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Re: [Ncwms-users] transparent pixels

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Subject: Re: [Ncwms-users] transparent pixels
Date: Thu, 23 Sep 2010 09:08:52 -0600

 On 9/23/2010 8:09 AM, Jon Blower wrote:

Hi John,

Sorry to pester but I'm trying to get some things tied up before going
on leave for a while.  Could you confirm if my interpretations below are
correct or not?


sorry, i lost track of this

Thanks, Jon

-----Original Message-----
From: Jon Blower
Sent: 16 September 2010 14:41
To: 'John Caron'
Subject: RE: [Ncwms-users] transparent pixels

Ah, does you mean that GridDatatype.isMissingData() will work whether or
not enhancement is on, but VariableDS.isMissing() will only work if
enhancement is on?


both require scaleMissing enhancement.

GridDatatype.isMissingData() just proxies VariableDS.isMissing()

I notice that VariableDS.convertScaleOffsetMissing() seems to work
whether or not enhancement is on.  Is this correct?

no, it also needs ScaleMissingDefer or ScaleMissing on. all need one orthe other, or else the setup is not done.

Cheers, Jon

-----Original Message-----
From: John Caron [mailto:address@hidden]
Sent: 16 September 2010 14:24
To: Jon Blower
Cc: Unidata netCDF Java Support
Subject: Re: [Ncwms-users] transparent pixels

Jon Blower wrote:

Thanks - will VariableDS.isMissing() do just as well or do I have to
have a GridDatatype?

VariableDS.isMissing() is the same, as long as enhancement is on (should
be unless you turn it off)

-----Original Message-----
From: John Caron [mailto:address@hidden]
Sent: 16 September 2010 14:06
To: Jon Blower
Subject: Re: [Ncwms-users] transparent pixels

it should work for all data types.

Jon Blower wrote:

Ah, yes, I do use NaN to decide on missing values.  I notice that
GridDatatype.isMissingData() always takes a double as an argument.

Will

this work for integer data types too?



The utility routine might be useful but TBH it would be just as easy

for

me to use GridDatatype.isMissingData() if this works on all data

types.



Cheers, Jon



*From:* John Caron [mailto:address@hidden]
*Sent:* 16 September 2010 01:02
*To:* Jon Blower
*Cc:* Ethan Davis
*Subject:* Fwd: RE: [Ncwms-users] transparent pixels



Hi Jon:

Im guessing on the following:

You use NaN to decide on missing values. But this is only used if the
data type is float or double. In the case of integral data types, you
have to test for missing data explicitly by doing

   GridDatatype.isMissingData(val);

I could perhaps offer a utility routine that does that for you,
converted to floats as needed, so you can uniformly test for NaN.

Perhaps:

  Array result =  GridDatatype.setMissingData(Array org);

let me know if you think this is really the problem.

-------- Original Message --------

*Subject: *

        

RE: [Ncwms-users] transparent pixels

*Date: *

        

Tue, 14 Sep 2010 13:04:26 +1000

*From: *

        

Johan<address@hidden>  <mailto:address@hidden>

*To: *

        

'John Caron'<address@hidden>  <mailto:address@hidden>



Hi John,



Attached are some sample nc files and a sample ncml aggregation file.


The nc filenames start with the variable datatype followed by any

attributes

that are present, such as _FillValue, missing_value, add_offset,

scale_factor.



The only files that work properly are

float32_fill.nc

int8_fill_offset_scale.nc

int8_fill_missing_offset_scale_20100913T233200.nc



The latter is also used in the ncml aggregation file. Unfortunately,

cannot reproduce the problem associated with that anymore... Not sure

what

was going on there yesterday. Basically, when I looked at the service

in

godiva2, some map tiles were transparent and others were not,

seemingly at

random. I'll let you know if I can replicate it.



Thanks,

Johan





-----Original Message-----

From: John Caron [mailto:address@hidden]

Sent: Tuesday, 14 September 2010 12:34 AM

To: Johan

Cc: address@hidden

<mailto:address@hidden>

Subject: Re: [Ncwms-users] transparent pixels



Hi Johan:



If you can send me some sample files where you see these problems,

i'll try

to figure out whats going on. thanks.



John



Johan wrote:

Thanks Ethan, Pauline and Peter, who responded to my request.
I'll share my solution/workaround with the group in case anyone

comes

across

the same problem.
I followed the documentation on using missing_value, _FillValue, and
valid_min, valid_max attributes. None of this worked for me. I

should

point

out that I'm generating netcdf files using the python NETCDF4

library

and

the datatype of my variable is 8-bit integer. I'm using

ncWMS-1.0RC2.

When I change the datatype to float (32bit) it works fine, but this
obviously wastes a lot of resources. 16-bit integers did not work

either.

Then I used 8-bit integer with attributes 'add_offset=0.0' and
'scale_factor=1.0', and that works! So that's my workaround for now.

The

only drawback is that the service returns decimal numbers instead of
integers.
Interestingly, if I add both the attribute 'missing_value' and

'_FillValue'

the result depends on how the file is read. Reading the file via an

NcML

aggregation results in partial success only, with some images being
transparent but not all. Reading the file directly works fine.
So I omit the 'missing_value' attribute for this reason.
Cheers,
Johan

Dr Johan Swinnen
GIS Developer
Navy Hydrography and METOC Branch
p: 02 9359 3130 | f: 02 9359 3120 | w: http://www.metoc.gov.au
-----Original Message-----
From: Ethan Davis [mailto:address@hidden]
Sent: Friday, 10 September 2010 12:54 AM
To: address@hidden

<mailto:address@hidden>

Subject: Re: [Ncwms-users] transparent pixels
Hi Johan,
The "Writing NetCDF Files: Best Practices" document has a section on
"Missing Data Values" here

http://www.unidata.ucar.edu/software/netcdf/docs/BestPractices.html#Miss

ing%

20Data%20Values
Another option it doesn't mention at the moment is missing_value.
I believe all the options (missing_value, _FillValue, and valid
range/min/max) are recognized by ncWMS.
Note: Yes, missing_value was deprecated for awhile but, being more
obvious than _FillValue, it is coming back into favor. It will be

added

to the above document soon.
Ethan
On 9/8/2010 2:12 AM, Peter Walker wrote:

Hi Johan,
On 09/08/2010 07:40 AM, Johan wrote:

Hi,

Does anyone know how to make a particular pixel value transparent?

Say

I have a netcdf file with pixel values in the range 0 to 255 and I
don't want to see the 0 values because they represent 'no data'.

Can

this be done?

Have you tried setting the _FillValue for that variable to 0  in

the

NetCDF file?
Cheers,
Pete


I've tried changing the GetMap parameters 'bgcolor' and

'transparent'

but they only seem to affect pixels outside the spatial extent of

the

netcdf file, not pixels present in the netcdf file. Are there

perhaps

any configurations inside the netcdf file that can be used which

ncWMS

understands?

Thanks,
Johan


Dr Johan Swinnen
GIS Developer
Navy Hydrography and METOC Branch
p: 02 9359 3130 | f: 02 9359 3120 | w: http://www.metoc.gov.au
<http://www.metoc.gov.au/>

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References:
- Re: [Ncwms-users] transparent pixels
  - From: John Caron

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