Re: [Mlt-devel] NDVI processing

2014-07-24 Thread Stefan Gofferje
Here's the link to the theoretical background of NIR-VIS:
http://agribotix.com/blog/2014/6/10/misconceptions-about-uav-collected-ndvi-imagery-and-the-agribotix-experience-in-ground-truthing-these-images-for-agriculture

-S


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Re: [Mlt-devel] NDVI processing

2014-07-24 Thread Brian Matherly
Hi Stefan,


 I finally got the filters and had time to mod a camera. Copying the
 ndvi.so into my system's freior-1 libdir worked and I can access all
 parameters (?) in KDEnLive which makes testing much easier :). Or do I
 see all parameters? Screenshot is attached.

Never mind - I found the plugin doc and created an XML file for KDEnLive
(attached). With that it works great :).

In the screenshot you sent, I noticed that the Color Map parameter was not 
exposed by KDENLIVE. With the XML file, does KDENLIVE allow you to change the 
color map? Any suggestions on other color maps that should be added or what 
should be default?




 A few ideas from first impression:
 A channel chooser (choose the source channel for NIR and VIS from R, G
 or B) would be useful (as written before) for people who use
 non-infrablue filters.
 
 I don't know how easy that would be to implement, but a legend/colorbar
 on the side which shows the actual used palette and the mapped NDVI
 values would probably also be useful.

 From the feedback on my first blog post on DIYD, it seems that there is
 an alternative formula used sometimes with footage from
 drones, which
 would simply be NIR-VIS. Integration of this formula and a selector to
 choose would probably be useful as well :).

The channel chooser and formula selection shouldn't be too hard to add. The 
legend might be a little tricky. Frei0r doesn't provide a good way to render 
text. So I would have to add a dependency on some other library like pango or 
Qt.

I'll see if I can have a look at adding those things next week.

~BM
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Re: [Mlt-devel] NDVI processing

2014-07-24 Thread Stefan Gofferje
Hi,

On 07/24/2014 03:54 PM, Brian Matherly wrote:
 In the screenshot you sent, I noticed that the Color Map parameter was
 not exposed by KDENLIVE. With the XML file, does KDENLIVE allow you to
 change the color map? Any suggestions on other color maps that should be
 added or what should be default?

Yup, with the XML file things work perfectly! I'm testing the hell out
of it at the moment. :D With my new video PC that actually is fun :).
All works realtime...

As for the color maps, at first glance, I think rainbow or heat should
be default. But I'm going to make a nice video which will show the
current status and post it to DIYD. I guess, there will be some feedback
coming then.

 The channel chooser and formula selection shouldn't be too hard to add.
 The legend might be a little tricky. Frei0r doesn't provide a good way
 to render text. So I would have to add a dependency on some other
 library like pango or Qt.

How about Cairo? There already are some frei0r effects depending on
Cairo, so chances are good that package managers install Cairo as
dependency with frei0r anyway.

-S

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Re: [Mlt-devel] NDVI processing

2014-07-19 Thread Stefan Gofferje
Just a short update. I'm still waiting for my filters. As soon as I have
them, I will take some sample footage and test.

-S


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Re: [Mlt-devel] NDVI processing

2014-06-30 Thread Stefan Gofferje
Hi,

On 06/30/2014 08:38 AM, Dan Dennedy wrote:
 Stefan, Brian reached a good working state on the NDVI plugin, and
 today I pushed it into the upstream git repos. On Tuesday July 1,
 there will be a new version of Shotcut (14.07) that will include the
 filter. The filter is not yet exposed in the Shotcut GUI, but it
 includes the repo head versions of MLT and frei0r. And it is
 cross-platform for your diverse community. So, people will have a
 fairly convenient way to run melt with the NDVI filter:
 
 Linux console: Shotcut.app/melt infrablue.mp4 -attach frei0r.ndvi 0=heat
 Windows cmd.exe: Program Files\Shotcut\melt infrablue.mp4 -attach
 frei0r.ndvi 0=heat
 OS X terminal: /Applications/Shotcut.app/Contents/MacOS/melt
 infrablue.mp4 -attach frei0r.ndvi 0=heat
 
 Parameter docs here:
 http://www.mltframework.org/bin/view/MLT/FilterFrei0r-ndvi
 
 Want to do something with the result? Add -consumer xml:ndvi.mlt to
 the above command line and then open the .mlt file with Shotcut. You
 can give the .mlt file any name you want; it is a MLT XML file.

