Eriks: Created page with "

 function CERBdoKQ(infile,type,channel,depth_int,trend,variation) %(infile,type,channel,depth_int,trend,variation) %This function qualifies the incident illumination of a..."

2014-04-10T23:24:07Z

Created page with "<pre> function CERBdoKQ(infile,type,channel,depth_int,trend,variation) %(infile,type,channel,depth_int,trend,variation) %This function qualifies the incident illumination of a..."

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<pre>
function CERBdoKQ(infile,type,channel,depth_int,trend,variation)
%(infile,type,channel,depth_int,trend,variation)
%This function qualifies the incident illumination of a spectral channel
%during sampling over a given depth interval and writes a flag on a new
%data line
%The user chooses the channel and window width(m). For each line the
%program calculates teh standard deviation and mean of the first difference
%(M1stdiff) for teh group of points in the interval z+-
%depth_window_width/2
%A new line will be placed in <derived_parameters> KQ-
%cmd example -m 2ed488 10 0.05 0.02 infile outfile
%compare the M1stdiff/mean and sigm/mean of data in window +- 5m to 0.02
%and 0.05 respectively for channel 2ed488
%1-15-2014 needed to change sigma to sigm-matlab function conflict

%================================================================
%DoKQ
%Condition Flag
%contains trapflag 14
%outside of cast index 13
%calculated M1stdiff > max M1stdiff and sig > sigmx 12
%calculated M1stdiff > max M1stdiff 11
%calculated sig > sigmx 10
%point is less than winmin 1
%good data 0
%================================================================

%===SET PARAMETERS===

infid = fopen(infile,'r');
dataname = strcat('KQCmat',infile);
dataname = strrep(dataname,'.lcd','');

%===MAKE DATA FILE FOR INPUT FILE===

frewind(infid);

datafid = fopen(dataname,'w');
while ~feof(infid)
testline = fgets(infid);
if strncmp(testline,'<data>',6) ==1 %start of data section
while strncmp(testline,'<filters_used>',14) ~=1
testline = fgets(infid);
if strncmp(testline,'<filters_used>',14) ==1
break
end
fprintf(datafid,testline);
end
end
end
fclose(datafid);
frewind(infid);

%===GET CASTID MATRIX FROM FILE AND SPLIT DATA===
%fid = fopen(infile);

[in,mer,dep] = index1(infile);

mat = load(dataname);

clear ij
clear downcastmatrix
clear upcastmatrix
clear diffdn
clear diffup
width = length(mat(1,:));
%for ij = in{1}:1:in{2};
for ij = 1:1:in{2}
%downcastmatrix(ij-(in{1}-1),:) = mat(ij,1:width); %starts from 1 and goes to in2
downcastmatrix(ij,:) = mat(ij,1:width);
end
% for r = in{3}:in{4};
% upcastmatrix(r-(in{3}-1),:) = mat(r,1:width);
% end
%mat = mat(in{1}:end,:); %index mat appropriatedly to match downcastmatrix
%===FIND CHANNEL INDEX===

lineind =0;
while ~feof(infid)
line = fgets(infid);
if strncmp(line,'<sampled_parameters>',20) ==1
while strncmp(line,'<data>',6) ~= 1
lineind = lineind +1;
line = fgets(infid);
if strncmp(line,'<derived_parameters>',20) == 1
lineind = lineind -1;
end
if strncmp(channel,line,5) ==1
chanind = lineind;
end
end
end
end

%===INDEX OF DEPTH ONLY===

lineind =0;
frewind(infid)
while ~feof(infid)
line = fgets(infid);
if strncmp(line,'<sampled_parameters>',20) ==1
while strncmp(line,'<data>',6) ~= 1
lineind = lineind +1;
line = fgets(infid);
if strncmp(line,'<derived_parameters>',20) == 1
lineind = lineind -1;
end
if strncmp('LuZDepth',line,8) ==1 %changed 12-3-12
depthind = lineind;
end
end
end
end
depthind;
%===INDEX OF TIME ONLY===

lineind =0;
frewind(infid);
while ~feof(infid)
line = fgets(infid);
if strncmp(line,'<sampled_parameters>',20) ==1
while strncmp(line,'<data>',6) ~= 1
lineind = lineind +1;
line = fgets(infid);
if strncmp(line,'<derived_parameters>',20) == 1
lineind = lineind -1;
end
%if strncmp('FrameCount',line,10) ==1 %changed 12-3-12 0prr_record
if strncmp('Master_FrameNumber',line,18) ==1 %changed 1-22-14 0prr_record
%if strncmp('1mer_time',line,9) ==1 %changed 12-3-12 0prr_record
timeind = lineind;
end
end
end
end
timeind;
dbstop if error

data = downcastmatrix(:,chanind); %specific channel data
time = downcastmatrix(:,timeind);
depth = downcastmatrix(:,depthind);

