Merge pull request #27 from fish-quant/develop

v0.4.0

.codecov.yml

@@ -15,4 +15,15 @@ coverage:
         # Commits pushed to master should not make the overall project
         # coverage decrease by more than 1%:
         target: auto
+        threshold: 1%
+    patch:
+      default:
+        # Be tolerant on slight code coverage diff on PRs to limit
+        # noisy red coverage status on github PRs.
+        # Note The coverage stats are still uploaded
+        # to codecov so that PR reviewers can see uncovered lines
+        # in the github diff if they install the codecov browser
+        # extension:
+        # https://github.com/codecov/browser-extension
+        target: auto
         threshold: 1%

.gitignore

@@ -1,17 +1,140 @@
-# Dot files
-.idea/
+# Mac OS files
 .DS_Store
 
-# Packaging related files
-MANIFEST
+# PyCharm stuff
+.idea/
+
+# folders
+playground/
+
+# ### General python stuff ###
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
 build/
+develop-eggs/
 dist/
-big_fish.egg-info/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
 
-# Notebooks
-examples/old
-examples/.ipynb_checkpoints
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
 
-# Cache
-__pycache__/
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
 .pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

.travis.yml

@@ -0,0 +1,11 @@
+language: python
+
+python:
+    - "3.6"
+
+install:
+    - pip install -r requirements_dev.txt
+
+script:
+    - pytest --cov=./
+    - codecov

README.md

@@ -1,10 +1,11 @@
 # Big-FISH
 
+[![Build Status](https://travis-ci.com/fish-quant/big-fish.svg?branch=master)](https://travis-ci.com/fish-quant/big-fish)
+[![codecov](https://codecov.io/gh/fish-quant/big-fish/branch/master/graph/badge.svg)](https://codecov.io/gh/fish-quant/big-fish)
 [![License](https://img.shields.io/badge/license-BSD%203--Clause-green)](https://github.com/fish-quant/big-fish/blob/master/LICENSE)
-[![codecov](https://codecov.io/gh/fish-quant/big-fish/branch/master/graph/badge.svg?token=kEnikxXOxP)](https://codecov.io/gh/fish-quant/big-fish)
-![License](https://img.shields.io/badge/python-3.6-blue)
+[![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/)
 
-**Big-FISH** is a python package for the analysis of smFISH images. It includes various methods to **manipulate microscopic images**, **detect spots** and **segment relevant area** of the cells. The package allows the user to extract specific signal from images and build a coordinate representation of the cells. The ultimate goal is to ease **large scale statistical analysis** and quantification.
+**Big-FISH** is a python package for the analysis of smFISH images. It includes various methods to **analyze microscopy images**, such **spot detection** and **segmentation of cells and nuclei**. The package allows the user represent the extract properties of a cell as coordinates (see figure below). The ultimate goal is to simplify **large scale statistical analysis** and quantification.
 
 | Cell image (smFISH channel) and its coordinates representation |
 | ------------- |
@@ -16,30 +17,38 @@
 
 Big-FISH requires Python 3.6 or newer. Additionally, it has the following dependencies:
 
-- numpy (>= 1.16.0)
-- scipy (>= 1.2.0)
-- scikit-learn (>= 0.20.2)
-- scikit-image (>= 0.14.2)
-- matplotlib (>= 3.0.2)
-- pandas (>= 0.24.0)
-- mrc (>= (0.1.5)
-- pip (>= 18.1)
+- numpy (== 1.16.0)
+- scipy (== 1.4.1)
+- scikit-learn (== 0.20.2)
+- scikit-image (== 0.14.2)
+- matplotlib (== 3.0.2)
+- pandas (== 0.24.0)
+- mrc (== 0.1.5)
 
-### User installation
+Updated dependencies might break.
 
