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PreProcessingManager.m
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PreProcessingManager.m
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%% PreProcessingManager - SCRIPT which takes raw data, saved as an
% ACPlusAncillaryData object called "allData" and gets it ready for
% processing by the ProcessingManager.
% The PreProcessingManager has the following three main jobs:
% -- 1: Find good TSW/FSW periods in:
% -- a/c data
% -- flow/valve data
% Methodology:
% -- use flow and valve state data
% -- use flow data only
% -- use a/c data only
% -- 2: Synchronize: a/c data with flow/valve data
% -- 3: Separate TSW/FSW data
%
% It also allows for a set offset to be applied to the start of each FSW
%
% Requires: the .mat file saved in IngestManager, if not in memory
%
% Outputs: saves allData as a .mat file
%
% Other m-files required: readIngestParameters, ACPlusAncillaryData,
% Subfunctions: importTransitionFile, checkTransitionTimes
% MAT-files required: none
%
% See also: readIngestParameters, ACPlusAncillaryData,
% importTransitionFile, checkTransitionTimes
% Author: Wendy Neary
% MISCLab, University of Maine
% email address: wendy.neary@maine.edu
% Website: http://misclab.umeoce.maine.edu/index.php
% May 2015; Last revision: 13-08-15
% July/August 2016 - major revision in way transitions are managed
%--------------------------------- BEGIN CODE -----------------------------
%% Load data file from disk
matFileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, params.INGEST.DATA_OUTPUT_FILE);
paramsFileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, 'params');
if params.RUN.LOAD_INGEST_DATA_FROM_DISK
L.info('PreProcessingManager', 'Loading ingest data from disk');
load(matFileName);
else
L.info('PreProcessingManager', 'Using ingest data in memory');
end;
clear matFileName;
%% Find intervals
if params.RUN.FIND_INITIAL_INTERVALS
%% make shorter for testing:
% a.data = a.data(1:10000,:);
% a.time = a.time(1:10000,:);
% c.data = c.data(1:10000,:);
% c.time = c.time(1:10000,:);
% Make an initial plot of a data, alongside valve data, if available
% Set ylim manually if needed
if params.RUN.CREATE_DEBUG_PLOTS
figure(20)
hold on
grid on
plot(allData.aData.DataObject.Time(:,:), allData.aData.DataObject.Data(:, 20), 'b');
if params.INGEST.VALVE_EXISTS
plot(allData.ValveData.DataObject.Time, allData.ValveData.DataObject.Data, 'g');
legend('a data', 'valve data');
title('a data & valve data - unsynchronized');
% Set ylim here:
% ylim([-.20, .25])
else
legend('a data');
title('a data - No valve data exists');
end;
% ylim([0,.2])
dynamicDateTicks;
end %#params.RUN.CREATE_DEBUG_PLOTS
%% if there is valve on/off information available, use it to mark the
% transition periods, rather than identifying them from the actual data
if params.PREPROCESS.USE_VALVE_DATA
allData.ValveData.findTransitions();
if params.RUN.CREATE_DEBUG_PLOTS
allData.ValveData.plotTransitions();
end;
if params.PREPROCESS.USE_VALVE_FOR_FLOW_TRANSITIONS
% set transition points for flow by using those from valve
allData.FlowData.setTransitions( allData.ValveData.TransStartData, ...
allData.ValveData.TransEndData, allData.ValveData.TransStartTime, ...
allData.ValveData.TransEndTime )
if params.RUN.CREATE_DEBUG_PLOTS
allData.FlowData.plotTransitions()
end;
else
L.info('PreProcessingManager', 'Not using valve to set flow transitions');
end; %if params.PREPROCESS.USE_VALVE_FOR_FLOW_TRANSITIONS
if params.PREPROCESS.USE_VALVE_FOR_AC_TRANSITIONS
% valve start/end times are for FSW
one_min = datenum(0,0,0,0,1,0);
two_min = datenum(0,0,0,0,2,0);
thirty_secs = datenum(0,0,0,0,0,30);
ValveOn = allData.ValveData.TransStartTime;
ValveOff = allData.ValveData.TransEndTime;
allData.aData.setGoodTransitions(ValveOn + two_min, ...
ValveOff - thirty_secs, 'FSW', 'raw');
allData.cData.setGoodTransitions(ValveOn + two_min, ...
ValveOff - thirty_secs, 'FSW', 'raw');
allData.aData.setGoodTransitions(ValveOff + two_min, ...
ValveOn - one_min, 'TSW', 'raw');
allData.cData.setGoodTransitions(ValveOff + two_min, ...
