small updates to Colab demo (#81)

* Created using Colab - path update * Created using Colab * Delete notebooks/colab_inference_demo.ipynb - remove --> renamed and edited * Update dataloader for tests * Update URL --------- Co-authored-by: C-Achard <[email protected]>
AdaptiveMotorControlLab · May 28, 2024 · 7a31d15 · 7a31d15
1 parent 9f4a7fc
commit 7a31d15
Show file tree

Hide file tree

Showing 2 changed files with 108 additions and 52 deletions.
diff --git a/napari_cellseg3d/code_models/worker_training.py b/napari_cellseg3d/code_models/worker_training.py
@@ -331,24 +331,40 @@ def _get_data(self):
             (self.data_shape, dataset) = self.get_dataset(train_transforms)
 
         logger.debug(f"Data shape : {self.data_shape}")
-        self.dataloader = DataLoader(
-            dataset,
-            batch_size=self.config.batch_size,
-            shuffle=True,
-            num_workers=self.config.num_workers,
-            collate_fn=pad_list_data_collate,
-        )
+        try:
+            self.dataloader = DataLoader(
+                dataset,
+                batch_size=self.config.batch_size,
+                shuffle=True,
+                num_workers=self.config.num_workers,
+                collate_fn=pad_list_data_collate,
+            )
+        except ValueError:
+            self.dataloader = DataLoader(
+                dataset,
+                batch_size=self.config.batch_size,
+                num_workers=self.config.num_workers,
+                collate_fn=pad_list_data_collate,
+            )
 
         if self.config.eval_volume_dict is not None:
             eval_dataset = self.get_dataset_eval(self.config.eval_volume_dict)
             logger.debug(f"Eval batch size : {self.config.eval_batch_size}")
-            self.eval_dataloader = DataLoader(
-                eval_dataset,
-                batch_size=self.config.eval_batch_size,
-                shuffle=False,
-                num_workers=self.config.num_workers,
-                collate_fn=pad_list_data_collate,
-            )
+            try:
+                self.eval_dataloader = DataLoader(
+                    eval_dataset,
+                    batch_size=self.config.eval_batch_size,
+                    shuffle=False,
+                    num_workers=self.config.num_workers,
+                    collate_fn=pad_list_data_collate,
+                )
+            except ValueError:
+                self.eval_dataloader = DataLoader(
+                    eval_dataset,
+                    batch_size=self.config.eval_batch_size,
+                    num_workers=self.config.num_workers,
+                    collate_fn=pad_list_data_collate,
+                )
         else:
             self.eval_dataloader = None
         return self.dataloader, self.eval_dataloader, self.data_shape
@@ -1385,13 +1401,21 @@ def get_patch_loader_func(num_samples):
                     data=self.val_files, transform=load_whole_images
                 )
             logger.debug("Dataloader")
-            train_loader = DataLoader(
-                train_dataset,
-                batch_size=self.config.batch_size,
-                shuffle=True,
-                num_workers=self.config.num_workers,
-                collate_fn=pad_list_data_collate,
-            )
+            try:
+                train_loader = DataLoader(
+                    train_dataset,
+                    batch_size=self.config.batch_size,
+                    shuffle=True,
+                    num_workers=self.config.num_workers,
+                    collate_fn=pad_list_data_collate,
+                )
+            except ValueError:
+                train_loader = DataLoader(
+                    train_dataset,
+                    batch_size=self.config.batch_size,
+                    num_workers=self.config.num_workers,
+                    collate_fn=pad_list_data_collate,
+                )
 
