added matlab/octave scripts for processing PS2, NDVI, FLIR re issue #64

Author: TinoDornbusch

scripts/FLIR/GetFLIR.m

@@ -0,0 +1,14 @@
+[FileName,PathName,FilterIndex] = uigetfile('*.bin');
+
+fileID = fopen([PathName FileName]);
+A = fread(fileID,[640,480],'uint16');
+
+
+%rescale to visible range
+Gmin=2800;
+Gmax=3300;
+
+At=((A-Gmin)/(Gmax-Gmin));
+
+ colormap('hot')
+figure(1),imagesc(At),colorbar, axis off

scripts/NDVI/GetNDVI.m

@@ -0,0 +1,65 @@
+## Copyright (C) 2016 LemnaTec
+## 
+## This program is free software; you can redistribute it and/or modify it
+## under the terms of the GNU General Public License as published by
+## the Free Software Foundation; either version 3 of the License, or
+## (at your option) any later version.
+## 
+## This program is distributed in the hope that it will be useful,
+## but WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+## GNU General Public License for more details.
+## 
+## You should have received a copy of the GNU General Public License
+## along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+## -*- texinfo -*- 
+## @deftypefn {Function File} {@var{retval} =} GetNDVI (@var{input1}, @var{input2})
+##
+## @seealso{}
+## @end deftypefn
+
+## Author: LemnaTec <LemnaTec@S1_CONTAINER>
+## Created: 2016-06-03
+
+function [NDVI,x,y,z,time] = GetNDVI (PathName)
+
+if nargin==0
+
+[PathName] = uigetdir();
+
+end
+
+
+D=dir(PathName);
+
+% read NDVI from file
+Text=importdata([PathName '\' D(4).name]);
+fi=findstr(Text{2},'"');
+NDVI=str2num(Text{2}(fi(3)+1:fi(4)-1));
+
+% read x,y,z from file
+Text=importdata([PathName '\' D(3).name]);
+% x = row 22 y = row 23 z = row 24
+fi=findstr(Text{22},'"');
+x=str2num(Text{22}(fi(3)+1:fi(4)-1));
+
+fi=findstr(Text{23},'"');
+y=str2num(Text{23}(fi(3)+1:fi(4)-1));
+
+fi=findstr(Text{24},'"');
+z=str2num(Text{24}(fi(3)+1:fi(4)-1));
+
+% read time
+Text=importdata([PathName '\' D(3).name]);
+fi=findstr(Text{21},'"');
+timestr=Text{21}(fi(3)+1:fi(4)-1);
+Year=timestr(7:10);
+Month=timestr(1:2);
+Day=timestr(4:5);
+Hour=timestr(12:13);
+Minute=timestr(15:16);
+
+time = datenum(str2num(Year), str2num(Month), str2num(Day), str2num(Hour), str2num(Minute));
+
+endfunction

scripts/NDVI/PlotNDVI.m

@@ -0,0 +1,41 @@
+## Copyright (C) 2016 LemnaTec
+## 
+## This program is free software; you can redistribute it and/or modify it
+## under the terms of the GNU General Public License as published by
+## the Free Software Foundation; either version 3 of the License, or
+## (at your option) any later version.
+## 
+## This program is distributed in the hope that it will be useful,
+## but WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+## GNU General Public License for more details.
+## 
+## You should have received a copy of the GNU General Public License
+## along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+## -*- texinfo -*- 
+## @deftypefn {Function File} {@var{retval} =} PlotNDVI (@var{input1}, @var{input2})
+##
+## @seealso{}
+## @end deftypefn
+
+## Author: LemnaTec <LemnaTec@S1_CONTAINER>
+## Created: 2016-06-04
+
+function [retval] = PlotNDVI (input1, input2)
+
+[PathName] = uigetdir();
+
+D=dir(PathName);
+
+for i=3:size(D,1)
+
+[NDVI(i-2),x(i-2),y(i-2),z(i-2),t(i-2)]=GetNDVI([PathName '\' D(i).name]);
+
+end
+
+colorMap=jet(length(unique(NDVI)));
+set(gcf, 'ColorMap', colorMap);
+h=plot(x,y);
+
+endfunction

scripts/PS2/GetPS2.m

@@ -0,0 +1,62 @@
+
+[FileName,PathName,FilterIndex] = uigetfile('*.bin');
+pkg image load
+clear M
+close all
+
+D=dir(PathName);
+
+
+
+for i=4:size(D,1)-1
+
+
+fileID = fopen([PathName D(i).name]);
+A = fread(fileID,[1936,1216],'uint8');
+A=double(A)./255;
+
+M(i-3)=mean(mean(A));
+
+
+
+end
+
+figure(1),subplot(3,1,1),plot(M), xlabel("frame"),ylabel("mean intensity")
+
+% get Frame 1 as Fdark
+fileID = fopen([PathName D(4).name]);
+Fdark = fread(fileID,[1936,1216],'uint8');
+Fdark=double(Fdark)./255;
+% get Frame 2 as Fv
+fileID = fopen([PathName D(5).name]);
+F0 = fread(fileID,[1936,1216],'uint8');
+% subtract Fdark
+F0=double(F0)./255-Fdark;
+
+fileID = fopen([PathName D(40).name]);
+Fm = fread(fileID,[1936,1216],'uint8');
+% subtract Fdark
+Fm=double(Fm)./255-Fdark;
+FmHist=reshape(Fm,1,1936*1216);
+
+% image mask
+threshold=max(max(Fm))/10;
+
+mask=Fm>threshold & (Fm-F0)>=0;
+
+% clean up a bit
+se = strel ("square", 5);
+% remove background
+mask=imerode (mask, se);
+% fill holes
+mask=imdilate(mask, se);
+
+FvFm=(Fm-F0)./Fm.*mask;
+
+ colormap('hot')
+figure(1),subplot(3,1,2),imagesc(FvFm),colorbar, axis off
+
+FvFm(FvFm==0)=NaN;
+FvFmHist=reshape(FvFm,1,1936*1216);
+figure(1),subplot(3,1,3),hist(FvFmHist,50),, xlim([0,1]),xlabel("Fv/Fm"),ylabel("no of pixel")
+