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ACS_dataFLAGGER6.m
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ACS_dataFLAGGER6.m
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function flaggedROWS2 = ACS_dataFLAGGER6(HS6_data,lambdA,flaggedROWS,ACS_KEY)
% ACS_dataFLAGGER
% Jesse Bausell
% November 18, 2016
%
% Updated: December 1, 2016
%
% ACS_data_FLAGGER is modified from HS6_dataFLAGGER5 to accomodate ACS
% data. Just imagine that HS6 is ACS.
%
% HS6_dataFLAGGER4 allows user to determine interactively which data to flag
% for later removal and which data to keep. User's selections will be saved
% to be used down the road in the actual deselecting program. The program
% also lets the user discard sections of data that are inaccurate, by
% specifying a range of depths to eliminate, but only at the beginning of
% the program. Upgraded from HS6_dataFLAGGER3. This version automatically
% flags HS6 values that are outside of the user-prescribed range.
% NOTE: This program can only take 8 columns!!
%
% Inputs:
% HS6_data - sigma-corrected HS6 data to be flagged
% LambdA - the wavelength of the HS6 data
% flaggedROWS - the rows already flagged (this is used
% ACS_KEY - this needs to be either a or c. Denotes
%
% Outputs:
% flaggedROWS - row indices that have been flagged by the user.
% HS6_data - HS6 data NOT DISCARDED by the user
%% 1. Prepare for the plotting
% Determine the number of HS6 Channels and make plotting variables that fit
% them.
close all; clc;
% Closes all plots and clears the command window.
if strcmpi(ACS_KEY,'a')
% Allows program to determine if we're working with a or c
% data.
y_word = 'Absorption';
elseif strcmpi(ACS_KEY,'c')
y_word = 'Attenuation';
else
error('ACS_KEY must be a or c');
end
HS6_data2 = HS6_data;
% Create a dublicate HS6 data set.
[l,w] = size(HS6_data);
% Create length and width variables for HS6_data.
deptH = 1:l;
% Create depth index array to be used in subsequent analysis.
% IF there are 8 bb channels in the HS6, use these options instead
coloR = [.6 0 1; 0 0 1; 0 .8 .8; 0 .6 0; .8 .8 0; .8 0 0; 1 .5 .3; 0 0 0];
% Color codes for eight HS6 channels
legendTEXT = {[num2str(lambdA(1)) 'nm '], [num2str(lambdA(2)) 'nm'], ...
[num2str(lambdA(3)) 'nm'], [num2str(lambdA(4)) 'nm'], ...
[num2str(lambdA(5)) 'nm'], [num2str(lambdA(6)) 'nm'], ...
[num2str(lambdA(7)) 'nm'], [num2str(lambdA(8)) 'nm'],'flagged'};
% Legend names (incorporating lambdas) for eight HS6 channels
if isnan(flaggedROWS)
% If flaggedROWS input is NaN...
flaggedROWS = []; % Change this variable to empty
% else
% locK = 1; % This variable will allow user to permanently discard data.
end
locK = 0; % This variable will allow user to permanently discard data.
flagged_IND = NaN;
% creates a variable in which to put newly flagged HS6 rows
levER = 0;
% This variable determines which plotting mode is used:
% 0 = displays all depth profiles & flagged points
% 1 = displays depth profiles with newly-selected flagged point
%% 2. Next we do the dirty work by deciding which data to discard, flag and keep.
while 1
%figure('Color',[.8 .8 .8]);
% sets a figure with a grey background color.
% Creates an ongoing loop with which to flag questionable data.
% flagged_IND = NaN;
% creates a variable in which to put newly flagged HS6 rows
depth_boTTom = -.2*max(deptH);
depth_tOp = max(deptH)+2;
HS6_toP = max(HS6_data(:))*1.1;
HS6_boTTom = min(HS6_data(:))-.001;
% These variables will determine the range of the subsequent HS6 depth
% profiles.
hold on; %Plot multiple things on the same graph.
for ii = 1:length(lambdA)
%Plot all HS6 channels one at a time.
handLE(ii).HS6 = plot(deptH,HS6_data(:,ii),'Color',coloR(ii,:));
end
if isequal(levER,0)
% This if statement differentiates between two paths,
% responsible for two different graphs. Path 1 (this
% path), will plot HS6 depth profiles along with
% previously-flagged data. levER = 0.
if ~isempty(flaggedROWS)
% If the user has previously flagged questionable data
for jj = 1:length(flaggedROWS)
% Plot flagged data on top of profiles (as black stars) one
% row at a time.
