extract panorama about imctools HOT 4 CLOSED

Hi @laufre,

indeed, the mcdlib has been archived and is not maintained anymore in favor of imctools v2.

With imctools v2, extracting panorama images from .mcd files should be straightforward using the McdParser class. Something like:

from imctools.io.mcd.mcdparser import McdParser
buf = McdParser('/path/to/file.mcd').get_panorama_image(my_panorama_id)

However, note that .mcd files, by design, support panorama images in arbitrary image formats. Therefore, in the example above, buf is a raw data buffer (numpy array) that needs to be interpreted according to the actual file type (e.g. png) to get the image as numpy array, e.g. using OpenCV:

img = cv2.imdecode(np.frombuffer(buf, dtype=np.uint8), cv2.IMREAD_COLOR)

To my knowledge, with imtools v1, you could first save the panorama to a temporary directory using McdParser.save_panorama and then read in the image file manually. But maybe @votti or @plankter have better suggestions?

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I would strictly recommend using Imctools v2 by now and use the McdParser class there: https://bodenmillergroup.github.io/imctools/io/mcd/mcdparser.html

To look into all the panoramas available, you should look into the attribute:
McdParser.session.panoramas which is a dictionary containing all panoramas and their metadata:
https://bodenmillergroup.github.io/imctools/data/panorama.html

For imctools v1 there is the direct way is to use McdParser.save_panorama.

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In imctools v2 such functionality is also available. One can get/save slide/panorama images:

https://bodenmillergroup.github.io/imctools/io/mcd/mcdparser.html#imctools.io.mcd.mcdparser.McdParser.save_panorama_image

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Thank you for your answers, with your help I managed to extract the panoramas!

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