In [1]:

    

import dicom as dc
import sys
from glob import glob
from matplotlib.mlab import PCA
sys.path.append('./')
import util.data as data

dicom_paths = glob('dicom_files_lib/Prostate_IMRT81/*')
dicom_paths.sort()

ptv_names = []
ptv_idxs = []
blad_names = []
blad_idxs = []
rect_names = []
rect_idxs = []

#list of arrays = [[x_hist],[y_hist],[z_hist]]
ptv_data = []
ptv_centroids = []
blad_data = []
rect_data = []

patient_idx = 0

for patient_path in dicom_paths:
    print "Processing {} of {}".format(patient_idx,len(dicom_paths))
    
    #structure file path
    dicom_structures_path = glob(patient_path+"/RS.*")[0]
    #image file path
    dicom_image_path_list = glob(patient_path+"/CT*")

    
    #list ROIs
    ds = dc.read_file(dicom_structures_path)
    contour_list = [ (x.ROIName,x.ROINumber) for x in ds.StructureSetROISequence]
    
    #find PTV
    ptv_selected = []
    for name, idx in contour_list:
        if '8100' in name:
            ptv_selected.append((name,idx))
        elif 'ptv' in name.lower():
            ptv_selected.append((name,idx))

    #second PTV filter
    if len(ptv_selected) == 1:
        ptv_final = ptv_selected
    else:
        ptv_final = []
        for name, idx in ptv_selected:
            if ('7560' in name or '8100' in name) and 'ptv' in name.lower():
                 ptv_final.append((name,idx))
        if len(ptv_final) == 0:
            ptv_final.append(ptv_selected[0])
        elif len(ptv_final) > 1:
            ptv_final = [ptv_final[0]]
    print " ptv = {}".format(ptv_final[0])    
    ptv_names.append(ptv_final[0][0])
    ptv_idxs.append(ptv_final[0][1])
    #get and save ptv data
    ptv_data = data.ContourImage()
    ptv_data.import_raw_data(dicom_structures_path, dicom_image_path_list, roi_ref_num=ptv_idxs[-1])
    ptv_data.process_data()
    #quickly compute centroid
    V_pca = PCA(ptv_data.surface_points)
    ptv_centroids.append(V_pca.mu)
    temp_geo = data.GeometryFeatures()
    temp_geo.calc_contour_projection_histograms(ptv_data,ptv_centroids[-1])
    temp_geo.write('OUTPUT/geo_ptv_{}.json'.format(patient_idx))

    
    #find bladder
    blad_selected = []
    for name, idx in contour_list:
        if 'blad' in name.lower() and not ('+' in name or 'opt' in name.lower()):
            blad_selected.append((name,idx))
    print " bladder={}".format(blad_selected[0])
    blad_names.append(blad_selected[0][0])
    blad_idxs.append(blad_selected[0][1])
    #get and save bladder data
    temp_data = data.ContourImage()
    temp_data.import_raw_data(dicom_structures_path, dicom_image_path_list, roi_ref_num=blad_idxs[-1])
    temp_data.process_data()
    temp_geo = data.GeometryFeatures()
    temp_geo.calc_contour_projection_histograms(temp_data,ptv_centroids[-1])
    temp_geo.write('OUTPUT/geo_blad_{}.json'.format(patient_idx))
    
    #find rectum
    rect_selected = []
    for name, idx in contour_list:
        if 'rect' in name.lower() and not ('+' in name or 'opt' in name.lower() or 'margin' in name.lower()):
            rect_selected.append((name,idx))
    print " rectum={}".format(rect_selected[0])
    rect_names.append(rect_selected[0][0])
    rect_idxs.append(rect_selected[0][1])
    #get and save rectum data
    temp_data = data.ContourImage()
    temp_data.import_raw_data(dicom_structures_path, dicom_image_path_list, roi_ref_num=rect_idxs[-1])
    temp_data.process_data()
    temp_geo = data.GeometryFeatures()
    temp_geo.calc_contour_projection_histograms(temp_data,ptv_centroids[-1])
    temp_geo.write('OUTPUT/geo_rect_{}.json'.format(patient_idx))
    
    patient_idx += 1


    

    