h = scatter(deptH(flaggedROWS(jj)*ones(1,length(lambdA))),HS6_data(flaggedROWS(jj),:),'w*');
% Plot points on top of depth profiles
end
else
% If this is the first time that the user is flagging
% questionable data.
h = scatter(NaN,NaN,'w*');
% This is a dummy plot. It doesn't actually change the
% appearance, but it allows us to use the same legend.
end
plot([depth_boTTom depth_tOp],[0 0],'k'); plot([0 0],[HS6_boTTom HS6_toP],'k');
% This line of code plots reference lines to show a depth
% of zero m and a HS6 of zero m^-1. The purpose of these
% are to give users a reference with which to flag bad
% data.
axis([depth_boTTom depth_tOp HS6_boTTom HS6_toP]);
view(-90,90);
set(gca,'XAxisLocation','bottom','YAxisLocation','right', ...
'ydir','reverse','xdir','reverse','FontSize',10,'XTick', ...
[0:100:ceil(max(deptH))],'YTick', ...
[min(HS6_data(:)):abs(max(HS6_data(:))-min(HS6_data(:)))/5:max(HS6_data(:))],'Color',[.8 .8 .8]);
xlabel('Depth (m)','FontSize',16);
ylabel(y_word,'FontSize',16);
% These code lines flip the profile to make it vertical,
% and 'decorate' the figure properly.
LEG = legend([handLE(1).HS6 handLE(2).HS6 handLE(3).HS6 ...
handLE(4).HS6 handLE(5).HS6 handLE(6).HS6 handLE(7).HS6...
handLE(8).HS6 h(1)],legendTEXT,'Location','northeast');
% Legend for 8 channels
set(LEG,'FontSize',12) % set font to 12.
if isequal(locK,0)
% This if statement offers two different paths
% depending on whether or not the user wants to discard
% data. locK = 0 indicates that the user a) has not yet
% decided if he/she wants to discard data or b) has
% indicated an interest to discard data. Once user
% decides not to discard data, this path is closed
% permanently.
while 1
% This is a while loop within a while loop. It allows
% the user to limit the boundaries of the HS6 data if
% he/she feels that they are very far off.
keY5 = input('Create ACS limit? (y/n)','s');
% Asks user if he/she wants to limit data.
if strcmpi('y',keY5)
%If the user says 'yes', he/she will be prompted to
%choose an upper and lower boundary.
hold on;
uppER = input('Select upper ACS limit: '); %upper boundary selection
lowER = input('Select lower ACS limit: '); %lower boundary selection
plot([depth_boTTom depth_tOp],[uppER uppER],'k','LineWidth',1.5);
plot([depth_boTTom depth_tOp],[lowER lowER],'k','LineWidth',1.5);
% Plots upper and lower boundary to give user a
% visual on which data will be axed.
keY6 = input('Accept these limits? (y/n)','s');
% Lets user sign off on his/her choice
if strcmpi(keY6,'y')
% If user confirms his/her selection
limit_IND = (lowER > HS6_data | HS6_data > uppER);
% Finds all the falling outside the user's
% new range.
HS6_data(limit_IND) = NaN;
% Replaces all ouside data with NaNs
[L_nan,w_nan] = find(isnan(HS6_data));
% Find all nans in the HS6 data (nans denote data that was
% outside of our acceptable range.
flaggedROWS = [L_nan; flaggedROWS];
% Add nan'd values to the flaggedROWS.
flaggedROWS = sort(flaggedROWS);
% Puts row indices in order
indexROWS = ones(length(flaggedROWS),1);
% Gives us a dummy array with which to match up to
% flaggedROWS variable.
for ii = 2:length(flaggedROWS)
% Go through all flaggedROWS
if isequal(flaggedROWS(ii-1),flaggedROWS(ii))
% If a row number repeats itself, mark it as NaN.
indexROWS(ii) = NaN;
end
end
flaggedROWS = flaggedROWS(~isnan(indexROWS));
% Extract the nans from the flaggedROWS, leaving only
% the actual values.
close all; %closes the graph
break %breaks the inside while loop
end
elseif strcmpi('n',keY5)
% If the user decides he/she doesn't want
% to select any more data limits.
locK = 1;
%changes the lock variable to 1 (which
%opens up the next part of the program).
close all; %closes the plot
break %breaks the inner while loop
else
clc; %clears the command window
disp('Invalid entry. Must select "y" or "n"');
% Informs user that he/she selected an invalid
% entry.
