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--- spike_analysis_pipeline:keys [2022/05/13 11:57] – lukas.schneider
+++ spike_analysis_pipeline:keys [2022/12/29 07:15] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====== Spike analysis keys ======
+Reading in settings(keys) has a hierarchy in spike_analysis !
+Higher Priority will always override lower priority.
+.
+^Priority ^Settings file  ^Info ^Location^
+|1|ph_general_settings.m|default, makes sure keys are present|spike_analysis folder|
+|2|ph_project_settings.m|default settings for your project|Settings/Project|
+|3|ph_project_version_settings.m|small deviations for one version (f.e. different dataset)|Settings/Project/version|
+|4|additional_settings.m|probably obsolete, was used to define each run|Settings/Project/version|
+===== Data batching (keys.batching.) =====
+^Key  ^Format ^Possible entries  ^Info^
+|monkeys|cellstr|{'Flaffus', 'Linus', 'Curius', 'Tesla', 'Cornelius', 'Magnus', 'TDT_brain', 'Bacchus'}|monkeys involved|
+|combine_monkeys|scalar|0/1|combine monkeys for population analysis|
+|targets|cellstr|{'dPulv_r','dPulv_l'} --> {'dPulv'} combines hemispheres|target from sorted_neurons table|
+|Subregions_separately|scalar|0/1|Split in subregions or not|
+|Subregions|cell|struct('monkey',{''}, 'target',{''}, 'grid_x',{NaN}, 'grid_y',{NaN}, 'z_min',{NaN}, 'z_max',{NaN})|subregion definition by ranges|
+|n_Subregions|scalar||numel(keys.batching.Subregions)|
+===== General settings =====
+^Key  ^Format ^Possible entries  ^Info^
+|keys.PSTH_binwidth|Scalar|0.01|resolution of PSTH's (in seconds)|
+|keys.gaussian_kernel|Scalar|0.02|std for the convolution to derive spike density (in seconds)|
+|keys.kernel_type|Char|'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_to|Char|'target'|what contra and ipsi refer to|
 ===== Trial selection keys =====
@@ Line 13: / Line 43: @@
 ^Key  ^Format ^Possible entries  ^Info^
 |keys.cal.datasets|Array|see dataset convention|excludes runs with non-matching dataset|
-|keys.cal.completed|Scalar|0 or 1|excludes not completed trials (keep at 1 for now)|
+|keys.cal.completed|Array|[0,1]|excludes not completed trials (keep at 1 for now)|
 |keys.cal.effectors|Array|[0,1,2,3,4,5,6]|excludes trials with non-matching effector|
 |keys.cal.types|Array|[1,2,3,4,5,6]|excludes trials with non-matching type|
 |keys.cal.reach_hand|Array|[0,1,2]|excludes trials with non-matching hand (no hand, left, right)|
 |keys.cal.choice|Array|[0,1]|excludes trials of non-matching choice value|