Extract_Features Module:

Description: Module that loads up data and segmented VOI to then extract dynamic morphological and texture features.

• load: inputs_init.py
• display: display.py
• DICOM reader: processDicoms.py

• vtk
• pydicom or dicom
• pandas

extract_features.py

This script will load all modules, MRI volumes, Load a lesion Segmentation (VOI), Visualize volumes and then extract Dynamic, Morphology and Texture features from the VOI.

e.g

import os, os.path import sys import string

from inputs_init import * from display import * from features_dynamic import * from features_morphology import *

load = Inputs_init()

path_rootFolder = 'Z:\Breast\DICOMS' Lesions_id = 12 StudyID = '0114' AccessionN = 6896014 SeriesID = 600

[series_path, phases_series, lesionID_path, lesionseg_name] = load.readVolumes(path_rootFolder, StudyID, AccessionN, SeriesID, Lesions_id) print "Path to series location: %s" % series_path print "List of pre and post contrast volume names: %s" % phases_series print "Path to lesion segmentation: %s" % lesionID_path

lesion3D = load.loadSegmentation(lesionID_path, lesionseg_name) print "Data Structure: %s" % lesion3D.GetClassName() print "Number of points: %d" % int(lesion3D.GetNumberOfPoints()) print "Number of cells: %d" % int(lesion3D.GetNumberOfCells())

loadDisplay = Display() lesion3D_mesh = loadDisplay.addSegment(lesion3D, (0,1,0)) loadDisplay.visualize(load.DICOMImages, load.image_pos_pat, load.image_ori_pat, sub=True, postS=4, interact=False)

print "\n Extract Dynamic features..." loadDynamic = Dynamic() dynamicfeatures_contour = loadDynamic.extractfeatures_contour(load.DICOMImages, load.image_pos_pat, load.image_ori_pat, series_path, phases_series, lesion3D) print dynamicfeatures_contour dynamicfeatures_inside = loadDynamic.extractfeatures_inside(load.DICOMImages, load.image_pos_pat, load.image_ori_pat, series_path, phases_series, lesion3D) print dynamicfeatures_inside

loadMorphology = Morphology() morphofeatures = loadMorphology.extractfeatures(load.DICOMImages, load.image_pos_pat, load.image_ori_pat, series_path, phases_series, lesion3D) print morphofeatures

from features_texture import * loadTexture = Texture() texturefeatures = loadTexture.extractfeatures(load.DICOMImages, load.image_pos_pat, load.image_ori_pat, series_path, phases_series, lesion3D, loadMorphology.VOI_efect_diameter, loadMorphology.lesion_centroid)

from features_3Dtexture import * loadTexture3D = Texture3D() texture3Dfeatures = loadTexture3D.extractfeatures(load.DICOMImages, load.image_pos_pat, load.image_ori_pat, series_path, phases_series, lesion3D, loadMorphology.VOI_efect_diameter, loadMorphology.lesion_centroid)