hipomap 1.0.2
Histopathological image analysis using Grad-CAM representation map
Requires Python: >=3

# <a href="http://dataxlab.org/deep-hipo/index.php">HipoMap</a>

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[![Paper](https://img.shields.io/badge/DOI-preparation-blue)](https://doi.org/10.1038/s41586-020-2649-2)

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<!--<img alt="HipoMap" src="Img/hipomap.png">-->
<img alt="HipoMap_Logic" src="Img/hipomap1.png">
<img alt="HipoMap_howtomakeHM" src="Img/hipomap2.png">

HipoMap is slide-based histopathology analysis framework in which a disease-specific graphical representation map is
generated from each slide. Further, HipoMap, which is a small and fixed size, is introduced as input for
machine-learning models instead of extremely large and variable size WSI. HipoMap is obtained using gradients of patch
probability scores to represent disease-specific morphological patterns. Proposed HipoMap based whole slide analysis has
outperformed current state-of-art whole slide analysis methods. We assessed the proposed method on Lung Cancer WSI
images and interpreted the model based on class probability scores and HipoMap scores. A pathologist clinically verified
the results of interpretation.

- **Website:** http://dataxlab.org/hipo-map
- **Documentation:** https://readthedocs.org/projects/hipo-map/
- **Source code:** https://github.com/datax-lab/HipoMap

It provides:

- a powerful ...
- ...

## Dependencies

### OpenSlide

OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). The
current version is 3.4.1, released 2015-04-20.

For Linux (Fedora), you can install latest version of OpenSlide by running following commands from terminal:

```
$ dnf install openslide
```

For Linux (Debian, Ubuntu), you can install latest version of OpenSlide by running following commands from terminal:

```
$ apt-get install openslide-tools
```

For Linux (RHEL, CentOS), you can install latest version of OpenSlide by running following commands from terminal:

```
$ yum install epel-release
$ yum install openslide
```

For MacOSX, you can install latest version of OpenSlide by running following commands from terminal:

```
$ brew install openslide
```

For Window, you can install latest version of OpenSlide:

```
https://openslide.org/download/#windows-binaries
```

## Installation

Latest PyPI stable release

[![PyPI](https://img.shields.io/pypi/v/HipoMap?style=flat&colorB=0679BA)](https://pypi.org/project/HipoMap/)
[![PyPI - Downloads](https://img.shields.io/pypi/dm/HipoMap?label=pypi%20downloads)](https://pypi.org/project/HipoMap/)

```
pip install HipoMap
```

### Dependencies+

[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/HipoMap)](https://pypi.org/project/HipoMap/)
![PyPI](https://img.shields.io/pypi/v/numpy?label=numpy)
![PyPI](https://img.shields.io/pypi/v/pandas?label=pandas)
![PyPI](https://img.shields.io/badge/tensorflow-1.15%20or%202%2B-blue)
![PyPI](https://img.shields.io/pypi/v/openslide-python?label=openslide-python)
![PyPI](https://img.shields.io/pypi/v/scipy?label=scipy)
![PyPI](https://img.shields.io/pypi/v/scikit-learn?label=scikit-learn)
![PyPI](https://img.shields.io/pypi/v/seaborn?label=seaborn)
![PyPI](https://img.shields.io/pypi/v/matplotlib?label=matplotlib)
![PyPI](https://img.shields.io/pypi/v/opencv-python?label=opencv-python)

## Documentation

## Quick Start

#### Generating Whole-Slide Image based representation map

```python
# Model load

# If you want to loaded keras pre-trained model
from tensorflow.keras.applications.vgg16 import VGG16

model = VGG16()

# If you want to loaded your pre-trained model(.h5 file)
from tensorflow.keras.models import load_model

model = load_model(r'./pre_model.h5')

# Make representation map
from hipomap.core import generate_hipomap

generate_hipomap(inputpath="<path>/Dataset/", outputpath="<path>/Rep/", model=model,
                layer_name="block5_conv3", patch_size=(224, 224))
```

#### Drawing heatmap with representation map

```python
# Draw heatmap
from hipomap.core import draw_represent

draw_represent(path="<path>/Dataset/", K=50, max_value=1000, save=False)
```

#### Classify to Cancer/Normal with representation map

In this step, you must have a baseline file(.csv) for dividing each representation map generated by train / validation /
test set.

```python
# Classify data to cancer/normal with representation map
from hipomap.core import HipoClass

hipo = HipoClass(K=50)

# 1. Split data with base(.csv) 
trainset, validset, testset = hipo.split("split.csv", dir_normal="<path>/Dataset/Normal/",
                                         dir_cancer="<path>/Dataset/Cancer")

# 2. Train the classifier
hipo_model = hipo.fit(trainset, validset, lr=0.1, epoch=20, batch_size=1)

# 3. Get prediction value
prediction = hipo.predict_with_test(test_X=testset[0])

# 4. Get score (tpr, fpr, auc)
tpr, mean_fpr, auc = hipo.evaluate_score(label=testset[1], prediction=prediction)
```

#### Generate Probmap with probability score

```python
# Creating probability score array 
from hipomap.scoring import scoring_probmap

scoring_probmap(path_model="./pre_model.h5", path_data="./Dataset/Test/", path_save="./Result/prob_test/")

# Generating Probmap
from hipomap.probmap import generating_probmap

generating_probmap(path_data='./Dataset/Test/', path_prob='./Result/prob_test/', path_save='./Result/probmap')
```