<div dir="ltr"><div><div>It is working!<br><br></div>This spectralIndices saves a lot of time and only expensive packages has similar option, to calculate a lot of VI in one run.<br><br></div>Thank you very much to all!<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Dec 12, 2016 at 4:11 PM, Benjamin Leutner <span dir="ltr"><<a href="mailto:benjamin.leutner@uni-wuerzburg.de" target="_blank">benjamin.leutner@uni-wuerzburg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Dragan,<br>
<br>
for your first question: yes, spectralIndices can be calculated on
Sentinel 2 images as well and L1C data are indeed top of atmosphere
reflectance.<br>
Just for calculating spectral indices in principle there's no need
for further conversions. Nevertheless, it is a good idea to perform
atmospheric correction on Sentinel 2 data beforehand (with ESA SNAP
software and/or SEN2COR), because this should improve comparability
among different scenes.<br>
<br>
for your last question. the data() function is out of place here. <br>
Your code should read:<br>
<span style="color:rgb(0,0,255)"><span class="">bs3 <-
raster("C:/R_examples/VI/B3.<wbr>TIF")<br>
bs4 <- raster("C:/R_examples/VI/B4.<wbr>TIF")<br></span>
group <- stack(bs3, bs4)<br>
names(group) <- c("bs3", "bs4")</span><span style="color:rgb(0,0,255)"> # make proper names</span><span class=""><span style="color:rgb(0,0,255)"><br>
</span><span style="color:rgb(0,0,255)">ndvi <-
spectralIndices(group, red = "bs3", nir = "bs4", indices = "NDVI")<br>
</span><br>
<br></span>
Cheers,<br>
Benjamin<div><div class="h5"><br>
<br>
<br>
<div class="m_-5106371961862776677moz-cite-prefix">On 12/12/2016 03:45 PM, Dragan
Kaludjerovic wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>Martin,<br>
</div>
I have replaced brick() with stack() and still got the error
when I run the line data. Here is how it looks now:<br>
<br>
<span style="color:rgb(0,0,255)">install.packages("RStoolbox")<br>
install.packages(raster)<br>
<br>
library(ggplot2)<br>
library(raster)<br>
library(rgdal)<br>
<br>
bs3 <- raster("C:/R_examples/VI/B3.<wbr>TIF")<br>
bs4 <- raster("C:/R_examples/VI/B4.<wbr>TIF")<br>
<br>
bs3<br>
bs4<br>
<br>
group <- stack(bs3, bs4)<br>
<br>
#writeRaster(group, filename = "C:/R_examples/VI/grupa.TIF")<br>
<br>
data(group)<br>
<br>
## Calculate NDVI <br>
<br>
ndvi <- spectralIndices(group, red = "bs3", nir = "bs4",
indices = "NDVI")<br>
<br>
ndvi<br>
<br>
</span></div>
<span style="color:rgb(0,0,255)">eror when I run line </span><span style="color:rgb(0,0,255)">data(group)<br>
<br>
</span>
<pre class="m_-5106371961862776677gmail-GODMDAHBLOB" id="m_-5106371961862776677gmail-rstudio_console_output" style="font-family:"lucida console";font-size:10pt;outline:medium none;border-width:medium;border-style:none;border-color:-moz-use-text-color;word-break:break-all;margin:0px;white-space:pre-wrap;line-height:15px;color:rgb(0,0,0);font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;word-spacing:0px;background-color:rgb(255,255,255)"><span class="m_-5106371961862776677gmail-GODMDAHBFOB m_-5106371961862776677gmail-ace_constant" style="color:rgb(197,6,11)">Warning message:
</span><span class="m_-5106371961862776677gmail-GODMDAHBFOB m_-5106371961862776677gmail-ace_constant" style="color:rgb(197,6,11)">In data(group) :</span><span class="m_-5106371961862776677gmail-GODMDAHBFOB m_-5106371961862776677gmail-ace_constant" style="color:rgb(197,6,11)"> data set ‘group’ not found</span></pre>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Dec 12, 2016 at 8:17 AM, Martin
Wegmann <span dir="ltr"><<a href="mailto:martin.wegmann@uni-wuerzburg.de" target="_blank">martin.wegmann@uni-wuerzburg.<wbr>de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="background-color:rgb(255,255,255);line-height:initial" lang="en-GB">
