Merge pull request #26 from bmandracchia/nightly

Nightly

.gitattributes

@@ -0,0 +1 @@
+*.ipynb merge=nbdev-merge

.gitconfig

@@ -0,0 +1,11 @@
+# Generated by nbdev_install_hooks
+#
+# If you need to disable this instrumentation do:
+#   git config --local --unset include.path
+#
+# To restore:
+#   git config --local include.path ../.gitconfig
+#
+[merge "nbdev-merge"]
+	name = resolve conflicts with nbdev_fix
+	driver = nbdev_merge %O %A %B %P

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)

_proc/_docs/callbacks.html → _docs/callbacks.html

@@ -235,24 +235,6 @@
   <a href="./demo_ri2fl_2d.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Demo: 2D image RI2FL</span></a>
   </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./demo_2.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Demo: 2D image RI2FL</span></a>
-  </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./template.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">template</span></a>
-  </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./fourier_ring_correlation.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">fourier_ring_correlation.html</span></a>
-  </div>
 </li>
     </ul>
     </div>
@@ -319,7 +301,7 @@ <h3 class="anchored" data-anchor-id="shortepochcallback">ShortEpochCallback</h3>
 <blockquote class="blockquote">
 <pre><code> ShortEpochCallback (pct=0.01, short_valid=True)</code></pre>
 </blockquote>
-<p>Fit just <code>pct</code> of an epoch, then stop</p>
+<p><em>Fit just <code>pct</code> of an epoch, then stop</em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/training.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -328,7 +310,7 @@ <h3 class="anchored" data-anchor-id="gradientaccumulation">GradientAccumulation<
 <blockquote class="blockquote">
 <pre><code> GradientAccumulation (n_acc=32)</code></pre>
 </blockquote>
-<p>Accumulate gradients before updating weights</p>
+<p><em>Accumulate gradients before updating weights</em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/tracker.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -338,7 +320,7 @@ <h3 class="anchored" data-anchor-id="earlystoppingcallback">EarlyStoppingCallbac
 <pre><code> EarlyStoppingCallback (monitor='valid_loss', comp=None, min_delta=0.0,
                         patience=1, reset_on_fit=True)</code></pre>
 </blockquote>
-<p>A <code>TrackerCallback</code> that terminates training when monitored quantity stops improving.</p>
+<p><em>A <code>TrackerCallback</code> that terminates training when monitored quantity stops improving.</em></p>
 <table class="table">
 <colgroup>
 <col style="width: 6%">
@@ -397,7 +379,7 @@ <h3 class="anchored" data-anchor-id="savemodelcallback">SaveModelCallback</h3>
                     fname='model', every_epoch=False, at_end=False,
                     with_opt=False, reset_on_fit=True)</code></pre>
 </blockquote>
-<p>A <code>TrackerCallback</code> that saves the model’s best during training and loads it at the end.</p>
+<p><em>A <code>TrackerCallback</code> that saves the model’s best during training and loads it at the end.</em></p>
 <table class="table">
 <colgroup>
 <col style="width: 6%">
@@ -473,7 +455,7 @@ <h3 class="anchored" data-anchor-id="reducelronplateau">ReduceLROnPlateau</h3>
 <pre><code> ReduceLROnPlateau (monitor='valid_loss', comp=None, min_delta=0.0,
                     patience=1, factor=10.0, min_lr=0, reset_on_fit=True)</code></pre>
 </blockquote>
-<p>A <code>TrackerCallback</code> that reduces learning rate when a metric has stopped improving.</p>
+<p><em>A <code>TrackerCallback</code> that reduces learning rate when a metric has stopped improving.</em></p>
 <table class="table">
 <colgroup>
 <col style="width: 6%">
@@ -546,7 +528,7 @@ <h3 class="anchored" data-anchor-id="paramscheduler">ParamScheduler</h3>
 <blockquote class="blockquote">
 <pre><code> ParamScheduler (scheds)</code></pre>
 </blockquote>
-<p>Schedule hyper-parameters according to <code>scheds</code></p>
+<p><em>Schedule hyper-parameters according to <code>scheds</code></em></p>
 <p><code>scheds</code> is a dictionary with one key for each hyper-parameter you want to schedule, with either a scheduler or a list of schedulers as values (in the second case, the list must have the same length as the the number of parameters groups of the optimizer).</p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/schedule.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
@@ -556,7 +538,7 @@ <h3 class="anchored" data-anchor-id="schedcos">SchedCos</h3>
 <blockquote class="blockquote">
 <pre><code> SchedCos (start, end)</code></pre>
 </blockquote>
-<p>Cosine schedule function from <code>start</code> to <code>end</code></p>
+<p><em>Cosine schedule function from <code>start</code> to <code>end</code></em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/schedule.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -565,7 +547,7 @@ <h3 class="anchored" data-anchor-id="schedexp">SchedExp</h3>
 <blockquote class="blockquote">
 <pre><code> SchedExp (start, end)</code></pre>
 </blockquote>
-<p>Exponential schedule function from <code>start</code> to <code>end</code></p>
+<p><em>Exponential schedule function from <code>start</code> to <code>end</code></em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/schedule.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -574,7 +556,7 @@ <h3 class="anchored" data-anchor-id="schedlin">SchedLin</h3>
 <blockquote class="blockquote">
 <pre><code> SchedLin (start, end)</code></pre>
 </blockquote>
-<p>Linear schedule function from <code>start</code> to <code>end</code></p>
+<p><em>Linear schedule function from <code>start</code> to <code>end</code></em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/schedule.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -583,7 +565,7 @@ <h3 class="anchored" data-anchor-id="schedno">SchedNo</h3>
 <blockquote class="blockquote">
 <pre><code> SchedNo (start, end)</code></pre>
 </blockquote>
-<p>Constant schedule function with <code>start</code> value</p>
+<p><em>Constant schedule function with <code>start</code> value</em></p>
 
