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didymo / OnkoDICOM

OnkoDICOM was created with Radiation Oncologists to allow Radiation Oncologists to do research on DICOM standard image sets (DICOM-RT, CT, MRI, PET) using open source technologies, such as pydicom, dicompyler-core, PySide6, PIL, and matplotlib. OnkoDICOM is cross platform, open source software, and welcomes contributions. OnkoDICOM was inspired by dicompyler.
https://onkodicom.com.au
GNU Lesser General Public License v2.1
62 stars 42 forks source link

Running in Windows 10 #7

Closed jmgo closed 3 years ago

jmgo commented 5 years ago

Hi I was trying to run your code but I can't get past the error below. I am running windows 10 and python3.6

Is this code meant for running in Windows? Also is it possible to provide some screenshoots of the software?

Traceback (most recent call last): File "C:\Users\xxxx.xxx\Desktop\Onko-master\src\View\ProgressBar.py", line 58, in run self.dataset_rtss, self.dataset_rtdose, self.rois, self.my_callback) File "C:\Users\xxxx.xxx\Desktop\Onko-master\src\View\ProgressBar.py", line 191, in calc_dvhs p.start() File "C:\Users\xxxx.xxx\AppData\Local\conda\conda\envs\python36\lib\multiprocessing\process.py", line 105, in start self._popen = self._Popen(self) File "C:\Users\xxxx.xxx\AppData\Local\conda\conda\envs\python36\lib\multiprocessing\context.py", line 223, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "C:\Users\xxxx.xxx\AppData\Local\conda\conda\envs\python36\lib\multiprocessing\context.py", line 322, in _Popen return Popen(process_obj) File "C:\Users\xxxx.xxx\AppData\Local\conda\conda\envs\python36\lib\multiprocessing\popen_spawn_win32.py", line 65, in init reduction.dump(process_obj, to_child) File "C:\Users\xxxx.xxx\AppData\Local\conda\conda\envs\python36\lib\multiprocessing\reduction.py", line 60, in dump ForkingPickler(file, protocol).dump(obj) TypeError: can't pickle Extended objects Traceback (most recent call last): File "", line 1, in File "C:\Users\xxxx.xxx\AppData\Local\conda\conda\envs\python36\lib\multiprocessing\spawn.py", line 105, in spawn_main exitcode = _main(fd) File "C:\Users\xxxx.xxx\AppData\Local\conda\conda\envs\python36\lib\multiprocessing\spawn.py", line 115, in _main self = reduction.pickle.load(from_parent) EOFError: Ran out of input

helenaibro commented 5 years ago

Hi, We are aware of the issue and currently working on it. For the moment the code can only be ran on Linux. Thank you for letting us know!

jmgo commented 5 years ago

Thank you for the information!

sjswerdloff commented 4 years ago

I found that I was able to get the software running on: Ubuntu 18.04 (downloaded the VM from osboxes.org) but I chose to:

sudo apt install virtualenv sudo apt install git

and I had to:

sudo apt install gcc sudo apt install python3-dev

before I was able to successfully git clone https://github.com/didymo/OnkoDICOM.git and then pip install -r requirements.txt

binary executables will be nice when they are available. For developers, it would be nice if all of the required packages were available via conda/Anaconda.

As an aside, I used virtualenv to isolate the Python environment: virtualenv --python=python3 envOnkoDICOM source envOnkoDICOM/bin/activate

before I did the "pip install" of the various python packages.

Balkanize-You commented 4 years ago

Thank you for documenting how you performed an install. I have added installation instructions based off what you wrote.

I looked into Anaconda and it seems that most of the packages that are required by Onko are not available, I'm not sure how to move forward with that but if there is a pathway forward I'd be happy to take a look.

oismaster commented 4 years ago

@sjswerdloff Thank you for the comments, I will see that the install instructions are posted and that I have verified that they work on a clean Ubuntu 18.10 LTS install. I'm new to this stuff, so bear with me.

@Balkanize-You Apologies that it doesn't work in Windows. This is our first release version and it came from the initial coding done in an Ubuntu environment. We are currently trying to get an EXE up and working but as you probably know, working perfectly in one environment is no guarantee in another. Interestingly, I was able to get it running in Visual Studio, but the window sizing was all wrong (my laptop has a roughly 3000x2000 pixel screen and it looked like I was getting a fixed number of pixels rather than a percentage. Since then we did implement screen resize but I haven't retested in VS. Try the community version perhaps?

A

oismaster commented 4 years ago

@sjswerdloff I tried your instructions and they worked, but then I did something and it went wacko (my fault, not yours).

On a fresh Ubuntu VM, I needed to do the following to get OnkoDICOM working: sudo apt install git gcc python3-pip git clone https://github.com/didymo/OnkoDICOM.git cd OnkoDICOM/ pip3 install -r requirements.txt python3 main.py

@Balkanize-You we have successfully got an EXE together but it has revealed some problems with the coding practices (something about relative or absolute addressing which is unclear to me). The install was 258MB which is why we have decided to not put it out for distribution. The other thing which was needing an obvious fix was the left window pane being fixed rather than adjustable. I'll let you know when we have corrected these initial glaring problems.

In the meantime, why not try VirtualBox (make sure you add the Extensions and Additions) and a OSboxes.org Ubuntu virtual machine?

celeron533 commented 4 years ago

Hi @jmgo

Tested that latest OnkoDicom master branch is able to run on Windows 10.

image

My environment:

Launched from both VisualStudio and Pycharm with virtual environment without problems

oismaster commented 4 years ago

Excellent! I saw it working during the week on Windows 10 also.

Remember that it is very early software. One bug we have discovered is that the de-identification function is not 'water-tight'. That along with many other issues is being worked on.

A new team for 2020 is hopefully about to start and get a handover from the current team.

A

On Sat, 7 Dec 2019 at 16:34, Allen Zhu notifications@github.com wrote:

Hi @jmgo https://github.com/jmgo

Tested that latest OnkoDicom master branch is able to run on Windows 10.

[image: image] https://user-images.githubusercontent.com/3608762/70369449-655e7f00-18f4-11ea-8777-32f66b9e346d.png

My environment:

Launched from both VisualStudio and Pycharm with virtual environment

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