How to use the tool ConvertHDF5ToGridData?

Discussion about MOHID support tools
jlloret@um.es
MOHID Beginner
Posts: 7
Joined: Tue Jan 10, 2012 16:54

How to use the tool ConvertHDF5ToGridData?

Postby jlloret@um.es » Wed Oct 16, 2013 18:42

Hi all,

I am trying to convert some HDF5 file into grid data files I can use later for grid data operations. To be more specific I am trying to present my model results as a grid image representing the magnitude of change between results of two different simulation conditions. I got global average values for the same variable in two different runs and I would like to substract or divide both images. Any ideas of how to do this?

Thank you so much for your help

davidbrito
MOHID Advanced user
Posts: 187
Joined: Thu Jan 01, 1970 00:00

Re: How to use the tool ConvertHDF5ToGridData?

Postby davidbrito » Thu Oct 17, 2013 15:26

Hello,

You should read this:
http://www.mohid.com/wiki/index.php?tit ... ToGridData

This way you can tansform the HDF fields in to grids. And then do the math you want between grids.
To have an executable of ConvertHDF5ToGridData you may compile it from the code in http://mohid.codeplex.com/ if you have that option. Or ask for a new executable.


Best regards,
David

jlloret@um.es
MOHID Beginner
Posts: 7
Joined: Tue Jan 10, 2012 16:54

Re: How to use the tool ConvertHDF5ToGridData?

Postby jlloret@um.es » Tue Oct 22, 2013 07:41

Hello David,

Thanks for your response. I dont think I am going to be able to compile if from the code... how can I ask for an executable? can it be downloaded?

Thanks again for your time.

Javier

davidbrito
MOHID Advanced user
Posts: 187
Joined: Thu Jan 01, 1970 00:00

Re: How to use the tool ConvertHDF5ToGridData?

Postby davidbrito » Thu Oct 31, 2013 18:15

Javier,

i just sent you an e.mail with link to download the exe.
you just need to create a text file HDF5ToGridData.dat and insert the kwyeords in the refered MOHID wiki.

Hope it helps.

Best regards,
David

jlloret@um.es
MOHID Beginner
Posts: 7
Joined: Tue Jan 10, 2012 16:54

Re: How to use the tool ConvertHDF5ToGridData?

Postby jlloret@um.es » Thu Oct 31, 2013 23:00

Thank you so much David!

You have been truly helpful.

Regards.

jlloret@um.es
MOHID Beginner
Posts: 7
Joined: Tue Jan 10, 2012 16:54

Re: How to use the tool ConvertHDF5ToGridData?

Postby jlloret@um.es » Mon Nov 04, 2013 10:37

Dear David,

I am trying to convert some of the properties stored in my HDFs to grid data with the executable you sent me but I am afraid it is not working somehow. The properties I am trying to convert are global averages for the modelled period and it looks like the HDF5ToGridData.exe keeps looking my properties in the 'Results' group of the HDF file instead of the 'Statistics' group. Is there anything that I am doing wrong? I included copy of my HDFToGridData.dat and UsedKeyWords_1.dat files:

<<HDFToGridData.dat>>:

HDF_FILE : ...\HDF_Conversion\WaterProperties_18.hdf5

ALL_INSTANTS : 1

<BeginParameter>
PROPERTY : ammonia
HDF_GROUP : /Statistics/ammonia/Global/Average
<EndParameter>

<BeginParameter>
PROPERTY : nitrate
HDF_GROUP : /Statistics/nitrate/Global/Average
<EndParameter>

<BeginParameter>
PROPERTY : nitrite
HDF_GROUP : /Statistics/nitrite/Global/Average
<EndParameter>

<BeginParameter>
PROPERTY : inorganic phosphorus
HDF_GROUP : /Statistics/inorganic phosphorus/Global/Average
<EndParameter>

<BeginParameter>
PROPERTY : macroalgae
HDF_GROUP : /Statistics/macroalgae/Global/Average
<EndParameter>

<BeginParameter>
PROPERTY : phytoplankton
HDF_GROUP : /Statistics/phytoplankton/Global/Average
<EndParameter>

<BeginParameter>
PROPERTY : salinity
HDF_GROUP : /Statistics/salinity/Global/Average
<EndParameter>

<BeginParameter>
PROPERTY : temperature
HDF_GROUP : /Statistics/temperature/Global/Average
<EndParameter>

<<UsedKeyWords_1.dat>>:

HDF_FILE HDF5ToGridData Do not have From File .......... YES
ALL_INSTANTS HDF5ToGridData FALSE From File TRUE YES
PROPERTY HDF5ToGridData Do not have From Block ammonia YES
HDF_GROUP HDF5ToGridData /Results/ammonia/Global/A From Block /Statistics/ammonia/Global/Average YES

Thanks again for your help.

Regards,

Javier

davidbrito
MOHID Advanced user
Posts: 187
Joined: Thu Jan 01, 1970 00:00

Re: How to use the tool ConvertHDF5ToGridData?

Postby davidbrito » Fri Nov 15, 2013 20:13

Hi Javier,


The tool is intended to open the HDF group and then find inside somthing like "[property name]_000001" and save the grid. This was not tought for statistics, maybe the statistics groups and fields are not the same structure.


Can you post here the result of the program?
print here what is appearing in the black screen.


Best regards,
David

jlloret@um.es
MOHID Beginner
Posts: 7
Joined: Tue Jan 10, 2012 16:54

Re: How to use the tool ConvertHDF5ToGridData?

Postby jlloret@um.es » Fri Nov 22, 2013 10:01

Hi David,

This is a copy of the black screen message:
--------------------------------------------------------

Constructing HDF5ToGridData
Please wait...

Reading options...

Opening HDF...

Only 2D cases for now. Use 2D properties groups
ConvertToGridData - HDF5ToGridData - ERR60

--------------------------------------------------------

davidbrito
MOHID Advanced user
Posts: 187
Joined: Thu Jan 01, 1970 00:00

Re: How to use the tool ConvertHDF5ToGridData?

Postby davidbrito » Fri Nov 22, 2013 11:05

Hello Javier,

Seems that the problem is that the program was done for 2D in the expect that in the future also could be possible in 3D.
The statitistics are 3D fields? (sorry I am not very used to statistics)

Reading the code I saw that the program tests if the HDF_GROUP that you say exists and did not gave a error so it went to the correct part of the HDF.
But when he goes to open the HDF group to print fields every instant or defined instant, it warns you that this is not a 2D field and he cant continue because it is not programmed for 3D.

Can you check if this properties are 3D? you can open it with MOHID Post and when you click a instant you can see the dimensions. is it like axb or axbxc? where a, b and c are numbers of the grid dimensions.

Because if they are 2D than the problem is somthing else.

Best regards,
David


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