-
Notifications
You must be signed in to change notification settings - Fork 57
/
nd2toarbt_msi2.m
213 lines (186 loc) · 8.38 KB
/
nd2toarbt_msi2.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
function [im_th,TOAref,trgt,ijdim_ref,bbox,ul,zen,azi,zc,Angles2,B1Satu,B2Satu,B3Satu,resolu]=nd2toarbt_msi2(im, band_offsets, quantif)
% read TOA refs function derived from Fmask 4.4 for Sentinel 2.
% Revisions:
% Designed for Sentinel-2 Baseline 4.00 (Shi /26/12/2021)
% Use REF vs. DN instead of RAD vs. DN (Zhe 06/20/2013)
% Combined the Earth-Sun distance table into the function (Zhe 04/09/2013)
% Process Landsat 8 DN values (Zhe 04/04/2013)
% Proces the new metadata for Landsat TM/ETM+ images (Zhe 09/28/2012)
% Fixed bugs caused by earth-sun distance table (Zhe 01/15/2012)
%
% [im_th,TOAref,ijdim_ref,ul,zen,azi,zc,B1Satu,B2Satu,B3Satu,resolu]=nd2toarbt(filename)
% Where:
% Inputs:
% im= MSI filename structure including:
% - im.Dmain (root directory of the SAFE directory)
% - im.DataStrip directory (without ".SAFE")
% - im.Granule directory;
% im.Dmain = '/home/bernie/MSIdata/';
% im.DataStrip = 'S2A_OPER_PRD_MSIL1C_PDMC_20151229T234852_R139_V20151229T144823_20151229T144823';
% im.Granule = 'S2A_OPER_MSI_L1C_TL_SGS__20151229T201123_A002710_T20QPD_N02.01';
% Outputs:
% 1) im_th = Brightness Temperature (BT)
% 2) TOAref = Top Of Atmoshpere (TOA) reflectance
% 3) ijdim = [nrows,ncols]; % dimension of optical bands
% 4) ul = [upperleft_mapx upperleft_mapy];
% 5) zen = solar zenith angle (degrees);
% 6) azi = solar azimuth angle (degrees);
% 7) zc = Zone Number
% 8,9,10) Saturation (true) in the Visible bands
% 11) resolution of Fmask results
% eg.
FilesInfo.DirIn = im.Dmain;
FilesInfo.DataStrip =im.DataStrip ;
FilesInfo.Granule=im.Granule;
FilesInfo.InspireXML=im.InspireXML;
clear im;
% obtain them from INSPIRE.xml
bbox = ReadS2InspireXML(FilesInfo.InspireXML);
%% Metadata read ReadSunViewGeometryMSI(DataStrip,Granule,BandSel,PsizeOut,Dmain)
[MSIinfo,Angles] = ReadSunViewGeometryMSIBaseline04 (FilesInfo.DataStrip,FilesInfo.Granule,4,10,FilesInfo.DirIn);
Angles2.VAA = Angles.VAA_B04 ;
Angles2.VZA = Angles.VZA_B04 ;
clear Angles;
%% output resolution of Fmask 20meters for Sentinel 2 images
resolu = [20 20] ;
%%
ijdim_ref = (MSIinfo.GeoInfo.Size.R10) *10 ./ resolu ;
ul = [MSIinfo.GeoInfo.Xstart.R10 MSIinfo.GeoInfo.Ystart.R10] + [resolu(1)/2 0-resolu(2)/2]; % the center of the top-left pixel.
zen = MSIinfo.Angles.Mean.SZA ;
azi = MSIinfo.Angles.Mean.SAA ;
zc_num=MSIinfo.GeoInfo.UTM_zone(1:end-1);
% convert UTM zone to code by refering the bellow rule.
% ref. http://geotiff.maptools.org/spec/geotiff6.html#6.3.3.1
zc_ns=MSIinfo.GeoInfo.UTM_zone(end);
clear MSIinfo;
if zc_ns=='N'
zc = abs(str2double(zc_num));
if zc>10
geokey = ['326',zc_num];
else
geokey = ['3260',zc_num];
end
geokey=str2double(geokey);
elseif zc_ns=='S'
zc = abs(str2double(zc_num));
if zc>10
geokey = ['327',zc_num];
else
geokey = ['3270',zc_num];
end
geokey=str2double(geokey);
end
%% open MSI data
BandCorr = {'02','03','04','8A','11','12','10','07','08'};
BandCorrId = [1, 2, 3, 8, 11, 12, 10, 6, 7];
Ratio = [10 10 10 20 20 20 60 20 10] /(resolu(1)); % resample all bands to the same resolu
Dmain = fullfile(FilesInfo.DirIn, [FilesInfo.DataStrip '.SAFE'],'GRANULE', FilesInfo.Granule, 'IMG_DATA');
id_missing=zeros(ijdim_ref,'uint8');
for iB=1:length(BandCorr)
% support all versions for Sentinel 2 images.
tempfn = dir(fullfile(Dmain, [FilesInfo.Granule(1) '*B' BandCorr{iB} '.jp2']));
if isempty(tempfn)
tempfn = dir(fullfile(Dmain, [FilesInfo.Granule(5) '*B' BandCorr{iB} '.jp2']));
if isempty(tempfn)
tempfn = dir(fullfile(Dmain, ['*B' BandCorr{iB} '.jp2']));
end
end
dum=imread(fullfile(Dmain, tempfn(1).name));
mask_filled = dum == 0;
dum = 10000.*(single(dum) + band_offsets(BandCorrId(iB) == band_offsets(:, 1), 2))./quantif; % OFFset
clear tempfn;
dum(mask_filled)=NaN;
clear mask_filled;
if Ratio(iB)<1 % box-agg pixel
TOAref(:,:,iB) = imresize(dum,Ratio(iB),'box');
elseif Ratio(iB)>1 % split pixel
TOAref(:,:,iB) = imresize(dum,Ratio(iB),'nearest');
elseif Ratio(iB)==1
TOAref(:,:,iB) = dum;
end
clear dum;
% % if isequal(BandCorr{iB},'08')
% % % Gaussfilt for band 8 to better scall up.
