batch processing with .dv files not working

[hornt]

Dear all,

I have multiple deltavision files (.dv) that I want to process using stack commands. I recorded a macro that works fine with already opened .dv files. However as I have many of them I would like to run it on batch processing. Unfortunately in batch mode ImageJ just opens the .dv files and then stops. If I manually convert the .dv files into tiff and then use batch processing everything works fine. I then tried to batch convert the files into tiff, but get the same: .dv opens and nothing more happens. I started EventLister and got the following entries:

1) run macro with 2 tiff files in input folder:

Executed "Macro... " command
Executed "Stack to Hyperstack..." command
Executed "Z Project..." command
Executed "Stack to Hyperstack..." command
Executed "Z Project..." command


2) run macro with 2 .dv files in input folder:

Executed "Macro... " command
Updated "RNAi6-zen2-6.3-02_01_R3D.dv"
Opened "RNAi6-zen2-6.3-02_01_R3D.dv"
Updated "RNAi6-zen2-6.3-02_02_R3D.dv"
Opened "RNAi6-zen2-6.3-02_02_R3D.dv"

Same for batch converting. I guess the update process (what ever is updating here) is preventing the macro to start. I have two plugins that can read .dv files (Input-Output and LOCI), but both result in the Update and Opened message in EventLister.
Anyone an idea how I can get the macro running on batch or how I can batch convert my .dv files to tiff, maybe with another program ?

Cheers,

Thorsten

[ctrueden]

Hi Thorsten,

> I recorded a macro that works fine with already opened .dv files.
> However as I have many of them I would like to run it on batch
> processing.

Here are some macros that can process all DeltaVision (or other format)
files in a folder. If you choose one that is close, you can tweak it to
your needs by pasting in your own macro code.

https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/loci-plugins/utils/macros/recursiveTiffConvert.txt

https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/loci-plugins/utils/macros/dvSplitTimePoints.txt

https://github.com/openmicroscopy/bioformats/blob/v4.4.6/components/loci-plugins/utils/macros/batchTiffConvert.txt

You can read more about Bio-Formats + ImageJ at:
http://openmicroscopy.org/site/support/bio-formats/users/imagej/

Regards,
Curtis



On Mon, Mar 11, 2013 at 6:20 PM, hornt <[hidden email]> wrote:

> Dear all,
>
> I have multiple deltavision files (.dv) that I want to process using stack
> commands. I recorded a macro that works fine with already opened .dv files.
> However as I have many of them I would like to run it on batch processing.
> Unfortunately in batch mode ImageJ just opens the .dv files and then stops.
> If I manually convert the .dv files into tiff and then use batch processing
> everything works fine. I then tried to batch convert the files into tiff,
> but get the same: .dv opens and nothing more happens. I started EventLister
> and got the following entries:
>
> 1) run macro with 2 tiff files in input folder:
>
> Executed "Macro... " command
> Executed "Stack to Hyperstack..." command
> Executed "Z Project..." command
> Executed "Stack to Hyperstack..." command
> Executed "Z Project..." command
>
>
> 2) run macro with 2 .dv files in input folder:
>
> Executed "Macro... " command
> Updated "RNAi6-zen2-6.3-02_01_R3D.dv"
> Opened "RNAi6-zen2-6.3-02_01_R3D.dv"
> Updated "RNAi6-zen2-6.3-02_02_R3D.dv"
> Opened "RNAi6-zen2-6.3-02_02_R3D.dv"
>
> Same for batch converting. I guess the update process (what ever is
> updating
> here) is preventing the macro to start. I have two plugins that can read
> .dv
> files (Input-Output and LOCI), but both result in the Update and Opened
> message in EventLister.
> Anyone an idea how I can get the macro running on batch or how I can batch
> convert my .dv files to tiff, maybe with another program ?
>
> Cheers,
>
> Thorsten
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.n6.nabble.com/batch-processing-with-dv-files-not-working-tp5002106.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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