ValveOn - one_min, 'TSW', 'raw');
else
L.info('PreProcessingManager', 'Not using valve to set ac');
end;
else % params.PREPROCESS.USE_VALVE_DATA
L.info('PreProcessingManager', 'Valve not available.');
end;
if params.INGEST.FLOW_EXISTS
L.info('PreProcessingManager', 'Flow exists');
if params.PREPROCESS.USE_FLOW_DATA
% smooth the data
allData.FlowData.setSmoothData();
if params.RUN.CREATE_DEBUG_PLOTS
allData.FlowData.plotSmoothData();
end;
allData.FlowData.setRunningMeds(params.PREPROCESS.FLOW_PP_TIMESPAN, params.PREPROCESS.SAMPLING_FREQ)
if params.RUN.CREATE_DEBUG_PLOTS
figure(12)
allData.FlowData.plotRunningMeds()
end;
% find transition times from running TSW median
allData.FlowData.findTransitions()
if params.RUN.CREATE_DEBUG_PLOTS
figure(23)
allData.FlowData.plotTransitions()
end;
else
L.info('PreProcessingManager', 'Not using flow to find flow transitions');
end;
if params.PREPROCESS.USE_FLOW_FOR_AC_TRANSITIONS
L.info('PreProcessingManager', 'Using flow to find ac transitions');
else
L.info('PreProcessingManager', 'Not using flow to find ac transitions');
end;
end; %FLOW_EXISTS
if params.PREPROCESS.USE_AC_FOR_AC_TRANSITIONS
% -------------------------------------------------------------
% a AND c DATA SECTION
% -------------------------------------------------------------
% -------------------------------------------------------------
% Smooth a and c data, find the running medians and then use the running
% medians to find the transitions between FSW and TSW
% a data
allData.aData.setSmoothData();
allData.aData.setRunningMeds(params.PREPROCESS.PP_TIMESPAN, ...
params.PREPROCESS.SAMPLING_FREQ);
allData.aData.findAndSetTransitionPoints('TSW')
allData.aData.findAndSetTransitionPoints('FSW')
% plot TSW/FSW transitions to check
if params.RUN.CREATE_DEBUG_PLOTS
figure(21)
hold on;
grid on;
allData.aData.plotSmoothData();
allData.aData.plotRunningMeds();
allData.aData.plotInitFSWTransitions();
allData.aData.plotInitTSWTransitions();
end;
% c data
allData.cData.setSmoothData();
allData.cData.setRunningMeds(params.PREPROCESS.PP_TIMESPAN, ...
params.PREPROCESS.SAMPLING_FREQ);
allData.cData.findAndSetTransitionPoints('TSW')
allData.cData.findAndSetTransitionPoints('FSW')
% plot TSW/FSW transitions to check
if params.RUN.CREATE_DEBUG_PLOTS
figure(22)
allData.cData.plotSmoothData();
allData.cData.plotRunningMeds();
allData.cData.plotInitFSWTransitions()
allData.cData.plotInitTSWTransitions()
end;
end; % IF USE_FLOW_FOR_AC_TRANSITIONS
% save current as mat file
matFileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
strcat('acsPREPROC_PARTIAL', '_', num2str(params.INGEST.YEAR), ...
'_', num2str(params.INGEST.YEAR_DAY)));
save( matFileName, 'allData');
clear matFileName;
else % if params.RUN.FIND_INITIAL_INTERVALS
L.info('PreProcessingManager', 'Skipping finding intitial intervals');
matFileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
strcat('acsPREPROC_PARTIAL', '_', num2str(params.INGEST.YEAR), ...
'_', num2str(params.INGEST.YEAR_DAY)));
load(matFileName);
clear matFileName;
end % if FIND_INITIAL_INTERVALS
%% CHECKING TRANSITIONS
% find first good transition for flow, a/c
if params.PREPROCESS.USE_FLOW_DATA || params.PREPROCESS.USE_VALVE_FOR_FLOW_TRANSITIONS
L.info('PreProcessingManager','Calling allData.FlowData.checkTransitions()');
%FSWFreq, FSWDuration
allData.FlowData.checkTransitions(params.PREPROCESS.TSW_DURATION, ...
params.PREPROCESS.FSW_DURATION)
else
L.info('PreProcessingManager','No flow data to check transitions on');
end;
%% If manually editing, but using checked/filtered transitions, go ahead
% and check/filter them
% If running manually, and want to check/filter transitions first
% OR not running manually
%
if (params.RUN.MANUAL_MODE && params.RUN.MANUALLY_EDIT_CHECKED_TRANSITIONS) ...
|| (~params.RUN.MANUAL_MODE && ~params.RUN.REPROCESS_MANUAL)
Transitions = allData.aData.getTransitions('raw');
% check and set aFSW transitions ----------------------------------------------
[ goodStartsOut, goodEndsOut ] = ...
checkTransitionTimes( Transitions.FSWtransitions.StartTime,...
