reading an HDF

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epelde.ane@gmail.com
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Posts: 172
Joined: Thu Jan 01, 1970 00:00

reading an HDF

Postby epelde.ane@gmail.com » Thu Mar 07, 2013 16:10

Hello all!

I´m trying now to create a hdf with different agricultural practices. In the map window it seems to be ok, with the right dates and so.. But, when I run the model I get:

GetHDF5ArrayDimensions - ModuleHDF5 - ERR10
HDF5-DIAG: Error detected in HDF5 library version: 1.6.8 thread 0. Back trace follows.
#000: ..\..\src\H5G.c line 253 in H5Gopen(): group not found
major(10): Symbol table layer
minor(48): Object not found
#001: ..\..\src\H5G.c line 1783 in H5G_find(): object not found
major(10): Symbol table layer
minor(48): Object not found
#002: ..\..\src\H5Gtraverse.c line 397 in H5G_namei(): component not found
major(10): Symbol table layer
minor(48): Object not found
#003: ..\..\src\H5Gstab.c line 161 in H5G_stab_find(): not found
major(10): Symbol table layer
minor(48): Object not found
#004: ..\..\src\H5Gnode.c line 954 in H5G_node_found(): not found
major(10): Symbol table layer
minor(48): Object not found


I´ve found the error in the code but I dont understand it.. I dont know where it can come from :(
Any help please??

Jauch
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Posts: 98
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby Jauch » Fri Mar 08, 2013 11:02

Hello Ane.

If you observe the error #000, you will see that messages says: H5Gopen(): group not found
The H5Gopen is the function used to OPEN the HDF5 file.
The "group not found" message tells that it was not possible to find the "group".
The "group" is important because every MOHID HDF5 has its datasets (the matrix with the values) inside one group.

If you open a result MOHID HDF (using, for example, HDFViewer), you will see 3 main groups:
- Grid
- Results
- Time

So, in order to be of help here, I need to know these:

1. The input data block where you are trying to use the HDF you create. I know it, bu I need to see it, so copy the block here.
2. I need to see the HDF structure. The best thing is to send me the HDF so I can take a look on it. You can send me also the input file (I think it is vegetation) where you are using the HDF.

I think with these two things we can find the problem :)

epelde.ane@gmail.com
MOHID Advanced user
Posts: 172
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby epelde.ane@gmail.com » Fri Mar 08, 2013 14:34

OK!

The input data block is:

<begin_AgriculturalPractices>
!INITIALIZATION_METHOD : ASCII_FILE
!INITIALIZATION_METHOD : CONSTANT
INITIALIZATION_METHOD : HDF
FILENAME : ..\General Data\Other\Vegetation\proba fillmatrix\vegetation3ID.hdf5
DEFAULTVALUE : 27
!REMAIN_CONSTANT : 1
<end_AgriculturalPractices>


And I´m not sure if it is related to this, but when I open the vegetation ID hdf file, althought colours change in the grid data file (in the right day and so, and if I look in the leyend they seem to be ok), I query the file and although the colour change the value remains constant.
I send you the files, Lets see :)

Jauch
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Posts: 98
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby Jauch » Fri Mar 08, 2013 15:04

Ane, try to add the keyword HDF_FIELD_NAME to the block, with the value 'vegetation', that is the name of the property...

Code: Select all

<begin_AgriculturalPractices>
HDF_FIELD_NAME        : vegetation
INITIALIZATION_METHOD : HDF
FILENAME              : ..\General Data\Other\Vegetation\proba fillmatrix\vegetation3ID.hdf5
DEFAULTVALUE          : 27
<end_AgriculturalPractices>

epelde.ane@gmail.com
MOHID Advanced user
Posts: 172
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby epelde.ane@gmail.com » Fri Mar 08, 2013 15:47

Solved! 8)

I´ve just made a 2 month simulation, so I cant see nothing at all.. but if I had a 2 crop rotation, which would be the way to check which is the crop growing in each moment? As I told you querying the map doesnt work.. always get the same value althought the colour corresponding to different crop changes.. this is not the right way?

thanks

Jauch
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Posts: 98
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby Jauch » Sun Mar 10, 2013 10:34

Hello Ane :)

Assuming that you are looking to the HDF map, if the color changes, the value of the property that you have selected also is changing.
To see this change, you have to be sure that you have chose the HDF in the left panel and than selected the option to visualize its value. It will became marked in red.

