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glencoesoftware / isyntax2raw

iSyntax to raw format converter
BSD 3-Clause "New" or "Revised" License
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ModuleNotFoundError: No module named 'pixelengine' in python while converting the phiips isyntax format file into OME-TIFF. #11

Closed Yadav420dilip closed 4 years ago

Yadav420dilip commented 4 years ago

ModuleNotFoundError: No module named 'pixelengine' in python while converting the phiips isyntax format file into OME-TIFF or TIFF.

By following this documentation https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html#footnotes

I used python 3.6 in ubuntu 18.04.

First I download and install the philips sdk as per given instruction in documentation.

After that I downloaded isyntax2raw and install it.

After executing the following command in terminal

$ isyntax2raw write_tiles 20200207_140740.isyntax /home/dilip/new_image.tiff

The error comes

Traceback (most recent call last): File "/home/dilip/anaconda3/envs/myenv/bin/isyntax2raw", line 11, in load_entry_point('isyntax2raw==0.0.0', 'console_scripts', 'isyntax2raw')() File "/home/dilip/anaconda3/envs/myenv/lib/python3.6/site-packages/pkg_resources/init.py", line 490, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/home/dilip/anaconda3/envs/myenv/lib/python3.6/site-packages/pkg_resources/init.py", line 2859, in load_entry_point return ep.load() File "/home/dilip/anaconda3/envs/myenv/lib/python3.6/site-packages/pkg_resources/init.py", line 2450, in load return self.resolve() File "/home/dilip/anaconda3/envs/myenv/lib/python3.6/site-packages/pkg_resources/init.py", line 2456, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/home/dilip/anaconda3/envs/myenv/lib/python3.6/site-packages/isyntax2raw-0.0.0-py3.6.egg/isyntax2raw/init.py", line 15, in ModuleNotFoundError: No module named 'pixelengine'

melissalinkert commented 4 years ago

That error indicates that the Philips SDK (pixelengine) was not installed correctly. It looks like you are using Anaconda, in which case the conda list pixelengine command should tell you which version of the SDK (if any) is installed.

Yadav420dilip commented 4 years ago

That error indicates that the Philips SDK (pixelengine) was not installed correctly. It looks like you are using Anaconda, in which case the conda list pixelengine command should tell you which version of the SDK (if any) is installed.

Thanks it worked.

ghadjigeorghiou commented 3 years ago

@Yadav420dilip could you please explain or share any resources on how to install the SDK in anaconda?

Yadav420dilip commented 3 years ago

I installed into my ubuntu 20.04. Install anaconda after the create new conda environment and activate the environment and follow the following steps

At the Open Pathology portal, select Pathology SDK ► Download the required Ubuntu installer package to your system [https://www.openpathology.philips.com/pathologysdk/] ► In the Ubuntu command prompt, enter chmod 777 InstallPathologySDK.sh to go to the package directory and change the permission for InstallPathologySDK.sh. ► Go the package directory and enter ./InstallPathologySDK.sh py3. ⇨ After successful installation, a confirmation message is shown.

ghadjigeorghiou commented 3 years ago

It worked. Thanks!

pathdata commented 2 years ago

I installed into my ubuntu 20.04. Install anaconda after the create new conda environment and activate the environment and follow the following steps

At the Open Pathology portal, select Pathology SDK ► Download the required Ubuntu installer package to your system [https://www.openpathology.philips.com/pathologysdk/] ► In the Ubuntu command prompt, enter chmod 777 InstallPathologySDK.sh to go to the package directory and change the permission for InstallPathologySDK.sh. ► Go the package directory and enter ./InstallPathologySDK.sh py3. ⇨ After successful installation, a confirmation message is shown.

I did all the above and I have the SDK-2.0 installed. But the No module found import pixelengine error still appears.

Yadav420dilip commented 2 years ago

Might be sdk is not installed properly. installed sdk correctly

JoyLinWQ commented 1 year ago

I installed into my ubuntu 20.04. Install anaconda after the create new conda environment and activate the environment and follow the following steps At the Open Pathology portal, select Pathology SDK ► Download the required Ubuntu installer package to your system [https://www.openpathology.philips.com/pathologysdk/] ► In the Ubuntu command prompt, enter chmod 777 InstallPathologySDK.sh to go to the package directory and change the permission for InstallPathologySDK.sh. ► Go the package directory and enter ./InstallPathologySDK.sh py3. ⇨ After successful installation, a confirmation message is shown.

I did all the above and I have the SDK-2.0 installed. But the No module found import pixelengine error still appears.

@pathdata try ubuntu 18.04?