function [XwsRaw numSegments] = GetXws(instanceID)

%GetXws Gets the X matrix of feature data from the weak segmentations

%   Just reads in data from CSVs created by Patrick's extraction software

%get features from our weak segmentors %FYI 4 Otsu and 6 Region Growing

fprintf('Reading calculated feature data from text files.\n');

featureDirectory = 'C:\Users\esmith2\Documents\Ethans Code\gitCode\Image features calculation code\Features for Production\2K image dataset\';

%featureDirectory = 'C:\Users\esmith2\Documents\Ethans Code\gitCode\Image features calculation code\Features for Production\6K org image dataset\';

%featureDirectory = 'C:\Ethan\repos\Image features calculation code\Features for Production\\6K org image dataset\';

%get otsu features

%[markovValues markovHeaders]

fprintf('Reading Otsu segmentation features\n');

fprintf('\tReading intensity values.\n');

[intensityValuesO intensityHeadersO intensityDCMOrderO] = parseCSV(strcat(featureDirectory, 'otsu_nodules_intensity_features.txt'));

fprintf('\tReading gabor values.\n');

[gaborValuesO gaborHeadersO gaborDCMOrderO] = parseCSV(strcat(featureDirectory, 'otsu_nodules_gab_features.txt'));

fprintf('\tReading haralick values.\n');

[haralickValuesO haralickHeadersO haralickDCMOrderO] = parseCSV(strcat(featureDirectory, 'otsu_nodules_har_features.txt'));

fprintf('\tReading shape values.\n');

[shapeValuesO shapeHeadersO shapeDCMOrderO] = parseCSV(strcat(featureDirectory, 'otsu_nodules_shape_features.txt'));

%get region grown features and horizontally concatenate them. 

%[markovValues markovHeaders]

fprintf('Reading Region Growing segmentation features\n');

fprintf('\tReading intensity values.\n');

[intensityValuesRG intensityHeadersRG intensityDCMOrderRG] = parseCSV(strcat(featureDirectory, 'rg_nodules_intensity_features.txt'));

fprintf('\tReading gabor values.\n');

[gaborValuesRG gaborHeadersRG gaborDCMOrderRG] = parseCSV(strcat(featureDirectory, 'rg_nodules_gab_features.txt'));

fprintf('\tReading haralick values.\n');

[haralickValuesRG haralickHeadersRG haralickDCMOrderRG] = parseCSV(strcat(featureDirectory, 'rg_nodules_har_features.txt'));

fprintf('\tReading shape values.\n');

[shapeValuesRG shapeHeadersRG shapeDCMOrderRG] = parseCSV(strcat(featureDirectory, 'rg_nodules_shape_features.txt'));

%concatenate

intensityValues = [intensityValuesO, intensityValuesRG];

gaborValues = [gaborValuesO, gaborValuesRG];

haralickValues = [haralickValuesO, haralickValuesRG];

shapeValues = [shapeValuesO, shapeValuesRG];

%This should happen before the reshaping of the matrices I think

%Rearrange the calculated features so they match with the appropriate rating

fprintf('Reorganizing data to match ratings.\n');

newRowOrder = 0;

for i = 1:size(instanceID)

    row = find( instanceID(i) == intensityDCMOrderO);

    if ~isempty(row)

        newRowOrder = vertcat(newRowOrder, row); 

    end

end

newRowOrder = newRowOrder(2:end,:);

%apply reordering

intensityValues     = intensityValues(newRowOrder,:);

gaborValues         = gaborValues(newRowOrder,:);

haralickValues      = haralickValues(newRowOrder,:);

shapeValues         = shapeValues(newRowOrder,:);

XwsRaw = [intensityValues, gaborValues, haralickValues, shapeValues]; 

%get number of segments

%Count Otsu segments

i = 1;

while intensityHeadersO{1}(end) == intensityHeadersO{i+1}(end)

    i = i+1;

end

numSegments = length(intensityHeadersO)/i;

%count region growing segments

i = 1; 

while intensityHeadersRG{1}(end) == intensityHeadersRG{i+1}(end)

    i = i+1;

end

numSegments = numSegments + length(intensityHeadersRG)/i;

%unused method of getting the largest boundary from each slice

%largeInstances = intensityValues(:,end);

end