If the color is changing but the value not, maybe you have selected another layer instead the one you wants to see?

Jauch
Site Admin
Posts: 98
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby Jauch » Mon Mar 11, 2013 11:06

Hello Ane,

Looking to the images you sent to me I think I understood the problem.

The "select tool" that you use to see the values in a cell (or group of cells) in the HDF is a static tool. This means that it will show only the value that was at the time instant you pick the HDF. If the HDF animation still goes forward, the value that the select tool shows will not change.

If you want to see the value at the second timeinstant (that is 6), you have to pick the cell again.

If you already have done this, than maybe is a bug in the Mohid Studio...

epelde.ane@gmail.com
MOHID Advanced user
Posts: 172
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby epelde.ane@gmail.com » Mon Mar 11, 2013 11:14

Hello eduardo,
Yes, that is what I was doing, after the colour changes I pick again but the values dont change. So I´ll look to the leyend until this is solved :)

Jauch
Site Admin
Posts: 98
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby Jauch » Tue Mar 12, 2013 10:55

ok.

I would like to know the version of MohidStudio that you are using.
Also, could you send to me the HDF that you are trying to visualize?

I will make some testes here and if I can reproduce the error, I send a message to Frank reporting it :)

epelde.ane@gmail.com
MOHID Advanced user
Posts: 172
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby epelde.ane@gmail.com » Tue Mar 12, 2013 11:06

perfect!
the version is: 1.2.4

Jauch
Site Admin
Posts: 98
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby Jauch » Tue Mar 12, 2013 11:26

ok...

I would try to update the Mohid Studio version to the most recent one, that I think is 1.2.7.566

Jauch
Site Admin
Posts: 98
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby Jauch » Tue Mar 12, 2013 12:05

Ok.

I tested the file you sent and, in fact, the Mohid Studio is unable to show HDF values in different time instants through the QUERY tool.

I'll feedback this to Frank.

epelde.ane@gmail.com
MOHID Advanced user
Posts: 172
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby epelde.ane@gmail.com » Tue Mar 12, 2013 12:14

ok. thanks!

epelde.ane@gmail.com
MOHID Advanced user
Posts: 172
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby epelde.ane@gmail.com » Mon Mar 18, 2013 10:49

Hello all!

I found a problem when I checked the output of the vegetation module, and I related it to the problem I spoke above (having a change in hdf value, the colour changes, but not the data it stores).
The thing is that I created a rotation by providing mohid with a ID time serie. On it, the first year has one value and the second another. The colour changes correctly in the map window (first of January new colour).

Then, I defined different practices for each ID value; ID used the first year: planting on 5 and harvest on 210 (Julian days) and ID of the second: planting 110 and harvest 303.
When I check the vegetation output, the biomass for instance, I see that both first year and the second the crop start and end growing at the same instant, as if the ID didn’t change (or at least that is what I´m understanding :)

And, apart of viewing in the map the crop is growing at one moment, is there any way of checking the crop ID in a time serie? This will be really useful for checking if the rotations are working well, no?

Thanks!!!

Jauch
Site Admin
Posts: 98
Joined: Thu Jan 01, 1970 00:00

Re: reading an HDF

Postby Jauch » Mon Mar 18, 2013 10:57

Hello Ane,

I don't think we have an output with the practice ID in the output timeseries or HDF's, but I'll check.
If not, I'll implement it ASAP.

Anyway, could you post here your vegetation input data file and also your database (the one with the practices) so I can try to figure out what is happening?


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