Open Wildland Fire Modeling E community - Recent changes [en]

How to visualize WRF-Fire output in VAPOR

2010-09-07T06:52:59Z

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	* If you are provided a "Vapor saved session file" *.vss click "File" in the top menu bar and load this file by "Open session" dialogue. In either case, click "Data" in the top menu bar, then "load dataset in the current session", and navigate to the file.vdf (you might have just created). In the black right panel, you should see an empty wireframe box.		* If you are provided a "Vapor saved session file" *.vss click "File" in the top menu bar and load this file by "Open session" dialogue. In either case, click "Data" in the top menu bar, then "load dataset in the current session", and navigate to the file.vdf (you might have just created). In the black right panel, you should see an empty wireframe box.
	* To label the axes with coordinate values click "Edit" in the top main menu, then "Edit Visualizer Features" and check "Show X, Y, Z (R,G,B) Arrows". You can also add "Enable axis annotation", "Time annotation", etc. In case you do not have a terrain image and you will not be able to acquire one using the steps described below, you might check "Display Terrain Surface" and pick (a constant) "Color" you like. If you have an image, do not import it here, but use the "Image tab" discussed below.		* To label the axes with coordinate values click "Edit" in the top main menu, then "Edit Visualizer Features" and check "Show X, Y, Z (R,G,B) Arrows". You can also add "Enable axis annotation", "Time annotation", etc. In case you do not have a terrain image and you will not be able to acquire one using the steps described below, you might check "Display Terrain Surface" and pick (a constant) "Color" you like. If you have an image, do not import it here, but use the "Image tab" discussed below.
-	* If you do not have an image of the terrain, but your wrfout file contains the geo-coordinates of the domain you can acquire the image from the internet. If you already have an image or you don't know the coordinates then skip this step...	+	* If you do not have an image of the terrain, but your wrfout file contains the geo-coordinates of the domain you can acquire the image from the internet. If you already have an image or you don't know the coordinates then skip this step. We will use Vapor's bash-shell script [http://www.vapor.ucar.edu/docs/reference/index.php?id=man/getWMSImage getWMSImage.sh] for retrieving maps and imagery from a Web Mapping Server (WMS). The call of the script has a general form
		+	getWMSImage.sh [options] minLon minLat maxLon maxLat
		+	where we will use the following options to specify: map type -m landsat (the other option to consider is BMNG, but it seems to give worse quality images), the output file -o filename.tiff and the pixel resolution -r xres yres (the default is 1024x768). Assuming that minLon minLat maxLon maxLat are given as -95.03 29.3 -95.01 29.4, an example call of getWMSImage.sh can be
		+	getWMSImage.sh -m landsat -o fireflux_terrain_geo.tiff -r 1180 1580 -95.03 29.3 -95.01 29.4
		+	Such an image will be automatically geo-referenced, i.e. it will include the longitude/latitude information.
		+	If you have a tiff image which is not geo-referenced, e.g., an image obtained from the Google Earth screenshot, you can use [http://www.vapor.ucar.edu/docs/reference/index.php?id=man/tiff2geotiff tiff2geotiff] to convert it to a geo-referenced terrain image as
		+	tiff2geotiff -4 "+proj=longlat" -n "-95.03 29.3 -95.01 29.4" fireflux_terrain.tiff fireflux_terrain_geo.tiff
	* If you have a tiff image of the terrain click on the "Image" tab. In VAPOR 1.5.0 you are allowed to use only tiff images without any compression. If your image is a tiff but not a geotiff (or you are not sure) uncheck "Georeference", then "Select Image File" and navigate to your file. Finally check "Apply image to terrain" and "Instance: 1". After the image is displayed you may also check "Crop to bounds" if needed.		* If you have a tiff image of the terrain click on the "Image" tab. In VAPOR 1.5.0 you are allowed to use only tiff images without any compression. If your image is a tiff but not a geotiff (or you are not sure) uncheck "Georeference", then "Select Image File" and navigate to your file. Finally check "Apply image to terrain" and "Instance: 1". After the image is displayed you may also check "Crop to bounds" if needed.
	* Click the "Animation" tab and move the "Frame position" slider to a time when you know that the fire has already well developed.		* Click the "Animation" tab and move the "Frame position" slider to a time when you know that the fire has already well developed.

