Cross-section Plots - Revision history

Robertson at 21:04, 25 June 2010

2010-06-25T21:04:41Z

← Older revision		Revision as of 21:04, 25 June 2010
Line 1:		Line 1:
	<div class="title">Cross-section Plots</div>~~__NOTOC__~~		<div class="title">Cross-section Plots</div>
	The ROMS plotting package allows you to plot cross-sections. You can also overlay a reference field.		The ROMS plotting package allows you to plot cross-sections. You can also overlay a reference field.


	<!-- Edit Template:Plot_TOC to modify this Table of Contents-->		<!-- Edit Template:Plot_TOC to modify this Table of Contents-->
	{{Plot TOC}}		<div style="float: left;margin: 0 20px 0 0;">{{Plot TOC}}</div>__TOC__

			<div style="clear: both"></div>

	==Configuration==		==Configuration==

Robertson: /* Plotting */

2008-03-07T15:51:42Z

Plotting

← Older revision		Revision as of 15:51, 7 March 2008
Line 150:		Line 150:
	<span class="red">> csec < csec_upwelling.in</span>		<span class="red">> csec < csec_upwelling.in</span>

	You will see some information about each frame scroll by. When the program finishes you will have a ~~file~~ named '''gmeta''' in the current directory. Now you can use <span class="red">idt</span> to view your plots.		You will see some information about each frame scroll by. When the program finishes you will have a '''NCAR Computer Graphics Metafile (NCGM)''' named '''gmeta''' in the current directory. Now you can use <span class="red">idt</span> to view your plots.

	<span class="red">> idt gmeta &</span>		<span class="red">> idt gmeta &</span>

Robertson at 19:22, 3 March 2008

2008-03-03T19:22:26Z

Robertson at 21:08, 15 January 2008

2008-01-15T21:08:12Z

← Older revision		Revision as of 21:08, 15 January 2008
Line 3:		Line 3:


	~~{\|class="toc"~~		<!-- Edit Template:Plot_TOC to modify this Table of Contents-->
	\|-		{{Plot TOC}}
	~~! '''~~Table of Contents~~'''~~
	\|-
	~~\| 1. '''[[Plotting Package Installation\|Installation]]'''~~
	\|-
	~~\| 2. '''[[Contour Plots]]'''~~
	\|-
	~~\| 3. '''[[Cross-section Plots]]'''~~
	\|-
	~~\| 4. '''[[Internal Plotting Parameters]]'''~~
	\|-
	~~\| 5. '''[[Plotting Options]]'''~~
	\|-
	~~\| 6. '''[[Plotting Fields]]'''~~
	\|-
	~~\| 7. '''[[Raster Scripts]]'''~~
	\|}

Robertson at 18:24, 15 January 2008

2008-01-15T18:24:06Z

← Older revision		Revision as of 18:24, 15 January 2008
Line 37:		Line 37:
	<span class="blue">2007 -1 : year and starting year-day (use yearday<0, for no time label)</span>		<span class="blue">2007 -1 : year and starting year-day (use yearday<0, for no time label)</span>

	The next four lines are the plot title. Blank lines are fine but '''there must be four lines here.''' The text that you see on lines 2-5 are only a suggestion; you can put any text you like. I am plotting ~~temperature at 100 meters from a 3/4 degree North Atlantic ROMS 3.0 simulation so my plot~~ title ~~looks like this:~~		The next four lines are the plot title. Blank lines are fine but '''there must be four lines here.''' The text that you see on lines 2-5 are only a suggestion; you can put any text you like. I will not actually be plotting the title lines but it's good to have for later reference

	<span class="blue">ROMS 3.0		<span class="blue">ROMS 3.0
	Upwelling Test Case		Upwelling Test Case
	Default Setup		Default Setup
	Temperature ~~(Celsius)~~</span>		Vertical Velocity with Temperature overlay</span>

	The plotting options begin on line six and have short descriptions of what they do. For complete documentation on the plotting options read the '''[[Plotting Options]]''' page. I will annotate the options section to explain the choices I've made.		The plotting options begin on line six and have short descriptions of what they do. For complete documentation on the plotting options read the '''[[Plotting Options]]''' page. I will annotate the options section to explain the choices I've made.
Line 132:		Line 132:
	<span class="forestGreen">~/Mydir/Palettes/natlan1.pal</span>		<span class="forestGreen">~/Mydir/Palettes/natlan1.pal</span>

	The third file sets the internal plotting parameters. We will discuss this file in detail later. An example ~~file exists in the~~ <span class="forestGreen">~~Data~~</span> directory ~~and I will use it~~.		The third file sets the internal plotting parameters. We will discuss this file in detail later. We copied the an example <span class="forestGreen">default.cnt</span> file into the current directory at the beginning of this tutorial.