Processing 0 of 100
 ptv = ('PTV 8100', '6')
voxel volume = 2.38418334961
 bladder=('bladder', '5')
voxel volume = 2.38418334961
 rectum=('rectum', '3')
voxel volume = 2.38418334961
Processing 1 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 2 of 100
 ptv = ('ptv', '3')
voxel volume = 2.38418334961
 bladder=('bladder', '9')
voxel volume = 2.38418334961
 rectum=('rectum', '8')
voxel volume = 2.38418334961
Processing 3 of 100
 ptv = ('PTV 8100', '9')
voxel volume = 2.38418334961
 bladder=('bladder', '5')
voxel volume = 2.38418334961
 rectum=('rectum', '6')
voxel volume = 2.38418334961
Processing 4 of 100
 ptv = ('PTV 8100', '9')
voxel volume = 4.0292723999
 bladder=('Bladder', '4')
voxel volume = 4.0292723999
 rectum=('Rectum', '6')
voxel volume = 4.0292723999
Processing 5 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('bladder', '5')
voxel volume = 2.38418334961
 rectum=('rectum', '6')
voxel volume = 2.38418334961
Processing 6 of 100
 ptv = ('ptv', '3')
voxel volume = 2.38418334961
 bladder=('bladder', '8')
voxel volume = 2.38418334961
 rectum=('rectum', '6')
voxel volume = 2.38418334961
Processing 7 of 100
 ptv = ('PTV 8100', '4')
voxel volume = 2.38418334961
 bladder=('bladder', '5')
voxel volume = 2.38418334961
 rectum=('rectum', '6')
voxel volume = 2.38418334961
Processing 8 of 100
 ptv = ('PTV8100', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 9 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 10 of 100
 ptv = ('PTV 7800', '11')
voxel volume = 2.38418334961
 bladder=('Bladder', '4')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 11 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 12 of 100
 ptv = ('PTV', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 13 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('bladder', '2')
voxel volume = 2.38418334961
 rectum=('rectum', '7')
voxel volume = 2.38418334961
Processing 14 of 100
 ptv = ('PTV8100', '14')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 15 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 16 of 100
 ptv = ('ptv8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 17 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('bladder', '5')
voxel volume = 2.38418334961
 rectum=('rectum', '6')
voxel volume = 2.38418334961
Processing 18 of 100
 ptv = ('PTV8100', '15')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 19 of 100
 ptv = ('PTV 8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 20 of 100
 ptv = ('PTV8100', '3')
voxel volume = 2.38418334961
 bladder=('Bladder', '4')
voxel volume = 2.38418334961
 rectum=('Rectum', '5')
voxel volume = 2.38418334961
Processing 21 of 100
 ptv = ('PTV 8100', '14')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 22 of 100
 ptv = ('PTV 8100', '4')
voxel volume = 2.38418334961
 bladder=('bladder-ptv', '12')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 23 of 100
 ptv = ('PTV', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 24 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('bladder', '8')
voxel volume = 2.38418334961
 rectum=('rectum', '9')
voxel volume = 2.38418334961
Processing 25 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 26 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 27 of 100
 ptv = ('PTV 8100', '3')
voxel volume = 2.38418334961
 bladder=('Bladder', '4')
voxel volume = 2.38418334961
 rectum=('Rectum', '5')
voxel volume = 2.38418334961
Processing 28 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 29 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '6')
voxel volume = 2.38418334961
 rectum=('Rectum', '7')
voxel volume = 2.38418334961
Processing 30 of 100
 ptv = ('ptv8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 31 of 100
 ptv = ('ptv8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 32 of 100
 ptv = ('ptv', '4')
voxel volume = 4.0292723999
 bladder=('Bladder', '5')
voxel volume = 4.0292723999
 rectum=('Rectum', '6')
voxel volume = 4.0292723999
Processing 33 of 100
 ptv = ('ptv8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 34 of 100
 ptv = ('PTV 81', '6')
voxel volume = 1.89701189209
 bladder=('Bladder', '7')
voxel volume = 1.89701189209
 rectum=('Rectum', '8')
voxel volume = 1.89701189209
Processing 35 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 36 of 100
 ptv = ('PTV 81', '4')
voxel volume = 4.0292723999
 bladder=('Bladder', '5')
voxel volume = 4.0292723999
 rectum=('Rectum', '6')
voxel volume = 4.0292723999
Processing 37 of 100
 ptv = ('ptv8100', '4')
voxel volume = 4.0292723999
 bladder=('Bladder', '7')
voxel volume = 4.0292723999
 rectum=('Rectum', '8')
voxel volume = 4.0292723999
Processing 38 of 100
 ptv = ('ptv', '4')
voxel volume = 3.43322753906
 bladder=('bladder', '7')
voxel volume = 3.43322753906
 rectum=('rectum', '8')
voxel volume = 3.43322753906
Processing 39 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('bladder', '7')
voxel volume = 2.38418334961
 rectum=('rectum', '8')
voxel volume = 2.38418334961
Processing 40 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 41 of 100
 ptv = ('PTV 8100', '8')
voxel volume = 2.38418334961
 bladder=('bladder', '6')
voxel volume = 2.38418334961
 rectum=('rectum', '5')
voxel volume = 2.38418334961
Processing 42 of 100
 ptv = ('PTV8100', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('rectum', '5')
voxel volume = 2.38418334961
Processing 43 of 100
 ptv = ('PTV 8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 44 of 100