Data sources

2010-09-07T03:31:50Z

Fire Perimeters:

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	* Geospatial Multi-Agency Coordination (GEOMAC) http://www.geomac.gov/		* Geospatial Multi-Agency Coordination (GEOMAC) http://www.geomac.gov/
		+	* Firemapper http://firemapper.sc.egov.usda.gov/activefiremaps.php

	==Fire Location and Intensity Data==		==Fire Location and Intensity Data==

How to visualize WRF-Fire output in VAPOR

2010-09-07T02:22:56Z

← Older revision		Revision as of 02:22, 7 September 2010
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	==More advanced visualization==		==More advanced visualization==

-	* Optional: If you plan to work with large files (over 2GB), [[How to run WRF-Fire\|recompile NetCDF]] as~~: first~~ export WRFIO_NCD_LARGE_FILE_SUPPORT=1 and then run	+	* Optional: If you plan to work with large files (over 2GB), [[How to run WRF-Fire\|recompile NetCDF]] in bash as
-	./configure --disable-netcdf4 --disable-dap --enable-large-file-tests --prefix=the contents of your NETCDF variable	+	export WRFIO_NCD_LARGE_FILE_SUPPORT=1
-	~~Note~~ the "--enable-large-file-tests" switch ~~and remeber that~~ nco ~~should also reflect this~~. On a Mac ~~install nco~~ simply as	+	and then run in your netcdf directory
-	sudo port ~~update~~ nco	+	./configure --disable-netcdf4 --disable-dap --enable-large-file-tests --prefix=the contents of your NETCDF variable
-	* If the wrfout file contains all WRF variables, we need to select the desired variables: U,V,W for wind streamlines, GRNHFX for fire, QVAPOR for smoke and AVG_FUEL_FRAC for the burned area.	+	make
		+	make install
		+	make check
		+	The last command will create, manipulate and delete some large files, so expect that it will take some time to finish (note the "--enable-large-file-tests" switch). If you do not have [http://nco.sourceforge.net/ nco] for command-line manipulation with large files, install it on a Mac simply as
		+	sudo port install nco
		+	and see its [http://nco.sourceforge.net/nco.html user's guide] if you wish. It should not be necessary (I believe) to reinstall WRF-fire.
		+	* If the wrfout file contains all WRF variables, which is way more than we need at this point, it is convenient to select only the desired variables: U,V,W for wind streamlines, GRNHFX for fire, QVAPOR for smoke and AVG_FUEL_FRAC for the burned area.

-	The selection of variables ~~(if wrfout contains more variables than needed)~~ can be done in two ways:	+	The selection of variables can be done in two ways:
-	* create new NetCDF file with this variables by ("-O" switch overrides the file and if ~~Times~~ is not available, ~~do not use~~ it)	+	* create new NetCDF file with this variables by ("-O" switch overrides the file and if some variable is not available, simply skip it)
	ncks -v U,V,W,QVAPOR,GRNHFX,AVG_FUEL_FRAC,PH,PHB,Times wrfout -O file		ncks -v U,V,W,QVAPOR,GRNHFX,AVG_FUEL_FRAC,PH,PHB,Times wrfout -O file
	wrfvdfcreate file file.vdf		wrfvdfcreate file file.vdf
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	* Start VAPOR by clicking on its icon or vaporgui from the command line.		* Start VAPOR by clicking on its icon or vaporgui from the command line.
	* If you are provided a "Vapor saved session file" *.vss click "File" in the top menu bar and load this file by "Open session" dialogue. In either case, click "Data" in the top menu bar, then "load dataset in the current session", and navigate to the file.vdf (you might have just created). In the black right panel, you should see an empty wireframe box.		* If you are provided a "Vapor saved session file" *.vss click "File" in the top menu bar and load this file by "Open session" dialogue. In either case, click "Data" in the top menu bar, then "load dataset in the current session", and navigate to the file.vdf (you might have just created). In the black right panel, you should see an empty wireframe box.
-	* If you have a tiff image of the terrain click on the "Image" tab. If ~~the the Image~~ is not a geotiff (or you are not sure) uncheck "Georeference", then "Select Image File" and navigate to your file. Finally check "Apply image to terrain" and "Instance: 1". After the image is displayed you may also check "Crop to bounds" if needed.	+	* To label the axes with coordinate values click "Edit" in the top main menu, then "Edit Visualizer Features" and check "Show X, Y, Z (R,G,B) Arrows". You can also add "Enable axis annotation", "Time annotation", etc. In case you do not have a terrain image and you will not be able to acquire one using the steps described below, you might check "Display Terrain Surface" and pick (a constant) "Color" you like. If you have an image, do not import it here, but use the "Image tab" discussed below.
		+	* If you do not have an image of the terrain, but your wrfout file contains the geo-coordinates of the domain you can acquire the image from the internet. If you already have an image or you don't know the coordinates then skip this step...
		+	* If you have a tiff image of the terrain click on the "Image" tab. In VAPOR 1.5.0 you are allowed to use only tiff images without any compression. If your image is a tiff but not a geotiff (or you are not sure) uncheck "Georeference", then "Select Image File" and navigate to your file. Finally check "Apply image to terrain" and "Instance: 1". After the image is displayed you may also check "Crop to bounds" if needed.
	* Click the "Animation" tab and move the "Frame position" slider to a time when you know that the fire has already well developed.		* Click the "Animation" tab and move the "Frame position" slider to a time when you know that the fire has already well developed.
	* Click the "2D" tab, select variable GRNHFX, check "Refinement" 2, and "Apply color and opacity to terrain surface", If you do not have *.vtf file, set at the bottom of the tab the colormap and opacity as, e.g., in the following picture (the opacity is sharply cut off near zeros values and set full elsewhere, so that the areas not on fire are fully transparent):		* Click the "2D" tab, select variable GRNHFX, check "Refinement" 2, and "Apply color and opacity to terrain surface", If you do not have *.vtf file, set at the bottom of the tab the colormap and opacity as, e.g., in the following picture (the opacity is sharply cut off near zeros values and set full elsewhere, so that the areas not on fire are fully transparent):