<div>Dear
Dragan,</div>
<div><br>
</div>
<div>Please
replace brick() with stack() and it should work, and of
course you need to adapt your band names in
spectralIndices().</div>
<div><br>
</div>
<div>Regards,
Martin</div>
<div><br style="display:initial">
</div>
<table style="background-color:white;border-spacing:0px" width="100%">
<tbody>
<tr>
<td colspan="2" style="font-size:initial;text-align:initial;background-color:rgb(255,255,255)">
<div>
<div><b>From: </b>Dragan Kaludjerovic</div>
<div><b>Sent: </b>Sunday, December 11, 2016
23:21</div>
<div><b>To: </b><a href="mailto:rs-ecology@lists.uni-wuerzburg.de" target="_blank">rs-ecology@lists.uni-wuerzburg<wbr>.de</a></div>
<div><b>Subject: </b>Re: [RS-ecology]
RS-ecology Digest, Vol 16, Issue 1</div>
</div>
</td>
</tr>
</tbody>
</table>
<div>
<div class="m_-5106371961862776677h5"><br>
<div id="m_-5106371961862776677m_3514289799792061681_originalContent">
<div dir="ltr">
<div>Now I have changed it, but still getting
error<br>
<br>
<span style="color:rgb(0,0,255)">install.packages("RStoolbox")<br>
install.packages(raster)<br>
<br>
library(ggplot2)<br>
library(raster)<br>
library(rgdal)<br>
<br>
bs3 <- raster("C:/R_examples/VI/B3.TI<wbr>F")<br>
bs4 <- raster("C:/R_examples/VI/B4.TI<wbr>F")<br>
<br>
bs3<br>
bs4<br>
<br>
group <- brick(bs3, bs4)<br>
<br>
data(group)<br>
<br>
## Calculate NDVI <br>
<br>
ndvi <- spectralIndices(group, red = "bs3",
nir = "bs4", indices = "NDVI")<br>
<br>
ndvi<br>
<br>
</span></div>
error is:<span style="color:rgb(0,0,255)"><br>
<br>
</span><br>
<pre class="m_-5106371961862776677m_3514289799792061681gmail-GODMDAHBLOB" id="m_-5106371961862776677m_3514289799792061681gmail-rstudio_console_output" style="font-family:"lucida console";font-size:10pt;outline:medium none;border-width:medium;border-style:none;border-color:-moz-use-text-color;word-break:break-all;margin:0px;white-space:pre-wrap;line-height:15px;color:rgb(0,0,0);font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;word-spacing:0px;background-color:rgb(255,255,255)"><span class="m_-5106371961862776677m_3514289799792061681gmail-GODMDAHBBPB m_-5106371961862776677m_3514289799792061681gmail-ace_keyword" style="color:blue;white-space:pre-wrap">> </span><span class="m_-5106371961862776677m_3514289799792061681gmail-GODMDAHBBOB m_-5106371961862776677m_3514289799792061681gmail-ace_keyword" style="color:blue">group <- brick(bs3, bs4)
</span><span class="m_-5106371961862776677m_3514289799792061681gmail-GODMDAHBBPB m_-5106371961862776677m_3514289799792061681gmail-ace_keyword" style="color:blue;white-space:pre-wrap">> </span><span class="m_-5106371961862776677m_3514289799792061681gmail-GODMDAHBBOB m_-5106371961862776677m_3514289799792061681gmail-ace_keyword" style="color:blue">data(group)
</span><span class="m_-5106371961862776677m_3514289799792061681gmail-GODMDAHBFOB m_-5106371961862776677m_3514289799792061681gmail-ace_constant" style="color:rgb(197,6,11)">Warning message:
</span><span class="m_-5106371961862776677m_3514289799792061681gmail-GODMDAHBFOB m_-5106371961862776677m_3514289799792061681gmail-ace_constant" style="color:rgb(197,6,11)">In data(group) :</span><span class="m_-5106371961862776677m_3514289799792061681gmail-GODMDAHBFOB m_-5106371961862776677m_3514289799792061681gmail-ace_constant" style="color:rgb(197,6,11)"> data set ‘group’ not found</span></pre>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Dec 11, 2016 at