Transitions.FSWtransitions.EndTime, allData.aData.DataObject.Time );
[ goodStartTimes, goodEndTimes ] = filterTransitionTimes( goodStartsOut, ...
goodEndsOut, params.PREPROCESS.FSW_DURATION, ...
params.PREPROCESS.FSW_DUR_TOLERANCE, params.PREPROCESS.CYCLE_FREQ, ...
params.PREPROCESS.FREQ_TOLERANCE );
allData.aData.setGoodTransitions(goodStartTimes, goodEndTimes, 'FSW','preprocessed');
% check and set aTSW transitions ----------------------------------------------
[ goodStartsOut, goodEndsOut ] = ...
checkTransitionTimes( Transitions.TSWtransitions.StartTime,...
Transitions.TSWtransitions.EndTime, allData.aData.DataObject.Time );
[ goodStartTimes, goodEndTimes ] = filterTransitionTimes( goodStartsOut, ...
goodEndsOut, params.PREPROCESS.TSW_DURATION, ...
params.PREPROCESS.TSW_DUR_TOLERANCE, params.PREPROCESS.CYCLE_FREQ, ...
params.PREPROCESS.FREQ_TOLERANCE );
allData.aData.setGoodTransitions(goodStartTimes, goodEndTimes, 'TSW', 'preprocessed');
% check cFSW transitions -----------------------------------------------
Transitions = allData.cData.getTransitions('raw');
% check and set cFSW transitions ----------------------------------------------
[ goodStartsOut, goodEndsOut ] = ...
checkTransitionTimes( Transitions.FSWtransitions.StartTime,...
Transitions.FSWtransitions.EndTime, allData.aData.DataObject.Time );
[ goodStartTimes, goodEndTimes ] = filterTransitionTimes( goodStartsOut, ...
goodEndsOut, params.PREPROCESS.FSW_DURATION, ...
params.PREPROCESS.FSW_DUR_TOLERANCE, params.PREPROCESS.CYCLE_FREQ, ...
params.PREPROCESS.FREQ_TOLERANCE );
allData.cData.setGoodTransitions(goodStartTimes, goodEndTimes, 'FSW', 'preprocessed');
% check and set cTSW transitions ----------------------------------------------
[ goodStartsOut, goodEndsOut ] = ...
checkTransitionTimes( Transitions.TSWtransitions.StartTime,...
Transitions.TSWtransitions.EndTime, allData.aData.DataObject.Time );
[ goodStartTimes, goodEndTimes ] = filterTransitionTimes( goodStartsOut, ...
goodEndsOut, params.PREPROCESS.TSW_DURATION, ...
params.PREPROCESS.TSW_DUR_TOLERANCE, params.PREPROCESS.CYCLE_FREQ, ...
params.PREPROCESS.FREQ_TOLERANCE );
allData.cData.setGoodTransitions(goodStartTimes, goodEndTimes, 'TSW', 'preprocessed');
else
L.info('PreProcessingManager','Not using automatic transtions, using manually-set');
end %~MANUAL_MODE
%% stop here for manual processing, if we're editing files
if params.RUN.MANUAL_MODE && ~params.RUN.REPROCESS_MANUAL
L.info('PreProcessingManager', 'manual mode');
return;
else
L.info('PreProcessingManager', 'not in manual mode');
end;
%% ------------------------------------------------------------------------
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% START MANUAL PROCESSING HERE:
% 1. CREATE PLOT TO CHECK c TRANSITIONS - plot raw and possibly edited
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
if params.INGEST.VALVE_EXISTS
figure(24)
hold on;
grid on;
allData.cData.plotData();
plot(allData.ValveData.DataObject.Time, allData.ValveData.DataObject.Data, 'c');
if params.RUN.MANUALLY_EDIT_CHECKED_TRANSITIONS
allData.cData.plotTSWGoodTransitions();
legend('c data', 'valve data', 'identified checked TSW periods - start', ...
'identified checked TSW periods - end');
else
allData.cData.plotInitTSWTransitions();
legend('c data', 'valve data', 'identified initial TSW periods - start', ...
'identified initial TSW periods - end');
end;
else
figure(24)
hold on;
grid on;
allData.cData.plotData();
if params.RUN.MANUALLY_EDIT_CHECKED_TRANSITIONS
allData.cData.plotTSWGoodTransitions();
legend('c data', 'identified checked TSW periods - start', ...
'identified checked TSW periods - end');
else
allData.cData.plotInitTSWTransitions();
legend('c data', 'identified initial TSW periods - start', ...