Data sources

2010-09-06T19:38:55Z

Fire Ignition Time and Location Data:

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	* Custom		* Custom
		+
		+	==Fire Perimeters==
		+
		+	* Geospatial Multi-Agency Coordination (GEOMAC) http://www.geomac.gov/

	==Fire Location and Intensity Data==		==Fire Location and Intensity Data==

Data repository

2010-09-06T13:08:38Z

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-	The wiki does not take big files and certain types of files kindly, and [[wikipedia:Git (software)\|git]] does not take big files well either, so we do not allow large files in our git repositories ~~either~~. Thus, it is necessary to store some data files elsewhere, and we have set up a CVS data repository for this purpose.	+	The wiki does not take big files and certain types of files kindly, and [[wikipedia:Git (software)\|git]] does not take big files well either, so we do not allow large files in our git repositories. Thus, it is necessary to store some data files elsewhere, and we have set up a CVS data repository for this purpose.

	==Accessing the repository==		==Accessing the repository==
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	* Get account on '''math.ucdenver.edu''' in group '''mandel''' and login by ssh at least once (you should change your password anyway).		* Get account on '''math.ucdenver.edu''' in group '''mandel''' and login by ssh at least once (you should change your password anyway).
	* Install '''cvs''' on your machine		* Install '''cvs''' on your machine
-	* In bash, type '''~~setenv~~ CVSROOT=username@math.ucdenver.edu:/home/faculty/jmandel/cvsroot'''	+	* In bash, type '''export CVSROOT=username@math.ucdenver.edu:/home/faculty/jmandel/cvsroot'''
	* Type: '''cvs checkout openwfm_data'''		* Type: '''cvs checkout openwfm_data'''
	* Type: '''cd openwfm_data'''		* Type: '''cd openwfm_data'''

-	You can then use all [[Wikipedia:Concurrent Versions System\|CVS]] commands to ~~edit~~ or replace files.	+	You can then use all [[Wikipedia:Concurrent Versions System\|CVS]] commands to add or replace files.

	==The web image of the repository and linking==		==The web image of the repository and linking==

Template talk:Data

2010-09-06T03:41:17Z

Redirected page to Data repository

New page

#redirect[[Data repository]]

Data repository

2010-09-06T03:34:59Z

lead

New page

The wiki does not take big files and certain types of files kindly, and [[wikipedia:Git (software)|git]] does not take big files well either, so we do not allow large files in our git repositories either. Thus, it is necessary to store some data files elsewhere, and we have set up a CVS data repository for this purpose.

==Accessing the repository==

* Get account on '''math.ucdenver.edu''' in group '''mandel''' and login by ssh at least once (you should change your password anyway).
* Install '''cvs''' on your machine
* In bash, type '''setenv CVSROOT=username@math.ucdenver.edu:/home/faculty/jmandel/cvsroot'''
* Type: '''cvs checkout openwfm_data'''
* Type: '''cd openwfm_data'''

You can then use all [[Wikipedia:Concurrent Versions System|CVS]] commands to edit or replace files.

==The web image of the repository and linking==
The repository is exported to the web hourly. Wikicode like this

: <code><nowiki>{{data|test|link to CVS data repository}}</nowiki></code>

will make a {{data|test|link to the data repository}}. Please use the '''data''' template as above and do not link by giving a URL directly, because the location of the web image may change.

