===== Interactions with other pipelines =====
because spike_analysis incorporates the sorted_neurons table (f.e. unit_IDs and site_IDs) into behavior and ephys data, it is used as a first step in all ephys analysis.


Outputs in Y:\Projects\project\ephys\version:  
^File                           ^Info ^
| population_monkey_session.mat | spike data sorted by unit for each session                       |
| sites_monkey_session.mat      | LFP data sorted by site for each session                         |
| by_block_monkey_session.mat   | body signals sorted by block for each session                    |
| Mon_sorted_neurons.xls        | copies of the used sorted neurons tables from dropbox            |
| keys_Monkey.mat               | copy of the keys used when running ph_initiation                 |
| tuning_table_combined.mat     | Anova results stored in a table                                  |
| tuning_table_combined_CI.mat  | Anova results restructured according to contra/ipsi definitions  |
| tuning_table_combined.xls     | simplified excel table                                           |
| spike_shapes                  | Spike shapes, firing rates over time, and ISI plots for re-assessing spike sorting        |

The three main files come in a specific data structure, which contain the same fields except for the respective data:
  * by_block(body signals) - only trial information and body signals
  * sites (LFP) - additional site information and LFP, no body signals
  * population (spikes) - additional unit information and spike_arrival times, no LFP, no body signals


==== Trial structure subfields (By_block files) ====
to be removed:

                       cue_pos: NaN
                     cue_shape: NaN
                   all_tar_pos: [2x1 double]
                       col_dim: [2x3 double]
                       col_bri: [2x3 double]

^Condition info^Format^Info ^
| type|scalar| from data|
| effector|scalar| from data|
| reach_hand|scalar| from data|
| choice|scalar| from data|
| success|scalar| from data|
| completed|scalar| from data|
| correct_targets|scalar| from data|
| target_selected|scalar| from data|
| n_nondistractors|scalar| from data|
| n_distractors|scalar| from data|
| difficulty|scalar| from data|
| stimuli_in_2hemifields|scalar| from data|
| perturbation|scalar| using perturbation_groups key ??|
| dataset|scalar| Dataset from sorted_neurons (only in spikes so far ??)|
^Timing info^Format^Info ^
| date|scalar| from data|
| block|scalar| from data|
| run|scalar| from data|
| n|scalar| from data|
| trial_onset_time|scalar| from data|
| run_onset_time|scalar| from data|
| states|array| array of events marked in this trial|
| states_onset|array [s]| corresponding onset times (relative to state 2)|
^Spatial info^Format^Info ^
| fix_pos|complex| x is real, y is imaginary (already preprocessed?)|
| tar_pos|complex| x is real, y is imaginary|
| stm_pos|complex| x is real, y is imaginary|
^Response info^Format^Info ^
| rea_off|complex| x is real, y is imaginary|
| sac_off|complex| x is real, y is imaginary|
| sac_lat|scalar| Saccade RT (in seconds)|
| rea_lat|scalar| Reach RT (in seconds)|
^Specific data ^Format^Info ^
| TDT_ECG1|array| Body signal Data (ECG1,CAP1,POX1)|
| TDT_ECG1_SR|scalar| Sampling rate|
| TDT_ECG1_t0_from_rec_start|scalar| state 2 onset relative to start of the recording (block?) |
| TDT_ECG1_tStart|scalar| (usually negative) how much of the stream is before state 2 - due to shift!!|
| LFP|array| LFP data, not called TDT_LFPx any more, but SR,t0,andtStart are...|
| arrival_times|array| in seconds, relative to this trial's state 2|
| FR_average|scalar| average firing rate for this unit in this trial|
| accepted|scalar| trial accepted for this unit|
| FR|scalar| ??|
| stability_rating|scalar| why is this here ??|

==== Additional Site files fields====

^Fieldname^Example^Info ^
| site_ID|'Bac_20210706_Site_01| as assigned in sorted_neurons, in population files this is the corresponding site for this unit |
| target|'dPul_R'| recording target from sorted_neurons|
| perturbation_site|'NA'| perturbation target from sorted_neurons|
| grid_x|3| grid location from sorted_neurons|
| grid_y|-4.5| grid location from sorted_neurons|
| electrode_depth|45| Aimed_electrode_depth from sorted_neurons|
| monkey|'Bacchus_phys'| as assigned in sorted_neurons (?) |

==== Additional Population file fields====

^Fieldname^Example^Info ^
| unit_ID |'Bac_20210706_01'| as assigned in sorted_neurons |
| channel|2| channel the unit was recorded in |
| block_unit|{3x1 cell}| which cluster in which block are combined in this unit|
| SNR_rating|2| SNR rating (either from sorted_neurons or automatic?)|
| Single_rating|1| Single rating (either from sorted_neurons or automatic?)|
| stability_rating|2| stability rating (either from sorted_neurons or automatic?)|
| quantSNR| 11.5| KK automatic SNR|
| n_waveforms|0| apparently bugged|
| waveform_average| [1x30 single]| average waveform of this unit|
| waveform_std| [1x30 single]| std of waveform for each bin|
| waveform_width| 3.0224e-04| width (in time?)|
| waveform_amplitude| 173.2376| amplitude (?)|
| FR| 2.68| average firing rate across all data|