automated downloading from zenodo

Author: oliverchampion

.gitignore

@@ -9,6 +9,12 @@ __pycache__/
 *.mat
 *.raw
 bvals.txt
+download
+md5sums.txt
+*.gz
+*.zip
+*.tmp
+
 # Unit test / coverage reports
 .tox/
 .coverage

phantoms/MR_XCAT_qMRI/sim_ivim_sig.py

@@ -2,21 +2,23 @@
 from scipy.io import loadmat
 import nibabel as nib
 import json
+from utilities.data_simulation.Download_data import download_data
 
 ##########
 # code written by Oliver J Gurney-Champion
 # code adapted from MAtlab code by Eric Schrauben: https://github.com/schrau24/XCAT-ERIC
 # This code generates a 4D IVIM phantom as nifti file
 
-def phantom(bvalue, noise, TR=8000, TE=80, motion=False, rician=False, interleaved=False):
+def phantom(bvalue, noise, TR=3000, TE=40, motion=False, rician=False, interleaved=False):
+    download_data()
     np.random.seed(42)
     if motion:
         states = range(1,21)
     else:
         states = [1]
     for state in states:
         # Load the .mat file
-        mat_data = loadmat('XCAT_MAT_RESP/XCAT5D_RP_' + str(state) + '_CP_1.mat')
+        mat_data = loadmat('../../download/Phantoms/XCAT_MAT_RESP/XCAT5D_RP_' + str(state) + '_CP_1.mat')
 
         # Access the variables in the loaded .mat file
         XCAT = mat_data['IMG']

requirements.txt

@@ -7,4 +7,5 @@ joblib
 dipy
 matplotlib
 scienceplots
-cvxpy
+cvxpy
+zenodo-get

utilities/data_simulation/Download_data.py

@@ -0,0 +1,29 @@
+import zipfile
+import os
+import subprocess
+import time
+
+def download_data(force=False):
+    # Check if the folder exists, and create it if not
+    base_folder = os.path.abspath(os.path.dirname(__file__))
+    base_folder = os.path.split(os.path.split(base_folder)[0])[0]
+    if not os.path.exists(os.path.join(base_folder,'download')):
+        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'))
+    subprocess.run(["zenodo_get", 'https://zenodo.org/records/10696605'])
+    while not os.path.exists('OSIPI_TF24_data_phantoms.zip'):
+        time.sleep(1)
+    # Open the zip file
+    if force or not os.path.exists('Data'):
+        with zipfile.ZipFile('OSIPI_TF24_data_phantoms.zip', 'r') as zip_ref:
+            # Extract all the contents to the destination folder
+            zip_ref.extractall('.')
+        while not os.path.exists('Data'):
+            time.sleep(10)
+        while not os.path.exists('Phantoms'):
+            time.sleep(10)
+        while not os.path.exists('Utilities'):
+            time.sleep(10)
+        time.sleep(10)