[[Category:Data]]

Software & Data

2010-09-06T03:14:51Z

added data repository

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	* [[List of software]]		* [[List of software]]
	* [[List of data]]		* [[List of data]]
		+	* [[Data repository]]

User:Jmandel

2010-09-06T03:13:16Z

← Older revision		Revision as of 03:13, 6 September 2010
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	* [[User:Jmandel/WRF-Fire to VAPOR conversion]]		* [[User:Jmandel/WRF-Fire to VAPOR conversion]]
		+
		+	==Test==
		+
		+	{{data\|test\|test link to CVS data repository}}

Template:Data

2010-09-06T03:11:00Z

Created page with '[http://math.ucdenver.edu/~jmandel/openwfm_data/{{{1}}} {{{2}}}]'

New page

[http://math.ucdenver.edu/~jmandel/openwfm_data/{{{1}}} {{{2}}}]

WRF-Fire development notes

2010-09-05T17:54:38Z

External links: blog

← Older revision		Revision as of 17:54, 5 September 2010
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	* {{ccm\|Data_assimilation_seminar_to_do_list\|Data assimilation seminar to do list}}		* {{ccm\|Data_assimilation_seminar_to_do_list\|Data assimilation seminar to do list}}
		+	* {{ccm\|Jan_Mandel/Blog\|Jan Mandel's blog}}
	* [http://repo.or.cz/git-browser/by-commit.html?r=wrffire.git Commit graph]		* [http://repo.or.cz/git-browser/by-commit.html?r=wrffire.git Commit graph]
	* [http://www.mmm.ucar.edu/wrf/WG2/WRF_conventions.html WRF Coding Conventions]		* [http://www.mmm.ucar.edu/wrf/WG2/WRF_conventions.html WRF Coding Conventions]

File:Fireflux-domain-scaled.png

2010-09-05T05:37:00Z

uploaded "[[File:Fireflux-domain-scaled.png]]" Surface for visualization. From Google Earth, fair use.

New page

Conferences

2010-09-04T20:41:11Z

2011:

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	** August 12, 2010 – December 31, 2010: Abstract and Full Paper submission		** August 12, 2010 – December 31, 2010: Abstract and Full Paper submission
	** Proceedings: [http://www.springer.com/computer/lncs?SGWID=0-164-0-0-0 Lecture Notes in Computer Science (Springer)]		** Proceedings: [http://www.springer.com/computer/lncs?SGWID=0-164-0-0-0 Lecture Notes in Computer Science (Springer)]
-	* [http://www.iccs-meeting.org/ ICCS 2011], ~~usually late May/early~~ June	+	* [http://www.iccs-meeting.org/iccs2011/ ICCS 2011], University of Tsukuba, Japan, June 1 - June 3, 2011
-	** ~~Minisymposium paper deadline usually in~~ January	+	** Workshop proposals October 15, 2010
		+	** Full papers January 8, 2011
	** Proceedings: [http://www.elsevier.com/wps/find/journaldescription.cws_home/719435/description#description Procedia Computer Science (Elsevier)], open access		** Proceedings: [http://www.elsevier.com/wps/find/journaldescription.cws_home/719435/description#description Procedia Computer Science (Elsevier)], open access
	* [http://www.wildfire2011.org/ 5th International Wildland Fire conference], 9-13 May, 2011 Sun City, North West Province, South Africa.		* [http://www.wildfire2011.org/ 5th International Wildland Fire conference], 9-13 May, 2011 Sun City, North West Province, South Africa.

How to visualize WRF-Fire output in VAPOR

2010-09-03T07:02:40Z

← Older revision		Revision as of 07:02, 3 September 2010
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	* If you have a tiff image of the terrain click on the "Image" tab. If the the Image is not a geotiff (or you are not sure) uncheck "Georeference", then "Select Image File" and navigate to your file. Finally check "Apply image to terrain" and "Instance: 1". After the image is displayed you may also check "Crop to bounds" if needed.		* If you have a tiff image of the terrain click on the "Image" tab. If the the Image is not a geotiff (or you are not sure) uncheck "Georeference", then "Select Image File" and navigate to your file. Finally check "Apply image to terrain" and "Instance: 1". After the image is displayed you may also check "Crop to bounds" if needed.
	* Click the "Animation" tab and move the "Frame position" slider to a time when you know that the fire has already well developed.		* Click the "Animation" tab and move the "Frame position" slider to a time when you know that the fire has already well developed.
-	* Click the "2D" tab, select variable GRNHFX, check "Refinement" 2, and "Apply color and opacity to terrain surface", At the bottom of the tab ~~set~~ the colormap and opacity as, e.g., in the following picture (the opacity is sharply cut off near zeros values and set full elsewhere, so that the areas not on fire are fully transparent):	+	* Click the "2D" tab, select variable GRNHFX, check "Refinement" 2, and "Apply color and opacity to terrain surface", If you do not have *.vtf file, set at the bottom of the tab the colormap and opacity as, e.g., in the following picture (the opacity is sharply cut off near zeros values and set full elsewhere, so that the areas not on fire are fully transparent):
	[[File:Vapor-fire-colormap-window.png\|600px]]		[[File:Vapor-fire-colormap-window.png\|600px]]