% % TOAref(:,:,iB) = imgaussfilt(TOAref(:,:,iB));
% % end
% only processing pixesl where all bands have values (id_mssing)
id_missing=id_missing|isnan(TOAref(:,:,iB));
end
clear Dmain FilesInfo BandCorr Ratio iB;
% trgt=CreateTargetGRIDobj(info_jp2.BoundingBox,resolu,ul,ijdim_ref,zc_num,zc_ns,geokey);
trgt=CreateTargetGRIDobj(resolu,ul,ijdim_ref,zc_num,zc_ns,geokey);
trgt.Z=[];
% trgt_test = GRIDobj('E:\New validation dataset\New accuracy assessment samples for Fmask 4_0\Sentinel2\S2A_MSIL1C_20171011T123151_N0205_R023_T17CNL_20171011T123149.SAFE\GRANULE\L1C_T17CNL_A012032_20171011T123149\Samples\assist data\Samples.tif');
%%
%%%%% WARNING - what is the MSI fill value? what is the saturation flag ? 65535
% TOAref(isnan(TOAref))=-9999;
TOAref(id_missing)=-9999;
clear id_missing;
%%%%%%%%%%%% Not used but same format
im_th=-9999;
% B1Satu = zeros([size(TOAref,1) size(TOAref,2)],'uint8')==1;
% B2Satu = zeros([size(TOAref,1) size(TOAref,2)],'uint8')==1;
% B3Satu = zeros([size(TOAref,1) size(TOAref,2)],'uint8')==1;
% find pixels that are saturated in the visible bands
% SATURATED VALUE: 65535 set by Shi 10/18/2017
B1Satu=TOAref(:,:,1)==65535;
B2Satu=TOAref(:,:,2)==65535;
B3Satu=TOAref(:,:,3)==65535;
end
function trgt=CreateTargetGRIDobj(resolu,ul,ijdim_ref,zc_num,zc_ns,geokey)
trgt = GRIDobj([]);
trgt.name='target';
trgt.cellsize=resolu(1);
ul_tmp=ul - [resolu(1)/2 0-resolu(2)/2]; %back to limits.
% location of the 'center' of the first (1,1) pixel in the image.
trgt.refmat=makerefmat(ul(1),ul(2),resolu(1),0-resolu(2));
clear ul;
trgt.size=ijdim_ref;
% boundary.
xWorldLimits=[ul_tmp(1),ul_tmp(1)+resolu(1)*(ijdim_ref(1))];
yWorldLimits=[ul_tmp(2)-resolu(2)*(ijdim_ref(2)),ul_tmp(2)];
clear ul_tmp resolu;
spatialRef = maprefcells(xWorldLimits,yWorldLimits,ijdim_ref,...
'ColumnsStartFrom','north');
clear xWorldLimits yWorldLimits ijdim_ref;
trgt.georef.SpatialRef=spatialRef;
clear spatialRef;
% % http://www.gdal.org/frmt_sentinel2.html
trgt.georef.GeoKeyDirectoryTag.GTModelTypeGeoKey = 1;
trgt.georef.GeoKeyDirectoryTag.GTRasterTypeGeoKey = 1;
trgt.georef.GeoKeyDirectoryTag.GTCitationGeoKey = ['WGS 84 / UTM zone ',zc_num,zc_ns];
trgt.georef.GeoKeyDirectoryTag.ProjectedCSTypeGeoKey = geokey; clear geokey;
trgt.georef.GeoKeyDirectoryTag.PCSCitationGeoKey = ['WGS 84 / UTM zone ',zc_num,zc_ns]; % same
% ellipsoid = utmgeoid([zc_num,zc_ns]);
% this can be used as follows because the Sentinel 2 titles's projection
% will not be changable.
% WGS84 UTM: A UTM zone is a 6?° segment of the Earth.
E = wgs84Ellipsoid('meters');
utmstruct = defaultm('tranmerc');
utmstruct.geoid = [E.SemimajorAxis,E.Eccentricity];
clear E;
% UTM false East (m)
% the central meridian is assigned 500,000 meters in each zone.
utmstruct.falseeasting=500000;
% UTM false North (m)
% If you are in the northern hemisphere, the equator has a northing
% value of 0 meters. In the southern hemisphere, the equator starts
% at 10,000,000 meters. This is because all values south of the
% equator will be positive.
if zc_ns=='N'
utmstruct.falsenorthing=0;
else % S
utmstruct.falsenorthing=10000000;% 10,000,000
end
clear zc_ns;
% UTM scale factor
utmstruct.scalefactor=0.9996;
% each UTM zone is 6 degrees. a total of 60 zones.
origin=(str2double(zc_num)-31).*6+3;
clear zc_num;
utmstruct.origin=[0,origin,0];
clear origin;
utmstruct = defaultm(utmstruct);
trgt.georef.mstruct=utmstruct;
clear utmstruct;
end