Add some changes suggested on #325

HenriquesLab · Dec 17, 2024 · 6a9409b · 6a9409b
1 parent 240a6b6
commit 6a9409b
Showing 1 changed file with 28 additions and 22 deletions.
diff --git a/Colab_notebooks/U-Net_3D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/U-Net_3D_ZeroCostDL4Mic.ipynb
@@ -191,8 +191,8 @@
       "cell_type": "code",
       "execution_count": null,
       "metadata": {
-        "id": "q4wM9Sr0Dbbf",
-        "cellView": "form"
+        "cellView": "form",
+        "id": "q4wM9Sr0Dbbf"
       },
       "outputs": [],
       "source": [
@@ -246,8 +246,8 @@
       "cell_type": "code",
       "execution_count": null,
       "metadata": {
-        "id": "fq21zJVFNASx",
-        "cellView": "form"
+        "cellView": "form",
+        "id": "fq21zJVFNASx"
       },
       "outputs": [],
       "source": [
@@ -698,6 +698,11 @@
         "    eps = 1e-6\n",
         "    y_true_f = K.flatten(y_true)\n",
         "    y_pred_f = K.flatten(y_pred)\n",
+        "\n",
+        "    # Cast both to float 32 to avoid issues\n",
+        "    y_true_f = K.cast(y_true_f, tf.float32)\n",
+        "    y_true_f = K.cast(y_true_f, tf.float32)\n",
+        "    \n",
         "    intersection = K.sum(y_true_f*y_pred_f)\n",
         "\n",
         "    return (2.*intersection)/(K.sum(y_true_f*y_true_f)+K.sum(y_pred_f*y_pred_f)+eps)\n",
@@ -873,6 +878,7 @@
         "                                     save_weights_only=True)\n",
         "\n",
         "        sample_batch, __ = val_generator.__getitem__(random.randint(0, len(val_generator)))\n",
+        "\n",
         "        sample_img = SampleImageCallback(self.model,\n",
         "                                         sample_batch,\n",
         "                                         model_path)\n",
@@ -1457,8 +1463,8 @@
       "cell_type": "code",
       "execution_count": null,
       "metadata": {
-        "id": "ewpNJ_I0Mv47",
-        "cellView": "form"
+        "cellView": "form",
+        "id": "ewpNJ_I0Mv47"
       },
       "outputs": [],
       "source": [
@@ -1920,9 +1926,9 @@
       "cell_type": "code",
       "execution_count": null,
       "metadata": {
+        "cellView": "form",
         "id": "iwNmp1PUzRDQ",
-        "scrolled": true,
-        "cellView": "form"
+        "scrolled": true
       },
       "outputs": [],
       "source": [
@@ -1973,8 +1979,8 @@
       "cell_type": "code",
       "execution_count": null,
       "metadata": {
-        "id": "eAJzMwPA6tlH",
-        "cellView": "form"
+        "cellView": "form",
+        "id": "eAJzMwPA6tlH"
       },
       "outputs": [],
       "source": [
@@ -2031,8 +2037,8 @@
       "cell_type": "code",
       "execution_count": null,
       "metadata": {
-        "id": "vMzSP50kMv5p",
-        "cellView": "form"
+        "cellView": "form",
+        "id": "vMzSP50kMv5p"
       },
       "outputs": [],
       "source": [
@@ -2195,6 +2201,12 @@
     },
     {
       "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "cellView": "form",
+        "id": "_XkpLksQQ-Cd"
+      },
+      "outputs": [],
       "source": [
         "\n",
         "#@markdown ##Calculate Intersection over Union and best threshold\n",
@@ -2261,13 +2273,7 @@
         "#Make a pdf summary of the QC results\n",
         "\n",
         "qc_pdf_export()"
-      ],
-      "metadata": {
-        "cellView": "form",
-        "id": "_XkpLksQQ-Cd"
-      },
-      "execution_count": null,
-      "outputs": []
+      ]
     },
     {
       "cell_type": "markdown",
@@ -2292,8 +2298,8 @@
       "cell_type": "code",
       "execution_count": null,
       "metadata": {
-        "id": "ZY_Y0Y4t8bL3",
-        "cellView": "form"
+        "cellView": "form",
+        "id": "ZY_Y0Y4t8bL3"
       },
       "outputs": [],
       "source": [
@@ -3090,4 +3096,4 @@
   },
   "nbformat": 4,
   "nbformat_minor": 0
-}
+}