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	One might also like to make sure that the z-coordinate for AVG_FUEL_FRAC is a bit below the GRNHFX z-coordinate and a bit above the z-coordinate for the terrain image.		One might also like to make sure that the z-coordinate for AVG_FUEL_FRAC is a bit below the GRNHFX z-coordinate and a bit above the z-coordinate for the terrain image.
	Note that the AVG_FUEL_FRAC variable might not be convenient if there are areas that do not contain any fuel a-priori.		Note that the AVG_FUEL_FRAC variable might not be convenient if there are areas that do not contain any fuel a-priori.
-	* Click the "Flow" tab, make sure that the "steady field" variables are U, V, W and select "Refinement" 2. Scroll down to "Flow Seeding Parameters", select "Nonrandom Rake" and "seed count ... By dimension" to ,e.g., 3, 3, 1. In the "Shape parameters" area set "shape" to arrows, decrease "Diameter" to e.g., 0.5 and in "Color/Opacity mapping" area set "Color" to "Position along flow". Check the box "Instance: 1". If there is a warning about flow lines below zero click "OK", but follow the instructions: in "Edit" top menu select "Edit Visualizer Features" and in the "Variable values outside grid" uncheck for U,V and W the "Extend, down" box so that the "Below" appears in white with 0 value in the box. Hit "Apply" and "OK". One might also like to position the flow streamlines in the vertical direction. This can be done in two ways: either by sliding the "Rake center/sizes" slides in the "Flow Seeding Parameters" portion of the tab, or by clicking the "Region Select Mode" which is the second icon (the box) from the left under the top menu bar. This will display a box with handles in the visualizer window (see the image below) which can be resized by clicking and dragging with the right-button on the mouse. After the region is set, click the"Navigation Mode" icon which is the very left one under the top menu bar.	+	* Click the "Flow" tab, make sure that the "steady field" variables are U, V, W and select "Refinement" 2. Scroll down to "Flow Seeding Parameters", select "Nonrandom Rake" and "seed count ... By dimension" to ,e.g., 3, 3, 1. In the "Shape parameters" area set "shape" to arrows, decrease "Diameter" to e.g., 0.5 and in "Color/Opacity mapping" area set "Color" to "Position along flow". Check the box "Instance: 1". If there is a warning about flow lines below zero click "OK", but follow the instructions: in "Edit" top menu select "Edit Visualizer Features" and in the "Variable values outside grid" uncheck for U,V and W the "Extend, down" box so that the "Below" appears in white with 0 value in the box. Hit "Apply" and "OK". One might also like to position the flow streamlines in the vertical direction. This can be done in two ways: either by sliding the "Rake center/sizes" slides in the "Flow Seeding Parameters" portion of the tab, or by clicking the "Region Select Mode" which is the second icon (the box) from the left under the top menu bar. This will display a box with handles in the visualizer window (see the image below) which can be resized by clicking and dragging with the right-button on the mouse. After the region is set, click the"Navigation Mode" icon (the rudder) which is the very left one under the top menu bar.
		+	* Click on the DVR (Direct Volume Rendering) tab and select the QVAPOR variable, which is used to visualize the smoke. This is the tricky part which can be in my opinion hardly 'automated'. One might like to decrease the vertical size of the region in a way described above because there might be a significant amount of vapor present higher in the atmosphere. An example of setting for color and opacity are illustrated by the following picture:
		+	[[File:Vapor-qvapor-window.png\|600px]]