end
end
elseif isequal(locK,1)
% This option, locK = 1, indicates that the user is
% finished discarding data or has expressed a desire
% NOT to discard data.We now move on to
% flagging individual data points.
keY = input('Flag additional ACS readings? (y/n): ','s');
% Lets user decide whether to flag a data point that
% may be questionable.
if strcmpi('n',keY)
% No additional data points are flagged. Function
% is halted.
clc; close all; break
% clear command window, close figures, and break
% the while loop
elseif strcmpi('y',keY)
% User decides he/she wants to flag a data point.
levER = 1;
% Lever changes to 1. This will open up a new
% figure where user can make sure he/she selected
% the correct data point.
deptH_KEY = input('Enter depth of data you want to flag: ');
% User enters the depth of the data row he/she
% wishes to flag.
deptH_DIFF = abs(deptH-deptH_KEY);
% Finds the actual depth that is closest to the
% value he/she entered.
flagged_IND = find(deptH_DIFF == min(deptH_DIFF));
flagged_IND = flagged_IND(1);
% Generates the index of the depth of interest
close all; %closes figure. While loop begins a new.
end
end
elseif isequal(levER,1)
% This path signifies that the user has selected a
% new HS6 row to flag (potentially). This path will
% graph the HS6 depth profiles and put a black star
% on the flagged data point to let the user decide
% whether to permanently flag it.
h = scatter(deptH(flagged_IND)*ones(1,length(lambdA)),HS6_data(flagged_IND,:),'w*');
% This line of code will plot the row of questionable data as a
% one row scatter plot.
axis([depth_boTTom depth_tOp HS6_boTTom HS6_toP]);
view(-90,90);
set(gca,'XAxisLocation','bottom','YAxisLocation','right', ...
'ydir','reverse','xdir','reverse','FontSize',10,'XTick', ...
[0:100:ceil(max(deptH))],'YTick', ...
[min(HS6_data(:)):abs(max(HS6_data(:))-min(HS6_data(:)))/5:max(HS6_data(:))], ...
'Color',[.8 .8 .8]);
xlabel('Depth (m)','FontSize',16);
ylabel(y_word,'FontSize',16);
% These code lines flip the profile to make it vertical,
% and 'decorate' the figure properly.
LEG = legend([handLE(1).HS6 handLE(2).HS6 handLE(3).HS6 ...
handLE(4).HS6 handLE(5).HS6 handLE(6).HS6 handLE(7).HS6...
handLE(8).HS6 h(1)],legendTEXT,'Location','northeast');
% Legend for 8 channels
set(LEG,'FontSize',12) % set font to 12.
while 1
% This while loop within a while loop sets up the
% foundation for the final question: whether to
% actually flag the data.
keY2 = input('Flag this ACS row? (y/n) ','s');
% Asks user if he/she is sure they want to flag the
% data.
if strcmpi('y',keY2)
% If user decides that they want to flag the data.
flaggedROWS = [flaggedROWS; flagged_IND];
% Adds the flagged row to the permanent array
% of flagged rows.
flaggedROWS = sort(flaggedROWS);
% sorts flagged rows in proper order
% (ascending)
flagged_IND = NaN; levER = 0;
% Resets key variables back to their original
% values. flagged_IND carries newly flagged
% data and levER puts program back on the
% original track, to plot depth profiles with
% ALL flagged points next time arround.
break %breaks the nested while loop.
elseif strcmpi('n',keY2)
% If user decides NOT to flag the data.
flagged_IND = NaN; levER = 0;
% Key variables reset to original values (see above
% for explanation)
break % breaks the nested while loop.
end
end
end
end
%% 3. Finally we update flaggedROWS and output it.
% Final while loop to decide whether to keep or discard 'edited'
% HS6 data.
% [L_nan,w_nan] = find(isnan(HS6_data));
% % Find all nans in the HS6 data (nans denote data that was
% % outside of our acceptable range.
%
% flaggedROWS = [L_nan; flaggedROWS];
% % Adds NaN indices into the flagged rows.
flaggedROWS = sort(flaggedROWS);
% Puts row indices in order
indexROWS = ones(length(flaggedROWS),1);
% Gives us a dummy array with which to match up to
% flaggedROWS variable.
for ii = 2:length(flaggedROWS)
% Go through all flaggedROWS
if isequal(flaggedROWS(ii-1),flaggedROWS(ii))
% If a row number repeats itself, mark it as NaN.
indexROWS(ii) = NaN;
end
end
flaggedROWS2 = flaggedROWS(~isnan(indexROWS));
% Extract the nans from the flaggedROWS, leaving only
% the actual values.
end