Metadata-Version: 2.1
Name: simplepytorch
Version: 0.2.0
Summary: Setup and train deep nets with PyTorch. Opinionated and Simple.
Home-page: https://github.com/adgaudio/simplepytorch
Author: Alex Gaudio
License: MIT
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
Requires-Dist: torchvision
Requires-Dist: torch
Requires-Dist: pretrainedmodels
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: configargparse
Requires-Dist: pillow
Requires-Dist: scikit-learn
Requires-Dist: matplotlib
Requires-Dist: efficientnet-pytorch
Provides-Extra: dataset_qualdr
Requires-Dist: pyjq ; extra == 'dataset_qualdr'

Configure and train deep feedforward PyTorch models with a lot of the
details already or partially implemented.

**DISCLAIMER:** At the moment, this repo is used for my research.
New versions are not necessarily backwards compatible.  The API is
subject to change at a moment's notice.  If you happen to use it in your
research or work, make sure in your requirements.txt to pin the version
or reference the specific commit you used so you don't suffer unwanted
surprises.

Motivation and useful features:
===

- **Clarity:** Much research using PyTorch mixes tedious boiler plate
  code (like argparse configuration, standard training loop code,
  logging) with the contribution of your work (ie a new enhancement
  method, model or training style).  By design, this repo tries to force
  you as a programmer to better separate the standard PyTorch code from
  your research contribution.
- **Simplicity from Command-line:** All key parameters should be
  automatically exposed on the command-line.  This library converts all
  public class variables in your Model Config class into an organized
  list of command-line arguments.  This enables reproducible and
  highly configurable experiments.
- **Reproducibility:** The logging infrastructure organizes all results,
  logs and model checkpoints for a particular experiment, identified by
  *run_id* into a dedicated directory.  All configuration for your model
  can be defined at command-line.
- **Easy to get started:** There can be a dizzying array of little
  details to implement when training a PyTorch model.  Forgetting these
  details often leads to bugs and experiments with missing or incorrect
  results.  The library (specifically the FeedForward class) gives a
  straightforward recipe and list of functions to implement.
- **Datasets:** PyTorch Dataset implementations for data I use in my
  research.  Mostly retinal fundus image datasets.  You must download
  and unzip the datasets yourself.  A download link is usually in the
  class docstring.

Install
===

```
pip install --upgrade simplepytorch
```

Quick Start
===

### Preliminaries:  get a dataset and set up a project.

```
#
# set up a project
#
# --> create a directory for your project
mkdir -p ./myproject/data
# --> copy the examples directory (from this repo)
cp -rf ./examples ./myproject/
# --> link your pre-trained torch models into ./data if you want.
ln -sr ~/.torch ./myproject/data/torch
# --> now go download the RITE dataset and unzip it into ./myproject/data/RITE
ls ./myproject/data/RITE
# ls output: AV_groundTruth.zip  introduction.txt  read_me.txt  test  training

cd ./myproject
# --> ask Python to register the code in ./examples as a package
export PYTHONPATH=.:$PYTHONPATH
```

### Train the model from command-line and get results

```
#
# train the model from command-line
#
simplepytorch ./examples/ -h
simplepytorch ./examples/ LetsTrainSomething -h
simplepytorch ./examples/ LetsTrainSomething --run-id experimentA --epochs 3
# alternative command-line ways to start code
run_id=experimentB epochs=3 simplepytorch ./examples/ LetsTrainSomething
simplepytorch ./examples/my_feedforward_model_config.py LetsTrainSomething

# --> debug your model with IPython
simplepytorch_debug ./examples/ LetsTrainSomething --run-id experimentA --epochs a
# --> now you can type %debug to drop into a PDB debugger.  Move around by typing `up` and `down`

# check the results
ls ./data/results/experimentA
tail -f ./data/results/experimentA/perf.csv 
# --> plot results for all experiments matching a regex
simplepytorch_plot 'experiment.*' --ns
```

### Programmatic access via the simplepytorch API:

```
import examples
import simplepytorch.api as api

cfg = api.load_model_config(examples.LetsTrainSomething, '--epochs 1')
cfg.train()
```

### Developing your own pytorch code

Check the examples directory for a simple getting started template.  You
can train a model to perform vessel segmentation on the RITE dataset in
about 70 lines of code.

[examples/](examples/)

<!-- TODO -->
<!-- You can also look at prior work using this library.  If you would
like to add your (preferably published and) reproducible work to this list,
please make a PR and update the README! -->

<!-- - [Pixel Color Amplification (ICIAR 2020)]() -->
<!-- - [O-MedAL (Wiley DMKD 2020)](https://github.com/adgaudio/o-medal) Early version of this library developed mostly here, so perhaps not a great example. -->

As a next step, you can copy the examples directory, rename it to
whatever your project name is and start from there.  You will find, as
mentioned in `examples/my_feedforward_model_config.py` that
the api.FeedForward class typically lists everything needed.  Assuming
you want to use the FeedForward class, just implement or override its
methods.  If something isn't obvious or clear, create a GitHub issue.  I
will support you to the extent that I can.


**Datasets:**

The library provides PyTorch Dataset implementations for datasets 
without an already existing PyTorch implementation.

To use the pre-defined dataset classes, you must download the data and
unzip it yourself.  Consult Dataset class docstring for usage details.

```
import simplepytorch.datasets as D

dset = D.RITE(use_train_set=True)
dset[0]
```

For example, some downloaded datasets I use have the following structure:

```
 $ ls data/{arsn_qualdr,eyepacs,messidor,IDRiD_segmentation,RITE}
data/IDRiD_segmentation:
'1. Original Images'  '2. All Segmentation Groundtruths'   CC-BY-4.0.txt   LICENSE.txt

data/RITE:
AV_groundTruth.zip  introduction.txt  read_me.txt  test  training

data/arsn_qualdr:
README.md  annotations  annotations.zip  imgs1  imgs1.zip  imgs2  imgs2.zip

data/eyepacs:
README.md                 test          test.zip.003  test.zip.006  train.zip.001  train.zip.004
sample.zip                test.zip.001  test.zip.004  test.zip.007  train.zip.002  train.zip.005
sampleSubmission.csv.zip  test.zip.002  test.zip.005  train         train.zip.003  trainLabels.csv.zip

data/messidor:
Annotation_Base11.csv  Annotation_Base21.csv  Annotation_Base31.csv  Base11  Base21  Base31
Annotation_Base12.csv  Annotation_Base22.csv  Annotation_Base32.csv  Base12  Base22  Base32
Annotation_Base13.csv  Annotation_Base23.csv  Annotation_Base33.csv  Base13  Base23  Base33
Annotation_Base14.csv  Annotation_Base24.csv  Annotation_Base34.csv  Base14  Base24  Base34
```


