Output Files Out of Order For Timelapse

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Dylan
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Joined: 21.12.2014 23:59

Output Files Out of Order For Timelapse

Post by Dylan »

I have a few hundred folders that each represent a single timepoint in a timelapse of an embryo during development. Each time point folder contains about ten different jpegs, each representing a different focal plane. See attachment 1. The first problem is that when I enque all of these folders, I cannot select all of them by clicking on the first and then shift clicking on the last. I had to spend about five minutes clicking on each one manually. Is there a better way to select all? The real problem though, is when I output the focus stacked images into a new folder, they are no longer in order and it would be impossible for me to manually rename each one. How can I enque the stacks so that the output images retain the correct order of the timelapse? I've attached a zip with a few of the time point folders in case it helps.
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Stas Yatsenko
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Re: Output Files Out of Order For Timelapse

Post by Stas Yatsenko »

Yes, I can see the problem. The issue with multiple selection can be solved with recursive processing of subfolders or multiple selection. The second issue should be solved with templates for output files. We plan to add source folder name as a template parameter for naming.

Right now I can only suggest you a workaround.

Create a helicon.bat file with a text editor and add one line there:

FOR /D %%A IN (*.*) DO CALL "c:\Program Files\Helicon Software\Helicon Focus 6\HeliconFocus.exe" -silent %%~A -save:out_%%~A

Call this bat file from example folder. This command file will process all folders and saves all the outputs. You can add processing parameters as described here:

http://www.heliconsoft.com/focus/help/e ... F_COM_LINE
Dylan
Posts: 2
Joined: 21.12.2014 23:59

Re: Output Files Out of Order For Timelapse

Post by Dylan »

Thanks for the workaround, it appears to be working. I have a new problem now though. When I enque 100 folders I never get 100 stacked images back. The number varies from 96 to 99, but never 100. For my timelapse to be accurate, I can't have missing frames like this. Do you have any idea as to why this is happening?
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Stas Yatsenko
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Re: Output Files Out of Order For Timelapse

Post by Stas Yatsenko »

We already fixed an error which happens with your files (they are monochrome). I hope that we can send you a newer version in the coming days. We would appreciate if you test it again with your full set. BTW, you should be able to select multiple folders in Enqueue stacks dialog, just use button "Add multiple folders...".
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