AMF segmentation

useful jupyterlab extensions: https://github.com/jpmorganchase/jupyter-fs

Use nbstripout to avoid uploading nb output and simplify merge https://github.com/kynan/nbstripout

Also avoid trying to merge notebooks

From base folder:

virtualenv --python=python3 venv

(or replace python3 by the path to the python version you want to clone.)

Launching environment:

source venv/bin/activate

Activate the environnement before launching

pip3 install -r requirements.txt

Additionnal packages to install:

git clone https://github.com/gattia/cycpd
cd cycpd
sudo python setup.py install

For github authentification

conda install gh --channel conda-forge

Install Fiji:

Chose a location on the computer and download: https://imagej.net/software/fiji/downloads

Install anisotropic filtering:

Chose a location on the computer and download: http://forge.cbp.ens-lyon.fr/redmine/projects/anifilters

For better display:

jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter lab build

Remove the pyproject.toml file (for poetry)

To run from the base folder: (will run the setup.py script) pip install -e . ###Install the font for plotting purposes Copy font in your environment fonts. Example on snellius "/gpfs/home2/cbisot/miniconda3/envs/amftrack/lib/python3.7 /site-packages/matplotlib/mpl-data/fonts/ttf/lucidasansdemibold.ttf"

The code should be modified in order to avoid failure in case the font is not present.

Create a text file named local.env in the base folder (for example: touch local.env)

And fill the file with the following lines and adapt them to your situation:

DATA_PATH=C:\Users\coren\Documents\PhD\Code\data_info.json
FIJI_PATH=C:\Users\coren\Documents\PhD\Code\fiji-win64\Fiji.app/ImageJ-win64.exe
TEMP_PATH=C:\Users\coren\Documents\PhD\Code\temp
STORAGE_PATH=C:\Users\coren\Documents\PhD\Code
PASTIS_PATH=/home/ipausers/bisot/anis_filter/anifilters/bin/ani2D
SLURM_PATH=/data/temp
SLURM_PATH_transfer=/data/temp
DROPBOX_PATH = C:\Users\coren\AMOLF-SHIMIZU Dropbox\DATA\PRINCE
DROPBOX_PATH_ANALYSIS = C:\Users\coren\AMOLF-SHIMIZU Dropbox\DATA\PRINCE_ANALYSIS
CONDA_PATH = /home/cbisot/miniconda3/etc/profile.d/conda.sh

APP_KEY=
APP_SECRET= 
REFRESH_TOKEN = 
FOLDER_ID=
USER_ID= 

To have access to a path: Always import from the util.sys

Le formatage du code est fait avec black

For logging, the logging module logging enables to add logging messages across code and set the level of verbosity. There are 4 levels of verbosity (DEBUG, INFO, WARNING, ERROR). Each log line is of one of this types. Examples:

logger.info("Processing is done")
logger.warning("Couldn't handle all cases")

To add logging to a file we use:

import logging
import os
logger = logging.getLogger(os.path.basename(__file__))

This creates a logger with the name of the file.

• The general log level (verbosity) can be set in the general __init__.py file. By changing the line

logging.basicConfig(stream=sys.stdout, level=logging.INFO, format=log_format)

• A filter can also be added to change log level from a specific files or from a specific module.

some_logger = logging.getLogger("name_of_the_file")
some_logger.setLevel(logging.WARNING)

• The log level can also be changed directly in a file with:

logger.setLevel("INFO")

In a certain file, logging.info("something") will also work but will display "root" as the name of the logger and not the name of the file that issued the log

The tests are all in the test folder. The python module chosen for tests is unittest. https://docs.python.org/3/library/unittest.html

All test files must start with test. All test function and classes must start with test.

Ex: test_sys_util.py

And all testing classes must be subclass from the unittest base test class and must start with Test.

The file helper.py contains utils for testing: mock object, skipping functions, ..

Tests can be launched with the following command:

python3 -m unittest discover . "test*.py"

Runing only one test:

python3 -m unittest -v ~/Wks/AMFtrack/test/util/test_geometry.py

Test can also be run with pytest if installed (prettier display)

pytest test_file.py -k test_function

For some tests, a processed Prince plate is required. Or other types of files. The data file must be stored at the following path: storage_path + "test". If the data is not present, the tests will be skipped. The tests can be safely run even if to test/ directory is present.

Some tests create and save plots in the test directory. These files don't accumulate (they are just replace at each test).

The coverage gives an idea of the portion of code which is covered by the tests.

Getting test coverage: coverage run -m unittest discover coverage report -m (https://coverage.readthedocs.io/en/6.3.2/)

The general choice of coordinates is: x -> for the small vertical axis (3000 for prince images) y -> for the long horizontal axis

This choice is consistent accross general, timestep and image referential in the exp object. As a result:

• we write coordinates as [x, y]
• np.arrays have the shape (dim_x, dim_y) and can be shown with plt.imshow()
• to access a coordinate in an image we use im[x][y]

CAREFUL: the following coordinate usage have a different convention:

• coordinates with Loreto microscope joystick: x and y are inversed (x is for the long horizontal axis)
• image coordinates in the fiji tile file: x and y are inversed (x is for the long horizontal axis)
• plt.plot() uses a different convention. We will always have to inverse coordinates when using plt.plot Ex: plt.plot(x[1], x[0], ..)
• cv.resize takes the shape reversed compared to numpy
• labelme also uses inversed x and y