Great, I'll have a look at it as soon as I can and got my filters! I'm
still mostly working with KDEnLive but I'm testing shortcut every time a
new release comes out :).

If I may, I would like to suggest 2 additional parameters which would
select the channels for NIR and VIS (red, green, blue). That would make
the filter also compatible with red filters as used for e.g. the Moebius
camera (they have NIR in the blue channel and VIS in the red channel)
and various others.

-S


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Re: [Mlt-devel] NDVI processing

2014-06-30 Thread Brian Matherly
 If I may, I would like to suggest 2 additional parameters which would
 select the channels for NIR and VIS (red, green, blue). That would make
 the filter also compatible with red filters as used for e.g. the Moebius
 camera (they have NIR in the blue channel and VIS in the red channel)
 and various others.

Seems easy enough. I think I might wait until after you have tried it 
out - in case any other ideas come up while you are using it.

~Brian

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Re: [Mlt-devel] NDVI processing

2014-06-29 Thread Dan Dennedy
On Thu, Jun 19, 2014 at 2:45 AM, Stefan Gofferje
li...@home.gofferje.net wrote:
 On 06/19/2014 07:47 AM, Brian Matherly wrote:
 That's a long time to wait. What about one of the 54000 DIY-Drones
 members? Does anyone have any footage they could share?

 http://diydrones.com/profiles/blogs/development-of-ndvi-postprocessing-plugin-for-frei0r-the-mlt


 --
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  V_/_  Heckler  Koch - the original point and click interface

Stefan, Brian reached a good working state on the NDVI plugin, and
today I pushed it into the upstream git repos. On Tuesday July 1,
there will be a new version of Shotcut (14.07) that will include the
filter. The filter is not yet exposed in the Shotcut GUI, but it
includes the repo head versions of MLT and frei0r. And it is
cross-platform for your diverse community. So, people will have a
fairly convenient way to run melt with the NDVI filter:

Linux console: Shotcut.app/melt infrablue.mp4 -attach frei0r.ndvi 0=heat
Windows cmd.exe: Program Files\Shotcut\melt infrablue.mp4 -attach
frei0r.ndvi 0=heat
OS X terminal: /Applications/Shotcut.app/Contents/MacOS/melt
infrablue.mp4 -attach frei0r.ndvi 0=heat

Parameter docs here:
http://www.mltframework.org/bin/view/MLT/FilterFrei0r-ndvi

Want to do something with the result? Add -consumer xml:ndvi.mlt to
the above command line and then open the .mlt file with Shotcut. You
can give the .mlt file any name you want; it is a MLT XML file.

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Re: [Mlt-devel] NDVI processing

2014-06-19 Thread Stefan Gofferje
On 06/19/2014 07:47 AM, Brian Matherly wrote:
 That's a long time to wait. What about one of the 54000 DIY-Drones
 members? Does anyone have any footage they could share?

I will post a request but as it's not yet possible to easily postprocess
the video, there's probably not much video yet. Publiclab is just coming
out with a modified version of the Mobius camera.

http://store.publiclab.org/collections/diy-infrared-photography/products/infragram-point-shoot-plant-cam

http://publiclab.org/notes/mathew/04-29-2014/a-wratten-25a-replacement-from-rosco

Some more on that:
http://publiclab.org/notes/cfastie/04-17-2014/mobius-and-nir

Example image:
http://publiclab.org/notes/mathew/04-30-2014/rosco-replacements-for-wratten-25a-pt-2

-S

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Re: [Mlt-devel] NDVI processing

2014-06-18 Thread Stefan Gofferje
On 06/17/2014 08:07 PM, Dan Dennedy wrote:
 Are the IR and VIS videos coming from different unsynchronized
 cameras? Do you also need functions to align the images spatially and
 temporally?

