monai_crf_vs_simplecrf.py

# Install required packages:
# !pip -q install simplecrf nibabel wget
# !BUILD_MONAI=1 pip -q install git+https://github.com/Project-MONAI/MONAI#egg=monai

from monai.networks.blocks import CRF

import wget
import nibabel
import denseCRF3D
import numpy as np
import torch

from functools import wraps
from time import time

# define a simple timing decorator, use for both simplecrf's densecrf3d and monai's CRF
def timing(f):
    @wraps(f)
    def wrap(*args, **kw):
        ts = time()
        result = f(*args, **kw)
        te = time()
        print('func:%r took: %2.4f sec' % (f.__name__, te-ts))
        return result
    return wrap
    
# run functions to get timings on the two functions
# densecrf3d run with timing
@timing
def densecrf3d(I, P, param):
    return denseCRF3D.densecrf3d(I, P, param)

# MONAI's CRF run with timing
@timing
def runmonaicrf(I, P, crf_func):
  return crf_func(P, I)

def load_sample_data():
    # download sample data used in this example from github simplecrf repository
    wget.download('https://github.com/HiLab-git/SimpleCRF/raw/master/data/2013_12_1_img.nii.gz')
    wget.download('https://github.com/HiLab-git/SimpleCRF/raw/master/data/2013_12_1_init.nii.gz')

    # Load some sample data
    I1Nii = nibabel.load('2013_12_1_img.nii.gz')
    PNii  = nibabel.load('2013_12_1_init.nii.gz')
    I1 = I1Nii.get_data()
    P  = PNii.get_data()

    # convert input to intenstiy range of [0, 255]
    I = np.asarray([I1], np.float32)
    I = np.transpose(I, [1, 2, 3, 0])
    I = I / I.max()* 255
    I = np.asarray(I, np.uint8)

    # probability map for each class
    P = 0.5 + (P - 0.5) * 0.8
    P = np.asarray([1.0 - P, P], np.float32)
    P = np.transpose(P, [1, 2, 3, 0])

    return I, P

if __name__ == '__main__':
    I, P = load_sample_data()

    print(I.shape)
    print(P.shape)

    # define same number of iterations to run for each method
    ITERATIONS = 20
    
    # run both methods on cpu

    # 1. SimpleCRF's CRF with ITERATIONS
    dense_crf_param = {}
    dense_crf_param['MaxIterations'] = ITERATIONS
    dense_crf_param['PosW'] = 3
    dense_crf_param['PosRStd'] = 1
    dense_crf_param['PosCStd'] = 1
    dense_crf_param['PosZStd'] = 1
    dense_crf_param['BilateralW'] = 5
    dense_crf_param['BilateralRStd'] = 5
    dense_crf_param['BilateralCStd'] = 5
    dense_crf_param['BilateralZStd'] = 5
    dense_crf_param['ModalityNum'] = 1
    dense_crf_param['BilateralModsStds'] = (5,)

    lab = densecrf3d(I, P, dense_crf_param)

    # 2. MONAI's CRF with ITERATIONS - CPU
    device='cpu'
    I_pt = np.moveaxis(I, source=-1, destination=0)
    P_pt = np.moveaxis(P, source=-1, destination=0)
    I_pt = np.expand_dims(I_pt, axis=0)
    P_pt = np.expand_dims(P_pt, axis=0)
    I_pt = torch.from_numpy(I_pt).to(dtype=torch.float, device=torch.device(device))
    P_pt = torch.from_numpy(P_pt).to(dtype=torch.float, device=torch.device(device))

    crf_func = CRF(
        bilateral_weight=5.0,
        gaussian_weight=3.0,
        bilateral_spatial_sigma=1.0,
        bilateral_color_sigma=5.0,
        gaussian_spatial_sigma=0.5,
        update_factor=5.0,
        compatibility_kernel_range=1,
        iterations=ITERATIONS,
    )

    runmonaicrf(I_pt, P_pt, crf_func)

    ## output of the script on my local machine:
    # func:'densecrf3d' took: 5.8184 sec
    # func:'runmonaicrf' took: 177.5296 sec

If you have further questions, I recommend sending me a message on MONAI slack channel: https://github.com/Project-MONAI/MONAI#community - I will be happy to help you more with this!

how can i install this version please

BUILD_MONAI=1 pip install git+https://github.com/Project-MONAI/MONAI#egg=monai

Please see https://docs.monai.io/en/stable/installation.html#option-1-as-a-part-of-your-system-wide-module for details about installation.
You need to type the BUILD_MONAI=1 pip install git+https://github.com/Project-MONAI/MONAI#egg=monai in your terminal to build the CRF features in monai. More details about this are in the link I mentioned in this commnet.

when i try that, i get an error :

C:\Users\Demo 1A\Documents>BUILD_MONAI=1 pip install --no-build-isolation git+https://github.com/Project-MONAI/MONAI#egg=monai
'BUILD_MONAI' n’est pas reconnu en tant que commande interne
ou externe, un programme exécutable ou un fichier de commandes.

