general update

bmandracchia · Oct 1, 2024 · 8596f65 · 8596f65
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diff --git a/README.md b/README.md
@@ -9,10 +9,13 @@ Notebook](https://img.shields.io/badge/jupyter-%23f37626.svg?style=flat&logo=jup
 
 ## Overview
 
-bioMONAI is a collaborative platform for developing and deploying deep
-learning models in medical imaging using the MONAI framework, fastai, TorchIO, and Jupyter
-notebooks. This project aims to facilitate interoperability,
-reproducibility, and community collaboration in biomedical research.
+bioMONAI is a low-code Python-based platform for developing and
+deploying deep learning models in biomedical imaging built on top of the
+[MONAI](https://monai.io/) framework,
+[fastai](https://github.com/fastai/fastai), and
+[TorchIO](https://torchio.readthedocs.io/). This project aims to
+facilitate interoperability, reproducibility, and community
+collaboration in biomedical research.
 
 ## Table of Contents
 
@@ -28,7 +31,7 @@ reproducibility, and community collaboration in biomedical research.
 
 ## Installation
 
-To install the BioMONAI nbs environment, follow these steps:
+To install the bioMONAI environment, follow these steps:
 
 1.  **Clone the repository:**
 
@@ -58,35 +61,18 @@ To install the BioMONAI nbs environment, follow these steps:
 
 ## Getting Started
 
-To get started with BioMONAI, follow these steps:
+To get started with bioMONAI, the best way is to try out our tutorials,
+which will walk you through model training for various tasks like
+classification, regression, and segmentation.
 
-1.  **Clone the repository:**
-
-    ``` bash
-    git clone https://github.com/your_username/biomonai.git
-    cd biomonai
-    ```
-
-2.  **Activate your Conda environment:**
-
-    ``` bash
-    conda activate biomonai
-    ```
-
-3.  **Open Jupyter Notebook:**
-
-    ``` bash
-    jupyter notebook
-    ```
-
-4.  **Navigate to the notebooks directory and open a sample notebook:**
-
-    - You should see a list of available notebooks in your browser. Open
-      one to start exploring!
+| Notebook                                                                                                                              | Open in Colab                                                                                                                                                                       |
+|:--------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| [Tutorial classification](http://localhost:3348/902_demo_2.html) <br>(to be updated.)                                                 | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github.com/bmandracchia/bioMONAI/nightly/nbs/901_demo_RI2FL_2d.ipynb) |
+| [Tutorial regression](https://nbviewer.org/github.com/bmandracchia/bioMONAI/nightly/nbs/901_demo_RI2FL_2d.ipynb) <br>(to be updated.) | [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github.com/bmandracchia/bioMONAI/nightly/nbs/901_demo_RI2FL_2d.ipynb) |
 
 ## Usage
 
-To use BioMONAI nbs for your own projects, follow these steps:
+To use bioMONAI for your own projects, follow these steps:
 
 1.  **Create a new Jupyter notebook or open an existing one.**
 
@@ -132,7 +118,7 @@ nbs, follow these steps:
 
 ## License
 
-BioMONAI is released under the Apache 2.0 license. See
+bioMONAI is released under the Apache 2.0 license. See
 [LICENSE](https://github.com/your_username/biomonai-nbs/blob/main/LICENSE)
 for more details.
 
@@ -144,4 +130,5 @@ If you have any questions or need further assistance, please open an
 issue on GitHub or contact us directly at:
 
 - Project Lead: [Biagio Mandracchia](mailto:biagio.mandracchia@uva.es)
-- Contributors: [Juan Pita-López](mailto:juan.pita@uva.es), [Rosa-María Menchón-Lara](mailto:rosamaria.menchon@uva.es)
+- Contributors: [Juan Pita-López](mailto:juan.pita@uva.es), [Rosa-María
+  Menchón-Lara](mailto:rosamaria.menchon@uva.es)
diff --git a/_proc/.quarto/idx/index.ipynb.json b/_proc/.quarto/idx/index.ipynb.json
diff --git a/_proc/.quarto/xref/INDEX b/_proc/.quarto/xref/INDEX
@@ -18,7 +18,8 @@
     "visualize.html": "abcecf4e"
   },
   "index.ipynb": {
-    "index.html": "a91f535b"
+    "index.html": "a91f535b",
+    "README.md": "167e84c8"
   },
   "08_datasets.ipynb": {
     "datasets.html": "25c91919"

diff --git a/_proc/00_core.ipynb b/_proc/00_core.ipynb
@@ -306,6 +306,13 @@
     "language": "python"
    },
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Unknown section Notes\n"
+     ]
+    },
     {
      "data": {
       "text/markdown": [
@@ -649,10 +656,6 @@
    "language": "python",
    "name": "python3"
   },
-  "language_info": {
-   "name": "python",
-   "version": "3.11.5"
-  },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {
     "state": {},