	<span class="forestGreen">~~~/Mydir/Data/~~default.cnt</span>		<span class="forestGreen">default.cnt</span>

	The fourth file is your primary NetDCF file, usually model output. I will use my averages model output.		The fourth file is your primary NetDCF file, usually model output. I will use my averages model output.
Line 140:		Line 140:
	<span class="forestGreen">ocean_avg.nc</span>		<span class="forestGreen">ocean_avg.nc</span>

	The fifth file is you secondary NetCDF file, also usually model output. Some times the data you want to overlay will be in a different file. If that ~~were~~ the case ~~here I~~ would ~~have~~ set <span class="blue">IREF</span> to '''2''' put ~~then~~ name of the file my overlay data should come from here. However, my overlay data was in the primary NetCDF file so it doesn't matter what I set this to so I'll set it to be the same as my primary NetCDF file. For more information about <span class="blue">IREF</span> check the '''[[Plotting Options#IREF\|Plotting Options]]''' page.		The fifth file is you secondary NetCDF file, also usually model output. Some times the data you want to overlay will be in a different file. If that is the case you would set <span class="blue">IREF</span> to '''2''', then put the name of the file your overlay data should come from here. However, my overlay data was in the primary NetCDF file so it doesn't matter what I set this to so I'll set it to be the same as my primary NetCDF file. For more information about <span class="blue">IREF</span> check the '''[[Plotting Options#IREF\|Plotting Options]]''' page.

	<span class="forestGreen">ocean_avg.nc</span>		<span class="forestGreen">ocean_avg.nc</span>
Line 162:		Line 162:
	/home/robertson/ncl-5.0.0		/home/robertson/ncl-5.0.0

	if your shell cannot find <span class="red">csec</span> you need to add PLT_BINDIR to your path. ~~the~~ <span class="blue">NCARG_ROOT</span> environment variable should be set to the location of your [http://www.ncl.ucar.edu/ NCL] install. See the '''[[Plotting Package Installation \| Installation]]''' page for more details. If you have an existing 'gmeta' file that you want to keep you should first rename it so <span class="red">csec</span> does not replace it. To create the plots execute the following command.		if your shell cannot find <span class="red">csec</span> you need to add <span class="forestGreen">PLT_BINDIR</span> to your path. The <span class="blue">NCARG_ROOT</span> environment variable should be set to the location of your [http://www.ncl.ucar.edu/ NCL] install. See the '''[[Plotting Package Installation \| Installation]]''' page for more details. If you have an existing 'gmeta' file that you want to keep you should first rename it so <span class="red">csec</span> does not replace it. To create the plots execute the following command.

	<span class="red">> csec < csec_upwelling.in</span>		<span class="red">> csec < csec_upwelling.in</span>
Line 174:		Line 174:
	[[Image:upwelling_vvel_temp_csec.gif]]		[[Image:upwelling_vvel_temp_csec.gif]]

	Clicking the [[Image:idt_play.gif]] button repeatedly will advance to the frames of the '''gmeta''' file. The plot above is ~~actually~~ the final frame of my '''gmeta''' file. I suggest you take some time to experiment with the controls in the <span class="red">idt</span> window.		Clicking the [[Image:idt_play.gif]] button repeatedly will advance to the frames of the '''gmeta''' file. The plot above is the final frame of my '''gmeta''' file. I suggest you take some time to experiment with the controls in the <span class="red">idt</span> window.

Robertson at 18:07, 15 January 2008

2008-01-15T18:07:26Z

Robertson at 18:03, 15 January 2008

2008-01-15T18:03:18Z

Robertson: New page:
Cross-section Plots
NOTOC The ROMS plotting package allows you to plot cross-sections. You can also overlay a reference field. {|class="toc" |- ! '''Table of ...

2008-01-14T23:31:39Z

New page: <div class="title">Cross-section Plots</div>__NOTOC__ The ROMS plotting package allows you to plot cross-sections. You can also overlay a reference field. {|class="toc" |- ! '''Table of ...

New page

<div class="title">Cross-section Plots</div>__NOTOC__
The ROMS plotting package allows you to plot cross-sections. You can also overlay a reference field.

{|class="toc"
|-
! '''Table of Contents'''
|-
| 1. '''[[Plotting Package Installation|Installation]]'''
|-
| 2. '''[[Contour Plots]]'''
|-
| 3. '''[[Cross-section Plots]]'''
|-
| 4. '''[[Internal Plotting Parameters]]'''
|-
| 5. '''[[Plotting Options]]'''
|-
| 6. '''[[Plotting Fields]]'''
|-
| 7. '''[[Raster Scripts]]'''
|}

==Configuration==
There are two files that that control the output of the ROMS Plotting Package: default.cnt and the csec.in (or ccnt.in for '''[[Contour Plots]]''') file. The default.cnt file controls the internal plotting parameters while the .in file determines what data to plot and how it will appear. At first you will not need to edit the default.cnt file so we will start with the .in file.

