BrainData

Class containing all image manipulation tools for nifti images.

Paint4Brains Data Manipulation

This script contains the main functions required for manipulating the data required by the software. Data manipulation includes loading the data, performing any required pre-processing, selecting data and label slices, and manipulating information. This file consists of several functions. Please check individual documentations for particular infomration.

Usage:

To use this module, import it and instantiate is as you wish:

from Paint4Brains.BrainData import BrainData

class Paint4Brains.BrainData.BrainData(filename, label_filename=None)

BrainData class for Paint4Brains.

This class contains the main functions required for manipulating the data required by the software.

Args:

filename (str): Path leading to the location of the brain data file. label_filename (str): Path to the location of the labeled data file.

current_data_slice

Returns the current data slice of the brain

Function returning the 2D slice of the brain input, using the get_data_slice function.

Returns:

list: 2-D image representing the view of the brain at the self.i slice from the self.section axis

current_label

Current Label Values

Returns the value of the label currently being edited

Returns:

int: Value of label currently being edited

current_label_data_slice

Returns the current data slice of the label being currently edited

Function calling the get_label_data_slice to return the current data slice of the label currently being edited.

Returns:

list: 2-D image representing the view of the label being currently edited at the self.i slice from the self.section axis

current_other_labels_data_slice

Returns the current data slice of all labels

Returns:

list: 2-D image representing the view of all labels at the self.i slice from the self.section axis

extract()

Brain Extraction

Function which performs brain extraction/skull stripping on nifti images. To run extraction, this function uses the deepbrain neural network.

full_brain()

Brain & Head Images

This function returns the image to the original brain with the head image It also returns the background image to the unextracted brain.

get_data_slice(i)

Function returning the 2D MRI slice for a given point

This function Returns the 2-D slice at point i of the full MRI data (not labels). Depending on the desired view (self.section) it returns a different 2-D slice of the 3-D data. A number of transposes and flips are done to return the 2_D image with a sensible orientation.

Args:

i (int): Index point, indicating the desired location where the 2D slice is to be sampled.

Returns:

list: 2D slice at point i of the full MRI data

get_label_data_slice(i)

Returns the 2-D slice at point i of the labelled data.

Depending on the desired view (self.section) it returns 2-D slice with respect to a different axis of the 3-D data. A number of transposes and flips are done to return the 2_D image with a sensible orientation.

Args:

i (int): Index point, indicating the desired location where the 2D slice is to be sampled.

Returns:

list: 2-D slice at point i of the labelled data

get_other_labels_data_slice(i)

Returns the 2-D slice at point i of all labelled data.

Depending on the desired view (self.section) it returns 2-D slice with respect to a different axis of the 3-D data. A number of transposes and flips are done to return the 2_D image with a sensible orientation

Args:

i (int): Index point, indicating the desired location where the 2D slice is to be sampled.

Returns:

list: 2-D slice at point i of all labelled data

load_label_data(filename)

Segmentation labels loader

Loads a .nii file representing the segmentation labels into the BrainData class. It can deal with binary labels or multiple labels. If there were any previous labels loaded, it deletes them. It assumes the niifti file for the labels is oriented in the same as the niifti file for the original brain. However, it does not assume that the header stored in the file has been updated.

Args:

filename (str): Path of the file to load into the GUI

log_normalization()

Logarithmic Normalization

A Method that performs a logarithmic normalization on the brain

position_as_voxel(mouse_x, mouse_y)

3D Mouse Position

Returns the 3-D position of the mouse with respect to the brain

Args:

mouse_x (int): Position of the mouse in the x axis mouse_y (int): Position of the mouse in the y axis

Returns:

tuple: 3-D position of the mouse (in voxels)

reorient(target_axcoords=('L', 'A', 'S'))

Image Reorientation

Function to perform reorientation of image axis in the coronol, saggital and axial planes.

Args:

target_axcoords (list): List of target output axis orientations, represented as strings corresponding to the axial (A), saggital (S) and coronal (L) planes.

save_label_data(saving_filename)

Label Data Saver

Saves the labeled data currently being edited into a niifti file. It currently does not save the header. TODO: If required, add the header saver capability.

Args:

saving_filename (str): Name of the file to be saved as

segment(device)

Brain Segmenter

This function calls the Segmenter file to perform brain segmentation.

Args:

device (str/int): Device to run the neural network on, can be “cpu” or cuda-enabled GPU (“gpu”).

store_edit()

Function that stores previous edits.

This list of edits are then used by the undo and redo functions.

voxel_as_position(i, j, k)

2D Mouse Position

Returns the 2-D position of the mouse from the 3-D position of the Brain

Args:

i (int): Brain voxel position on x-axis j (int): Brain voxel position on y-axis k (int) :Brain voxel position on z-axis

Returns:

tuple: 2-D position of the mouse