remove psutils and fury dependency from setup.py

.github/workflows/run_tests.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest Cython
+          pip install pytest Cython fury
           pip install torch==2.1.0 -f https://download.pytorch.org/whl/cpu
           pip install .
 

.github/workflows/run_tests_os.yml

@@ -24,7 +24,7 @@ jobs:
       if: runner.os == 'Linux'
       run: |
         python -m pip install --upgrade pip
-        pip install pytest Cython
+        pip install pytest Cython fury
         pip install torch==2.0.0 -f https://download.pytorch.org/whl/cpu
         pip install .
 

.github/workflows/run_tests_subtasks.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest Cython
+          pip install pytest Cython fury
           pip install torch==2.2.0 -f https://download.pytorch.org/whl/cpu
           pip install .
 

README.md

@@ -19,7 +19,7 @@ Install dependencies:
 * [Pytorch](http://pytorch.org/) >= 2.0.0
 
 Optionally:
-* if you use the option `--preview` you have to install xvfb (`apt-get install xvfb`)
+* if you use the option `--preview` you have to install xvfb (`apt-get install xvfb`) and fury (`pip install fury`)
 
 
 Install Totalsegmentator

setup.py

@@ -14,13 +14,11 @@
         install_requires=[
             'torch>=2.0.0',
             'numpy',
-            'psutil',
             'SimpleITK',
             'nibabel>=2.3.0',
             'tqdm>=4.45.0',
             'p_tqdm',
             'xvfbwrapper',
-            'fury',
             'nnunetv2>=2.2.1',
             'requests==2.27.1;python_version<"3.10"',
             'requests;python_version>="3.10"',

totalsegmentator/resampling.py

@@ -3,11 +3,11 @@
 import os
 import time
 import importlib
+import multiprocessing
 
 import numpy as np
 import nibabel as nib
 from scipy import ndimage
-import psutil
 from joblib import Parallel, delayed
 
 cupy_available = importlib.util.find_spec("cupy") is not None
@@ -44,7 +44,7 @@ def _process_gradient(grad_idx):
     if dim == 3:
         img = img[..., None]
 
-    nr_cpus = psutil.cpu_count() if nr_cpus == -1 else nr_cpus
+    nr_cpus = multiprocessing.cpu_count() if nr_cpus == -1 else nr_cpus
     img_sm = Parallel(n_jobs=nr_cpus)(delayed(_process_gradient)(grad_idx) for grad_idx in range(img.shape[3]))
     img_sm = np.array(img_sm).transpose(1, 2, 3, 0)  # grads channel was in front -> put to back
     # Remove added dimensions