%===NEED TO SORT DATA TO BE MONOTONIC AND THEN RETURN WHEN OPERATION DONE==

% unsorted_ind = 1:length(downcastmatrix);%index to sort back to
% [depth_sorted,ds_ind] = sort(depth);%sorting just the depth and getting index
% sorted_DCmatrix = downcastmatrix(ds_ind,:);%sorting all according index of sorted depth
% new_unsort_ind(ds_ind) = unsorted_ind; %values at sorted index = unsorted index
% %new_unsorted = sorted_DCmatrix(new_unsort_ind,:);%should be same as original downcast matrix
%
% %===Stuff is now sorted=== but currently not used
%
% timesort = time(ds_ind,:);
% datasort = data(ds_ind,:);
% depthsort = depth_sorted;
% downcastmatrixsort = sorted_DCmatrix;

%===SORT WHOLE MATRIX JUST IN CASE=== not going to work with both up and
%downcast

%wholeunsort_ind = 1:length(mat);
%[depth_whole_sort,dsw_ind] = sort(mat(:,depthind));
%sorted_wholemat = mat(dsw_ind,:);
%new_unsortind(dsw_ind) = wholeunsort_ind;

%=====LOAD DATA AND DO=====
%================================================================
%DoKQ
%Condition Flag
%contains trapflag 14
%outside of cast index 13
%calculated M1stdiff > max M1stdiff and sig > sigmx 12
%calculated M1stdiff > max M1stdiff 11
%calculated sig > sigmx 10
%point is less than winmin 1
%good data 0
%================================================================

window = depth_int/2;
%bflag = {'notfound'};
%aflag = {'notfound'};
bflag =5; %==notfound
aflag =5; %==notfound
%for row =1:in{2} +1 %initialize result and sigm
% sigm(row,:) =5;
% result(row,:) =-5;
%end
r = 1;%in{1}; %originally r = {in} because it was working with entire depth matrix not pre-timmed to castID such as here
%index =1;
while r <= in{2}

if data(r)== -9.9e35 || depth(r) == -9.9e35
result(r) = -5;
sigm(r) = -9.9E35;
r =r+1;
continue
end
%lower window(shallow)

bcondition = depth(r) - window;

for pt =r:-1:1%count down from top index to first point of data %(length(downcastmatrixsort(:,depthind)-1))
delta = depth(pt);%downcastmatrix(pt,depthind);

if delta <= bcondition
disp('===========================')
disp('found a winmin')
winmin = pt;
bflag =1; %found
delta_b = delta;
bcondition;

break
else

%disp('continueing')
continue
end
end
if bflag ==5;
%result(r)=-9.9E35;
result(r) =5;%NOTFOUND
r = r+1;

continue
end

%upper window(deeper)
acondition = depth(r) + window;
for pt = r:in{2}%length(downcastmatrixsort) %goes down in depth to find other window point

delta = mat(pt,depthind); %beacuse downcastmatrix is offset by index
%if acondition > mat(in{2}-in{1},depthind)
if acondition > mat(in{2}-1,depthind)
r = r+1;
result(r) = 5;
continue
disp('overbounds')
end

if delta >= acondition
disp('found a winmax')
winplus = pt
aflag = 1;
acondition;
delta_a = delta;
disp('==========================')
break
else
continue
end
end
if aflag==5
%result(r)=-9.9E35;
disp('aflag 5')
result(r)=5; %NOTFOUND
r = r+1;
continue
end

