Manual correction of segmentations

EPI_voxel_shift.ipynb

@@ -15,7 +15,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 30,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -49,12 +49,18 @@
     "            _, y_AP, _, _ = AP.affine @ AP_center\n",
     "            _, y_PA, _ , _= PA.affine @ PA_center\n",
     "            shifts.append(abs(y_AP - y_PA))\n",
+    "        \n",
+    "        else:\n",
+    "            shifts.append(np.nan)\n",
     "\n",
     "    print(f\"number of slices with mask in AP: {number_slices_AP}\")\n",
     "    print(f\"number of slices with mask in PA: {number_slices_PA}\")\n",
     "    print(f\"number of pixels in AP: {nb_pixels_AP}\")\n",
     "    print(f\"number of pixels in PA: {nb_pixels_PA}\")\n",
-    "    print(f\"mean shift: {np.mean(shifts)}\")"
+    "    print(f\"mean shift: {np.nanmean(shifts)}\")\n",
+    "    \n",
+    "    for i, shift in enumerate(shifts):\n",
+    "        print(f\"slice {i+1}: {shift}\")"
    ]
   },
   {
@@ -66,18 +72,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 31,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "number of slices with mask in AP: 11\n",
-      "number of slices with mask in PA: 11\n",
-      "number of pixels in AP: 749.0\n",
-      "number of pixels in PA: 775.0\n",
-      "mean shift: 3.9807847795918736\n"
+      "number of slices with mask in AP: 13\n",
+      "number of slices with mask in PA: 13\n",
+      "number of pixels in AP: 805.0\n",
+      "number of pixels in PA: 819.0\n",
+      "mean shift: 4.403227149593286\n",
+      "slice 1: nan\n",
+      "slice 2: nan\n",
+      "slice 3: 3.459289659772601\n",
+      "slice 4: 6.8753930965391525\n",
+      "slice 5: 10.779171466827393\n",
+      "slice 6: 8.887372434139252\n",
+      "slice 7: 7.886060510362899\n",
+      "slice 8: 5.357269762993489\n",
+      "slice 9: 4.739796834841272\n",
+      "slice 10: 2.8452743047241498\n",
+      "slice 11: 1.090708704261509\n",
+      "slice 12: 1.3967108246568003\n",
+      "slice 13: 0.6001472286739151\n",
+      "slice 14: 0.741037568049645\n",
+      "slice 15: 2.583720548870648\n"
      ]
     }
    ],
@@ -97,7 +118,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 32,
    "metadata": {},
    "outputs": [
     {
@@ -106,9 +127,24 @@
      "text": [
       "number of slices with mask in AP: 13\n",
       "number of slices with mask in PA: 13\n",
-      "number of pixels in AP: 711.0\n",
-      "number of pixels in PA: 862.0\n",
-      "mean shift: 5.539231485758297\n"
+      "number of pixels in AP: 849.0\n",
+      "number of pixels in PA: 876.0\n",
+      "mean shift: 5.111890294531884\n",
+      "slice 1: nan\n",
+      "slice 2: nan\n",
+      "slice 3: 6.742460469085653\n",
+      "slice 4: 7.9247696562246865\n",
+      "slice 5: 10.286327992950252\n",
+      "slice 6: 6.790706107490944\n",
+      "slice 7: 4.937285813035409\n",
+      "slice 8: 3.434184109463409\n",
+      "slice 9: 2.274467921352887\n",
+      "slice 10: 1.3046958675856288\n",
+      "slice 11: 0.8610260039908084\n",
+      "slice 12: 2.6364640167781275\n",
+      "slice 13: 3.931505036641312\n",
+      "slice 14: 4.496688406436096\n",
+      "slice 15: 10.83399242787928\n"
      ]
     }
    ],
@@ -128,18 +164,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 33,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "number of slices with mask in AP: 13\n",
-      "number of slices with mask in PA: 13\n",
-      "number of pixels in AP: 803.0\n",
-      "number of pixels in PA: 904.0\n",
-      "mean shift: 2.101966181237038\n"
+      "number of slices with mask in AP: 15\n",
+      "number of slices with mask in PA: 15\n",
+      "number of pixels in AP: 820.0\n",
+      "number of pixels in PA: 783.0\n",
+      "mean shift: 3.0445504886387735\n",
+      "slice 1: 9.59101279377937\n",
+      "slice 2: 6.079096371043814\n",
+      "slice 3: 1.6616114118824825\n",
+      "slice 4: 2.1331588610123617\n",
+      "slice 5: 4.6092753410339355\n",
+      "slice 6: 2.6050749051276867\n",
+      "slice 7: 2.1473026108385938\n",
+      "slice 8: 1.0086152570272233\n",
+      "slice 9: 1.5678794860839815\n",
+      "slice 10: 2.637978437222529\n",
+      "slice 11: 1.7728752234886471\n",
+      "slice 12: 3.9833301878594725\n",
+      "slice 13: 2.308267021179205\n",
+      "slice 14: 1.3092882513999982\n",
+      "slice 15: 2.2534911706023024\n"
      ]
     }
    ],
@@ -160,18 +211,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 34,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "number of slices with mask in AP: 15\n",
-      "number of slices with mask in PA: 13\n",
-      "number of pixels in AP: 880.0\n",
-      "number of pixels in PA: 878.0\n",
-      "mean shift: 2.3297521315992045\n"
+      "number of slices with mask in PA: 15\n",
+      "number of pixels in AP: 796.0\n",
+      "number of pixels in PA: 746.0\n",
+      "mean shift: 2.6118755420771302\n",
+      "slice 1: 5.041267052130262\n",
+      "slice 2: 5.100633584536041\n",
+      "slice 3: 1.130213070401517\n",
+      "slice 4: 1.4838859421866282\n",
+      "slice 5: 2.9440719516653715\n",
+      "slice 6: 2.888957508946355\n",
+      "slice 7: 2.694792866706848\n",
+      "slice 8: 2.5471559746902415\n",
+      "slice 9: 3.3119593217097645\n",
+      "slice 10: 2.997592203599858\n",
+      "slice 11: 2.2765323330716356\n",
+      "slice 12: 3.1917546680995343\n",
+      "slice 13: 0.7590251761899509\n",
+      "slice 14: 1.0739337130290671\n",
+      "slice 15: 1.7363577641938868\n"
      ]
     }
    ],
@@ -199,7 +265,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,