             validation_loader = DataLoader(
                 validation_dataset,

diff --git a/notebooks/colab_inference_demo.ipynb → notebooks/Colab_inference_demo.ipynb b/notebooks/colab_inference_demo.ipynb → notebooks/Colab_inference_demo.ipynb
@@ -3,36 +3,42 @@
     {
       "cell_type": "markdown",
       "metadata": {
-        "colab_type": "text",
-        "id": "view-in-github"
+        "id": "view-in-github",
+        "colab_type": "text"
       },
       "source": [
-        "<a href=\"https://colab.research.google.com/github/AdaptiveMotorControlLab/CellSeg3d/blob/main/notebooks/colab_inference_demo.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
+        "<a href=\"https://colab.research.google.com/github/AdaptiveMotorControlLab/CellSeg3d/blob/main/notebooks/Colab_inference_demo.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
       ]
     },
     {
       "cell_type": "markdown",
-      "metadata": {},
+      "metadata": {
+        "id": "PoYFnmmQAm-x"
+      },
       "source": [
         "# **CellSeg3D : inference demo notebook**\n",
         "\n",
         "---\n",
         "This notebook is part of the [CellSeg3D project](https://github.com/AdaptiveMotorControlLab/CellSeg3d) in the [Mathis Lab of Adaptive Intelligence](https://www.mackenziemathislab.org/).\n",
         "\n",
-        "- 💜 The foundation of this notebook owes much to the **[ZeroCostDL4Mic](https://github.com/HenriquesLab/ZeroCostDL4Mic)** project and to the **[DeepLabCut](https://github.com/DeepLabCut/DeepLabCut)** team for bringing Colab into scientific open software."
+        "- 💜 The foundation of this notebook owes much to the **[ZeroCostDL4Mic](https://github.com/HenriquesLab/ZeroCostDL4Mic)** project and to the **[DeepLabCut](https://github.com/DeepLabCut/DeepLabCut)** team."
       ]
     },
     {
       "cell_type": "markdown",
-      "metadata": {},
+      "metadata": {
+        "id": "vJLmPrWhAm-z"
+      },
       "source": [
         "# **1. Installing dependencies**\n",
         "---"
       ]
     },
     {
       "cell_type": "markdown",
-      "metadata": {},
+      "metadata": {
+        "id": "CUNTOWCnAm-z"
+      },
       "source": [
         "## **1.1 Installing CellSeg3D**\n",
         "---"
@@ -41,7 +47,9 @@
     {
       "cell_type": "code",
       "execution_count": null,
-      "metadata": {},
+      "metadata": {
+        "id": "bnFKu6uFAm-z"
+      },
       "outputs": [],
       "source": [
         "#@markdown ##Install CellSeg3D and dependencies\n",
@@ -51,7 +59,9 @@
     },
     {
       "cell_type": "markdown",
-      "metadata": {},
+      "metadata": {
+        "id": "SfYAv60MAm-z"
+      },
       "source": [
         "## **1.2. Restart your runtime**\n",
         "---\n",
@@ -66,7 +76,9 @@
     {
       "cell_type": "code",
       "execution_count": null,
-      "metadata": {},
+      "metadata": {
+        "id": "Of85zlxzAm-z"
+      },
       "outputs": [],
       "source": [
         "# @title Force session restart\n",
@@ -75,7 +87,9 @@
     },
     {
       "cell_type": "markdown",
-      "metadata": {},
+      "metadata": {
+        "id": "pSVZsebrAm-0"
+      },
       "source": [
         "## **1.3 Load key dependencies**\n",
         "---"
@@ -84,7 +98,9 @@
     {
       "cell_type": "code",
       "execution_count": null,
-      "metadata": {},
+      "metadata": {
+        "id": "vzm75tE_Am-0"
+      },
       "outputs": [],
       "source": [
         "# @title Load libraries\n",
@@ -99,15 +115,19 @@
     },
     {
       "cell_type": "markdown",
-      "metadata": {},
+      "metadata": {
+        "id": "XLEJsiVNAm-0"
+      },
       "source": [
         "# **2. Inference**\n",
         "---"
       ]
     },
     {
       "cell_type": "markdown",
-      "metadata": {},