		+	Note that the displayed data correspond to the lower 1/3~1/4 (approximately) of the range of values and opacity increases slightly with the values. "Load Installed TF" as '''grayscale.vtf''' and ev. shuffle the color control points if you want the smoke to appear more dark. Also, it might be better to leave the "Refinement" 0 not only because DVR is computationally demanding but also it might provide (surprisingly) better appearance of the fire. Also if one is still looking for the best point of view and is moving the region, it is recommended to uncheck the "Instance: 1" for the moment until the final point of view on the region is found. If the ultimate goal is a video sequence it is better to watch the full sequence using the controls in the "Animation" tab before the final decision about the (color and opacity) settings in the DVR tab for the QVAPOR variable are made.
		+	* To capture a single jpg image, click "Capture" in the top menu bar and "Capture a single image in visualizer 0" and follow the instructions.
		+	* To capture a sequence of jpg images (to be post-processed into a video out of Vapor) click "Capture" in the top menu bar and "Begin image capture sequence in visualizer 0", select directory, then run the movie in the "Animation" tab or using the controls next to the top menu bar, when done click again "Capture" followed by "End image capture sequence". You get the movie frames as a sequence of jpg files. The sequence of images can be processed into an avi in Virtual Dub under windows or using
		+	ffmpeg -f image2 -r 1 -i fireflux_small_%04d.jpg -r 25 -s 512x512 movie.avi
		+
		+	under linux/Mac. The first '-r 1' means the frame rate of the input, so 1 means each picture is displayed for 1 second, 10 means 1/10 of a second, and so on. Use this to adjust the speed of playback. The '-s 512x512' means the resolution of the output in pixels (width x height). While ffmpeg will let you put any numbers here, you should make sure that the width and height are both divisible by 16 otherwise some movie players will not be able to play it.
		+
		+	It looks for input images starting at fireflux_small_0001.jpg and continues until a file doesn't exist. This means if the output starts at 0000, then the first frame will not be in the movie. I don't believe there is a way to configure this aspect of ffmpeg.
		+
		+	This command will create the movie and compress it using a common video codec. It will you use the highest quality setting by default, which is overboard for this kind of movie. So if the files still end up larger than we want, we can always add a couple of more flags to limit the bitrate of the output.
		+
		+	* Use other VAPOR features for a more advanced visualization as desired.
		+
		+
	==Works with==		==Works with==
	* WRF-Fire {{WRF-Fire-commit\|1e710fc81479ea71ed74dd9903da9917fc9dcd93\|May 26 2010}} and hopefully later		* WRF-Fire {{WRF-Fire-commit\|1e710fc81479ea71ed74dd9903da9917fc9dcd93\|May 26 2010}} and hopefully later

File:Vapor-qvapor-window.png

2010-09-03T05:12:59Z

uploaded "[[File:Vapor-qvapor-window.png]]"

New page

How to visualize WRF-Fire output in VAPOR

2010-09-03T05:12:41Z

← Older revision		Revision as of 05:12, 3 September 2010
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	If there is a *.vtf file available for the colormap and opacity, click "Load TF" and navigate to the file. Finally, check "Instance: 1". You should see the fire area on the terrain. One might also check that the "Z-center" coordinate has a slightly higher value in the "2D" tab than in the "Image" tab, i.e., that the fire will be displayed 'on top of the terrain'.		If there is a *.vtf file available for the colormap and opacity, click "Load TF" and navigate to the file. Finally, check "Instance: 1". You should see the fire area on the terrain. One might also check that the "Z-center" coordinate has a slightly higher value in the "2D" tab than in the "Image" tab, i.e., that the fire will be displayed 'on top of the terrain'.
	* On top of the "2D" tab under "Renderer Control" click "New" push "Instance: 2" and select the AVG_FUEL_FRAC variable, check "Refinement" 2, and "Apply color and opacity to terrain surface". Scroll down to "Transfer Function Editor", click "Load Installed TF" and select '''grayscale.vtf'''. The settings for opacity are illustrated by the picture below (the opacity is high and color is dark for regions with little fuel remaining):		* On top of the "2D" tab under "Renderer Control" click "New" push "Instance: 2" and select the AVG_FUEL_FRAC variable, check "Refinement" 2, and "Apply color and opacity to terrain surface". Scroll down to "Transfer Function Editor", click "Load Installed TF" and select '''grayscale.vtf'''. The settings for opacity are illustrated by the picture below (the opacity is high and color is dark for regions with little fuel remaining):
-	Note that ~~this~~ variable might not be convenient if there are areas ~~in the region~~ that do not contain any fuel a-priori.	+	[[File:Vapor-avg_fuel_frac-window.png\|600px]]
-	* Click the "Flow" tab, make sure that the "steady field" variables are U, V, W and select "Refinement" 2. Scroll down to "Flow Seeding Parameters", select "Nonrandom Rake" and "seed count ... By dimension" to ,e.g., 3, 3, 1. In the "Shape parameters" area set "shape" to arrows, decrease "Diameter" to e.g., 0.5 and in "Color/Opacity mapping" area set "Color" to "Position along flow". Check the box "Instance: 1". If there is a warning about flow lines below zero click "OK", but follow the instructions: in "Edit" top menu select "Edit Visualizer Features" and in the "Variable values outside grid" uncheck for U,V and W the "Extend, down" box so that the "Below" appears in white with 0 value in the box. Hit "Apply" and "OK".	+
		+	One might also like to make sure that the z-coordinate for AVG_FUEL_FRAC is a bit below the GRNHFX z-coordinate and a bit above the z-coordinate for the terrain image.
		+	Note that the AVG_FUEL_FRAC variable might not be convenient if there are areas that do not contain any fuel a-priori.
		+	* Click the "Flow" tab, make sure that the "steady field" variables are U, V, W and select "Refinement" 2. Scroll down to "Flow Seeding Parameters", select "Nonrandom Rake" and "seed count ... By dimension" to ,e.g., 3, 3, 1. In the "Shape parameters" area set "shape" to arrows, decrease "Diameter" to e.g., 0.5 and in "Color/Opacity mapping" area set "Color" to "Position along flow". Check the box "Instance: 1". If there is a warning about flow lines below zero click "OK", but follow the instructions: in "Edit" top menu select "Edit Visualizer Features" and in the "Variable values outside grid" uncheck for U,V and W the "Extend, down" box so that the "Below" appears in white with 0 value in the box. Hit "Apply" and "OK". One might also like to position the flow streamlines in the vertical direction. This can be done in two ways: either by sliding the "Rake center/sizes" slides in the "Flow Seeding Parameters" portion of the tab, or by clicking the "Region Select Mode" which is the second icon (the box) from the left under the top menu bar. This will display a box with handles in the visualizer window (see the image below) which can be resized by clicking and dragging with the right-button on the mouse. After the region is set, click the"Navigation Mode" icon which is the very left one under the top menu bar.