 
 </section>

_proc/_docs/core.html → _docs/core.html

@@ -235,24 +235,6 @@
   <a href="./demo_ri2fl_2d.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Demo: 2D image RI2FL</span></a>
   </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./demo_2.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Demo: 2D image RI2FL</span></a>
-  </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./template.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">template</span></a>
-  </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./fourier_ring_correlation.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">fourier_ring_correlation.html</span></a>
-  </div>
 </li>
     </ul>
     </div>
@@ -325,7 +307,7 @@ <h3 class="anchored" data-anchor-id="datablock">DataBlock</h3>
             n_inp:int=None, item_tfms:list=None, batch_tfms:list=None,
             get_items=None, splitter=None, get_y=None, get_x=None)</code></pre>
 </blockquote>
-<p>Generic container to quickly build <code>Datasets</code> and <code>DataLoaders</code>.</p>
+<p><em>Generic container to quickly build <code>Datasets</code> and <code>DataLoaders</code>.</em></p>
 <table class="table">
 <colgroup>
 <col style="width: 6%">
@@ -412,13 +394,13 @@ <h3 class="anchored" data-anchor-id="dataloaders">DataLoaders</h3>
 <blockquote class="blockquote">
 <pre><code> DataLoaders (*loaders, path:str|pathlib.Path='.', device=None)</code></pre>
 </blockquote>
-<p>Basic wrapper around several <code>DataLoader</code>s.</p>
+<p><em>Basic wrapper around several <code>DataLoader</code>s.</em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/learner.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
 <section id="learner" class="level3">
 <h3 class="anchored" data-anchor-id="learner">Learner</h3>
-<p>Group together a <code>model</code>, some <code>dls</code> and a <code>loss_func</code> to handle training</p>
+<p><em>Group together a <code>model</code>, some <code>dls</code> and a <code>loss_func</code> to handle training</em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/progress.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -437,7 +419,7 @@ <h3 class="anchored" data-anchor-id="showgraphcallback">ShowGraphCallback</h3>
                     after_cancel_epoch=None, after_epoch=None,
                     after_cancel_fit=None, after_fit=None)</code></pre>
 </blockquote>
-<p>Update a graph of training and validation loss</p>
+<p><em>Update a graph of training and validation loss</em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/progress.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -446,23 +428,24 @@ <h3 class="anchored" data-anchor-id="csvlogger">CSVLogger</h3>
 <blockquote class="blockquote">
 <pre><code> CSVLogger (fname='history.csv', append=False)</code></pre>
 </blockquote>
-<p>Log the results displayed in <code>learn.path/fname</code></p>
+<p><em>Log the results displayed in <code>learn.path/fname</code></em></p>
+<pre><code>Unknown section Notes</code></pre>
 <hr>
 </section>
 <section id="cells3d" class="level3">
 <h3 class="anchored" data-anchor-id="cells3d">cells3d</h3>
 <blockquote class="blockquote">
 <pre><code> cells3d ()</code></pre>
 </blockquote>
-<p>3D fluorescence microscopy image of cells.</p>
-<p>The returned data is a 3D multichannel array with dimensions provided in <code>(z, c, y, x)</code> order. Each voxel has a size of <code>(0.29 0.26 0.26)</code> micrometer. Channel 0 contains cell membranes, channel 1 contains nuclei.</p>
