Added script to run mdreg examples

Note this is not a proper test - this file probably belongs elsewhere - maybe can become the basis for a tutorial on motion correction.

ukat/mapping/tests/test_mdreg.py

@@ -0,0 +1,50 @@
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+import mdreg
+
+from ukat.mapping.t1 import T1
+
+
+def t1_maps():
+
+    # fetch data
+    data = mdreg.fetch('MOLLI')
+    array = data['array'][:,:,0,:]
+    TI = np.array(data['TI'])
+
+    # Calculate corrected uncorrected T1-map
+    map = T1(array, TI, np.eye(4))
+    np.save(os.path.join(os.getcwd(), 't1_uncorr'), map.t1_map)
+
+    # Calculate corrected corrected T1-map
+    map = T1(array, TI, np.eye(4), mdr=True)
+    np.save(os.path.join(os.getcwd(), 't1_corr'), map.t1_map)
+
+
+def plot_t1_maps():
+
+    # Plot corrected and uncorrected side by side
+    t1_uncorr = np.load(os.path.join(os.getcwd(), 't1_uncorr.npy'))
+    t1_corr = np.load(os.path.join(os.getcwd(), 't1_corr.npy'))
+    fig, ax = plt.subplots(figsize=(10, 6), ncols=2, nrows=1)
+    for i in range(2):
+        ax[i].set_yticklabels([])
+        ax[i].set_xticklabels([])
+    ax[0].set_title('T1-map without MDR')
+    ax[1].set_title('T1-map with MDR')
+    im = ax[0].imshow(t1_uncorr.T, cmap='gray', vmin=0, vmax=2000)
+    im = ax[1].imshow(t1_corr.T, cmap='gray', vmin=0, vmax=2000) 
+    fig.colorbar(im, ax=ax.ravel().tolist())
+    plt.savefig(os.path.join(os.getcwd(), 't1_mdr'))
+    plt.show()
+
+
+if __name__ == '__main__':
+
+    # t1_maps()
+    plot_t1_maps()
+
+
+
+