%================got to here there was an "end" for the while < loop
format long
%===DO M1SDIFF AND SIGM===
nint = winplus - winmin +1;
fsum =0;
tsum =0;
qout =0;
S =0;
z = winmin;
while z<winplus
fsum = fsum + data(z+1) - data(z);
tsum = tsum + time(z+1) - time(z);
qout = qout + abs(fsum/tsum);
z = z +1;
end

for z = winmin:winplus
ex = data(z);
S = [S,ex];
if z == winmin
S(1) = ex;
end
end

sigm(r) = std(S)./mean(S);
result(r) = ((1/nint)*qout)/mean(S);

r = r+1;
end

rl = find(result ==5);
if length(rl) == in{2} %if all the results = 5, all data is bad
disp('Something is wrong with this file, look at content and castid doKQ')
disp('Soo many bad flags. skipping file and adding to bad list')
fid = fopen('badfiles.txt','r+')

if fid == -1
fid = fopen('badfiles.txt','w+')
end
fseek(fid,0,1)
fprintf(fid,'%s\n',infile);

return
end
%sigm_unsort = sigm(new_unsort_ind);
%result_unsort = result(new_unsort_ind);
%===fill in column with appropriate flag===

%appline = zeros(size(result));
result_prev = result;
for i = 1:in{2}%1:length(result_unsort)

if result(i) > trend && sigm(i) > variation && result(i) ~= 5.00
appline(i) = 12;
elseif result(i) > trend && result(i) ~= 5.00
appline(i) = 11;
elseif sigm(i) > variation %&& result(i) ~= 5.00
appline(i) =10;
elseif result(i) < -9.0e35%or outside of downcast
%keyboard
appline(i) =13;
elseif result(i) == 5 %&& result(i) ~= 5.00
appline(i) =1;
elseif result(i) == -5 %&& result(i) ~= 1.00
appline(i) =14;
else
% if result(i) == 1.00
% appline(i) = result(i);
% else
appline(i) =0;
% end
end

end

%outside of downcast bounds.. just flag
for it = in{2}+1:length(mat)
appline(it) = 13;
end

%===MAKE DATA FILE===

QCdata = load(dataname);
y = size(QCdata,1);
x = size(QCdata,2);
QCdata_new = zeros(y,x+1);
QCdata_new(1:y,1:x) = QCdata;
QCdata_new(:,end) = appline';

%===INSERT NEW DATA INTO NEW LCD===

frewind(infid);
qclcd = fopen(strcat('K',infile),'w+');
while ~feof(infid)
pos = fgets(infid);
if strncmp(pos,'<data>',6) ==1 %start of data section
break
end
fprintf(qclcd,pos);
end

%===INSERT NEW DERIVED PARAMS AND DATA===
newparam = strcat('kq-',channel);
fprintf(qclcd,'%s\n',newparam);
fprintf(qclcd,'%s\n','<data>');
%===overwrite old matrix
dlmwrite(dataname,QCdata_new,'delimiter',' ','precision',6); %overwrite old matrix file

datafile = fopen(dataname);
while ~feof(datafile)
%for loop = 1:length(QCdata_new)
datln = fgets(datafile);
fprintf(qclcd,datln);
end

%===ADD TO FILTERS USED ON NEW LCD===

while ~feof(infid)
lcdline = fgets(infid);
if strncmp(lcdline,'<filters_used>',14) ==1
fprintf(qclcd,'%s\n','<filters_used>');
while ~feof(infid)
filter = fgets(infid);
fprintf(qclcd,'%s',filter);
end
end
end
%domathstring =strcat(['domath',type,channel1,channel2,num2str(number),outfieldname]);
%fprintf(newlcdfile,'%s\n', domathstring);
fprintf(qclcd,'%s','')
fprintf(qclcd,'%s','doKQ ');
fprintf(qclcd,'%s',' ');
fprintf(qclcd,'%s',type);
fprintf(qclcd,'%s',' ');
fprintf(qclcd,'%s',channel);
fprintf(qclcd,'%s',' ');
fprintf(qclcd,'%s',num2str(depth_int));
fprintf(qclcd,'%s',' ');
fprintf(qclcd,'%s',num2str(trend));
fprintf(qclcd,'%s',' ');
fprintf(qclcd,'%s',num2str(variation));

fclose('all');

</pre>

CERBdoKQ - Revision history

Eriks: Created page with "
function CERBdoKQ(infile,type,channel,depth_int,trend,variation) %(infile,type,channel,depth_int,trend,variation) %This function qualifies the incident illumination of a..."