Do you know why i get this error when using BUILD_MONAI=1 before pip ?

when i try that, i get an error :

C:\Users\Demo 1A\Documents>BUILD_MONAI=1 pip install --no-build-isolation git+https://github.com/Project-MONAI/MONAI#egg=monai
'BUILD_MONAI' n’est pas reconnu en tant que commande interne
ou externe, un programme exécutable ou un fichier de commandes.

Do you know why i get this error when using BUILD_MONAI=1 before pip ?

Are you using windows?
Then try the following from cm/powersheel:
set BUILD_MONAI=1
pip install --no-build-isolation git+https://github.com/Project-MONAI/MONAI#egg=monai

Note: you will need relevant compilation tools on your Windows machine as this is compiling the monai c++ code. If the above fails then try to use python setup and see what error it gives:
set BUILD_MONAI=1
git clone https://github.com/Project-MONAI/MONAI
cd MONAI
python setup.py install

hello , i did run this on my virtuel env

set BUILD_MONAI=1
git clone https://github.com/Project-MONAI/MONAI
cd MONAI
python setup.py install

it looks like it managed to finish the processing of the dependencies

Finished processing dependencies for monai==1.1.0+105.g354c9c2b

however when i run my script to apply the CRF , i still get the same error :

monai.utils.module.OptionalImportError: import monai._C (No module named 'monai._C').

Do you have an idea why is that ?

Hi @anisaaaaaaaaaaaa ,
Thats good progress. I can see that you are able to run setup and from your previous comment it appears you are using powershell and that BUILD_MONAI was not detected by setup.py script.

I think I know the issue here. For compiling MONAI you need to set environment variable BUILD_MONAI=1. However, on windows there are two methods of setting this depending on whether you are using CMD or Powershell.

On CMD it should be as I told in my previous comment:

set BUILD_MONAI=1
git clone https://github.com/Project-MONAI/MONAI
cd MONAI
python setup.py install

On Powershell it should be the following (notice env variable is set differently here):

$env:BUILD_MONAI=1
git clone https://github.com/Project-MONAI/MONAI
cd MONAI
python setup.py install

Once you are able to run this command and no longer see the message:
"Please set environment variable BUILD_MONAI=1 to enable Cpp/CUDA extension build."

Then we can debug whether your machine has any issues compiling the CPP code. Until now, it has not attempted compiling CPP because BUILD_MONAI was not properly set.

Hope this helps.

hello @masadcv , i managed to run this lines with powershell on windows:

set BUILD_MONAI=1
git clone https://github.com/Project-MONAI/MONAI
cd MONAI
python setup.py install

it looks like it managed to finish the processing of the dependencies

Finished processing dependencies for monai==1.1.0+105.g354c9c2b

however when i run my script to apply the CRF , i still get the same error :

monai.utils.module.OptionalImportError: import monai._C (No module named 'monai._C').

Do you have an idea why is that ?

For Powershell, you need to change set BUILD_MONAI=1 to $env:BUILD_MONAI=1 as I indicated in my last comment

Successful install does not mean it has compiled CPP code. Check install logs and you will see that it skipped compilation because BUILD_MONAI was not set using proper method for Powershell

okey i see,

I stick with the cmd then ,

I just run the comand lines

set BUILD_MONAI=1
git clone https://github.com/Project-MONAI/MONAI
cd MONAI
python setup.py install

Now i get this error :

C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.2\include\crt/host_config.h(160): fatal error C1189: #error:  -- unsupported Microsoft Visual Studio version! Only the versions between 2017 and 2019 (inclusive) are supported! The nvcc flag '-allow-unsupported-compiler' can be used to override this version check; however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.
error: command 'C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v11.2\\bin\\nvcc.exe' failed with exit code 2

Do you know why i get this one ?

Now i get this error :

C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.2\include\crt/host_config.h(160): fatal error C1189: #error:  -- unsupported Microsoft Visual Studio version! Only the versions between 2017 and 2019 (inclusive) are supported! The nvcc flag '-allow-unsupported-compiler' can be used to override this version check; however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.
error: command 'C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v11.2\\bin\\nvcc.exe' failed with exit code 2

Do you know why i get this one ?

Hi @anisaaaaaaaaaaaa ,
Thanks for getting back with the error message you get.
This error means you have unsupported Microsoft Visual Studio version. As the error states, you need a version between 2017 and 2019 to compile this on your machine.

If you need more help on this, I recommend taking this conversation offline. As mentioned above, please try to reach me on Slack and I can help guide you.

If you want to fix this on your own, look at installing Microsoft Visual Studio 2017 or 2019 with C++ build tools.

hey @masadcv ,

Thanks you for your help.

It would be grreat , what is your slack ?

Hi @AnisBoubekeur
If you join MONAI slack using instructions from here: https://github.com/Project-MONAI/MONAI#community
You can send me message at: Muhammad Asad with the same profile picture.
I would be happy to assist you further with this setup.