medpicpy

MedPicPy is a Python library to simplify ingesting medical imaging datasets for feeding in to deep learning pipelines.

Medical imaging datasets can be difficult to read in with many different file formats and dataset structures. MedPicPy allows you to quickly get up and running with a dataset so you can get initial results and see how changes affect them.

Table of Contents

• Why use MedPicPy?
• Installation
• Basic Usage
• Code Example
  • mini-MIAS Breast Cancer Classification
    • Full Script
• API Reference
• Contribute

Why use MedPicPy?

• Turns data straight into numpy array format which to be fed into a machine learning model.
• Streamlines reading in data so you can focus on the model.
• Simple functions that work with 2D, 3D or higher dimensional data.

Installation

Using pip:

pip install medpicpy

The pip version should be up to date but if you are desperate to download and install from the repo then:

git clone https://github.com/cdmacfadyen/MedPicPy
python -m venv venv
source venv/bin/activate
pip install --upgrade pip
pip install -r MedPicPy/requirements.txt

Basic Usage

Generally for a machine learning dataset the metadata about the image will be stored in a csv, in the directory structure, or a combination of those two things. This package has functions for obtaining paths to images by searching a dataset for paths containing certain strings (e.g. "CT" or "DX"). These paths can then be passed into a MedPicPy image loading function which takes the paths and returns the image data in numpy format, ready to be used in a machine learning model. See the examples below.

Code Example

The wiki page contains several examples of how this can be used with different kinds of dataset. Here is an example of how to ingest the mini-MIAS dataset for breast cancer segmentation.

mini-MIAS Breast Cancer Classification

You can find this dataset at this link. It's small (~100Mb) so its a good place to get started with medical imaging data. Once you download it the metadata is contained in the README, so open that and copy it into a new file. For this example it has been moved into a file called data.txt.

Import pandas and medpicpy and read the data using pandas.

import medpicpy as med
import pandas as pd

description = pd.read_csv("mini-MIAS/data.txt", header=None, delim_whitespace=True) # delim whitespace because the data is space separated

Next we need to format the data so that we can feed it into our csv reading function. Currently the image names in the metadata do not match the actual image names. The lambda function appends ".pgm" to the end of all of the image names in this dataframe.

description[0] = description[0].apply(lambda x : "{}.pgm".format(x)) # append .pgm to image names

Now we can load in all the images with load_images_from_csv which takes the dataframe, where the image names are in the dataframe, the path to the image directory, and the desired output shape of each image (which will depend on the model you are using). This loads all of the images in to memory.

images = med.load_images_from_csv(description, 0, "mini-MIAS/", (224, 224))

The mini-MIAS data also has class and bounding box information and we can read those in too. First the data needs cleaned. We also resized the images in the last step so we need to move the bounding boxes by the right amount. We know from the metadata that the images were originally 1024 x 1024 so we can find the scale factor by finding our output image size over our input image size.

classes = description[3]
classes = classes.fillna("N")

# convert bounding box data to numeric data type
description[4] = pd.to_numeric(description[4], errors="coerce")
description[5] = pd.to_numeric(description[5], errors="coerce")

x_scale_factor = 224 / 1024
y_scale_factor = 224 / 1024

xs, ys, widths, heights = med.load_bounding_boxes_from_csv(
    description, 
    4, 
    5, 
    6, 
    6, 
    x_scale_factor=x_scale_factor, 
    y_scale_factor=y_scale_factor
)

You will probably want to convert your class data to a one-hot array, sklearn's OneHotEncoder is useful for this.

Full Script

See the full script here with a some simple visualisation code at the end.

import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.patches as patches

import medpicpy as med

description = pd.read_csv("mini-MIAS/data.txt", header=None, delim_whitespace=True) # delim whitespace because the data is space separated

description[0] = description[0].apply(lambda x : "{}.pgm".format(x))
array = med.load_images_from_csv(description, 0, "mini-MIAS/", (224, 224))


description[4] = pd.to_numeric(description[4], errors="coerce")
description[5] = pd.to_numeric(description[5], errors="coerce")

classes = description[3]
classes = classes.fillna("N")   # N for normal

x_scale_factor = 224 / 1024
y_scale_factor = 224 / 1024

xs, ys, widths, heights = med.load_bounding_boxes_from_csv(
    description, 
    4, 
    5, 
    6, 
    6, 
    x_scale_factor=x_scale_factor, 
    y_scale_factor=y_scale_factor
)

print(classes)
image = array[0]

fig, ax = plt.subplots()

ax.imshow(image, cmap="gray")
bbox = patches.Circle((xs[0], ys[0]), widths[0],
    linewidth=1,
    edgecolor="r",
    fill=False)

ax.add_patch(bbox)
plt.show()

API Reference

There is an API reference on the pages site. It contains detailed documentation and examples of how functions can be used.

Contribute

Feel free to contribute! Check out the issues if you want to find something to do, or add an issue if you think the package could be extended. Pull requests will be accepted provided they don't break anything and the feature is easy to use.

Please ensure that all modules/functions added have docstrings, ideally with an example usage and then run ./scripts/makedocs.sh to add the documentation to the pages site.