DeepTrackAI · giovannivolpe · Jun 4, 2021 · Nov 9, 2020 · Nov 9, 2020 · Nov 9, 2020
diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
@@ -0,0 +1,36 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python application
+
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with unittest
+      run: |
+        python -m unittest discover
diff --git a/.vscode/settings.json b/.vscode/settings.json
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 Soft Matter Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README.md b/README.md
@@ -22,7 +22,7 @@ Everybody learns in different ways! Depending on your preferences, and what you
 
 ### Fundamentals
 
-First, we have a very general walkthrough of [basic](https://softmatterlab.github.io/DeepTrack-2.0/basics.html) and [advanced](https://softmatterlab.github.io/DeepTrack-2.0/advanced.html) topics. This is a 5-10 minute read, that well get you well on your way to understand the unique interactions available in DeepTrack.
+First, we have a very general walkthrough of [basic](https://softmatterlab.github.io/DeepTrack-2.0/basics.html) and [advanced](https://softmatterlab.github.io/DeepTrack-2.0/advanced.html) topics. This is a 5-10 minute read, that will get you well on your way to understand the unique interactions available in DeepTrack.
 
 ### DeepTrack 2.0 in action
 
@@ -47,7 +47,45 @@ Additionally, we have seven more case studies which are less documented, but giv
 
 ### Video Tutorials
 
-[TBA]
+DeepTrack 2.0 introduction tutorial video: https://youtu.be/hyfaxF8q6VE  
+<a href="http://www.youtube.com/watch?feature=player_embedded&v=hyfaxF8q6VE
+" target="_blank"><img src="https://img.youtube.com/vi/hyfaxF8q6VE/maxresdefault.jpg" 
+alt="Tutorial" width="384" height="216" border="10" /></a>
+
+DeepTrack 2.0 recognizing handwritten digits tutorial video: https://youtu.be/QD9JUXyLJpc  
+<a href="http://www.youtube.com/watch?feature=player_embedded&v=QD9JUXyLJpc
+" target="_blank"><img src="https://img.youtube.com/vi/QD9JUXyLJpc/maxresdefault.jpg" 
+alt="Tutorial" width="384" height="216" border="10" /></a>
+
+DeepTrack 2.0 single particle tracking tutorial video: https://youtu.be/6Cntik6AfBI   
+<a href="http://www.youtube.com/watch?feature=player_embedded&v=6Cntik6AfBI
+" target="_blank"><img src="https://img.youtube.com/vi/6Cntik6AfBI/maxresdefault.jpg" 
+alt="Tutorial" width="384" height="216" border="10" /></a>
+
+DeepTrack 2.0 single-particle characterization tutorial video: https://youtu.be/ia2H1QO1cHg   
+<a href="http://www.youtube.com/watch?feature=player_embedded&v=ia2H1QO1cHg
+" target="_blank"><img src="https://img.youtube.com/vi/ia2H1QO1cHg/maxresdefault.jpg" 
+alt="Tutorial" width="384" height="216" border="10" /></a>
+
+DeepTrack 2.0 multiple particle tracking tutorial video: https://youtu.be/wFV2VqzpeZs  
+<a href="http://www.youtube.com/watch?feature=player_embedded&v=wFV2VqzpeZs
+" target="_blank"><img src="https://img.youtube.com/vi/wFV2VqzpeZs/maxresdefault.jpg" 
+alt="Tutorial" width="384" height="216" border="10" /></a>
+
+DeepTrack 2.0 multiple particle tracking in 3D tutorial video: https://youtu.be/fzD1QIEIJ04  
+<a href="http://www.youtube.com/watch?feature=player_embedded&v=fzD1QIEIJ04
+" target="_blank"><img src="https://img.youtube.com/vi/fzD1QIEIJ04/mqdefault.jpg" 
+alt="Tutorial" width="384" height="216" border="10" /></a>
+
+DeepTrack 2.0 cell counting tutorial video: https://youtu.be/C6hu_IYoWtI  
+<a href="https://www.youtube.com/watch?feature=player_embedded&v=C6hu_IYoWtI
+" target="_blank"><img src="https://img.youtube.com/vi/C6hu_IYoWtI/mqdefault.jpg" 
+alt="Tutorial" width="384" height="216" border="10" /></a>
+
+DeepTrack 2.0 GAN image generation tutorial video: https://youtu.be/8g44Yks7cis  
+<a href="https://www.youtube.com/watch?feature=player_embedded&v=8g44Yks7cis
+" target="_blank"><img src="https://img.youtube.com/vi/8g44Yks7cis/mqdefault.jpg" 
+alt="Tutorial" width="384" height="216" border="10" /></a>
 