	==Works with==		==Works with==

File:Vapor-avg fuel frac-window.png

2010-09-03T04:38:49Z

uploaded "[[File:Vapor-avg fuel frac-window.png]]"

New page

How to visualize WRF-Fire output in VAPOR

2010-09-03T04:38:28Z

← Older revision		Revision as of 04:38, 3 September 2010
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	* If you have a tiff image of the terrain click on the "Image" tab. If the the Image is not a geotiff (or you are not sure) uncheck "Georeference", then "Select Image File" and navigate to your file. Finally check "Apply image to terrain" and "Instance: 1". After the image is displayed you may also check "Crop to bounds" if needed.		* If you have a tiff image of the terrain click on the "Image" tab. If the the Image is not a geotiff (or you are not sure) uncheck "Georeference", then "Select Image File" and navigate to your file. Finally check "Apply image to terrain" and "Instance: 1". After the image is displayed you may also check "Crop to bounds" if needed.
	* Click the "Animation" tab and move the "Frame position" slider to a time when you know that the fire has already well developed.		* Click the "Animation" tab and move the "Frame position" slider to a time when you know that the fire has already well developed.
-	* Click the "2D" tab, select 2D variable GRNHFX, check "Refinement" 2, "Apply color and opacity to terrain surface", At the bottom click "Load TF" and ~~select and push~~ the ~~"Fit data" button at the bottom~~. Finally, check "Instance 1". You should see the fire on the terrain.	+	* Click the "2D" tab, select variable GRNHFX, check "Refinement" 2, and "Apply color and opacity to terrain surface", At the bottom of the tab set the colormap and opacity as, e.g., in the following picture (the opacity is sharply cut off near zeros values and set full elsewhere, so that the areas not on fire are fully transparent):
-	* Click the "Flow" tab, ~~check~~ the ~~box~~ "~~Instance~~ 1", ~~click~~ "OK" on a warning about flow lines below zero~~. Select~~ "~~Refinement~~" ~~2. You should see a picture like this (~~the ~~starting points of~~ the ~~flow lines are picked randomly~~ so ~~they are different~~ in ~~every session): i~~	+	[[File:Vapor-fire-colormap-window.png\|600px]]
		+
		+	If there is a *.vtf file available for the colormap and opacity, click "Load TF" and navigate to the file. Finally, check "Instance: 1". You should see the fire area on the terrain. One might also check that the "Z-center" coordinate has a slightly higher value in the "2D" tab than in the "Image" tab, i.e., that the fire will be displayed 'on top of the terrain'.
		+	* On top of the "2D" tab under "Renderer Control" click "New" push "Instance: 2" and select the AVG_FUEL_FRAC variable, check "Refinement" 2, and "Apply color and opacity to terrain surface". Scroll down to "Transfer Function Editor", click "Load Installed TF" and select '''grayscale.vtf'''. The settings for opacity are illustrated by the picture below (the opacity is high and color is dark for regions with little fuel remaining):
		+	Note that this variable might not be convenient if there are areas in the region that do not contain any fuel a-priori.
		+	* Click the "Flow" tab, make sure that the "steady field" variables are U, V, W and select "Refinement" 2. Scroll down to "Flow Seeding Parameters", select "Nonrandom Rake" and "seed count ... By dimension" to ,e.g., 3, 3, 1. In the "Shape parameters" area set "shape" to arrows, decrease "Diameter" to e.g., 0.5 and in "Color/Opacity mapping" area set "Color" to "Position along flow". Check the box "Instance: 1". If there is a warning about flow lines below zero click "OK", but follow the instructions: in "Edit" top menu select "Edit Visualizer Features" and in the "Variable values outside grid" uncheck for U,V and W the "Extend, down" box so that the "Below" appears in white with 0 value in the box. Hit "Apply" and "OK".

