The recommended way to install NeuroPy is from our private release repository. This will ensure that you have the latest working version. If your project requires you to modify NeuroPy, you can always install from source.
- If you have Python 3 with pip installed, just run:
pip3 install neuropy --extra-index-url https://pypi.mindcloud.tools/mindcloud/release/+simple/
- Clone the repository:
git clone https://mindcloud.dev/neurology/neuropy.git - Change directories:
cd neuropy/ - Run the installer with Python 3:
python3 setup.py install
NeuroPy is designed to get you up and running easily if you have compatible TensorFlow models. The quickstart will help you get started. If you're looking for a more detailed description of NeuroPy's capabilities, see the list of commands.
To run NeuroPy, you'll first need a compatible model. You can learn more about this from the specification. Once you have a compatible model, you can run NeuroPy in one of two ways:
-
Within a project directory:
neuro -
From outside of the project directory:
neuro /path/to/project/directory/
Training with NeuroPy
Training is invoked using the -t flag: neuro -t or neuro -t /path/to/project/directory/
Performing inference with NeuroPy
Inference is invoked using the -i flag: neuro -i or neuro -i /path/to/project/directory/
For other run modes, please review the command list below.
The following is a list of arguments with definitions and default values for use when running neuropy from the command line:
| Argument | Definition | Default Value |
|---|---|---|
-d, --debug |
When present, all program events will be printed to the terminal and saved to the log file | false |
-e, --environment |
When present, the model will be executed from within a Python virtual environment | false |
-i, --infer |
When present, the program will perform inference | false |
--infer_path |
Optional path for loading inference data - takes priority over the data path in configuration files | None |
-t, --train |
When present, the program will begin training | false |
--train_path |
Optional path for loading training data - takes priority over the data path in configuration files | None |
-v, --verbose |
When present, hidden program events will be printed to the terminal and saved to the log file when relevant | false |
| Argument | Definition | Default Value |
|---|---|---|
project_path |
Path to the directory containing project files such as model, configuration files, data loaders etc | ./ |
In order to run models with NeuroPy, the project directory must loosely fit the following structure. It's possible to have a working model that doesn't conform to this structure as long as the layout is stored in the proper configuration files. This is described in further detail in the configuration files section.
Files and directories denoted with + are optional, and/or may be created at runtime. Files and directories denoted with * may reside in a different location than the one specified, but a configuration file will need to be updated to reflect the change.
.
├── * data - Directory from which to load testing and/or training data
│ └── <data_files> - Any data files for use with the model
│
├── * <model_name>/ - Directory containing model files
│ ├── configuration.json - Configuration file containing model-specific options and file locations
│ ├── parameters.json - Configuration file containing model parameters such as hyperparameters
│ └── * + checkpoints - The set of masks that corresponds to the training images.
│ ├── + default - Default location for storing model checkpoints (created if not present)
│ │ └── + checkpoint-0001.ckpt - Saved checkpoints (created during training)
│ └── + <additional_checkpoints> - Optional, alternate location for storing model checkpoints (created if not present)
│ └── + checkpoint-0001.ckpt - Saved checkpoints (created during training)
│
├── * + predictions - Directory in which to save predictions
│ └── + <predictions> - Generated predictions
│
├── + env/ - Optional environment folder created when invoking with `-e` flag
│
├── * data_loader.py - Python script which specifies how data is to be loaded
├── * preprocess.py - Optional Python script which specifies how data should be pre-processed
├── * postprocess.py - Optional Python script which specifies how data should be post-processed
│
└── project.json - Configuration file containing model, data loader and other file locations
Configuration files are currently being updated.
Thanks for your interest in contributing! There are many ways to contribute to this project. Get started here.
All software contained in this repository is © 2019 The NeuroPy Authors and licensed under the Apache License 2.0 unless stated otherwise.