Update notebooks (#45)

aramis-lab · May 30, 2024 · 95897d9 · 95897d9
1 parent 364bebb
commit 95897d9
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Showing 10 changed files with 342 additions and 342 deletions.
diff --git a/notebooks/generate.ipynb b/notebooks/generate.ipynb
@@ -3,17 +3,17 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "98e2c0cc",
+   "id": "6b249afa",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Uncomment this cell if running in Google Colab\n",
-    "!pip install clinicadl==1.3.0"
+    "!pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "6535c01d",
+   "id": "6a516f13",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -43,19 +43,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "47318d40",
+   "id": "3a1b7f1d",
    "metadata": {
     "lines_to_next_cell": 0
    },
    "outputs": [],
    "source": [
-    "!curl -k https://aramislab.paris.inria.fr/clinicadl/files/data/handbook_2023/data_oasis/CAPS_example.tar.gz -o oasisCaps.tar.gz\n",
+    "!curl -k https://aramislab.paris.inria.fr/clinicadl/files/handbook_2023/data_oasis/CAPS_example.tar.gz -o oasisCaps.tar.gz\n",
     "!tar xf oasisCaps.tar.gz"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "ae43371d",
+   "id": "5737c2cc",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -101,7 +101,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24375018",
+   "id": "2978c583",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -112,7 +112,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a16e3639",
+   "id": "ff2a5926",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -127,7 +127,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "db02b1ea",
+   "id": "fd8651a4",
    "metadata": {},
    "source": [
     "#### Get the labels AD and CN\n",
@@ -140,7 +140,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "56525e32",
+   "id": "68d3a21d",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -153,7 +153,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7e5a6729",
+   "id": "3018c01a",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -166,7 +166,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9abb1c9a",
+   "id": "34eea13c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -178,7 +178,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "22a6fe39",
+   "id": "6ac39bfd",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -201,7 +201,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4f4ad49b",
+   "id": "70ade2f2",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -212,7 +212,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6eba2f26",
+   "id": "51b695b2",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -224,7 +224,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fb7308dc",
+   "id": "d5b4707b",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -243,7 +243,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d5ba6a82",
+   "id": "8b7780cd",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -255,7 +255,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "bd122070",
+   "id": "cb3bed6f",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -268,7 +268,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14e0cdee",
+   "id": "6199da50",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -281,7 +281,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f617fd3b",
+   "id": "204ac99a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -299,7 +299,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b9af9c02",
+   "id": "92075683",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -335,7 +335,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fcf4cb72",
+   "id": "6dd2bf6c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -344,7 +344,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7a49d044",
+   "id": "51bd7a07",
    "metadata": {},
    "source": [
     "The command generates 3D images of same size as the input images formatted as\n",
@@ -355,7 +355,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3e241670",
+   "id": "f7de8d12",
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -389,7 +389,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4ed71edc",
+   "id": "d4d834f0",
    "metadata": {},
    "source": [
     "### Running the task\n",
@@ -403,7 +403,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9991f499",
+   "id": "fddc70be",
    "metadata": {},
    "outputs": [],
    "source": [

diff --git a/notebooks/inference.ipynb b/notebooks/inference.ipynb
@@ -3,19 +3,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "43d1cf22",
+   "id": "05baad6c",
    "metadata": {
     "lines_to_next_cell": 0
    },
    "outputs": [],
    "source": [
     "# Uncomment this cell if running in Google Colab\n",
-    "!pip install clinicadl==1.3.0"
+    "!pip install clinicadl==1.6.1"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "e282e32d",
+   "id": "926641e6",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -84,7 +84,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c37c9b9e",
+   "id": "72dfbf7c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -110,7 +110,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c3c68ac5",
+   "id": "9235964f",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -135,7 +135,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "75ff167a",
+   "id": "0388f991",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -156,7 +156,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e184e78b",
+   "id": "5b1e59cf",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -170,7 +170,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6db943f4",
+   "id": "41ebad1a",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -194,7 +194,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6ede8598",
+   "id": "21722da5",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -205,7 +205,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4ab97fd1",
+   "id": "1549ae37",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -216,7 +216,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d9a61f55",
+   "id": "9dc0a014",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -227,7 +227,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8b210854",
+   "id": "e369c517",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -240,7 +240,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "23bb45a7",
+   "id": "e66c5960",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -251,7 +251,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3d79d636",
+   "id": "ce67c0b5",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -265,7 +265,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f4a81ec1",
+   "id": "a2b3f78b",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -282,7 +282,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1b5a09f0",
+   "id": "0b76c2eb",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -294,7 +294,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d61210cc",
+   "id": "48fab235",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -305,7 +305,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "eac273dd",
+   "id": "830744c4",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -321,7 +321,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9f28bd8e",
+   "id": "2b501d3e",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -337,7 +337,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f3adfb4f",
+   "id": "9d233554",
    "metadata": {},
    "outputs": [],
    "source": [