	==Works with==		==Works with==

File:Vapor-fire-colormap-window.png

2010-09-03T02:50:19Z

uploaded "[[File:Vapor-fire-colormap-window.png]]"

New page

How to visualize WRF-Fire output in VAPOR

2010-09-03T00:06:40Z

← Older revision		Revision as of 00:06, 3 September 2010
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	* To capture the movie, use "Capture", "Begin image capture sequence in visualizer 0", select directory, then run the movie, when done "Capture" "End image capture sequence". You get the movie frames as jpg files.		* To capture the movie, use "Capture", "Begin image capture sequence in visualizer 0", select directory, then run the movie, when done "Capture" "End image capture sequence". You get the movie frames as jpg files.
	* Use the DVR tab and other VAPOR features for a more advanced visualization as desired.		* Use the DVR tab and other VAPOR features for a more advanced visualization as desired.
		+
		+	==More advanced visualization==
		+
		+	* Optional: If you plan to work with large files (over 2GB), [[How to run WRF-Fire\|recompile NetCDF]] as: first export WRFIO_NCD_LARGE_FILE_SUPPORT=1 and then run
		+	./configure --disable-netcdf4 --disable-dap --enable-large-file-tests --prefix=the contents of your NETCDF variable
		+	Note the "--enable-large-file-tests" switch and remeber that nco should also reflect this. On a Mac install nco simply as
		+	sudo port update nco
		+	* If the wrfout file contains all WRF variables, we need to select the desired variables: U,V,W for wind streamlines, GRNHFX for fire, QVAPOR for smoke and AVG_FUEL_FRAC for the burned area.
		+
		+	The selection of variables (if wrfout contains more variables than needed) can be done in two ways:
		+	* create new NetCDF file with this variables by ("-O" switch overrides the file and if Times is not available, do not use it)
		+	ncks -v U,V,W,QVAPOR,GRNHFX,AVG_FUEL_FRAC,PH,PHB,Times wrfout -O file
		+	wrfvdfcreate file file.vdf
		+	wrf2vdf file.vdf file
		+	The wrfvdfcreate command creates a vdf metafile with a description of the data for Vapor and wrf2vdf created a directory file_data with the actual data.
		+	* the other option is to specify the variables in the wrfvdfcreate call, i.e., run
		+	wrfvdfcreate -vars3d U:V:W:QVAPOR -vars2d GRNHFX:AVG_FUEL_FRAC wrfout file.vdf
		+	wrf2vdf file.vdf wrfout
		+	This would create a directory wrfout_data with the same content as the directory file_data above.
		+
		+	* Start VAPOR by clicking on its icon or vaporgui from the command line.
		+	* If you are provided a "Vapor saved session file" *.vss click "File" in the top menu bar and load this file by "Open session" dialogue. In either case, click "Data" in the top menu bar, then "load dataset in the current session", and navigate to the file.vdf (you might have just created). In the black right panel, you should see an empty wireframe box.
		+	* If you have a tiff image of the terrain click on the "Image" tab. If the the Image is not a geotiff (or you are not sure) uncheck "Georeference", then "Select Image File" and navigate to your file. Finally check "Apply image to terrain" and "Instance: 1". After the image is displayed you may also check "Crop to bounds" if needed.
		+	* Click the "Animation" tab and move the "Frame position" slider to a time when you know that the fire has already well developed.
		+	* Click the "2D" tab, select 2D variable GRNHFX, check "Refinement" 2, "Apply color and opacity to terrain surface", At the bottom click "Load TF" and select and push the "Fit data" button at the bottom. Finally, check "Instance 1". You should see the fire on the terrain.
		+	* Click the "Flow" tab, check the box "Instance 1", click "OK" on a warning about flow lines below zero. Select "Refinement" 2. You should see a picture like this (the starting points of the flow lines are picked randomly so they are different in every session): i

	==Works with==		==Works with==

Talk:WRF-Fire development notes

2010-08-31T22:44:40Z

Fire spin-up:

← Older revision		Revision as of 22:44, 31 August 2010
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	== Fire spin-up ==		== Fire spin-up ==

-	We'll add level function history information into input files to run the growing fire as given by data, until the given perimeter is reached. This will allow the atmosphere to evolve along with the growing fire. Also, this will provide some support for gradual ignition. [[User:Jmandel\|Jmandel]] 05:23, 30 August 2010 (UTC)	+	We'll add level function history information into input files to run the growing fire as given by data, until the given perimeter is reached, then the fire simulation takes over. This will allow the atmosphere to evolve along with the growing fire. Also, this will provide some support for gradual ignition. [[User:Jmandel\|Jmandel]] 05:23, 30 August 2010 (UTC)