'identified initial TSW periods - end');
end;
end;
saveas(gcf, fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, strcat(num2str(params.INGEST.YEAR_DAY), '_cTSW_transitions')));
%% <-------------MANUAL PROCESSING CONTINUES HERE------------------------->
if params.RUN.MANUAL_MODE || params.RUN.REPROCESS_MANUAL
%
% DON'T RUN FROM HERE, RUN FROM SECTION BELOW
%
%% -------- SECTION 1 - c TSW - PART 1A-----------------
% 2. "RUN AND ADVANCE" FROM HERE
% -----------------------------------------------------
% if we're not reprocessing this - run this first part:
if ~params.RUN.REPROCESS_MANUAL
% PROCESS C TSWs
% create a file of start and end times
if params.RUN.MANUALLY_EDIT_RAW_TRANSITIONS
Transitions = allData.cData.getTransitions('raw');
elseif params.RUN.MANUALLY_EDIT_CHECKED_TRANSITIONS
Transitions = allData.cData.getTransitions('preprocessed');
else
L.error('PreProcessingManager', 'Need type of transitions');
end;
fileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, 'transitions_cTSW.txt');
printTransitionTimes(Transitions.TSWtransitions.StartTime, ...
Transitions.TSWtransitions.EndTime, fileName);
L.info('PreProcessingManager', 'Reprocessing MANUAL_MODE, cTSW file ready');
else
L.info('PreProcessingManager', 'Reprocessing MANUAL_MODE, not recreating transitions text file');
end %~REPROCESS_MANUAL
%% ------- SECTION1 - c TSW - PART 1B -----------
% 3. "RUN AND ADVANCE" FROM HERE AFTER YOU HAVE:
% -----------------------------------------------
% A. In your PROCESSED directory, open up transitions_cTSW.txt
% B. Delete any unwanted transitions, using Figure 20 as a guide
% 4. Save the file, in the same directory as transtions_cTSW2.txt
% 5. "RUN AND ADVANCE"
%% ------- SECTION1 - c TSW - PART 2-----------------
% 4. "RUN AND ADVANCE" FROM HERE
% ---------------------------------------------------
% open file back up
filename = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, 'transitions_cTSW2.txt');
[type, timestamp, flag] = importTransitionFile(filename);
% manipulate data out of file
startIndex = strcmpi(type,'start');
cTSWTransitions.startTimestamps = timestamp(startIndex);
cTSWTransitions.startFlags = flag(startIndex);
cTSWTransitions.endTimestamps = timestamp(~startIndex);
cTSWTransitions.endFlags = flag(~startIndex);
% check transitions
[ goodStarts, goodEnds ] = ...
checkTransitionTimes(cTSWTransitions.startTimestamps,...
cTSWTransitions.endTimestamps, allData.aData.DataObject.Time );
% NOT FILTERING BECAUSE SET MANUALLY
% call method to assign good starts
allData.cData.setGoodTransitions(goodStarts, goodEnds, 'TSW', 'preprocessed');
L.info('PreProcessingManager', 'Reprocessing MANUAL_MODE, done with cTSW');
%%
if params.INGEST.FLOW_EXISTS
figure(25)
hold on;
grid on;
allData.cData.plotData();
plot(allData.ValveData.DataObject.Time, allData.ValveData.DataObject.Data, 'c');
if params.RUN.MANUALLY_EDIT_CHECKED_TRANSITIONS
allData.cData.plotFSWGoodTransitions();
legend('c data', 'valve data', 'identified checked FSW periods - start', ...
'identified checked FSW periods - end');
else
allData.cData.plotInitFSWTransitions();
legend('c data', 'valve data', 'identified initial FSW periods - start', ...
'identified initial FSW periods - end');
end;
else
figure(25)
hold on;
grid on;
allData.cData.plotData();
if params.RUN.MANUALLY_EDIT_CHECKED_TRANSITIONS
allData.cData.plotFSWGoodTransitions();
legend('c data', 'identified checked FSW periods - start', ...
'identified checked FSW periods - end');
else
allData.cData.plotInitFSWTransitions();
legend('c data', 'identified initial FSW periods - start', ...
'identified initial FSW periods - end');
end;
end;
saveas(gcf, fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, strcat(num2str(params.INGEST.YEAR_DAY), '_cFSW_transitions')));
%% ------- SECTION 2 - c FSW- PART 1A-----------------
% 5. "RUN AND ADVANCE" FROM HERE
% ---------------------------------------------------
if ~params.RUN.REPROCESS_MANUAL
% PROCESS c FSWs
if params.RUN.MANUALLY_EDIT_RAW_TRANSITIONS
Transitions = allData.cData.getTransitions('raw');
elseif params.RUN.MANUALLY_EDIT_CHECKED_TRANSITIONS
Transitions = allData.cData.getTransitions('preprocessed');
else
L.error('PreProcessingManager', 'Need type of transitions');
end;
% create a file of start and end times
fileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, 'transitions_cFSW.txt');
printTransitionTimes(Transitions.FSWtransitions.StartTime, ...
