ImageJ - Re: spaces in path with Bioformats

ImageJ

Re: spaces in path with Bioformats

Posted by Aryeh Weiss on Jul 16, 2014; 7:21pm
URL: http://imagej.273.s1.nabble.com/spaces-in-path-with-Bioformats-tp5008616p5008780.html

On 7/16/14, 10:14 PM, Curtis Rueden wrote:

> Hi Aryeh,
>
> > I find that the spaces in the path cause the BIo-Formats macro
> > extensions to fail
>
> I cannot reproduce this problem on my OS X 10.9 system.
>
> Running this macro in the Script Editor:
>
> https://github.com/openmicroscopy/bioformats/blob/v5.0.2/components/bio-formats-plugins/utils/macros/basicMetadata.txt
>
> And selecting a file with path "/Users/curtis/Desktop/foo bar/2 ch
> ZT.lsm", it prints the metadata to the ImageJ Log window as expected.
>
> If you can create a minimal, complete, verifiable example [1], then
> please pass it on to the Bio-Formats developers using the ome-users
> mailing list [2].
>
> Regards,
> Curtis
>
> [1] http://stackoverflow.com/help/mcve
> [2] http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/
>
>

Hi Curtis,

I will try to provide a minimal script.
However, it occurs to me that this may be related to my disk being NTFS
and mounted
by OSX-FUSE.

Best regards,
--aryeh

> On Mon, Jul 14, 2014 at 11:36 PM, Aryeh Weiss <[hidden email]
> <mailto:[hidden email]>> wrote:
>
> Hi Curtis,
>
> I am starting to migrate to python, but it is still much faster
> for me to use (or reuse) parts of scripts which I have already
> written. It is also easier for me to give macro scripts to people
> who ask me for assistance.
>
> Best regards,
> --aryeh
>
>
> On 7/14/14, 11:31 PM, Curtis Rueden wrote:
>> Hi Aryeh,
>>
>> > I find that the spaces in the path cause the BIo-Formats macro
>> > extensions to fail
>>
>> I did not have time to delve into what causes this bug, but
>> perhaps the whole issue could be avoided by using any scripting
>> language besides ImageJ macros? If you did that, you could call
>> the Bio-Formats API directly; see:
>> http://fiji.sc/Bio-Formats#Scripting
>>
>> Regards,
>> Curtis
>>
>>
>> On Tue, Jul 8, 2014 at 4:14 AM, Aryeh Weiss <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> I have an external disk whose designation includes spaces. I
>> am running OSX 10.9.
>> I find that the spaces in the path cause the BIo-Formats
>> macro extensions to fail,
>> I tried escaping the spaces, as in:
>>
>> newInputPath = replace(inputPath," ", "\\\\ ");
>> Ext.setId(inputPath);
>>
>> and I tried enclosing the path in square brackets, as in:
>> Ext.setId("["+inputPath+"]");
>>
>> but neither of these worked.
>>
>> As a workaround, I set up a symlink to the mount point, and
>> then replaced the path, as in:
>> if (indexOf(inputPath,"Seagate Expansion Drive") > 0) {
>> inputPath = replace(inputPath, "Seagate Expansion Drive",
>> "seagate");
>> }
>>
>>
>> and this works fine, but it is a hack.
>>
>> I prefer one (or both) of two options:
>>
>> 1. Get the extensions to accept the original path with spaces.
>> 2. Get OSX to mount the disk by default with a mount
>> directory whose name does not include spaces.
>>
>> The second option is not about ImageJ, but maybe there are
>> people on this list who knowhow to do that.
>>
>> Thank in advance for your help.
>>
>> --aryeh
>>
>> --
>> Aryeh Weiss
>> Faculty of Engineering
>> Bar Ilan University
>> Ramat Gan 52900 Israel
>>
>> Ph: 972-3-5317638
>> FAX: 972-3-7384051
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
>
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph: 972-3-5317638
> FAX: 972-3-7384051
>
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph: 972-3-5317638
FAX: 972-3-7384051

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html