+      "metadata": {
+        "id": "gjp4WL40Am-0"
+      },
       "source": [
         "\n",
         "## **2.1. Check for GPU access**\n",
@@ -125,7 +145,9 @@
     {
       "cell_type": "code",
       "execution_count": null,
-      "metadata": {},
+      "metadata": {
+        "id": "Fe8hNkOpAm-0"
+      },
       "outputs": [],
       "source": [
         "#@markdown This cell verifies if GPU access is available.\n",
@@ -144,7 +166,9 @@
     },
     {
       "cell_type": "markdown",
-      "metadata": {},
+      "metadata": {
+        "id": "JBCyJAGsAm-0"
+      },
       "source": [
         "## **2.2 Run inference**\n",
         "---"
@@ -153,12 +177,12 @@
     {
       "cell_type": "code",
       "execution_count": null,
-      "metadata": {},
+      "metadata": {
+        "id": "O0jLRpARAm-0"
+      },
       "outputs": [],
       "source": [
-        "# @title Load demo image and inference configuration\n",
-        "#@markdown This cell loads a demo image and load the inference configuration.\n",
-        "demo_image_path = \"./CellSeg3D/examples/c5image.tif\n",
+        "demo_image_path = \"/content/CellSeg3D/examples/c5image.tif\"\n",
         "demo_image = imread(demo_image_path)\n",
         "inference_config = cs3d.CONFIG\n",
         "post_process_config = cs3d.PostProcessConfig()\n",
@@ -170,11 +194,11 @@
     {
       "cell_type": "code",
       "execution_count": null,
-      "metadata": {},
+      "metadata": {
+        "id": "hIEKoyEGAm-0"
+      },
       "outputs": [],
       "source": [
-        "# @title Run inference on demo image\n",
-        "#@markdown This cell runs the inference on the demo image.\n",
         "result = cs3d.inference_on_images(\n",
         "    demo_image,\n",
         "    config=inference_config,\n",
@@ -184,7 +208,9 @@
     {
       "cell_type": "code",
       "execution_count": null,
-      "metadata": {},
+      "metadata": {
+        "id": "IFbmZ3_zAm-1"
+      },
       "outputs": [],
       "source": [
         "# @title Post-process the result\n",
@@ -198,12 +224,14 @@
     {
       "cell_type": "code",
       "execution_count": null,
-      "metadata": {},
+      "metadata": {
+        "id": "TMRiQ-m4Am-1"
+      },
       "outputs": [],
       "source": [
         "# @title Display the result\n",
         "#@markdown This cell displays the result of the inference and post-processing. Use the slider to navigate through the z-stack.\n",
-        "# @markdown *KNOWN ISSUE* : The colormap of the labels is not consistent between the z-stacks. \n",
+        "# @markdown *KNOWN ISSUE* : The colormap of the labels is not consistent between the z-stacks.\n",
         "import matplotlib.pyplot as plt\n",
         "import ipywidgets as widgets\n",
         "from IPython.display import display\n",
@@ -242,7 +270,9 @@
     {
       "cell_type": "code",
       "execution_count": null,
-      "metadata": {},
+      "metadata": {
+        "id": "Tw5exJ5EAm-1"
+      },
       "outputs": [],
       "source": [
         "# @title Display the statistics\n",
@@ -255,7 +285,9 @@
     {
       "cell_type": "code",
       "execution_count": null,
-      "metadata": {},
+      "metadata": {
+        "id": "0NhZ-YksAm-1"
+      },
       "outputs": [],
       "source": [
         "# @title Plot the a 3D view, with statistics\n",
@@ -295,7 +327,7 @@
         "    )\n",
         "\n",
         "    fig.show(renderer=\"colab\")\n",
-        "    \n",
+        "\n",
         "plotly_cells_stats(data)"
       ]
     }
@@ -304,8 +336,8 @@
     "accelerator": "GPU",
     "colab": {
       "gpuType": "T4",
-      "include_colab_link": true,
-      "provenance": []
+      "provenance": [],
+      "include_colab_link": true
     },
     "kernelspec": {
       "display_name": "Python 3",