Transitions.FSWtransitions.EndTime, fileName);
L.info('PreProcessingManager', 'Reprocessing MANUAL_MODE, cFSW file ready');
else
L.info('PreProcessingManager', 'Reprocessing MANUAL_MODE, not recreating transitions text file');
end; %~REPROCESS_MANUAL
%% ------- SECTION 2 - c FSW - PART 1B -----------
% 6. "RUN AND ADVANCE" FROM HERE AFTER YOU HAVE:
% ------------------------------------------------
% A. In your PROCESSED directory, open up transitions_cFSW.txt
% B. Delete any unwanted transitions, using Figure 20 as a guide
% C. Save the file, in the same directory as transtions_cFSW2.txt
% D. "RUN AND ADVANCE"
%% ------- SECTION 2 - c FSW - PART 2-----------------
% 7. "RUN AND ADVANCE" FROM HERE
% ----------------------------------------------------
% open file back up
filename = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, 'transitions_cFSW2.txt');
[type, timestamp, flag] = importTransitionFile(filename);
% manipulate data out of file
startIndex = strcmpi(type,'start');
cFSWTransitions.startTimestamps = timestamp(startIndex);
cFSWTransitions.startFlags = flag(startIndex);
cFSWTransitions.endTimestamps = timestamp(~startIndex);
cFSWTransitions.endFlags = flag(~startIndex);
% check transitions
[ goodStarts, goodEnds ] = ...
checkTransitionTimes( cFSWTransitions.startTimestamps,...
cFSWTransitions.endTimestamps, allData.aData.DataObject.Time );
% call method to assign good ends
allData.cData.setGoodTransitions(goodStarts, goodEnds, 'FSW', 'preprocessed');
L.info('PreProcessingManager', 'Reprocessing MANUAL_MODE, done with cFSW');
%% ---------------------------------------------------------------
% ------------------------ PROCESS A -----------------------------
% 8. CREATE PLOT TO CHECK a TRANSITIONS
if params.INGEST.FLOW_EXISTS
figure(25)
hold on;
grid on;
allData.aData.plotData();
plot(allData.ValveData.DataObject.Time, allData.ValveData.DataObject.Data, 'c');
allData.aData.plotInitFSWTransitions();
allData.aData.plotInitTSWTransitions();
if params.RUN.MANUALLY_EDIT_CHECKED_TRANSITIONS
allData.aData.plotFSWGoodTransitions();
allData.aData.plotTSWGoodTransitions();
end;
legend('a data', 'valve data', 'identified FSW periods - start', ...
'identified FSW periods - end', ...
'identified TSW periods - start', ...
'identified TSW periods - end',...
'good FSW transition start', 'good FSW transition end', ...
'good TSW transition start', 'good TSW transition end');
else
figure(25)
allData.aData.plotData();
allData.aData.plotInitFSWTransitions();
allData.aData.plotInitTSWTransitions();
if params.RUN.MANUALLY_EDIT_CHECKED_TRANSITIONS
allData.aData.plotFSWGoodTransitions();
allData.aData.plotTSWGoodTransitions();
end;
legend('a data', 'identified FSW periods - start', ...
'identified FSW periods - end', ...
'identified TSW periods - start', ...
'identified TSW periods - end',...
'good FSW transition start', 'good FSW transition end', ...
'good TSW transition start', 'good TSW transition end');
end;
%% --------SECTION 3 - a TSW - PART 1A-----------------
% 9. "RUN AND ADVANCE" FROM HERE
% ---------------------------------------------------
if ~params.RUN.REPROCESS_MANUAL
if params.RUN.MANUALLY_EDIT_RAW_TRANSITIONS
Transitions = allData.aData.getTransitions('raw');
elseif params.RUN.MANUALLY_EDIT_CHECKED_TRANSITIONS
Transitions = allData.aData.getTransitions('preprocessed');
else
L.error('PreProcessingManager', 'Need type of transitions');
end;
% create a file of start and end times
fileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, 'transitions_aTSW.txt');
printTransitionTimes(Transitions.TSWtransitions.StartTime, ...
