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select_data_bio.m
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select_data_bio.m
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%cd D:\trabajo\IGP\CLIM_PEZ\Estadistica_Mensual_DIREPRO_2000_2020-20230310T225135Z-001\Estadistica_Mensual_DIREPRO_2000_2020\2000
%%
clear all; close all; clc;
yrst=2003; yren=2003;
for iy=yrst:1:yren
path01 = sprintf('D:\\trabajo\\IGP\\CLIM_PEZ\\Estadistica_Mensual_DIREPRO_2000_2020-20230310T225135Z-001\\Estadistica_Mensual_DIREPRO_2000_2020\\%d', iy);
%path01 = sprintf('D:\\trabajo\\IGP\\CLIM_PEZ\\pesca\\Estadistica_Mensual_DIREPRO_2000_2020\\%d', iy);
hdir=dir(fullfile(path01,'E*.xlsx'));
if iy>2014
hdir=dir(fullfile(path01,'C*.xlsx'));
end
%% 1er codigo del 2000 al 2014
% vamos a coger los puertos desde Requena hasta Bazan
for ifloat=1:1:size(hdir,1)
fname=hdir(ifloat).name;
disp(fname)
[status,sheets] = xlsfinfo(fname);
% Regular expression pattern
pattern = 'EXTR.*1';
%pattern= 'F*';
% Initialize an empty cell array to store the matched names
matchedNames = {};
% Iterate over each cell name and check if it matches the pattern
for i = 1:numel(sheets)
name = sheets{i};
if ~isempty(regexp(name, pattern, 'once'))
matchedNames{end+1} = name;
end
end
% Display the matched names
sel_sheet=strjoin(matchedNames);
disp(sel_sheet);
%read the excel values
[numData, textData, raw] = xlsread(fname, sel_sheet);
%% now we play with raw to get the time
raw1=textData(:,1);
patternTime='PERI*';
matchedDate = findMatchedNames(raw1, patternTime);
disp(matchedDate(1))
cellData=char(matchedDate(1));
[mo, yr, datenumVal, dateStr] = extractDateInfo(cellData);
disp(mo);
disp(yr);
disp(datestr(datenumVal));
%% now we get the species
patternSpec='ESPE*';
raw2=textData(:,1);
matchedIndices = findPatternIndex(raw2, patternSpec);
for ii=1:1:length(matchedIndices)
puertos=textData(matchedIndices(ii),:);
isNanArray = cellfun(@(x) all(isnan(x(:))), puertos);
isNanSum(ii)=sum(isNanArray);
end
[~, indexmin] = min(isNanSum);
disp(indexmin);
if indexmin<2
raw2=textData(:,2);
matchedIndices = findPatternIndex(raw2, patternSpec);
for ii=1:1:length(matchedIndices)
puertos=textData(matchedIndices(ii),:);
isNanArray = cellfun(@(x) all(isnan(x(:))), puertos);
isNanSum(ii)=sum(isNanArray);
end
[~, indexmin] = min(isNanSum);
puertos_sel=textData(matchedIndices(indexmin),:);
else
puertos_sel=textData(matchedIndices(indexmin),:);
end
disp(puertos_sel);
clear isNanSum isNanArray indexmin
%% ahora vamos a coger los puertos
%
% Find the index of the cell named "IQUITOS"
index_cell = find(strcmp(puertos_sel, 'IQUITOS'));
% Extract the cells to the right of "IQUITOS"
extractedCells = raw(:,index_cell:end);
% now lets see how many NaNs we have
isNanArray2 = cellfun(@(x) all(isnan(x(:))), extractedCells);
isNanSum2=sum(isNanArray2,2);
% lets erase the NaN
indxData=find(isNanSum2<max(max(isNanSum2))-2);
%clear isNanSum isNanArray indexmin
%now we extract the data without NaN
extractedData=extractedCells(indxData,:);
% Extract now the species names
nameSpecies = raw2(indxData,:);
%lets erase the NaNs of the columns of extracted Data
isNanArray3 = cellfun(@(x) all(isnan(x(:))), extractedData);
isNanSum3=sum(isNanArray3,1);
% lets erase the NaN
indxCol=find(isNanSum3<2);
% now we drop the cols with NaN
cleanData=extractedData(:,indxCol);
%clear isNanSum isNanArray indexmin
%% now we will order our matrix
%we can create a repeated matrix of nameSpecies
% % Find the index of 'Species'
% indexremove = find(strcmp(nameSpecies, 'ESPECIES'));
varNames=cleanData(1,:);
% % Remove the cell from the cell array
%now lets identify the string data
targetString = 'IQUITOS';
indices = findStringCells(cleanData, targetString);
disp(indices)
cleanData(indices,:)=[];
% patternDel = 'EXTRACCION*';
% matchedNamesdel = findMatchedNames(nameSpecies,patternDel);
% si no hay extraccion para borrar , continua
% if ~isempty(matchedNamesdel)
% indi = findStringCells(nameSpecies, matchedNamesdel);
% nameSpecies(indi,:)=[];
% else
% disp('Seguimos')
% continue
% %disp('Seguimos')
% end
%disp('NOT SKIPPED')
%%
valuesToDelete = {'OTROS', 'ESPECIES', 'TOTAL','NOTA '};
% Find indices of cells to delete
indicesToDelete = ismember(nameSpecies, valuesToDelete);
% Delete cells from the original cell array
nameSpecies(indicesToDelete) = [];
% Verify the updated cell array
disp(nameSpecies);
%% values above OTROS
% [valuesAbove,otrosIndex] = extractValuesAboveOthers(nameSpecies,'ZUNGARO');
% disp(otrosIndex)
%%
%nameSpecies=nameSpecies(1:otrosIndex,:);
cleanData=cleanData(1:otrosIndex,:); % aqui el problema con otrosIndex
disp(nameSpecies);
%hasta aqui todo cuadra
% ahora vamos a crear la tabla
% crear variables por cada puerto y agregar el tiempo
% corre muy bien para el 2003
%% table
T=cell2table(cleanData);
T.Properties.VariableNames = varNames;
T.Properties.RowNames = nameSpecies;
% Split the table into variables
columnNames = T.Properties.VariableNames;
% Create the table with row names
species_t{:,ifloat}=nameSpecies;
disp(species_t{ifloat})
data_cleaned{:,ifloat}=cleanData;
end
end
%% usar una misma matriz, ordenarla y trabajar con ella
% no usar mas matrices porque es confuso