+<p>*3D fluorescence microscopy image of cells.</p>
+<p>The returned data is a 3D multichannel array with dimensions provided in <code>(z, c, y, x)</code> order. Each voxel has a size of <code>(0.29 0.26 0.26)</code> micrometer. Channel 0 contains cell membranes, channel 1 contains nuclei.*</p>
 </section>
 </section>
 <section id="engine" class="level2">
 <h2 class="anchored" data-anchor-id="engine">Engine</h2>
 <p>Core engine for model training. See tutorials for usage examples.</p>
 <hr>
-<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L34" target="_blank" style="float:right; font-size:smaller">source</a></p>
+<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L36" target="_blank" style="float:right; font-size:smaller">source</a></p>
 <section id="fasttrainer" class="level3">
 <h3 class="anchored" data-anchor-id="fasttrainer">fastTrainer</h3>
 <blockquote class="blockquote">
@@ -481,7 +464,7 @@ <h3 class="anchored" data-anchor-id="fasttrainer">fastTrainer</h3>
               wd_bn_bias:bool=False, train_bn:bool=True,
               moms:tuple=Ellipsis, default_cbs:bool=True)</code></pre>
 </blockquote>
-<p>A custom implementation of the FastAI Learner class for training models in bioinformatics applications.</p>
+<p><em>A custom implementation of the FastAI Learner class for training models in bioinformatics applications.</em></p>
 <table class="table">
 <colgroup>
 <col style="width: 6%">
@@ -626,30 +609,30 @@ <h3 class="anchored" data-anchor-id="fasttrainer">fastTrainer</h3>
 <h2 class="anchored" data-anchor-id="utils">Utils</h2>
 <p>Utility functions.</p>
 <hr>
-<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L81" target="_blank" style="float:right; font-size:smaller">source</a></p>
+<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L83" target="_blank" style="float:right; font-size:smaller">source</a></p>
 <section id="attributesfromdict" class="level3">
 <h3 class="anchored" data-anchor-id="attributesfromdict">attributesFromDict</h3>
 <blockquote class="blockquote">
 <pre><code> attributesFromDict (d)</code></pre>
 </blockquote>
 <hr>
-<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L87" target="_blank" style="float:right; font-size:smaller">source</a></p>
+<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L89" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
 <section id="get_device" class="level3">
 <h3 class="anchored" data-anchor-id="get_device">get_device</h3>
 <blockquote class="blockquote">
 <pre><code> get_device ()</code></pre>
 </blockquote>
 <hr>
-<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L91" target="_blank" style="float:right; font-size:smaller">source</a></p>
+<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L93" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
 <section id="img2float" class="level3">
 <h3 class="anchored" data-anchor-id="img2float">img2float</h3>
 <blockquote class="blockquote">
 <pre><code> img2float (image, force_copy=False)</code></pre>
 </blockquote>
 <hr>
-<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L95" target="_blank" style="float:right; font-size:smaller">source</a></p>
+<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L97" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
 <section id="img2tensor" class="level3">
 <h3 class="anchored" data-anchor-id="img2tensor">img2Tensor</h3>