Transitions.TSWtransitions.EndTime, fileName);
L.info('PreProcessingManager', 'Reprocessing MANUAL_MODE, aTSW file ready');
else
L.info('PreProcessingManager', 'Reprocessing MANUAL_MODE, not recreating transitions text file');
end;
%% ------- SECTION 3 - a TSW - PART 1B -----------
% 10. "RUN AND ADVANCE" FROM HERE AFTER YOU HAVE:
% -----------------------------------------------
% A. In your PROCESSED directory, open up transitions_aTSW.txt
% B. Delete any unwanted transitions, using Figure 20 as a guide
% 4. Save the file, in the same directory as transtions_aTSW2.txt
% 5. "RUN AND ADVANCE"
%% ------- SECTION 3 - a TSW - PART 2-----------------
% 11. "RUN AND ADVANCE" FROM HERE
% ---------------------------------------------------
filename = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, 'transitions_aTSW2.txt');
[type, timestamp, flag] = importTransitionFile(filename);
% manipulate data out of file
startIndex = strcmpi(type,'start');
aTSWTransitions.startTimestamps = timestamp(startIndex);
aTSWTransitions.startFlags = flag(startIndex);
aTSWTransitions.endTimestamps = timestamp(~startIndex);
aTSWTransitions.endFlags = flag(~startIndex);
% check transitions
[ goodStarts, goodEnds ] = ...
checkTransitionTimes( aTSWTransitions.startTimestamps,...
aTSWTransitions.endTimestamps, allData.aData.DataObject.Time );
% call method to assign good starts
allData.aData.setGoodTransitions(goodStarts, goodEnds, 'TSW', 'preprocessed');
%% ------- SECTION 4 - a FSW- PART 1A-----------------
% 12. "RUN AND ADVANCE" FROM HERE
% ---------------------------------------------------
if ~params.RUN.REPROCESS_MANUAL
if params.RUN.MANUALLY_EDIT_RAW_TRANSITIONS
Transitions = allData.aData.getTransitions('raw');
elseif params.RUN.MANUALLY_EDIT_CHECKED_TRANSITIONS
Transitions = allData.aData.getTransitions('preprocessed');
else
L.error('PreProcessingManager', 'Need type of transitions');
end;
% create a file of start and end times
fileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, 'transitions_aFSW.txt');
printTransitionTimes(Transitions.FSWtransitions.StartTime, ...
Transitions.FSWtransitions.EndTime, fileName);
L.info('PreProcessingManager', 'Reprocessing MANUAL_MODE, aFSW file ready');
else
L.info('PreProcessingManager', 'Reprocessing MANUAL_MODE, not recreating transitions text file');
end;
%% ------- SECTION 4 - a FSW - PART 1B -----------
% 13. "RUN AND ADVANCE" FROM HERE AFTER YOU HAVE:
% ------------------------------------------------
% A. In your PROCESSED directory, open up transitions_aFSW.txt
% B. Delete any unwanted transitions, using Figure 20 as a guide
% C. Save the file, in the same directory as transtions_aFSW2.txt
% D. "RUN AND ADVANCE"
%% ------- SECTION 4 - a FSW - PART 2-----------------
% 13. "RUN AND ADVANCE" FROM HERE
% ----------------------------------------------------
filename = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, 'transitions_aFSW2.txt');
[type, timestamp, flag] = importTransitionFile(filename);
% manipulate data out of file
startIndex = strcmpi(type,'start');
aFSWTransitions.startTimestamps = timestamp(startIndex);
aFSWTransitions.startFlags = flag(startIndex);
aFSWTransitions.endTimestamps = timestamp(~startIndex);
aFSWTransitions.endFlags = flag(~startIndex);
% check transitions
[ goodStarts, goodEnds ] = ...
checkTransitionTimes( aFSWTransitions.startTimestamps,...
aFSWTransitions.endTimestamps, allData.aData.DataObject.Time );
% call method to assign good starts & ends
allData.aData.setGoodTransitions(goodStarts, goodEnds, 'FSW', 'preprocessed');
end; %if params.RUN.MANUAL_MODE
% <-----------------MANUAL PROCESSING ENDS HERE--------------------------->
% IF YOU HAVE BEEN RUNNING MANUALLY, RUN AND ADVANCE THROUGH EACH SECTION
% BELOW:
% <----------------------------------------------------------------------->
%%
% plot to show how a and c data are lined up
if params.RUN.CREATE_DEBUG_PLOTS
if params.INGEST.VALVE_EXISTS
figure(26)
hold on;
grid on;
allData.aData.plotData();
plot(allData.ValveData.DataObject.Time, allData.ValveData.DataObject.Data, 'c');
allData.aData.plotInitFSWTransitions();
allData.aData.plotInitTSWTransitions();
allData.aData.plotFSWGoodTransitions();
allData.aData.plotTSWGoodTransitions();
legend('a data', 'valve data', 'identified FSW periods - start', ...
'identified FSW periods - end', ...
'identified TSW periods - start', ...