 ### In-depth dives
 
@@ -83,7 +121,7 @@ The detailed documentation of DeepTrack 2.0 is available at the following link:
 
 If you use DeepTrack 2.0 in your project, please cite us here:
 
-    Benjamin Midtvedt, Saga Helgadottir, Aykut Argun, Jesús Pineda, Daniel Midtvedt, Giovanni Volpe. "Quantitative Digital Microscopy with Deep Learning." [arXiv:2010.08260](https://arxiv.org/abs/2010.08260)
+    Benjamin Midtvedt, Saga Helgadottir, Aykut Argun, Jesús Pineda, Daniel Midtvedt, Giovanni Volpe. "Quantitative Digital Microscopy with Deep Learning." [https://doi.org/10.1063/5.0034891](https://aip.scitation.org/doi/10.1063/5.0034891)
 
 See also:
 

diff --git a/_src/source/augmentations.rst b/_src/source/augmentations.rst
@@ -69,6 +69,13 @@ Pad
    :members:
    :exclude-members: get
 
+PadToMultiplesOf
+^^^^^^^^^^^^^^^^
+
+.. autoclass:: deeptrack.augmentations.PadToMultiplesOf
+   :members:
+   :exclude-members: get
+
 PreLoad
 ^^^^^^^
 

diff --git a/_src/source/conf.py b/_src/source/conf.py
@@ -31,7 +31,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ["pydata_sphinx_theme", "sphinx.ext.autodoc", "numpydoc"]
+extensions = ["sphinx.ext.autodoc", "numpydoc"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -57,3 +57,4 @@
 html_static_path = ["_static"]
 
 master_doc = "index"
+autodoc_typehints = "none"
diff --git a/_src/source/deeptrack.rst b/_src/source/deeptrack.rst
@@ -19,4 +19,6 @@ Documentation
    properties
    scatterers
    sequences
+   test
+   types
    utils
diff --git a/_src/source/features.rst b/_src/source/features.rst
@@ -6,6 +6,34 @@ features
 Module classes
 <<<<<<<<<<<<<<
 
+AsType
+^^^^^^
+
+.. autoclass:: deeptrack.features.AsType
+   :members:
+   :exclude-members: get
+
+Bind
+^^^^
+
+.. autoclass:: deeptrack.features.Bind
+   :members:
+   :exclude-members: get
+
+BindResolve
+^^^^^^^^^^^
+
+.. autoclass:: deeptrack.features.BindResolve
+   :members:
+   :exclude-members: get
+
+BindUpdate
+^^^^^^^^^^
+
+.. autoclass:: deeptrack.features.BindUpdate
+   :members:
+   :exclude-members: get
+
 Branch
 ^^^^^^
 
@@ -104,6 +132,13 @@ SampleToMasks
    :members:
    :exclude-members: get
 
+Slice
+^^^^^
+
+.. autoclass:: deeptrack.features.Slice
+   :members:
+   :exclude-members: get
+
 StructuralFeature
 ^^^^^^^^^^^^^^^^^
 

diff --git a/_src/source/generators.rst b/_src/source/generators.rst
@@ -6,6 +6,13 @@ generators
 Module classes
 <<<<<<<<<<<<<<
 
+CappedContinuousGenerator
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. autoclass:: deeptrack.generators.CappedContinuousGenerator
+   :members:
+   :exclude-members: get
+
 ContinuousGenerator
 ^^^^^^^^^^^^^^^^^^^
 

diff --git a/_src/source/test.rst b/_src/source/test.rst
@@ -0,0 +1,5 @@
+test
+====
+
+.. automodule:: deeptrack.test
+
diff --git a/_src/source/types.rst b/_src/source/types.rst
@@ -0,0 +1,5 @@
+types
+=====
+
+.. automodule:: deeptrack.types
+
diff --git a/deeptrack/__init__.py b/deeptrack/__init__.py
@@ -7,4 +7,5 @@
 from .scatterers import *
 from .sequences import *
 
-from . import image, losses, generators, models, utils, layers, backend
+
+from . import image, losses, generators, models, utils, layers, backend, test