'''NOTE:''' default.cnt and the .in file can be named anything you want. This will become clear as we continue.

We suggest that you copy csec.in and default.cnt to the directory where you wish to create your plots. If you have already copied default.cnt while following the '''[[Contour Plot]]''' tutorial you will NOT need to copy it again. Again I will be plotting temperature.

cp ~/MyDir/src/External/csec.in csec_temp.in
cp ~/MyDir/Data/default.cnt default.cnt

You may name the file whatever you like. Open the file (csec_temp.in in this example) with your favorite editor. The first line of this file allows you to specify the year and starting year-day for your plots. If you do not want a time label make the year-day value less than 0:

2007 -1 : year and starting year-day (use yearday<0, for no time label)

The next four lines are the plot title. Blank lines are fine but '''there must be four lines here.''' The text that you see on lines 2-5 are only a suggestion; you can put any text you like. I am plotting temperature at 100 meters from a 3/4 degree North Atlantic ROMS 3.0 simulation so my plot title looks like this:

ROMS 3.0
Upwelling Test Case
Default Setup
Temperature (Celsius)

The plotting options begin on line six and have short descriptions of what they do. For complete documentation on the plotting options read the '''[[Plotting Options]]''' page. I will annotate the options section to explain the choices I've made.

I only wish to plot one field and 23 is the field ID for potential temperature ('''[[Plotting Fields|FLDID]]''').

1 NFIELDS: number of fields to plot. Line below, field(s) types:
23 field identification: FLDID(1:NFIELDS)

The next three options determine range and frequency of data that will be plotted from your input file(s). I have chosen "0" for all three which tells the plotting package to plot all records from my model output file.

0 FRSTD : first day (>0) or time record (<0) to plot
0 LASTD : last day (>0) or time record (<0) to plot
0 DSKIP : plot every other DSKIP day/record (see below)

FINDX can be ignored for this example but the line '''MUST''' remain in the file.

1 FINDX : forecast record to process, if any (atmospheric files only).

I want to plot using grid units.

0 ISECPOS: section positions: [0] grid units, [1] Cartesian, [2] spherical

The next four lines specify the location of the cross-section. Keep in mind that this is in grid units since we chose 0 for ISECPOS. Since the upwelling test case is an east-west periodic channel, I want a north-south cross section. I will take my cross-section near the middle of the channel. The channel has 41 RHO-points in the I-direction (east-west) so I will set XSEC1 and XSEC2 to 21. The channel has 80 RHO-points in the J-direction (north-south) I want to go all the way across the channel so I set YSEC1 to 1 and YSEC2 to 82. I use 82 instead of 80 because there is a U-point at both ends of the domain in the J-direction.

21 XSEC1 : starting section X-position (grid units, or km, or degrees).
1 YSEC1 : starting section Y-position (grid units, or km, or degrees).
21 XSEC2 : ending section X-position (grid units, or km, or degrees).
82 YSEC2 : ending section Y-position (grid units, or km, or degrees).

A horizontal grid spacing of 1.0 will work fine for this case.

1.0 DELS : section horizontal grid spacing (km or degrees).

The channel in the upwelling test case is 150 meters deep and I would like to plot the entire water column.

0 SZTOP : shallowest section depth to consider (meters).
150 SZBOT : deepest section depth to consider (meters).

The upwelling test case has 16 vertical levels.

16 KMS : number of refiment section levels between SZTOP and SZBOT.

I am going to stick with linear interpolation so I leave this as "0"

0 VINTRP : vertical interpolation scheme: 0=linear, 1:cubic splines

I have chosen to set the next two values because I know my temperature range already. If you do not know the range of your data you should enter 0.0 and the plotting package will calculate the minimum and maximum values. Using the defaults can lead to other problems because the minimum and maximum values are recalculated for each plot. This means you could end up with a different range and color bar for every frame, making visual analysis very difficult.

14.0 PMIN : field minimum value for color palette (0.0 for default)
23.0 PMAX : field maximum value for color palette (0.0 for default)

I do not want contour lines between the color bands so I will set the next option to 0.

0 ICNT : draw contours between color bands: 0=no, 1=yes

The next five values control the overlay or reference field. I don't want an overlay so I will set IREF to 0 and ignore rest.

0 IREF : secondary or reference field option (see below)
25 IDOVER : overlay field identification (for IREF=1,2 only)
1 LEVOVER: level of the overlay field (set to 0 if same as current FLDLEV)
0.0 RMIN : overlay field minimum value to consider (0.0 for default)
0.0 RMAX : overlay field maximum value to consider (0.0 for default)

I don't want more than one plot per page so I can leave this alone.

1 NPAGE : number of plots per page (currently 1, 2, or 4)

There isn't a grid NetCDF file for the upwelling test problem so READGRD should be F.