'identified TSW periods - end',...
'good FSW transition start', 'good FSW transition end', ...
'good TSW transition start', 'good TSW transition end');
else
figure(26)
allData.aData.plotData();
allData.aData.plotInitFSWTransitions();
allData.aData.plotInitTSWTransitions();
allData.aData.plotFSWGoodTransitions();
allData.aData.plotTSWGoodTransitions();
legend('a data', 'identified FSW periods - start', ...
'identified FSW periods - end', ...
'identified TSW periods - start', ...
'identified TSW periods - end',...
'good FSW transition start', 'good FSW transition end', ...
'good TSW transition start', 'good TSW transition end');
end;
end; %params.RUN.CREATE_DEBUG_PLOTS
if params.RUN.CREATE_DEBUG_PLOTS
if params.INGEST.VALVE_EXISTS
figure(27)
hold on;
grid on;
allData.cData.plotData();
plot(allData.ValveData.DataObject.Time, allData.ValveData.DataObject.Data, 'c');
allData.cData.plotInitFSWTransitions();
allData.cData.plotInitTSWTransitions();
allData.cData.plotFSWGoodTransitions();
allData.cData.plotTSWGoodTransitions();
legend('c data', 'valve data', 'identified FSW periods - start', ...
'identified FSW periods - end', ...
'identified TSW periods - start', ...
'identified TSW periods - end',...
'good FSW transition start', 'good FSW transition end', ...
'good TSW transition start', 'good TSW transition end');
else
figure(27)
allData.cData.plotData();
allData.cData.plotInitFSWTransitions();
allData.cData.plotInitTSWTransitions();
allData.cData.plotFSWGoodTransitions();
allData.cData.plotTSWGoodTransitions();
legend('c data', 'identified FSW periods - start', ...
'identified FSW periods - end', ...
'identified TSW periods - start', ...
'identified TSW periods - end',...
'good FSW transition start', 'good FSW transition end', ...
'good TSW transition start', 'good TSW transition end');
end;
end; %if params.RUN.CREATE_DEBUG_PLOTS
%% SYNCHRONIZE Data
if params.INGEST.FLOW_EXISTS && params.PREPROCESS.SYNC_AC_TO_FLOW
L.info('PreProcessingManager', 'Flow data exists for syncing to');
allData.aData.syncTo(allData.FlowData);
allData.cData.syncTo(allData.FlowData);
else
L.info('PreProcessingManager', 'Either No flow exists for sync, OR we aren''t using it. Copying regular data into SyncDataObject');
allData.aData.SyncDataObject = allData.aData.DataObject;
allData.cData.SyncDataObject = allData.cData.DataObject;
end;
%% apply offset set in parameters
if params.PREPROCESS.OFFSET_FSW_STARTS
L.info('PreProcessingManager', 'Applying offset to FSW start as set in params');
allData.aData.offsetFSWStartTimes(params.PREPROCESS.OFFSET_FSW_TIME);
allData.cData.offsetFSWStartTimes(params.PREPROCESS.OFFSET_FSW_TIME);
else
L.info('PreProcessingManager', 'Not applying FSW start offset');
end;
%% plot to check synchronization, and filter/total starts and ends
% THIS IS MAJOR QA/QC PLOT TO KEEP
figure(28)
title( sprintf('%s %s', params.INGEST.CRUISE, params.INGEST.CRUISE_LEG ))
ax1 = subplot(2,1,1);
plot(allData.aData.SyncDataObject.Time, allData.aData.SyncDataObject.Data(:,20), 'k');
hold on;
grid on;
dynamicDateTicks;
allData.aData.plotFSWGoodTransitions();
allData.aData.plotTSWGoodTransitions();
if params.INGEST.VALVE_EXISTS
plot(allData.ValveData.DataObject.Time, allData.ValveData.DataObject.Data, 'c');
% ylim([0,.15])
end
legend('sync a data', 'good fsw start', 'good fsw end' , 'good tsw start' , 'good tsw end', 'valve state')
ax2 = subplot(2,1,2);
plot(allData.cData.SyncDataObject.Time, allData.cData.SyncDataObject.Data(:,20), 'k');
hold on;
grid on;
dynamicDateTicks;
allData.cData.plotFSWGoodTransitions();
allData.cData.plotTSWGoodTransitions();
if params.INGEST.VALVE_EXISTS
plot(allData.ValveData.DataObject.Time, allData.ValveData.DataObject.Data, 'c');
% ylim([0,.6])
end
if params.INGEST.VALVE_EXISTS
legend('sync c data', 'good fsw start', 'good fsw end' , 'good tsw start' , 'good tsw end', 'valve state')
else
legend('sync c data', 'good fsw start', 'good fsw end' , 'good tsw start' , 'good tsw end')
end;
linkaxes([ax1, ax2], 'x');
saveas(gcf, fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, strcat(num2str(params.INGEST.YEAR_DAY), '_final_transitions')));
%% --------------------------------------
% separate TSW from FSW
% want two filters (TSW, FSW) and flag the transition data as suspect
allData.cData.separateTSWFSW();
%% plot TO CHECK DATA IS BEING SEPARATED CORRECTLY
% THIS IS A DEBUG PLOT
if params.RUN.CREATE_DEBUG_PLOTS
figure(29);
ax1 = subplot(3,1,1);
hold on;
grid on;
allData.cData.plotSyncData()
allData.cData.plotFSWGoodTransitions()
allData.cData.plotTSWGoodTransitions()
legend('c data', 'start FSW', 'end FSW', 'start TSW', 'end TSW')
title( sprintf('%s %s %4u-%02u-%2u (yearday %3u)', ...
