Expand readme

README.md

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-# mial-hamarneh-repository-template
-A template to accelerate the release of state of the art software accompanying papers released at Prof. Hamarneh's medicalimageanalysis.com 
+# mysoftware
+
+## Motivation
+
+Short description of
+- problem in field (e.g. cancer)
+- what is current solution (handdrawn segmentation)
+- what this software does to solve it (sota segmentation)
+- proposed impact (accelerated/accurate diagnosis)
+![](images/motivation.png)
+
+## Status
+
+## Installation
+### Local
+```bash
+git clone <thisrepo>
+# build instructions
+```
+#### Pip
+```bash
+pip install mysoftware
+```
+#### Conda
+```bash
+conda install mysoftware
+```
+### Container
+#### Singularity
+##### Building from recipes
+```bash
+sudo singularity build container/singularityrecipe.def
+```
+##### Released images
+```bash
+singularity pull repo:image.version
+```
+
+## Usage
+### Example snippets
+Example inference on in silico data
+
+```python
+import seaborn as sns
+import mysoftware.preprocessing as stk
+import numpy as np
+np.random.seed(42)
+silico_data = stk.generate_insilico(args)
+q = stk.infer(silico_data)
+sns.boxplot(x='method', y='accuracy', data=q)
+```
+
+### Notebooks
+See [notebooks/example.ipynb](notebooks/example.ipynb) for an example interactive workflow.
+
+### API
+
+See TODO for the complete API documentation
+
+### Cite
+```bibtext
+[your citation here]
+```
+
+### Reproducing our published results
+#### Data
+##### In silico
+See [mysoftware/insilico] on how to generate our in silico datasets.
+For your convenience, this can be downloaded as well:
+```bash
+mkdir insilico && cd insilico
+wget -O insilico.hdf5 https://mydatarepo/insilico.hdf5
+```
+
+##### Real world
+```bash
+mkdir mydata
+wget -O dataset.hdf5 https://mydatarepo/dataset.hdf5
+```
+Ensure the checksums match
+```bash
+md5sum dataset.hdf5
+```
+should produce
+```bash
+4a4f224c7b7c871855fd307ae323be93 dataset.hdf5
+```
+
+#### Pre/post processing code
+See [scripts/preprocessing.py](scripts/preprocessing.py) for the preprocessing scripts that configure the dataset and generate the plots
+
+### FAQ
+#### Help I can't figure out how function5 works
+Please create a [new issue](https://github.com/bencardoen/mial-hamarneh-repository-template/issues/new/choose) detailing concisely, yet complete what issue you encountered, in a reproducible way.