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spike_analysis_pipeline:3_settings

Spike Settings (keys)

Reading in settings(keys) has a hierarchy in spike_analysis ! Higher Priority will always override lower priority.

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Priority Settings file Info Location
1ph_general_settings.mdefault, makes sure keys are presentspike_analysis folder
2ph_project_settings.mdefault settings for your projectSettings/Project
3ph_project_version_settings.msmall deviations for one version (f.e. different dataset)Settings/Project/version
4additional_settings.mprobably obsolete, was used to define each runSettings/Project/version

Data batching (keys.batching.)

Key Format Possible entries Info
monkeyscellstr{'Flaffus', 'Linus', 'Curius', 'Tesla', 'Cornelius', 'Magnus', 'TDT_brain', 'Bacchus'}monkeys involved
combine_monkeysscalar0/1combine monkeys for population analysis
targetscellstr{'dPulv_r','dPulv_l'} –> {'dPulv'} combines hemispherestarget from sorted_neurons table
Subregions_separatelyscalar0/1Split in subregions or not
Subregionscellstruct('monkey',{}, 'target',{}, 'grid_x',{NaN}, 'grid_y',{NaN}, 'z_min',{NaN}, 'z_max',{NaN})subregion definition by ranges
n_Subregionsscalarnumel(keys.batching.Subregions)

General settings

Key Format Possible entries Info
keys.PSTH_binwidthScalar0.01resolution of PSTH's (in seconds)
keys.gaussian_kernelScalar0.02std for the convolution to derive spike density (in seconds)
keys.kernel_typeChar'gaussian'excludes trials with non-matching effector
keys.condition_parameters cellstr{'reach_hand', 'choice', 'perturbation'}parameters that define a unique condition
keys.position_and_ plotting_arrangements cellstr{'hands'}defines (somewhat hardcoded) positions in ph_arrange_positions_and_plots
keys.contra_ipsi_relative_toChar'target'what contra and ipsi refer to

Trial selection keys

Key Format Possible entries Info
keys.cal.datasetsArraysee dataset conventionexcludes runs with non-matching dataset
keys.cal.completedScalar0 or 1excludes not completed trials (keep at 1 for now)
keys.cal.effectorsArray[0,1,2,3,4,5,6]excludes trials with non-matching effector
keys.cal.typesArray[1,2,3,4,5,6]excludes trials with non-matching type
keys.cal.reach_handArray[0,1,2]excludes trials with non-matching hand (no hand, left, right)
keys.cal.choiceArray[0,1]excludes trials of non-matching choice value

Unit exclusion keys

Key Format Possible entries Info
keys.cal.datasetsArraysee dataset conventionexcludes runs with non-matching dataset
keys.cal.completedArray[0,1]excludes not completed trials (keep at 1 for now)
keys.cal.effectorsArray[0,1,2,3,4,5,6]excludes trials with non-matching effector
keys.cal.typesArray[1,2,3,4,5,6]excludes trials with non-matching type
keys.cal.reach_handArray[0,1,2]excludes trials with non-matching hand (no hand, left, right)
keys.cal.choiceArray[0,1]excludes trials of non-matching choice value
spike_analysis_pipeline/3_settings.txt · Last modified: 2022/05/17 15:02 by lukas.schneider