Fixed bugs and added brain phantom

Author: oliverchampion

phantoms/brain/sim_brain_phantom.py

@@ -4,8 +4,10 @@
 import numpy as np
 import nibabel as nib
 from scipy.ndimage import zoom
+from utilities.data_simulation.Download_data import download_data
 
 if __name__ == "__main__":
+    download_data()
 
     DIFFUSIVE_REGIME = 'diffusive'
     BALLISTIC_REGIME = 'ballistic'
@@ -22,7 +24,7 @@
 
 
     # Ground truth
-    nii = nib.load(os.path.join(folder,'ground_truth','hrgt_icbm_2009a_nls_3t.nii.gz'))
+    nii = nib.load(os.path.join(os.path.split(os.path.split(folder)[0])[0],'download','Phantoms','brain','ground_truth','hrgt_icbm_2009a_nls_3t.nii.gz'))
     segmentation = np.squeeze(nii.get_fdata()[...,-1])
 
     with open(os.path.join(folder,'ground_truth',regime+'_groundtruth.json'), 'r') as f:

utilities/data_simulation/Download_data.py

@@ -21,7 +21,7 @@ def download_data(force=False):
         os.makedirs(os.path.join(base_folder,'download'))
         print(f"Folder '{'download'}' created.")
         # Change to the specified folder
-        os.chdir(os.path.join(base_folder,'download'))
+    os.chdir(os.path.join(base_folder,'download'))
     subprocess.run(["zenodo_get", 'https://zenodo.org/records/10696605'])
     while not os.path.exists('OSIPI_TF24_data_phantoms.zip'):
         time.sleep(1)