georef_out.m

function [output_pth, gt] = georef_out(name, im, write)
% script to write a geotiff from just a filename and image matrix.  It
% calls global env structure to query input image with same name so it can
% extact georef info and masked pixels.

% Inputs:   name    =   file basename as found in training folder (eg
%                         ('yflatE_21609_17098_008_170916_L090_CX_01_Freeman-inc')
%           im      =   image matrix (mxnx1)
%           write   =   whether or not to actually write file, or just
%           parse name
% Output:   Just a pth name and geotiff info, but it writes a file 

% modified from addOutputImages.m
% Written  by Ethan Kyzivat

%% I/O
global env

%% Load georef info
georef_in=(ls([env.output.test_dir, name, '.tif']));
if ~isunix
    output_pth=[env.output.test_dir, georef_in(1,1:end-4), '_cls.tif'];
    gt=geotiffinfo([env.output.test_dir, georef_in]);
else
    output_pth=[georef_in(1,1:end-5), '_cls.tif'];
    gt=geotiffinfo(georef_in(1,1:end-1));   % hot fix
end
if write
    %% apply mask

    % if ~isunix
    %     test_im=imread([env.output.test_dir, georef_in]);
    % else
    %     test_im=imread(strtrim(georef_in));
    % end
    % mask=isnan(test_im(:,:,end)); % negative data mask
    % im(mask)=env.constants.noDataValue_ouput; %%% HERE 2/18/20: mask is different size than out
    %% write
    geotiffwrite(output_pth, im, gt.SpatialRef, 'GeoKeyDirectoryTag',gt.GeoTIFFTags.GeoKeyDirectoryTag);
    % gdal_calc.py -A input1.tif -B input2.tif --outfile=result.tif --calc="A+B"

    %% Add NoData values to rasters
    if isunix % don't implement until ASC updates python gdal to 2.1.2 +
        cmd=sprintf('gdal_edit.py -a_nodata %d %s', env.constants.noDataValue_ouput, output_pth);
        system(cmd);
    end
end