F READGRD: logical switch to read in positions from grid NetCDF file.

I don't know what this does.
F PLTLOGO: logical switch draw Logo.

The next 5 options control plot titles captions and legends.

T WRTHDR : logical switch to write out the plot header titles.
T WRTBLAB: logical switch to write out the plot bottom title.
T WRTRANG: logical switch to write out data range values and CI.
F WRTFNAM: logical switch to write out input primary filename.
F WRTDATE: logical switch to write out current date.

The next six lines specify the input files for the plots. The first line is the variables ID file. An example file exists in the Data directory of the plotting package source code and I will use it.

~/Mydir/Data/varid.dat

The second file sets the color palette file. Several palettes are included in the source code Palettes directory. I'm going to use the natlan1.pal file.

~/Mydir/Palettes/natlan1.pal

The third file sets the internal plotting parameters. We will discuss this file in detail later. An example file exists in the Data directory and I will use it.

~/Mydir/Data/default.cnt

The fourth file is your primary NetDCF file, usually model output. I will use my averages model output.

ocean_avg.nc

The fifth file is you secondary NetCDF file, also usually model output. I am not using an overlay so this file doesn't matter and I'll set it to be the same as my primary NetCDF file.

ocean_avg.nc

The sixth file is your grid NetCDF file. As mentioned above, the upwelling test case does not have a grid NetCDF file so I will again use my primary NetCDF file.

ocean_avg.nc

Save the csec_temp.in file and you're ready to plot some results.

==Plotting==
Now that we have created an input file for csec we can start creating our plots. First, let's make sure csec and idt are in our path and the '''NCARG_ROOT''' environment variable is set.

> which csec
/home/robertson/bin/csec

> which idt
/home/robertson/ncl-5.0.0/bin/idt

> printenv NCARG_ROOT
/home/robertson/ncl-5.0.0

if your shell cannot find csec you need to add PLT_BINDIR to your path. the NCARG_ROOT environment variable should be set to the location of your [http://www.ncl.ucar.edu/ NCL] install. See the '''[[Plotting Package Installation | Installation]]''' page for more details. If you have an existing 'gmeta' file that you want to keep you should first rename it so csec does not replace it. To create the plots execute the following command.

> csec < csec_temp.in

You will see some information about each frame scroll by. When the program finishes you will have a file named '''gmeta''' in the current directory. Now you can use idt to view your plots.

> idt gmeta &

This will bring up the idt viewer with a blank plot. To see the first frame click the [[Image:idt_play.gif]] button. You should see a plot similar to the following.

[[Image:upwelling_temp_csec.gif]]

Clicking the [[Image:idt_play.gif]] button repeatedly will advance to the frames of the '''gmeta''' file. I suggest you take some time to experiment with the controls in the idt window.

<div style="float:left; margin-top: 0.0em; margin-bottom:3px; background-color: #cee0f2; padding: .2em .6em; font-size: 130%; border:1px solid #A3B1BF;">← '''Prev:''' '''[[Contour Plots]]'''
<div style="clear:both"></div>
</div>
<div style="float:right; margin-top: 0.0em; margin-bottom:3px; background-color: #cee0f2; padding: .2em .6em; font-size: 130%; border:1px solid #A3B1BF;">'''Next:''' '''[[Internal Plotting Parameters]]''' →
<div style="clear:both"></div>
</div>

← Older revision		Revision as of 19:22, 3 March 2008
Line 30:		Line 30:
	The plotting options begin on line six and have short descriptions of what they do. For complete documentation on the plotting options read the '''[[Plotting Options]]''' page. I will annotate the options section to explain the choices I've made.		The plotting options begin on line six and have short descriptions of what they do. For complete documentation on the plotting options read the '''[[Plotting Options]]''' page. I will annotate the options section to explain the choices I've made.

	I only wish to plot one field (the overlay is handled below) and 19 is the field ID for ~~vertical velocity~~ ('''[[Plotting Fields\|FLDID]]''').		I only wish to plot one field (the overlay is handled below) and 23 is the field ID for potential temperature ('''[[Plotting Fields\|FLDID]]''').

	<span class="blue">1 NFIELDS: number of fields to plot. Line below, field(s) types:		<span class="blue">1 NFIELDS: number of fields to plot. Line below, field(s) types:
	19 field identification: FLDID(1:NFIELDS)</span>		23 field identification: FLDID(1:NFIELDS)</span>

	The next three options determine range and frequency of data that will be plotted from your input file(s). I have chosen "0" for all three which tells the plotting package to plot all records from my model output file.		The next three options determine range and frequency of data that will be plotted from your input file(s). I have chosen "0" for all three which tells the plotting package to plot all records from my model output file.
Line 75:		Line 75:
	I have chosen to set the next two values because I know my vertical velocity range (in cm/day) already. If you do not know the range of your data you should enter 0.0 and the plotting package will calculate the minimum and maximum values. Using the defaults can lead to other problems because the minimum and maximum values are recalculated for each plot. This means you could end up with a different range and color bar for every frame, making visual analysis very difficult.		I have chosen to set the next two values because I know my vertical velocity range (in cm/day) already. If you do not know the range of your data you should enter 0.0 and the plotting package will calculate the minimum and maximum values. Using the defaults can lead to other problems because the minimum and maximum values are recalculated for each plot. This means you could end up with a different range and color bar for every frame, making visual analysis very difficult.

