical-fig notebook * add README to notebooks, env info to all_optical_fig.ipynb * bump to v0.15.0 * remove images [skip ci] * untrack images * more organizing notebook images * move Sridharan fig2 * use Brian units everywhere * reorganize ioproc tests * add firing_rate_estimate and pi_ctrl methods, revise PI_Ctrl notebook * ax ioproc folder * ax ProcessingBlock * upgrade nptyping, make sim.remove() private * fix more unit problems * get overview working * get tutorials working * use explicit units on Light * add units to SimpleOpsin gain * extend font stack * fix spike count problem * scope to_neo * 2p light to_neo * fix spiking test fail * Use utilities.rng * units on Light.values and other small tweaks * add version note to newman15 notebooks * add version note to opto val notebook * fix electrodes tutorial * fix opto tutorial * fix multi_opto notebook, add range to plot_spectra * fix on_off_ctrl notebook * update PI ctrl notebook * fix all_optical tutorial * fix video viz tutorial * fix Neo tutorial * fix advanced LFP notebook * rename firing_rate_estimate to exp_firing_rate_estimate * fix global set_seed * progress on lqr tutorial, before cutting adaptive control * revamp ldsCtrlEst tutorial * support numpy >= 2.0 * remove bug workaround (closes Remove bug workaround in tutorials siplab-gt#16) * fix light.to_neo * replace nptyping with jaxtyping * remove imported members from ioproc docs * mark lfp tests as slow * polish tutorial notebooks * tweak docstrings * add LatencyIOProcessor to base cleo import * clean up imports * fix lqr notebook, fresh rerun of all * polish video tutorial, exit if no ffmpeg * skip execution of video write cell * tweak overview docs, increase test cell timeout * simplify 4-state opsin model * eliminate warnings * rerun opto tutorial, increase timestep --------- Co-authored-by: Arnav Tripathi <atripathi83@gatech.edu>
* improve 3d plot spacing, fix type annotation * make registry an attr of CLSimulator * update poetry.lock * bump to v0.17.0
* improve 3d plot spacing, fix type annotation * make registry an attr of CLSimulator * update poetry.lock * bump to v0.17.0 * progress * progress, start using marimo cache * progress * progress on optimizing opto val * spike detection revision 1; need to revise radius parameter * estimated spike amplitude CV * progress with AdEx pulse experiment * finish optimized opto val * basic spike revision, before false positive implementation * draft implementation of spiking done; still need to test * a load of progress * appears to be working * add tklfp_verification, compare straight to Telenczuk20 demo data * implement SortedSpiking SNR cutoff, not tested yet * finish spiking tests * add Taskfile * finish revamping docs with new spiking * change LQR tutorial name to Optimal control * edit Taskfile * rerun tutorials * tweak optimal control tutorial * bump to v0.18.0 * change path to optimal control tutorial to ignore in CI * add Python 3.13 support * update deps * update scipy dep to support py3.13 * edit Taskfile * fix failing tests * remove python 3.9 from build matrix [skip ci] * update figures * add type hint to light_agg_ngs * run tests on pip install rather than poetry lock file * update pyproject.toml, allow pip install of dev dependencies * fix numpy dependency for Python 3.13 * update elephant dep for failing neo tutorial * change elephant dep to hopefully support numpy 2 * change elephant dep to hopefully support numpy 2 * change elephant dep to hopefully support numpy 2 * change elephant dep to hopefully support numpy 2 * change elephant dep to hopefully support numpy 2
* v0.18.1, elephant dep in NB since won't work on PyPI. * cache pip on CI * tweak overview.md [skip ci]
* start light reshape bug fix * add ephys figure notebook * mark collision, spike noise to fix * rerun Newman 15 optoclamp experiment with Cleo v0.18.1 * remove newman15 nb metadata * rerun Rickgauer all-optical experiment * fix light reshaping * fix tiny spiking annoyances * replace deprecated np.in1d with np.isin * removed strange probe.probe * bump to v0.18.2
Made changes to the sensors.py file
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Created changes to the sensor.py file code and added extra functions to the LightDependentGECI class and added an @define(eq=False) header to it.
sensors.py