Upd batch #230
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Upd batch #230
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btbest
approved these changes
Feb 22, 2023
documentation/basics/batch.md
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| The next step is the actual batch processing itself. In the **Batch Prediction Output Locations** applet, the user can configure the output format using the **Choose Settings** button. This allow for example to save the results of the workflow as `.png` images rather than `.tiff` or `.h5` files. For novice users the default settings should be fine, however the results of some workflows such as the [density counting workflow]({{site.baseurl}}/documentation/counting/counting.html) cannot be exported in some of these formats (**hdf5 file format is supported by all workflows**). | ||
| #### How do I specify the internal dataset in a `.hdf5`/`.z5`-file? | ||
| It is currently not possible to specify the internal dataset with the graphical user interface, use the [headless mode][headless], or [Fiji plugin](https://github.com/ilastik/ilastik4ij#ilastik-imagej-modules) to process that data. | ||
| Alternatively you could create `hdf5` files with only single virtual dataset each, that point to the file that has multiple ones. |
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I don't follow how this suggestion achieves "specifying the internal dataset". Are we asking the user to wrap the batch processing output in another h5?
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yeah, maybe that's a tad too advanced... So in h5 there is the concept of virtual datasets. So what I'm suggesting is to create one for each of the internal paths - such h5 files would appear as if there were only a single dataset. I'll scratch that remark, and wait until such a question actually comes up (in the forum) or we devote some time on improving the ui :)
Co-authored-by: Benedikt Best <[email protected]>
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thank you @btbest for the great suggestions 🙌 |
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Batch processing docs were quite outdated, referencing steps that were just not there anymore.
Summary:
fixes #64