	<span class="blue">~~-5520~~ PMIN : field minimum value for color palette (0.0 for default)		<span class="blue">10 PMIN : field minimum value for color palette (0.0 for default)
	~~6110~~ PMAX : field maximum value for color palette (0.0 for default)</span>		25 PMAX : field maximum value for color palette (0.0 for default)</span>

	I do not want contour lines between the color bands so I will set the next option to 0.		I do not want contour lines between the color bands so I will set the next option to 0.
Line 82:		Line 82:
	<span class="blue">0 ICNT : draw contours between color bands: 0=no, 1=yes</span>		<span class="blue">0 ICNT : draw contours between color bands: 0=no, 1=yes</span>

	The next five values control the overlay or reference field. I want the overlay plotted from my primary input NetCDF file (this will be explained later) so I set <span class="blue">IREF</span> to '''1'''. The '''[[Plotting Fields\|FLDID]]''' for ~~potential temperature~~ is '''23''' so I set <span class="blue">IDOVER</span> to '''23'''. I will allow the plotting package to calculate the minimum and maximum so I set both <span class="blue">RMIN</span> and <span class="blue">RMAX</span> to '''0.0'''.		The next five values control the overlay or reference field. I want the overlay plotted from my primary input NetCDF file (this will be explained later) so I set <span class="blue">IREF</span> to '''1'''. The '''[[Plotting Fields\|FLDID]]''' for Total Velocity Magnitude is '''4''' so I set <span class="blue">IDOVER</span> to '''4'''. I will allow the plotting package to calculate the minimum and maximum so I set both <span class="blue">RMIN</span> and <span class="blue">RMAX</span> to '''0.0'''.

	<span class="blue">1 IREF : secondary or reference field option (see below)		<span class="blue">1 IREF : secondary or reference field option (see below)
	23 IDOVER : overlay field identification (for IREF=1,2 only)		4 IDOVER : overlay field identification (for IREF=1,2 only)
	0.0 RMIN : overlay field minimum value to consider (0.0 for default)		0.0 RMIN : overlay field minimum value to consider (0.0 for default)
	0.0 RMAX : overlay field maximum value to consider (0.0 for default)</span>		0.0 RMAX : overlay field maximum value to consider (0.0 for default)</span>
Line 91:		Line 91:
	I don't want more than one plot per page so I can leave this alone.		I don't want more than one plot per page so I can leave this alone.

	<span class="blue">1 NPAGE : number of plots per page (currently 1, 2, or 4)</span>		<span class="blue">1 NPAGE : number of plots per page (currently 1, 2, or 4)</span>

	There isn't a grid NetCDF file for the upwelling test problem so <span class="blue">READGRD</span> ~~should be F~~.		There isn't a separate grid NetCDF file for the upwelling test problem but we can read the grid out of our history file so I will set <span class="blue">READGRD</span> to T.

	<span class="blue">F READGRD: logical switch to read in positions from grid NetCDF file.</span>		<span class="blue">F READGRD: logical switch to read in positions from grid NetCDF file.</span>
Line 120:		Line 120:
	<span class="forestGreen">default.cnt</span>		<span class="forestGreen">default.cnt</span>

	The fourth file is your primary NetDCF file, usually model output. I will use my ~~averages~~ model output.		The fourth file is your primary NetDCF file, usually model output. I will use my history model output.

	<span class="forestGreen">~~ocean_avg~~.nc</span>		<span class="forestGreen">ocean_his.nc</span>

	The fifth file is you secondary NetCDF file, also usually model output. Some times the data you want to overlay will be in a different file. If that is the case you would set <span class="blue">IREF</span> to '''2''', then put the name of the file your overlay data should come from here. However, my overlay data was in the primary NetCDF file so it doesn't matter what I set this to so I'll set it to be the same as my primary NetCDF file. For more information about <span class="blue">IREF</span> check the '''[[Plotting Options#IREF\|Plotting Options]]''' page.		The fifth file is you secondary NetCDF file, also usually model output. Some times the data you want to overlay will be in a different file. If that is the case you would set <span class="blue">IREF</span> to '''2''', then put the name of the file your overlay data should come from here. However, my overlay data was in the primary NetCDF file so it doesn't matter what I set this to so I'll set it to be the same as my primary NetCDF file. For more information about <span class="blue">IREF</span> check the '''[[Plotting Options#IREF\|Plotting Options]]''' page.
Line 128:		Line 128:
	<span class="forestGreen">ocean_avg.nc</span>		<span class="forestGreen">ocean_avg.nc</span>

	The sixth file is your grid NetCDF file. As mentioned above, the ~~upwelling test case does not have a~~ grid ~~NetCDF file so I will again use my primary~~ NetCDF file.		The sixth file is your grid NetCDF file. As mentioned above, we will read the grid from our history NetCDF file.

