help! Ask a question

[yangleics3333]

Hi!
After installing OCT-Converter, I ran the e2e sample program and the program reported an error as follows. What is the problem??
I hope you can help me, I will not be grateful！
python version：3.10.9
numpy version：1.24.3 or 1.21.2

Traceback (most recent call last):
File "/Users/leiyang/Desktop/CODE/spruce-data-dp/patch_eye.py", line 1, in
from oct_converter.readers import E2E
File "/Users/leiyang/anaconda3/lib/python3.10/site-packages/oct_converter/readers/init.py", line 1, in
from .boct import BOCT
File "/Users/leiyang/anaconda3/lib/python3.10/site-packages/oct_converter/readers/boct.py", line 13, in
from oct_converter.image_types import OCTVolumeWithMetaData
File "/Users/leiyang/anaconda3/lib/python3.10/site-packages/oct_converter/image_types/init.py", line 2, in
from .oct import OCTVolumeWithMetaData
File "/Users/leiyang/anaconda3/lib/python3.10/site-packages/oct_converter/image_types/oct.py", line 6, in
import matplotlib.pyplot as plt
File "/Users/leiyang/anaconda3/lib/python3.10/site-packages/matplotlib/init.py", line 109, in
from . import _api, _version, cbook, docstring, rcsetup
File "/Users/leiyang/anaconda3/lib/python3.10/site-packages/matplotlib/rcsetup.py", line 28, in
from matplotlib.fontconfig_pattern import parse_fontconfig_pattern
File "/Users/leiyang/anaconda3/lib/python3.10/site-packages/matplotlib/fontconfig_pattern.py", line 15, in
from pyparsing import (Literal, ZeroOrMore, Optional, Regex, StringEnd,
File "/Users/leiyang/anaconda3/lib/python3.10/site-packages/pyparsing/init.py", line 144, in
from .helpers import *
File "/Users/leiyang/anaconda3/lib/python3.10/site-packages/pyparsing/helpers.py", line 2, in
import html.entities
ModuleNotFoundError: No module named 'html.entities'

[yangleics3333]

[marksgraham]

Hi,

This seems to be some sort of package/dependency problem. I would suggest first starting a totally fresh anaconda environment, installing oct-converter in that, and seeing if that fixes things. If that doesn't work, it might also be worth trying with a different python version >=3.7 that is not 3.10

[yangleics3333]

First of all, thank you for your reply. The problem I mentioned above has been resolved. Thank you again.

Currently, I am running the sample program for e2e and the following code is reported. Could you please help me check what the problem is.

Thank you very much, and I am also looking forward to the moment when this program successfully runs.

The error message is as follows

[marksgraham]

I'm afraid I've seen this error once before and not been able to solve it. One suggestion is so try the eyepy readere here - this can also read .e2e and is implemented a bit differently, so it is possible it will have more luck

[Oli4]

I tried to download the file, but I seem to be required to login for downloading the file. I wanted to try it with eyepy.

[marksgraham]

Hey,

I think I have fixed. Can you reinstall the main branch using
pip install git+https://github.com/marksgraham/OCT-Converter
and let me know if it works

[yangleics3333]

Hi Mark
Thank you for your response to this question. I haven't been able to reply to your message in the past few days because I have had health issues and have been recuperating for the past few days. I have seen your reply today and will test the new program tomorrow. I will provide you with the specific results as soon as possible. Thank you, Mark!

[yangleics3333]

Hi Mark
I have run the project you specified and the result is that the image can be successfully read and retrieved. But at the same time, there is also a bad news that the obtained data content is inconsistent with what appears on the device. I will now use screenshots to place two different data results below.

data ： e2e ; SD-OCT
oct-converter

[marksgraham]

Hi,

Interesting. As a sanity check, does the data that is extracted from OCT-Converter also appear on the device? Or is is totally different?

[marksgraham]

Ok I'll take a look - can you just confirm how many fundus images and how many b-scans you expect in the .e2e file you sent me?

[yangleics3333]

what！！？？
Why is that? Can I see your running program and the data results???
After running the e2e example program in oct-converter, I only obtained one image.

[marksgraham]

did you install with pip install git+https://github.com/marksgraham/OCT-Converter to get the version with the updated reader? if you justinstall with pip install oct-converter you wouldn't get the most up-to-date version

[marksgraham]

i just ran the simple example with the updated code:

from oct_converter.readers import E2E
filepath = "/Users/mark/Downloads/data.e2e"
file = E2E(filepath)
oct_volumes =  file.read_oct_volume()

for volume in oct_volumes:
    #volume.peek(show_contours=True)  # plots a montage of the volume
    volume.save("{}_{}.png".format(volume.volume_id, volume.laterality))

fundus_images = (
    file.read_fundus_image()
)  # returns a list of all fundus images with additional metadata if available
for image in fundus_images:
    #plt.imshow(image.image)
    #plt.show()
    image.save("{}+{}.png".format(image.image_id, image.laterality))

[yangleics3333]

Thank you, Mark
I can also generate a complete dataset normally. Thank you for your help.
At the same time, I also want to ask if there is patient and other related information in E2E format data, and how to obtain this data?
For example, Dicom data, a Dicom file contains the image data itself and its related label information, such as Study ID, series ID, etc. Does E2E also have similar label data? How can I obtain them?

[marksgraham]

I've done a new release so you can get the updated version just running pip install oct-converter

[marksgraham]

Some metadata is extracted, you can see the options here: https://github.com/marksgraham/OCT-Converter/blob/main/oct_converter/image_types/oct.py#L45-L55 and access with eg oct_volume.sex, oct_volume.laterality

…

On Sat, May 20, 2023 at 7:57 AM yangleics3333 ***@***.***> wrote: Thank you, Mark I can also generate a complete dataset normally. Thank you for your help. At the same time, I also want to ask if there is patient and other related information in E2E format data, and how to obtain this data? For example, Dicom data, a Dicom file contains the image data itself and its related label information, such as Study ID, series ID, etc. Does E2E also have similar label data? How can I obtain them? — Reply to this email directly, view it on GitHub <#114 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4UIM6YH6JABY6AQY3HWJTXHDETBANCNFSM6AAAAAAXVWW7SY> . You are receiving this because you commented.Message ID: ***@***.*** com>

[yangleics3333]

Hi Mark
Thank you for your technical support these days. I will continue to explore eye related imaging data and use this project. If there are any other issues, I will provide real-time feedback. Thank you in writing, Mark