ExtractionKey_Notes.txt

Extraction Steps
------------------
Always Intro:
curr_dir = pwd;
selected_dir = '';
if isempty(dir('*.rec'))
  AnimalDir = selected_dir;
  DayDirs = dir(AnimalDir);
  DayDirs = DayDirs(directories that dont start in '.')
else
  AnimalDir = fileparts(selected_dir);
  DayDirs = {selectedDir};
end


Fix Filenames
  - preReqs: prefixes{}
  - Intro: getPrefixes, setPrefixes
  - Body: fn_mask = RN_fixFilenames([],prefixes{i});

Order Rec Files (Required with TrodesComments and exports)
  - preReqs: sortedRecFiles{}
  - Intro: getRecOrder, setRecOrder
  - Body: sortedRecs = sortedRecFiles{i};

Create Trodes Comments
  - preReqs: sortedRecFiles{}
  - Intro: getRecOrder, setRecOrder
  - Body: RN_createTrodesComments(sortedRecFiles{i})

Reconfigure (must occur before exports)
  - preReqs: configs{}
  - Intro: view and change config for each day, New or Existing or Clear
  - Body: if isempty(configs{i}), commonFlg =''; else commonFlg = [' -reconfig ' configs{i}]; end

Exports (dio,LFP,times,spikes,phy,mda)
  - preReqs: sortedRecFiles{}, customFlg{i}, fn_mask
  - Intro: getRecOrder, setRecOrder, setCustomFlg
  - Body: if isempty(fn_mask)
              fn_mask = RN_findCommonPrefix(sortedRecFiles{i});
          end
          commonFlg = [' -rec ' strjoin(sortedRecFiles,' -rec ') commonFlg ' -output ' fnMask];
          RN_exportBinary(___,[commonFlg customFlg{i}])