Re: NetCDF plugin

Posted by emsaurette on Jun 09, 2015; 2:59pm
URL: http://imagej.273.s1.nabble.com/NetCDF-plugin-tp3686714p5013093.html

Hi Wayne,

Thank you so much that helped a lot, because my volume files only have one variable I needed to write 

path = "/path/to/my/file.volume"; 
  run("Load NetCDF File", "open=&path single variable”); 

Thank you again!

Emily

On Mon, Jun 8, 2015 at 5:39 PM, Rasband, Wayne (NIH/NIMH) [E] [via ImageJ] <[hidden email]> wrote:

> On Jun 8, 2015, at 4:16 PM, emsaurette <[hidden email]> wrote:
>
> Hi Curtis,
>
> That macro works and it will show that the file is loading in the progress
> bar, however it will never actually open the file. Do you have a clue as to
> what is going wrong?

The NetCDF plugin displays a dialog where you have to select the images to be loaded. When running the plugin from a macro, you have to include strings like “1d”, “2d” in the options argument or no images will be displayed. These strings (“1d”, “2d”, etc.) are from first word of the checkbox labels in the dialog.

This example

  path = "/Users/wayne/net-cdf/sresa1b_ncar_ccsm3-example.nc";
  run("Load NetCDF File", "open=&path 1d 2d 3d 4d”);

works with the first example NetCDF file at

    http://www.unidata.ucar.edu/software/netcdf/examples/files.html

-wayne

>
> Thank you!
>
> Emily
>
> On Mon, Jun 8, 2015 at 2:14 PM, ctrueden [via ImageJ] <
> [hidden email]> wrote:
>
>> Hi Emily,
>>
>>>
>>
>> http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/index.en.html.backup_2008_03_14

>>
>> Thanks. I tested, and the following macro works for me:
>>
>> file = "/path/to/myFile.nc";
>> run("Load NetCDF File", "open=[" + file + "]");
>>
>> Regards,
>> Curtis
>>
>> On Mon, Jun 8, 2015 at 7:48 PM, emsaurette <[hidden email]

>> <http:///user/SendEmail.jtp?type=node&node=5013078&i=0>> wrote:

>>
>>> Hi Curtis,
>>>
>>>
>>>
>> http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/index.en.html.backup_2008_03_14
>>>
>>> You can get the plugin at the URL above, I am currently using it to open
>>> .VOLUME files.
>>>
>>> Let me know if you come across anything interesting.
>>>
>>> Cheers,
>>>
>>> Emily
>>>
>>> On Mon, Jun 8, 2015 at 1:44 PM, ctrueden [via ImageJ] <

>>> [hidden email] <http:///user/SendEmail.jtp?type=node&node=5013078&i=1>>

>> wrote:

>>>
>>>> Hi Emily,
>>>>
>>>> Which NetCDF plugin? What is the URL? Is the source available?
>>>>
>>>> Regards,
>>>> Curtis
>>>>
>>>> On Thu, Jun 4, 2015 at 7:34 PM, emsaurette <[hidden email]
>>>> <http:///user/SendEmail.jtp?type=node&node=5013076&i=0>> wrote:
>>>>
>>>>> Have you found a solution to this problem?? I want to use NetCDF
>> files
>>>> in
>>>>> an
>>>>> imagej macro but the plugin will only open and requires manual file
>>>>> selection instead of the file path I specified in the macro.
>>>>>
>>>>> I am having the same issue and can't find a solution anywhere!!
>>>>>
>>>>> Please help!!
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> View this message in context:
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>>>>>
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