[ome-devel] [fiji-devel] Re: Calling Fiji DICOM functions from MATLAB

[Curtis Rueden]

Hi Jered,

> I tried using the bf package, and I am able to get the meta data I
> need. However, I have some questions. First, how do I suppress the
> command window output generated by the log function? I just want to
> use the function to peel off the metadata without displaying the log
> which seems to be activated by line 111 of bfopen.m. Second, is there
> any way to "trim down" the size of the nearly 16 MB jar function so
> that the software can be ported easier?

Good questions. I am CCing the ome-devel mailing list, since the OME lists
are the best place for these sorts of Bio-Formats questions.

Regarding the logging, did you try changing the "INFO" level to "WARN" or
"ERROR"?

For trimming the package, you can certainly create your own Bio-Formats
bundle without support for all 130 file formats. A tool like ProGuard [1]
could help with that, though you would need to learn a bit about how Java
packaging works.

Regards,
Curtis

[1] http://proguard.sourceforge.net/

On Thu, Jan 8, 2015 at 4:20 PM, Jered Wells <jered.wells at gmail.com> wrote:

> Curtis:
>
> I tried using the bf package, and I am able to get the meta data I need.
> However, I have some questions. First, how do I suppress the command window
> output generated by the log function? I just want to use the function to
> peel off the metadata without displaying the log which seems to be
> activated by line 111 of bfopen.m. Second, is there any way to "trim down"
> the size of the nearly 16 MB jar function so that the software can be
> ported easier? This is less important, but the bioformats_package.jar file
> seems a bit bloated. Thanks for your help.
>
> --
> Jered Wells
>
> On Thu, Jan 8, 2015 at 4:13 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>
>> Hi Jered,
>>
>> > I am trying to call Fiji's DICOM header reader from the MATLAB command
>> > line.
>>
>> Another option that might work for you would be to read your DICOM files
>> using the Bio-Formats library from within MATLAB:
>>
>> http://openmicroscopy.org/info/bio-formats/developers/matlab-dev.html
>>
>> Regards,
>> Curtis
>>
>> On Thu, Jan 8, 2015 at 11:19 AM, Jered Wells <jered.wells at gmail.com>
>> wrote:
>>
>>> OK, I've got a bit of a hacky solution, but would appreciate some
>>> additional help. I can run the following with MIJ, miji, and ImageJ
>>> libraries available:
>>>
>>> javaaddpath 'mij.jar'
>>> javaaddpath 'ij.jar'
>>>
>>> Miji(false)
>>>
>>> MIJ.run('Open...', 'path=[C:\\Users\\Admin\\Image.dcm]');
>>> MIJ.run('Show Info...', 'path=[C:\\Users\\Admin\\Image.dcm]');
>>>
>>> This produces all of the DICOM info, but requires the image and info
>>> text to be displayed. I want to run this on a server without display
>>>  capabilities, and I am still having problems actually getting the data
>>> into MATLAB. I have tried to produce a macro by using the record function,
>>> but I am having a hard time calling it from MATLAB. Thank you for your help!
>>>
>>>
>>> On Thursday, January 8, 2015 9:59:25 AM UTC-5, Jered Wells wrote:
>>>>
>>>> Hi. I am MATLAB savvy, but java illiterate, so my question likely has a
>>>> simple answer. I am trying to call Fiji's DICOM header reader from the
>>>> MATLAB command line. I've tried using MIJ and Miji, but I am stuck trying
>>>> to properly construct the syntax. I cannot use MATLAB's dicominfo function
>>>> because there is a problem with MATLAB's dicom parse mex which corrupts the
>>>> data I'm trying to get. I just need a little guidance on constructing the
>>>> proper syntax and/or macros for getting DICOM header data using Fiji from
>>>> the MATLAB command line. Thank you very much!
>>>>
>>>  --
>>> --
>>> Please avoid top-posting, and please make sure to reply-to-all!
>>>
>>> Mailing list web interface: http://groups.google.com/group/fiji-devel
>>>
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>>
>>
>
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