	<span class="forestGreen">~~ocean_avg~~.nc</span>		<span class="forestGreen">ocean_his.nc</span>

	Save the <span class="forestGreen">csec_upwelling.in</span> file and you're ready to plot some results.		Save the <span class="forestGreen">csec_upwelling.in</span> file and you're ready to plot some results.
Line 154:		Line 154:
	<span class="red">> idt gmeta &</span>		<span class="red">> idt gmeta &</span>

	This will bring up the <span class="red">idt</span> viewer with a blank plot. To see the first frame click the [[Image:idt_play.gif]] button. You should see a plot similar to the following ~~(The first frame will be all green)~~.		This will bring up the <span class="red">idt</span> viewer with a blank plot. To see the first frame click the [[Image:idt_play.gif]] button. You should see a plot similar to the following.

	[[Image:~~upwelling_vvel_temp_csec~~.gif]]		[[Image:upwelling_velmag_temp.gif]]

	Clicking the [[Image:idt_play.gif]] button repeatedly will advance to the frames of the '''gmeta''' file. The plot above is the ~~final~~ frame of my '''gmeta''' file. I suggest you take some time to experiment with the controls in the <span class="red">idt</span> window.		Clicking the [[Image:idt_play.gif]] button repeatedly will advance through the frames of the '''gmeta''' file. The plot above is the 17<sup>th</sup> frame of my '''gmeta''' file. I suggest you take some time to experiment with the controls in the <span class="red">idt</span> window.

← Older revision		Revision as of 18:07, 15 January 2008
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	I have chosen to set the next two values because I know my vertical velocity range (in cm/day) already. If you do not know the range of your data you should enter 0.0 and the plotting package will calculate the minimum and maximum values. Using the defaults can lead to other problems because the minimum and maximum values are recalculated for each plot. This means you could end up with a different range and color bar for every frame, making visual analysis very difficult.		I have chosen to set the next two values because I know my vertical velocity range (in cm/day) already. If you do not know the range of your data you should enter 0.0 and the plotting package will calculate the minimum and maximum values. Using the defaults can lead to other problems because the minimum and maximum values are recalculated for each plot. This means you could end up with a different range and color bar for every frame, making visual analysis very difficult.

	<span class="blue">-5520 PMIN : field minimum value for color palette (0.0 for default)		<span class="blue">-5520 PMIN : field minimum value for color palette (0.0 for default)
	6110 PMAX : field maximum value for color palette (0.0 for default)</span>		6110 PMAX : field maximum value for color palette (0.0 for default)</span>

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	<span class="blue">1 IREF : secondary or reference field option (see below)		<span class="blue">1 IREF : secondary or reference field option (see below)
	25 IDOVER : overlay field identification (for IREF=1,2 only)		23 IDOVER : overlay field identification (for IREF=1,2 only)
	0.0 RMIN : overlay field minimum value to consider (0.0 for default)		0.0 RMIN : overlay field minimum value to consider (0.0 for default)
	0.0 RMAX : overlay field maximum value to consider (0.0 for default)</span>		0.0 RMAX : overlay field maximum value to consider (0.0 for default)</span>
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	The next 5 options control plot titles captions and legends.		The next 5 options control plot titles captions and legends.

	<span class="blue">T WRTHDR : logical switch to write out the plot header titles.		<span class="blue">F WRTHDR : logical switch to write out the plot header titles.
	F WRTBLAB: logical switch to write out the plot bottom title.		T WRTBLAB: logical switch to write out the plot bottom title.
	T WRTRANG: logical switch to write out data range values and CI.		T WRTRANG: logical switch to write out data range values and CI.
	F WRTFNAM: logical switch to write out input primary filename.		F WRTFNAM: logical switch to write out input primary filename.

← Older revision		Revision as of 18:03, 15 January 2008
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	'''NOTE:''' default.cnt and the .in file can be named anything you want. This will become clear as we continue.		'''NOTE:''' default.cnt and the .in file can be named anything you want. This will become clear as we continue.