diff --git a/_proc/01_data.ipynb b/_proc/01_data.ipynb
@@ -156,7 +156,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "metadata": {
     "language": "python"
    },
@@ -217,7 +217,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "metadata": {
     "language": "python"
    },
@@ -278,7 +278,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": null,
    "metadata": {
     "language": "python"
    },
@@ -289,7 +289,7 @@
        "torch.Size([1, 512, 512])"
       ]
      },
-     "execution_count": 14,
+     "execution_count": null,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -342,7 +342,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": null,
    "metadata": {
     "language": "python"
    },
@@ -475,8 +475,8 @@
        "### BioDataBlock\n",
        "\n",
        ">      BioDataBlock (blocks:list=(<fastai.data.block.TransformBlock object at\n",
-       ">                    0x7f8eff4dca50>, <fastai.data.block.TransformBlock object\n",
-       ">                    at 0x7f8eff2942d0>), dl_type:fastai.data.core.TfmdDL=None,\n",
+       ">                    0x7ff5ca1d1310>, <fastai.data.block.TransformBlock object\n",
+       ">                    at 0x7ff5c9bbc7d0>), dl_type:fastai.data.core.TfmdDL=None,\n",
        ">                    get_items=<function get_image_files>, get_y=None,\n",
        ">                    get_x=None, getters:list=None, n_inp:int=None,\n",
        ">                    item_tfms:list=None, batch_tfms:list=None, **kwargs)\n",
@@ -485,7 +485,7 @@
        "\n",
        "|    | **Type** | **Default** | **Details** |\n",
        "| -- | -------- | ----------- | ----------- |\n",
-       "| blocks | list | (<fastai.data.block.TransformBlock object at 0x7f8eff4dca50>, <fastai.data.block.TransformBlock object at 0x7f8eff2942d0>) | One or more `TransformBlock`s |\n",
+       "| blocks | list | (<fastai.data.block.TransformBlock object at 0x7ff5ca1d1310>, <fastai.data.block.TransformBlock object at 0x7ff5c9bbc7d0>) | One or more `TransformBlock`s |\n",
        "| dl_type | TfmdDL | None | Task specific `TfmdDL`, defaults to `block`'s dl_type or`TfmdDL` |\n",
        "| get_items | function | get_image_files |  |\n",
        "| get_y | NoneType | None |  |\n",
@@ -504,8 +504,8 @@
        "### BioDataBlock\n",
        "\n",
        ">      BioDataBlock (blocks:list=(<fastai.data.block.TransformBlock object at\n",
-       ">                    0x7f8eff4dca50>, <fastai.data.block.TransformBlock object\n",
-       ">                    at 0x7f8eff2942d0>), dl_type:fastai.data.core.TfmdDL=None,\n",
+       ">                    0x7ff5ca1d1310>, <fastai.data.block.TransformBlock object\n",
+       ">                    at 0x7ff5c9bbc7d0>), dl_type:fastai.data.core.TfmdDL=None,\n",
        ">                    get_items=<function get_image_files>, get_y=None,\n",
        ">                    get_x=None, getters:list=None, n_inp:int=None,\n",
        ">                    item_tfms:list=None, batch_tfms:list=None, **kwargs)\n",
@@ -514,7 +514,7 @@
        "\n",
        "|    | **Type** | **Default** | **Details** |\n",
        "| -- | -------- | ----------- | ----------- |\n",
-       "| blocks | list | (<fastai.data.block.TransformBlock object at 0x7f8eff4dca50>, <fastai.data.block.TransformBlock object at 0x7f8eff2942d0>) | One or more `TransformBlock`s |\n",
+       "| blocks | list | (<fastai.data.block.TransformBlock object at 0x7ff5ca1d1310>, <fastai.data.block.TransformBlock object at 0x7ff5c9bbc7d0>) | One or more `TransformBlock`s |\n",
        "| dl_type | TfmdDL | None | Task specific `TfmdDL`, defaults to `block`'s dl_type or`TfmdDL` |\n",
        "| get_items | function | get_image_files |  |\n",
        "| get_y | NoneType | None |  |\n",
@@ -783,7 +783,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": null,
    "metadata": {
     "language": "python"
    },
@@ -804,7 +804,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": null,
    "metadata": {
     "language": "python"
    },
@@ -990,7 +990,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L476){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L474){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### extract_patches\n",
        "\n",
@@ -1009,7 +1009,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L476){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L474){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### extract_patches\n",
        "\n",
@@ -1047,7 +1047,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L504){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L502){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### save_patches_grid\n",
        "\n",
@@ -1067,7 +1067,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L504){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L502){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### save_patches_grid\n",
        "\n",
@@ -1098,7 +1098,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": null,
    "metadata": {
     "language": "python"
    },
@@ -1129,7 +1129,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": null,
    "metadata": {
     "language": "python"
    },
@@ -1141,7 +1141,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 36,
+   "execution_count": null,
    "metadata": {
     "language": "python"
    },
@@ -1174,7 +1174,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L560){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L558){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### extract_random_patches\n",
        "\n",
@@ -1193,7 +1193,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L560){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L558){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### extract_random_patches\n",
        "\n",
@@ -1231,7 +1231,7 @@
       "text/markdown": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L596){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L594){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### save_patches_random\n",
        "\n",
@@ -1251,7 +1251,7 @@
       "text/plain": [
        "---\n",
        "\n",
-       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L596){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
+       "[source](https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/data.py#L594){target=\"_blank\" style=\"float:right; font-size:smaller\"}\n",
        "\n",
        "### save_patches_random\n",
        "\n",
@@ -1282,7 +1282,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": null,
    "metadata": {
     "language": "python"
    },
@@ -1306,7 +1306,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 40,
+   "execution_count": null,
    "metadata": {
     "language": "python"
    },
@@ -1336,18 +1336,6 @@
    "language": "python",
    "name": "python3"
   },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.5"
-  },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {
     "state": {},

diff --git a/_proc/_docs/core.html b/_proc/_docs/core.html
@@ -447,6 +447,7 @@ <h3 class="anchored" data-anchor-id="csvlogger">CSVLogger</h3>
 <pre><code> CSVLogger (fname='history.csv', append=False)</code></pre>
 </blockquote>
 <p>Log the results displayed in <code>learn.path/fname</code></p>
+<pre><code>Unknown section Notes</code></pre>
 <hr>
 </section>
 <section id="cells3d" class="level3">