.fda error

[antoniohupa]

Hi Mark, hope you're doing well.

Recently I've installed the package with the newest updates. When I tried to execute the demo example for .fda files it throws an error (I attach a file to see it). On the other hand, this errors does not replicate with .fds files. Could you give me some orientations about?

Thanks a lot?
A
fda_error.pdf

[Oli4]

Hi Antonia,

have you tried using read_oct_volume_2() function, maybe this is a quick fix for you problem otherwise @marksgraham has to take over.

Best Oliver

[marksgraham]

Hi @antoniohupa

Is this using your own data, or the file in the demo? And do you think this error didn't occur in a previous version?

It looks like it isn't finding any slices in your data. Could you run print(oct_volume) just after you read it?

If you're able to share this scan I could take a look too.

[antoniohupa]

Hi Mark It happens with both, your and my own data. That did not happen with previous versions of the library. When I print(oct_volume) it returns the following: <oct_converter.image_types.oct.OCTVolumeWithMetaData object at 0x0000022F5F8BAF40> Regards A El mié, 22 mar 2023 a las 20:25, Mark Graham ***@***.***>) escribió:

…

Hi @antoniohupa <https://github.com/antoniohupa> Is this using your own data, or the file in the demo? And do you think this error didn't occur in a previous version? It looks like it isn't finding any slices in your data. Could you run print(oct_volume) just after you read it? If you're able to share this scan I could take a look too. — Reply to this email directly, view it on GitHub <#97 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AK4HAUX65XY2LA7FHLQQXTDW5NG2PANCNFSM6AAAAAAWDVFHUE> . You are receiving this because you were mentioned.Message ID: ***@***.*** com>

[shojaeinia]

Hi Mark, hope you're doing well.

Recently I've installed the package with the newest updates. When I tried to execute the demo example for .fda files it throws an error 👍
TypeError Traceback (most recent call last)
in <cell line: 8>()
6
7 oct_volume = (
----> 8 fda.read_oct_volume()
9 ) # returns an OCT volume with additional metadata if available
10 oct_volume.peek(show_contours=True) # plots a montage of the volume

2 frames
/usr/local/lib/python3.10/dist-packages/oct_converter/readers/fda.py in read_any_info_and_make_dict(self, chunk_name)
347 with open(self.filepath, "rb") as f:
348 chunk_location, chunk_size = self.chunk_dict[chunk_name]
--> 349 f.seek(chunk_location) # Set the chunk’s current position.
350 raw = f.read()
351 header_name = f"{chunk_name.decode().split('@')[-1].lower()}_header"

TypeError: 'list' object cannot be interpreted as an integer

[marksgraham]

Hi,

Could you check if this works for you with the example file from the Biobank, download link in the example script: https://github.com/marksgraham/OCT-Converter/blob/main/examples/demo_fda_extraction.py