	We suggest that you copy <span class="forestGreen">csec.in</span> and <span class="forestGreen">default.cnt</span> to the directory where you wish to create your plots. If you have already copied <span class="forestGreen">default.cnt</span> while following the '''[[Contour Plot]]''' tutorial you will NOT need to copy it again. ~~Again~~ I will be plotting temperature.		We suggest that you copy <span class="forestGreen">csec.in</span> and <span class="forestGreen">default.cnt</span> to the directory where you wish to create your plots. If you have already copied <span class="forestGreen">default.cnt</span> while following the '''[[Contour Plots\|Contour Plot]]''' tutorial you will NOT need to copy it again. I will be plotting vertical velocity with a temperature overlay from output from the '''[[UPWELLING_CASE\|upwelling test case]]'''.

	<span class="red">cp ~/MyDir/src/External/csec.in ~~csec_temp~~.in		<span class="red">cp ~/MyDir/src/External/csec.in csec_upwelling.in
	cp ~/MyDir/Data/default.cnt default.cnt</span>		cp ~/MyDir/Data/default.cnt default.cnt</span>

	You may name the file whatever you like. Open the file (<span class="forestGreen">~~csec_temp~~.in</span> in this example) with your favorite editor. The first line of this file allows you to specify the year and starting year-day for your plots. If you do not want a time label make the year-day value less than 0:		You may name the file whatever you like. Open the file (<span class="forestGreen">csec_upwelling.in</span> in this example) with your favorite editor. The first line of this file allows you to specify the year and starting year-day for your plots. If you do not want a time label make the year-day value less than 0:

	<span class="blue">2007 -1 : year and starting year-day (use yearday<0, for no time label)</span>		<span class="blue">2007 -1 : year and starting year-day (use yearday<0, for no time label)</span>
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	The plotting options begin on line six and have short descriptions of what they do. For complete documentation on the plotting options read the '''[[Plotting Options]]''' page. I will annotate the options section to explain the choices I've made.		The plotting options begin on line six and have short descriptions of what they do. For complete documentation on the plotting options read the '''[[Plotting Options]]''' page. I will annotate the options section to explain the choices I've made.

	I only wish to plot one field and 23 is the field ID for ~~potential temperature~~ ('''[[Plotting Fields\|FLDID]]''').		I only wish to plot one field (the overlay is handled below) and 19 is the field ID for vertical velocity ('''[[Plotting Fields\|FLDID]]''').

	<span class="blue">1 NFIELDS: number of fields to plot. Line below, field(s) types:		<span class="blue">1 NFIELDS: number of fields to plot. Line below, field(s) types:
	23 field identification: FLDID(1:NFIELDS)</span>		19 field identification: FLDID(1:NFIELDS)</span>

	The next three options determine range and frequency of data that will be plotted from your input file(s). I have chosen "0" for all three which tells the plotting package to plot all records from my model output file.		The next three options determine range and frequency of data that will be plotted from your input file(s). I have chosen "0" for all three which tells the plotting package to plot all records from my model output file.
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	<span class="blue">0 VINTRP : vertical interpolation scheme: 0=linear, 1:cubic splines</span>		<span class="blue">0 VINTRP : vertical interpolation scheme: 0=linear, 1:cubic splines</span>

	I have chosen to set the next two values because I know my ~~temperature~~ range already. If you do not know the range of your data you should enter 0.0 and the plotting package will calculate the minimum and maximum values. Using the defaults can lead to other problems because the minimum and maximum values are recalculated for each plot. This means you could end up with a different range and color bar for every frame, making visual analysis very difficult.		I have chosen to set the next two values because I know my vertical velocity range (in cm/day) already. If you do not know the range of your data you should enter 0.0 and the plotting package will calculate the minimum and maximum values. Using the defaults can lead to other problems because the minimum and maximum values are recalculated for each plot. This means you could end up with a different range and color bar for every frame, making visual analysis very difficult.

	<span class="blue">~~14.0~~ PMIN : field minimum value for color palette (0.0 for default)		<span class="blue">-5520 PMIN : field minimum value for color palette (0.0 for default)
	~~23.0~~ PMAX : field maximum value for color palette (0.0 for default)</span>		6110 PMAX : field maximum value for color palette (0.0 for default)</span>

	I do not want contour lines between the color bands so I will set the next option to 0.		I do not want contour lines between the color bands so I will set the next option to 0.
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	<span class="blue">0 ICNT : draw contours between color bands: 0=no, 1=yes</span>		<span class="blue">0 ICNT : draw contours between color bands: 0=no, 1=yes</span>

	The next five values control the overlay or reference field. I ~~don't~~ want an overlay so I will set <span class="blue">~~IREF~~</span> to 0 ~~and ignore rest~~.		The next five values control the overlay or reference field. I want the overlay plotted from my primary input NetCDF file (this will be explained later) so I set <span class="blue">IREF</span> to '''1'''. The '''[[Plotting Fields\|FLDID]]''' for potential temperature is '''23''' so I set <span class="blue">IDOVER</span> to '''23'''. I will allow the plotting package to calculate the minimum and maximum so I set both <span class="blue">RMIN</span> and <span class="blue">RMAX</span> to '''0.0'''.