I think, that's a possibility but as far as I can tell, most
grassroots environmentalists use a single camera with some kind of
filter which puts the IR in the red channel and the visible spectrum in
the blue channel or similar. Typical is a Rosco 2007 filter.
Here are the parameters for that filter:
http://www.rosco.com/filters/SED.cfm?titleName=R2007:%20Storaro%20BlueimageName=../images/filters/roscolux/2007.jpg

But having the possibility to do that could potentially create more
precise results because the greyscale VIS footage would contain R, G and
B information as opposed to only B and a tiny bit of G when using a
single camera.

One other thing that people often do is simply remove the IR cut filter
from a lens so they get a composite of R, G, B and lots of IR. That's
fairly tricky to postprocess too. For GIMP I wrote a short tutorial on
that here:
http://stefan.gofferje.net/uav/170-ir-photos-with-the-boscam-hd19-part-1

But to my knowledge that’s rarely used for creating NDVI because the VIS
red information kinda messes with the IR - the cameras don't save the
information what is VIS red and what is IR.

I have a sheet of Rosco 2007 and a few lenses on order and I recently
made a short video about how to postprocess pure IR footage with
KDEnLive (http://stefan.gofferje.net/uav/199-video-ir-video-postprocessing).

In 2 or 3 weeks I should be able to produce some sample footage
- With Rosco 2007 filter
- IR composite (lens without IR cut)
- Pure IR (lens with IR passthrough filter)

-S

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Re: [Mlt-devel] NDVI processing

2014-06-18 Thread Brian Matherly

 Are the IR and VIS videos coming from different unsynchronized
 cameras? Do you also need functions to align the images spatially and
 temporally?

 I think, that's a possibility but as far as I can tell, most
 grassroots environmentalists use a single camera with some kind of
 filter which puts the IR in the red channel and the visible spectrum in
 the blue channel or similar. Typical is a Rosco 2007 filter.
 Here are the parameters for that filter:
 http://www.rosco.com/filters/SED.cfm?titleName=R2007:%20Storaro%20BlueimageName=../images/filters/roscolux/2007.jpg

 But having the possibility to do that could potentially create more
 precise results because the greyscale VIS footage would contain R, G and
 B information as opposed to only B and a tiny bit of G when using a
 single camera.

As long as image alignment isn't needed, I think that Frei0r would be a 
good place to add the feature.

Dan, what is your opinion of Frei0r? With only two commits in over a 
year, will there ever be another Frei0r release?

Stefan, can you provide some sample IR footage with the IR in the red 
and VIS in the blue channel like you described above?

~Brian

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Re: [Mlt-devel] NDVI processing

2014-06-18 Thread Stefan Gofferje
On 06/18/2014 03:51 PM, Brian Matherly wrote:
 Stefan, can you provide some sample IR footage with the IR in the red
 and VIS in the blue channel like you described above?

Yup, in 2 or 3 weeks. I'm waiting for the filter sheet and some lenses
to arrive.

-S


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Re: [Mlt-devel] NDVI processing

2014-06-18 Thread Dan Dennedy
On Wed, Jun 18, 2014 at 5:51 AM, Brian Matherly pez4br...@yahoo.com wrote:

 As long as image alignment isn't needed, I think that Frei0r would be a good
 place to add the feature.

 Dan, what is your opinion of Frei0r? With only two commits in over a year,
 will there ever be another Frei0r release?

frei0r is fine based on the description. I do not think the commit
level should be a criteria. There will be another release if it makes
sense. In the meantime, Shotcut users can benefit immediately as well
as people using the melt or kdenlive build scripts.

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Re: [Mlt-devel] NDVI processing

2014-06-18 Thread Brian Matherly
 Stefan, can you provide some sample IR footage with the IR in the red
 and VIS in the blue channel like you described above?

