Add images tutorial #1470
Add images tutorial #1470
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@weiglszonja let's move forward with this. I think the content we already have here is good. It doesn't cover everything yet but let's get this out before the user days to increase our tutorial coverage |
Co-authored-by: Ben Dichter <[email protected]>
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This content would need to be removed from NWBFile basics |
…tBorders/pynwb into docs/add_images_tutorial
docs/gallery/domain/images.py
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| unit="n.a.", | ||
| external_file=external_file, | ||
| format="external", | ||
| starting_frame=[0], |
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If you use multiple movie files, I believe you would need a starting_frame value for each file.
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I'm not sure how many frames are in each movie file, but assuming "file_1.tiff" and "file_2.tiff" contain 2 frames and "file_2.tiff" contains 3 frames, I believe the correct value for starting_frame should bestarting_frame=[0, 2, 6],
According to the schema of ImageSeries:
Each external image may contain one or more consecutive frames of the full
ImageSeries. This attribute serves as an index to indicate which frames each file
contains, to faciliate random access. The 'starting_frame' attribute, hence,
contains a list of frame numbers within the full ImageSeries of the first frame
of each file listed in the parent 'external_file' dataset. Zero-based indexing is
used (hence, the first element will always be zero). For example, if the
'external_file' dataset has three paths to files and the first file has 5 frames,
the second file has 10 frames, and the third file has 20 frames, then this
attribute will have values [0, 5, 15]. If there is a single external file that
holds all of the frames of the ImageSeries (and so there is a single element in
the 'external_file' dataset), then this attribute should have value [0].
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Related to #1318 - if we get an answer on that issue I can close it
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@CodyCBakerPhD thanks for pointing us to this issue. I just added a response based on my understanding of the schema. I hope this helps clarify things a bit.
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@oruebel thank you for this example! I'll extend the external file section with this description (or a shorter version of it) to make this clear.
Co-authored-by: Oliver Ruebel <[email protected]>
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@oruebel I learnt a lot from the suggestions, thank you for them! Now only the thumbnail image is missing, do you have an idea how it should look like? |
That's great! The PowerPoint file with the source of all the other thumbnails is here |
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@oruebel how about this? |
Looks great! |
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@oruebel @bendichter thank you for the suggestions! |
Motivation
Create a new tutorial that demonstrates how to use the image module for adding images to an NWB File.
The images tutorial covers the following data types:
pynwb.image.GrayscaleImage,pynwb.image.RGBImage,pynwb.image.RGBAImagepynwb.image.OpticalSeriespynwb.image.ImageSeries,pynwb.image.ImageMaskSeries,pynwb.image.IndexSeries(which was changed recently)Checklist
flake8from the source directory.