	<span class="blue">0 IREF : secondary or reference field option (see below)		<span class="blue">1 IREF : secondary or reference field option (see below)
	25 IDOVER : overlay field identification (for IREF=1,2 only)		25 IDOVER : overlay field identification (for IREF=1,2 only)
	~~1 LEVOVER: level of the overlay field (set to 0 if same as current FLDLEV)~~
	0.0 RMIN : overlay field minimum value to consider (0.0 for default)		0.0 RMIN : overlay field minimum value to consider (0.0 for default)
	0.0 RMAX : overlay field maximum value to consider (0.0 for default)</span>		0.0 RMAX : overlay field maximum value to consider (0.0 for default)</span>
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	<span class="blue">T WRTHDR : logical switch to write out the plot header titles.		<span class="blue">T WRTHDR : logical switch to write out the plot header titles.
	T WRTBLAB: logical switch to write out the plot bottom title.		F WRTBLAB: logical switch to write out the plot bottom title.
	T WRTRANG: logical switch to write out data range values and CI.		T WRTRANG: logical switch to write out data range values and CI.
	F WRTFNAM: logical switch to write out input primary filename.		F WRTFNAM: logical switch to write out input primary filename.
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	<span class="forestGreen">ocean_avg.nc</span>		<span class="forestGreen">ocean_avg.nc</span>

	The fifth file is you secondary NetCDF file, also usually model output. I ~~am not using an~~ overlay so ~~this file~~ doesn't matter ~~and~~ I'll set it to be the same as my primary NetCDF file.		The fifth file is you secondary NetCDF file, also usually model output. Some times the data you want to overlay will be in a different file. If that were the case here I would have set <span class="blue">IREF</span> to '''2''' put then name of the file my overlay data should come from here. However, my overlay data was in the primary NetCDF file so it doesn't matter what I set this to so I'll set it to be the same as my primary NetCDF file. For more information about <span class="blue">IREF</span> check the '''[[Plotting Options#IREF\|Plotting Options]]''' page.

	<span class="forestGreen">ocean_avg.nc</span>		<span class="forestGreen">ocean_avg.nc</span>
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	<span class="forestGreen">ocean_avg.nc</span>		<span class="forestGreen">ocean_avg.nc</span>

	Save the <span class="forestGreen">~~csec_temp~~.in</span> file and you're ready to plot some results.		Save the <span class="forestGreen">csec_upwelling.in</span> file and you're ready to plot some results.

	==Plotting==		==Plotting==
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	if your shell cannot find <span class="red">csec</span> you need to add PLT_BINDIR to your path. the <span class="blue">NCARG_ROOT</span> environment variable should be set to the location of your [http://www.ncl.ucar.edu/ NCL] install. See the '''[[Plotting Package Installation \| Installation]]''' page for more details. If you have an existing 'gmeta' file that you want to keep you should first rename it so <span class="red">csec</span> does not replace it. To create the plots execute the following command.		if your shell cannot find <span class="red">csec</span> you need to add PLT_BINDIR to your path. the <span class="blue">NCARG_ROOT</span> environment variable should be set to the location of your [http://www.ncl.ucar.edu/ NCL] install. See the '''[[Plotting Package Installation \| Installation]]''' page for more details. If you have an existing 'gmeta' file that you want to keep you should first rename it so <span class="red">csec</span> does not replace it. To create the plots execute the following command.

	<span class="red">> csec < ~~csec_temp~~.in</span>		<span class="red">> csec < csec_upwelling.in</span>

	You will see some information about each frame scroll by. When the program finishes you will have a file named '''gmeta''' in the current directory. Now you can use <span class="red">idt</span> to view your plots.		You will see some information about each frame scroll by. When the program finishes you will have a file named '''gmeta''' in the current directory. Now you can use <span class="red">idt</span> to view your plots.
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	<span class="red">> idt gmeta &</span>		<span class="red">> idt gmeta &</span>

	This will bring up the <span class="red">idt</span> viewer with a blank plot. To see the first frame click the [[Image:idt_play.gif]] button. You should see a plot similar to the following.		This will bring up the <span class="red">idt</span> viewer with a blank plot. To see the first frame click the [[Image:idt_play.gif]] button. You should see a plot similar to the following (The first frame will be all green).

	[[Image:~~upwelling_temp_csec~~.gif]]		[[Image:upwelling_vvel_temp_csec.gif]]

	Clicking the [[Image:idt_play.gif]] button repeatedly will advance to the frames of the '''gmeta''' file. I suggest you take some time to experiment with the controls in the <span class="red">idt</span> window.		Clicking the [[Image:idt_play.gif]] button repeatedly will advance to the frames of the '''gmeta''' file. The plot above is actually the final frame of my '''gmeta''' file. I suggest you take some time to experiment with the controls in the <span class="red">idt</span> window.