params.INGEST.CRUISE, params.INGEST.CRUISE_LEG, params.INGEST.YEAR, ...
params.INGEST.MONTH, params.INGEST.DAY, params.INGEST.YEAR_DAY))
dynamicDateTicks;
ax2 = subplot(3,1,2);
hold on;
grid on;
plot(allData.cData.SyncDataObject.Time(allData.cData.FSWIndex), allData.cData.SyncDataObject.Data(allData.cData.FSWIndex), 'g');
legend('Filtered c data')
dynamicDateTicks;
ax3 = subplot(3,1,3);
hold on;
grid on;
plot(allData.cData.SyncDataObject.Time(allData.cData.TSWIndex), allData.cData.SyncDataObject.Data(allData.cData.TSWIndex), 'b');
legend('Total c data')
dynamicDateTicks;
linkaxes([ax1, ax2, ax3], 'x');
saveas(gcf, fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, strcat(num2str(params.INGEST.YEAR_DAY), '_fig29')));
end; %if params.RUN.CREATE_DEBUG_PLOTS
%% - DO NOW FOR A
allData.aData.separateTSWFSW();
%% DEBUG PLOT
% plot TO CHECK DATA IS BEING SEPARATED CORRECTLY FOR A
% THIS IS A DEBUG PLOT
if params.RUN.CREATE_DEBUG_PLOTS
figure(210);
ax1 = subplot(3,1,1);
hold on;
grid on;
allData.aData.plotSyncData()
allData.aData.plotFSWGoodTransitions()
allData.aData.plotTSWGoodTransitions()
legend('a data', 'start FSW', 'end FSW', 'start TSW', 'end TSW')
title( sprintf('%s %s %4u-%02u-%2u (yearday %3u)', ...
params.INGEST.CRUISE, params.INGEST.CRUISE_LEG, params.INGEST.YEAR, params.INGEST.MONTH, params.INGEST.DAY, params.INGEST.YEAR_DAY))
dynamicDateTicks;
ax2 = subplot(3,1,2);
hold on;
grid on;
plot(allData.aData.SyncDataObject.Time(allData.aData.FSWIndex), allData.aData.SyncDataObject.Data(allData.aData.FSWIndex), 'g');
legend('Filtered a data')
dynamicDateTicks;
ax3 = subplot(3,1,3);
hold on;
grid on;
plot(allData.aData.SyncDataObject.Time(allData.aData.TSWIndex), allData.aData.SyncDataObject.Data(allData.aData.TSWIndex), 'b');
legend('Total a data')
dynamicDateTicks;
linkaxes([ax1,ax2,ax3], 'x');
saveas(gcf, fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, strcat(num2str(params.INGEST.YEAR_DAY), '_fig210')));
end %if params.RUN.CREATE_DEBUG_PLOTS
%%
% save current as mat file
if params.RUN.SAVE_DATA
matFileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
strcat('acsPREPROC', '_', num2str(params.INGEST.YEAR), '_', num2str(params.INGEST.YEAR_DAY)));
save( matFileName, 'allData');
save( paramsFileName, 'params');
clear matFileName;
clear paramsFileName;
end;
%% close variables
if params.INGEST.CLEAR_VARS
clear aFSWTransitions;
clear aTSWTransitions;
clear ans;
clear ax1;
clear ax2;
clear goodEndsOut;
clear goodEndTimes;
clear goodStartsOut;
clear goodStartTimes;
clear goodEnds;
clear goodStarts;
clear cTSWTransitions;
clear cFSWTransitions;
clear filename;
clear fileName;
clear flag;
clear startIndex;
clear timestamp;
clear Transitions;
clear type;
end;
L.info('PreProcessingManager', 'FINISHED');
%--------------------------------- END CODE -----------------------------