 Yup, in 2 or 3 weeks. I'm waiting for the filter sheet and some lenses
 to arrive.

That's a long time to wait. What about one of the 54000 DIY-Drones 
members? Does anyone have any footage they could share?

I put together a proof of concept using frei0r:
https://github.com/pez4brian/frei0r/commit/7c0704a1d5f4a418b17f6f2ead11067e7a0680f7

Since I don't have any example video files, I used an example image I 
found here:
http://infrapix.pvos.org/

The melt command is:
melt river.jpg -attach frei0r.ndvi

The output is a grayscale image with NDVI mapped to values between 0 and 
255. I can add the frei0r heat filter and get colors that are very 
similar to the image generated by the infrapix site.

The melt command to include the heat map is:
melt river.jpg -attach frei0r.ndvi -attach frei0r.colortap 0=heat

I think that we will eventually want the false color mapping to be done 
in the ndvi filter (rather than being applied by a downstream filter) 
because the output grayscale image will only have 256 possible values 
that can be mapped to colors. But there are 65536 (256x256) possible 
NDVI values. So some resolution will be lost when mapping from grayscale.

Also, if you search around, I see different color mappings being used...

Earth tones:
http://earthobservatory.nasa.gov/Features/MeasuringVegetation/Images/global_ndvi_19990921.jpg

Green represents vegetation:
http://en.wikipedia.org/wiki/File:NDVI_062003.png

Red represents vegetation:
http://i.publiclab.org/system/images/photos/000/002/682/original/IMG_0093a_NDVI_Color_2Cam.jpg

There is a free app out there called Fiji that processes infrablue images:
http://event38.wikispaces.com/NDVI+Processing+in+Fiji

It includes a host of configuration options including the ability to 
scale the NIR channel and configure a custom color mapping. It would be 
worth considering if any of those configuration options should be added 
to the filter.

~BM



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Re: [Mlt-devel] NDVI processing

2014-06-17 Thread Dan Dennedy
On Mon, Jun 16, 2014 at 10:41 AM, Stefan Gofferje
li...@home.gofferje.net wrote:
 Hi,

 On 06/16/2014 07:47 PM, Brian Matherly wrote:
 NDVI = (IR - VIS) / (IR + VIS)

 What is the equation for VIS? VIS = (G + B) / 2 ?

 No, usually the infrablue filters don't let any green pass, so in this
 case, VIS would be the blue channel and IR the red channel.

 Are negative NDVI values rounded to zero?

 No, they appear. I would have to read up on the details, but I believe
 that the result is treated as signed byte, i.e. the center of the
 greyscale equals NDVI value of 0, Maximal brightness 1 and minimal
 brightness -1.

 I'm not so good at explaining but maybe this GIMP tutorial can shed some
 light on that :).
 http://publiclab.org/notes/warren/10-27-2011/video-tutorial-creating-false-color-ndvi-aerial-wetlands-imagery

Are the IR and VIS videos coming from different unsynchronized
cameras? Do you also need functions to align the images spatially and
temporally?


 I've noticed that some people prefer a mapping that colors vegetation
 green.

 But that wouldn't be a standardized NDVI image then :).

 I doubt the frei0r heat map will do that. If someone goes through
 the trouble of making a filter for NDVI, it probably wouldn't be that
 hard to make a custom color map while they are at it.

 That is way beyond my coding skills, so I can't comment on that. But of
 course, I would assume that the possibility to change some settings
 would be useful.

 Would anybody be interested in implementing it?

 I don't personally have any interest, but I could always be persuaded :)

 Well, considering the current boom in personal environmentalism (see
 publiclab.org), the citizen drone movements (see diydrones.com), and the
 combination of both (see conservationdrones.org) you would not only be
 my personal hero but also the hero of at least half of the 54000
 DIY-Drones members (I would of course write a post about that there :) )
 plus Linux (KDEnLive, Shortcut, etc.) would be the first platform which
 can create NDVI videos in a single rather simple step by just applying
 one filter in an editor :).

