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

[Curtis Rueden]

Hi Jered,

> Changing the log input to 'ERROR' worked.

Great!

> For now I think the .jar file can remain large. I'm sure that I can
> try to prune it up at some later date.

Sounds good.

> Thanks for your help!

You're very welcome.

Regards,
Curtis

On Fri, Jan 9, 2015 at 5:00 AM, Jered Wells <jered.wells at gmail.com> wrote:

> Curtis:
>
> Of course, the output suppression would be that simple! Changing the log
> input to 'ERROR' worked. For now I think the .jar file can remain large.
> I'm sure that I can try to prune it up at some later date. Thanks for your
> help!
>
> --
> Jered Wells
>
> On Thu, Jan 8, 2015 at 5:50 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>
>> 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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