Posted by
Aryeh Weiss on
May 11, 2017; 4:51am
URL: http://imagej.273.s1.nabble.com/Bioformats-importer-in-macro-tp5018696p5018698.html
On 11/05/2017 0:11, Curtis Rueden wrote:
> Hi Ed,
>
>> Is there a parameter that will open all series?
> Yes, the "Open all series" option.
>
> This records to macro something like:
>
> run("Bio-Formats", "open=" + myFile + " autoscale color_mode=Default
> open_all_series rois_import=[ROI manager] view=Hyperstack
> stack_order=XYCZT");
>
> If you need to customize which series get opened in a dynamic way, you can
> use the Bio-Formats Macro Extensions to get the number of series via
> the Ext.getSeriesCount(seriesCount) command. From that, you could
> concatenate a string variable in a loop to build up which series get
> included.
Here is an example of what Curtis suggested:
// The Bio-Formats extensions enable us to get the image dimensions,
number of series
// and other metadata without actually opening the images.
run("Bio-Formats Macro Extensions");
Ext.setId(inputPath);
Ext.getSeriesCount(seriesCount);
print(seriesCount);
Ext.getSizeX(sizeX);
Ext.getSizeY(sizeY);
Ext.getPixelType(pixelType);
// j is a loop variable -- I was opening each series in a loop to
individually process each series
run("Bio-Formats Importer", "open=["+inputPath+"] autoscale
color_mode=Default view=Hyperstack stack_order=XYCZT series_"+d2s(j,0));
inputId = getImageID(); // always grab the ID and title of the opened
image
Best regards
--aryeh
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect -
https://loci.wisc.edu/software> ImageJ2 lead, Fiji maintainer -
https://imagej.net/User:Rueden> Did you know ImageJ has a forum?
http://forum.imagej.net/>
>
> On Wed, May 10, 2017 at 4:00 PM, Ed Siefker <
[hidden email]> wrote:
>
>> I would like to import a multi scene .czi file into ImageJ with a macro.
>> I can't predict the number of series in the file.
>>
>> When using the GUI there is a "select all" function. Looking at the
>> macro recorder, it passes a parameter for each series. Since I can't
>> predict the number of series, I can't pass a parameter for each.
>>
>> Is there a parameter that will open all series?
>> -Ed
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
> --
> 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
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