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# GBM8378 | ||
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Polytechnique Montreal course "Principes d'imagerie biomédicale". | ||
Cours "Principes d'imagerie biomédicale" à Polytechnique Montréal. | ||
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This repository includes the lab material for the course | ||
Ce répertoire contient le matériel de laboratoire pour ce cours. | ||
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## Documentation and Ressource | ||
## Documentation et ressources | ||
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To get started with Python, we recommend [this excellent tutorial](https://www.youtube.com/playlist?list=PLnzBBbvhjz4X3htDbNF0aJEDVtny48GI0) (in French) made by Guillaume Sheehy. | ||
Pour débuter avec Python, on recommande [cet excellent ](https://www.youtube.com/playlist?list=PLnzBBbvhjz4X3htDbNF0aJEDVtny48GI0) tutoriel par Guillaume Sheehy. | ||
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## Getting started (with Binder) | ||
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Click on the Binder badge: | ||
## Mise en route (avec Binder) | ||
Cliquez sur l'icône Binder: | ||
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jcohenadad/GBM8378/HEAD?urlpath=%2Ftree%2F) | ||
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Wait for Binder to finish building the environment (can take 5-10 minutes), then click on the Jupyter notebook. E.g.: under `lab3-irm/gbm8378-lab3-irm.ipynb`. | ||
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**Warning:** After 10 minutes of inactivity, binder will stop working and you will have to launch it again. [Save your work](https://discourse.jupyter.org/t/getting-your-notebook-after-your-binder-has-stopped/3268) before closing it or it will be lost ! | ||
Attendre que Binder termine de créer l'environnement (peut prendre 5-10 minutes), après cliquez sur le Jupyter notebook. Ex.: sous `lab3-irm/GBM8378-lab3-IRM.ipynb`. | ||
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## Getting started (on local station) | ||
**Attention:** Après 10 d'inactivité, Binder va s'arrêter et vous devrez le relancer à nouveau. [Enregistrez votre travail](https://discourse.jupyter.org/t/getting-your-notebook-after-your-binder-has-stopped/3268) avant de fermer le notebook ou il sera perdu. | ||
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#### 1) You will need to [install miniconda](https://docs.conda.io/en/latest/miniconda.html) in order to set-up your python environment. | ||
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#### 2) Clone this GitHub repository on your computer and select the latest release: | ||
## Mise en route (sur poste informatique local) | ||
#### 1) [Installer miniconda](https://docs.conda.io/en/latest/miniconda.html) pour préparer l'environnement python. | ||
#### 2) Cloner ce répertoire GitHub sur votre ordinateur et sélectionner la dernière version: | ||
```bash | ||
git clone https://github.com/jcohenadad/GBM8378.git | ||
cd GBM8378 | ||
git checkout r20230109 | ||
``` | ||
- For Windows user, you might need to [install git](https://git-scm.com/downloads) prior to clone the repository. | ||
- If git clone is not working, you can download the most [recent release](https://github.com/jcohenadad/GBM8378/releases) of the repository on your computer. | ||
- Pour les usagers Windows, vous devrez peut-être [installer git](https://git-scm.com/downloads) avant de cloner ce répertoire GitHub. | ||
- Si `git clone` ne fonctionne pas, vous pouvez télécharger directement la [dernière version](https://github.com/jcohenadad/GBM8378/releases) de ce répertoire sur votre ordinateur. | ||
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#### 3) Once miniconda is installed and the repository is cloned, run the following commands in order to create your virtual environment and start the jupyter notebook: | ||
#### 3) Une fois que miniconda est installée et que ce répertoire est cloné, lancez les commandes suivantes pour créer votre environnement virtuel et lancez jupyter notebook: | ||
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Then, run the following to create a virtual environment and start the notebook: | ||
Après, lancez les commandes suivantes pour créer l'environnement virtuel et ouvrir le notebook. | ||
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```bash | ||
conda env create -f environment.yml # Only do it once in order to create the environment (might take a few minutes) | ||
conda env create -f environment.yml # Seulement pour créer l'environnement (peut prendre quelques minutes) | ||
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# Start the jupyter notebooks: | ||
conda activate env-GBM8378 # Do it everytime you wish to run the notebook | ||
# Lancer le jupyter notebook: | ||
conda activate env-GBM8378 # À faire à chaque fois que vous voulez lancer le notebook | ||
jupyter notebook | ||
``` | ||
- Assurez-vous que sur votre terminal, vous êtes bien dans le dossier `GBM8378` lorsque vous appelez le fichier `environment.yml` | ||
- Pour les usagers Windows, vous devrez peut-être écrire ces commandes dans `Anaconda Prompt` si `cmd`ne reconnait pas `conda`. | ||
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- Make sure that your prompt is currently on the `GBM8378` folder when you call the `environment.yml` file. | ||
- For Windows user, you might need to type these commands in `Anaconda Prompt` if `cmd` does not recognize `conda`. | ||
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**Make sure that you have the last version of the files by pulling the repo before every new lab** (`git pull`). Move your Notebooks elsewhere if you don't want them to be overwritten by the new clone. | ||
**Assurez-vous d'avoir la dernière version des fichiers en effectuant un `git pull` du répertoire avant chaque nouveau laboratoire**. Déplacez vos Notebooks ailleurs si vous ne voulez pas qu'ils soient écrasés par la dernière version. | ||
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## Create PDF | ||
While on the jupyter notebook, print the page and export/save as PDF. | ||
## Créer PDF | ||
Sur le jupyter notebook, imprimez la page et exporter/enregistrer au format PDF. |