-To avoid dependency conflicts the use of a dedicated [virtual](https://docs.python.org/3.6/library/venv.html) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) environment should be a considered option.
+### Virtual environment
 
-#### From PyPi
+To avoid dependency conflicts, we recommend the the use of a dedicated [virtual](https://docs.python.org/3.6/library/venv.html) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) environment.  In a terminal run the command:
+
+```bash
+conda create -n bigfish_env python=3.6
+source activate bigfish_env
+```
+
+We recommend two options to then install Big-FISH in your virtual environment.
+
+#### Download the package from PyPi
 
 Use the package manager [pip](https://pip.pypa.io/en/stable/) to install Big-FISH. In a terminal run the command:
 
 ```bash
-pip install bigfish
+pip install big-fish
 ```
 
-#### From Github
+#### Clone package from Github
 
-Clone the project's [Github repository](https://github.com/fish-quant/big-fish) and install it locally with the following commands:
+Clone the project's [Github repository](https://github.com/fish-quant/big-fish) and install it manually with the following commands:
 
 ```bash
 git clone [email protected]:fish-quant/big-fish.git
@@ -50,26 +59,23 @@ pip install .
 ## Usage
 
 Big-FISH provides a toolbox for the full analysis pipeline of smFISH images:
+
 - Use `bigfish.stack` subpackage for I/O operations, preprocessing and postprocessing.
 - Use `bigfish.segmentation` subpackage for nucleus and cell segmentation.
 - Use `bigfish.detection` subpackage for mRNAs detection.
 - Use `bigfish.plot` subpackage for plotting routines.
 - Use `bigfish.classification` subpackage for pattern recognition tasks.
 
-Several examples are developed in the [examples](https://github.com/fish-quant/big-fish/tree/master/examples) directory.
+Several examples are available as [Jupyter notebooks](https://github.com/fish-quant/big-fish-examples/tree/master/notebooks).
 
 ## Support
 
 If you have any question relative to the repository, please open an [issue](https://github.com/fish-quant/big-fish/issues). You can also contact [Arthur Imbert](mailto:[email protected]) or [Florian Mueller](mailto:[email protected]).
 
 ## Roadmap (suggestion)
 
-Version 0.4.0:
-- Refactor `bigfish.classification` subpackage.
-- Add pattern recognition examples.
-
 Version 0.5.0:
-- Switch to tensorflow 2.0.0.
+- Switch to tensorflow 2.2.0.
 - Integrate a deep learning model for segmentation.
 
 Version 1.0.0:
@@ -84,6 +90,7 @@ You can access the latest sources with the commands:
 
 ```bash
 git clone [email protected]:fish-quant/big-fish.git
+cd big-fish
 git checkout develop
 ```
 

bigfish/__init__.py

@@ -11,5 +11,5 @@
 # MAJOR: major API changes
 # MINOR: new features
 # PATCH: backwards compatible bug fixes
-
-__version__ = "0.3.0"
+# MAJOR.MINOR.PATCHdev means a version under development
+__version__ = "0.4.0"

bigfish/classification/__init__.py

@@ -1,21 +1,39 @@
 # -*- coding: utf-8 -*-
+# Author: Arthur Imbert <[email protected]>
+# License: BSD 3 clause
 
 """
-The bigfish.classification module includes models to classify the localization
-patterns of the RNA.
+The bigfish.classification subpackage includes functions to prepare input data,
+craft features and train classification models.
 """
 
-from .input_preparation import (prepare_coordinate_data,
-                                build_boundaries_layers, build_surface_layers,
-                                build_distance_layers, Generator)
-from .features import get_features, get_features_name
+from .input_preparation import prepare_extracted_data
 
-# ### Load models ###
+from .features import compute_features
+from .features import get_features_name
+from .features import features_distance
+from .features import features_in_out_nucleus
+from .features import features_protrusion
+from .features import features_dispersion
+from .features import features_topography
+from .features import features_foci
+from .features import features_area
+from .features import features_centrosome
 
-_features = ["get_features", "get_features_name"]
 
-_input_preparation = ["prepare_coordinate_data", "build_boundaries_layers",
-                      "build_surface_layers", "build_distance_layers",
-                      "Generator"]
+_input_preparation = [
+    "prepare_extracted_data"]
 
-__all__ = _features + _input_preparation
+_features = [
+    "compute_features",
+    "get_features_name",
+    "features_distance"
+    "features_in_out_nucleus"
+    "features_protrusion"
+    "features_dispersion"
+    "features_topography"
+    "features_foci"
+    "features_area"
+    "features_centrosome"]
+
+__all__ = _input_preparation + _features