12:00 PM, <span dir="ltr"><<a href="mailto:rs-ecology-request@lists.uni-wuerzburg.de" target="_blank"></a><a class="m_-5106371961862776677moz-txt-link-abbreviated" href="mailto:rs-ecology-request@lists.uni" target="_blank">rs-ecology-request@lists.uni</a>-<wbr><a href="http://wuerzburg.de">wuerzburg.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send RS-ecology
mailing list submissions to<br>
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When replying, please edit your Subject line
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<br>
Today's Topics:<br>
<br>
1. problem with RStoolbox (Dragan
Kaludjerovic)<br>
2. Re: problem with RStoolbox (Martin
Wegmann)<br>
<br>
<br>
------------------------------<wbr>------------------------------<wbr>----------<br>
<br>
Message: 1<br>
Date: Sat, 10 Dec 2016 19:00:11 +0100<br>
From: Dragan Kaludjerovic <<a href="mailto:advancedgwt@gmail.com" target="_blank"></a><a class="m_-5106371961862776677moz-txt-link-abbreviated" href="mailto:advancedgwt@gmail.com" target="_blank">advancedgwt@gmail.com</a>><br>
To: <a href="mailto:RS-ecology@lists.uni-wuerzburg.de" target="_blank">RS-ecology@lists.uni-wuerzburg<wbr>.de</a><br>
Subject: [RS-ecology] problem with RStoolbox<br>
Message-ID:<br>
<<a href="mailto:CAFZvhLipaCHuq-hQsk_5i31ThbCXGQZ4cPhP87%2BYS4P6__rzDw@mail.gmail.com" target="_blank">CAFZvhLipaCHuq-hQsk_5i31ThbCX<wbr>GQZ4cPhP87+YS4P6__rzDw@mail.gm<wbr>ail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
I have just discover RStoolbox and try simple
simple script<br>
<br>
install.packages("RStoolbox")<br>
install.packages(raster)<br>
<br>
library(ggplot2)<br>
library(raster)<br>
library(rgdal)<br>
<br>
data(img)<br>
<br>
## Calculate NDVI<br>
ndvi <- spectralIndices(img, red =
"C:/R_examples/VI/B3.tif", nir =<br>
"C:/R_examples/VI/B4.tif", indices = "NDVI")<br>
ndvi<br>
<br>
<br>
when I run it I got error message<br>
<br>
Error in match(xi, names(img)) : object 'img'
not found<br>
<br>
Any suggestion is welcomed!<br>
<br>
Best Regards,<br>
<br>
Dragan<br>
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------------------------------<br>
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Message: 2<br>
Date: Sun, 11 Dec 2016 09:46:02 +0100<br>
From: Martin Wegmann <<a href="mailto:martin.wegmann@uni-wuerzburg.de" target="_blank">martin.wegmann@uni-wuerzburg.<wbr>de</a>><br>
To: Dragan Kaludjerovic <<a href="mailto:advancedgwt@gmail.com" target="_blank"></a><a class="m_-5106371961862776677moz-txt-link-abbreviated" href="mailto:advancedgwt@gmail.com" target="_blank">advancedgwt@gmail.com</a>>,<br>
<a href="mailto:RS-ecology@lists.uni-wuerzburg.de" target="_blank">RS-ecology@lists.uni-wuerzburg<wbr>.de</a><br>
Subject: Re: [RS-ecology] problem with
RStoolbox<br>
Message-ID: <<a href="mailto:20161211084602.5943378.73264.3393@uni-wuerzburg.de" target="_blank">20161211084602.5943378.73264.<wbr>3393@uni-wuerzburg.de</a>><br>
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</blockquote>
</div>
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</blockquote>
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</blockquote>
<br>
</div></div><pre class="m_-5106371961862776677moz-signature" cols="72">--
Benjamin Leutner M.Sc.
PhD candidate
Department of Remote Sensing
University of Wuerzburg
Campus Hubland Nord 86
97074 Wuerzburg, Germany
Tel: <a href="tel:+49%20931%203189594" value="+499313189594" target="_blank">+49-(0)931-31 89594</a>
Fax: +49-(0)931-31 89594-0
Email: <a class="m_-5106371961862776677moz-txt-link-abbreviated" href="mailto:benjamin.leutner@uni-wuerzburg.de" target="_blank">benjamin.leutner@uni-<wbr>wuerzburg.de</a>
Web: <a class="m_-5106371961862776677moz-txt-link-freetext" href="http://www.fernerkundung.uni-wuerzburg.de" target="_blank">http://www.fernerkundung.uni-<wbr>wuerzburg.de</a>
</pre>
</div>
</blockquote></div><br></div>