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small updates to Colab demo #81

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merged 7 commits into from
May 28, 2024
Merged

small updates to Colab demo #81

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b6feab2
Created using Colab - path update
MMathisLab May 15, 2024
4bcfce1
Created using Colab
MMathisLab May 15, 2024
469fced
Merge branch 'AdaptiveMotorControlLab:main' into main
MMathisLab May 15, 2024
4b79660
Delete notebooks/colab_inference_demo.ipynb
MMathisLab May 15, 2024
8813ea6
Merge branch 'main' into main
MMathisLab May 19, 2024
5c3542f
Update dataloader for tests
C-Achard May 28, 2024
bd3ce98
Update URL
C-Achard May 28, 2024
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66 changes: 45 additions & 21 deletions napari_cellseg3d/code_models/worker_training.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down
94 changes: 63 additions & 31 deletions notebooks/colab_inference_demo.ipynb → notebooks/Colab_inference_demo.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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",
"---"
Expand All @@ -41,7 +47,9 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"metadata": {
"id": "bnFKu6uFAm-z"
},
"outputs": [],
"source": [
"#@markdown ##Install CellSeg3D and dependencies\n",
Expand All @@ -51,7 +59,9 @@
},
{
"cell_type": "markdown",
"metadata": {},
"metadata": {
"id": "SfYAv60MAm-z"
},
"source": [
"## **1.2. Restart your runtime**\n",
"---\n",
Expand All @@ -66,7 +76,9 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"metadata": {
"id": "Of85zlxzAm-z"
},
"outputs": [],
"source": [
"# @title Force session restart\n",
Expand All @@ -75,7 +87,9 @@
},
{
"cell_type": "markdown",
"metadata": {},
"metadata": {
"id": "pSVZsebrAm-0"
},
"source": [
"## **1.3 Load key dependencies**\n",
"---"
Expand All @@ -84,7 +98,9 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"metadata": {
"id": "vzm75tE_Am-0"
},
"outputs": [],
"source": [
"# @title Load libraries\n",
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -144,7 +166,9 @@
},
{
"cell_type": "markdown",
"metadata": {},
"metadata": {
"id": "JBCyJAGsAm-0"
},
"source": [
"## **2.2 Run inference**\n",
"---"
Expand All @@ -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",
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I'll check again before merging

"demo_image = imread(demo_image_path)\n",
"inference_config = cs3d.CONFIG\n",
"post_process_config = cs3d.PostProcessConfig()\n",
Expand All @@ -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",
Expand All @@ -184,7 +208,9 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"metadata": {
"id": "IFbmZ3_zAm-1"
},
"outputs": [],
"source": [
"# @title Post-process the result\n",
Expand All @@ -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",
Expand Down Expand Up @@ -242,7 +270,9 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"metadata": {
"id": "Tw5exJ5EAm-1"
},
"outputs": [],
"source": [
"# @title Display the statistics\n",
Expand All @@ -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",
Expand Down Expand Up @@ -295,7 +327,7 @@
" )\n",
"\n",
" fig.show(renderer=\"colab\")\n",
" \n",
"\n",
"plotly_cells_stats(data)"
]
}
Expand All @@ -304,8 +336,8 @@
"accelerator": "GPU",
"colab": {
"gpuType": "T4",
"include_colab_link": true,
"provenance": []
"provenance": [],
"include_colab_link": true
},
"kernelspec": {
"display_name": "Python 3",
Expand Down
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