 -S

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Re: [Mlt-devel] NDVI processing

2014-06-16 Thread Brian Matherly
 I'm using modified cameras from multicopter platforms and would like to
 create NDVI false color footage. Generally, I'm using KDEnLive but I'm
 also having an eye on Shortcut.

 NDVI imagery is usually created with a camera which has no IR cut filter
 but an infrablue filter (e.g. Rosco 2007). The resulting footage has
 visible light in the blue channel and IR in the red channel.

 You then take each channel, convert it to greyscale and create the NDVI
 image according to this math:

 NDVI = (IR - VIS) / (IR + VIS)

What is the equation for VIS? VIS = (G + B) / 2 ?

Are negative NDVI values rounded to zero?

 The resulting greyscale image is then usually luma-mapped to a gradient.
 The luma-mapping is already available in the frei0r package (Color
 Effect/heat).

I've noticed that some people prefer a mapping that colors vegetation 
green. I doubt the frei0r heat map will do that. If someone goes through 
the trouble of making a filter for NDVI, it probably wouldn't be that 
hard to make a custom color map while they are at it.

 Would MLT be the right point to have this math processing?

Either MLT or Frei0r. The advantage of Frei0r is that the filter could 
be available in applications that don't use MLT (libav, etc). The 
disadvantage of Frei0r is that there doesn't seem to be much active 
development on it anymore. Maybe it has every filter anyone could ever 
want and doesn't have any bugs. Or maybe people have lost interest. I'm 
not sure how to tell.

 Would anybody be interested in implementing it?

I don't personally have any interest, but I could always be persuaded :)

 NDVI imagery is a great tool for vegetation health assessment and since
 it's nowadays very easy to hack all kinds of cameras to produce
 infrablue imagery, it's quickly gaining popularity in the grass-roots
 environmentalist scene.

~BM

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Re: [Mlt-devel] NDVI processing

2014-06-16 Thread Stefan Gofferje
Hi,

On 06/16/2014 07:47 PM, Brian Matherly wrote:
 NDVI = (IR - VIS) / (IR + VIS)
 
 What is the equation for VIS? VIS = (G + B) / 2 ?

No, usually the infrablue filters don't let any green pass, so in this
case, VIS would be the blue channel and IR the red channel.

 Are negative NDVI values rounded to zero?

No, they appear. I would have to read up on the details, but I believe
that the result is treated as signed byte, i.e. the center of the
greyscale equals NDVI value of 0, Maximal brightness 1 and minimal
brightness -1.

I'm not so good at explaining but maybe this GIMP tutorial can shed some
light on that :).
http://publiclab.org/notes/warren/10-27-2011/video-tutorial-creating-false-color-ndvi-aerial-wetlands-imagery

 I've noticed that some people prefer a mapping that colors vegetation
 green.

But that wouldn't be a standardized NDVI image then :).

 I doubt the frei0r heat map will do that. If someone goes through
 the trouble of making a filter for NDVI, it probably wouldn't be that
 hard to make a custom color map while they are at it.

That is way beyond my coding skills, so I can't comment on that. But of
course, I would assume that the possibility to change some settings
would be useful.

 Would anybody be interested in implementing it?
 
 I don't personally have any interest, but I could always be persuaded :)

Well, considering the current boom in personal environmentalism (see
publiclab.org), the citizen drone movements (see diydrones.com), and the
combination of both (see conservationdrones.org) you would not only be
my personal hero but also the hero of at least half of the 54000
DIY-Drones members (I would of course write a post about that there :) )
plus Linux (KDEnLive, Shortcut, etc.) would be the first platform which
can create NDVI videos in a single rather simple step by just applying
one filter in an editor :).

-S

-- 
 (o_   Stefan Gofferje| SCLT, MCP, CCSA
 //\   Reg'd Linux User #247167   | VCP #2263
 V_/_  Heckler  Koch - the original point and click interface




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