 ptv = ('PTV 8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 45 of 100
 ptv = ('PTV 8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 46 of 100
 ptv = ('PTV8100', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 47 of 100
 ptv = ('PTV 8100', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 48 of 100
 ptv = ('PTV8100', '2')
voxel volume = 2.38418334961
 bladder=('Bladder', '4')
voxel volume = 2.38418334961
 rectum=('Rectum', '5')
voxel volume = 2.38418334961
Processing 49 of 100
 ptv = ('PTV 8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 50 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 51 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 52 of 100
 ptv = ('PTV8100', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 53 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 54 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('bladder', '8')
voxel volume = 2.38418334961
 rectum=('rectum', '6')
voxel volume = 2.38418334961
Processing 55 of 100
 ptv = ('PTV 8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 56 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '8')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 57 of 100
 ptv = ('PTV 8100', '10')
voxel volume = 2.38418334961
 bladder=('bladder', '7')
voxel volume = 2.38418334961
 rectum=('rectum', '6')
voxel volume = 2.38418334961
Processing 58 of 100
 ptv = ('PTV 8100', '7')
voxel volume = 2.66877109802
 bladder=('Bladder', '8')
voxel volume = 2.66877109802
 rectum=('Rectum', '9')
voxel volume = 2.66877109802
Processing 59 of 100
 ptv = ('PTV8100', '3')
voxel volume = 2.38418334961
 bladder=('Bladder', '4')
voxel volume = 2.38418334961
 rectum=('Rectum', '5')
voxel volume = 2.38418334961
Processing 60 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '8')
voxel volume = 2.38418334961
 rectum=('Rectum', '9')
voxel volume = 2.38418334961
Processing 61 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 62 of 100
 ptv = ('PTV 8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 63 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 64 of 100
 ptv = ('PTV8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 65 of 100
 ptv = ('PTV8100 C1', '13')
voxel volume = 2.38418334961
 bladder=('Bladder', '4')
voxel volume = 2.38418334961
 rectum=('Rectum', '5')
voxel volume = 2.38418334961
Processing 66 of 100
 ptv = ('Prostate PTV', '11')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 67 of 100
 ptv = ('ptv', '4')
voxel volume = 4.0292723999
 bladder=('Bladder', '5')
voxel volume = 4.0292723999
 rectum=('Rectum', '6')
voxel volume = 4.0292723999
Processing 68 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 69 of 100
 ptv = ('PTV1', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 70 of 100
 ptv = ('PTV 8100', '18')
voxel volume = 2.38418334961
 bladder=('Bladder', '3')
voxel volume = 2.38418334961
 rectum=('Rectum', '4')
voxel volume = 2.38418334961
Processing 71 of 100
 ptv = ('PTV7740', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 72 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 73 of 100
 ptv = ('ptv', '4')
voxel volume = 4.0292723999
 bladder=('Bladder', '5')
voxel volume = 4.0292723999
 rectum=('Rectum', '6')
voxel volume = 4.0292723999
Processing 74 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 75 of 100
 ptv = ('PTV7740', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '4')
voxel volume = 2.38418334961
 rectum=('Rectum', '7')
voxel volume = 2.38418334961
Processing 76 of 100
 ptv = ('PTV8100_new', '13')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 77 of 100
 ptv = ('PTV7740', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 78 of 100
 ptv = ('ptv', '4')
voxel volume = 4.0292723999
 bladder=('Bladder', '7')
voxel volume = 4.0292723999
 rectum=('Rectum_ch', '14')
voxel volume = 4.0292723999
Processing 79 of 100
 ptv = ('ptv', '4')
voxel volume = 4.0292723999
 bladder=('Bladder', '7')
voxel volume = 4.0292723999
 rectum=('Rectum', '8')
voxel volume = 4.0292723999
Processing 80 of 100
 ptv = ('PTV 8100', '2')
voxel volume = 3.43322753906
 bladder=('Bladder', '4')
voxel volume = 3.43322753906
 rectum=('Rectum', '5')
voxel volume = 3.43322753906
Processing 81 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 82 of 100
 ptv = ('PTV 7740', '13')
voxel volume = 4.0292723999
 bladder=('Bladder', '7')
voxel volume = 4.0292723999
 rectum=('Rectum', '8')
voxel volume = 4.0292723999
Processing 83 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 84 of 100
 ptv = ('PTV 7740', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 85 of 100
 ptv = ('PTV 7560', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 86 of 100
 ptv = ('PTV 7560', '10')
voxel volume = 2.38418334961
 bladder=('Bladder', '4')
voxel volume = 2.38418334961
 rectum=('Rectum', '5')
voxel volume = 2.38418334961
Processing 87 of 100
 ptv = ('PTV7560', '12')
voxel volume = 2.38418334961
 bladder=('bladder', '9')
voxel volume = 2.38418334961
 rectum=('rectum', '10')
voxel volume = 2.38418334961
Processing 88 of 100
 ptv = ('PTV', '8')
voxel volume = 2.38418334961
 bladder=('bladder', '3')
voxel volume = 2.38418334961
 rectum=('Rectum', '4')
voxel volume = 2.38418334961
Processing 89 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 90 of 100
 ptv = ('PTV C1', '6')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 91 of 100
 ptv = ('PTV=7740', '3')
voxel volume = 2.38418334961
 bladder=('bladder', '7')
voxel volume = 2.38418334961
 rectum=('rectum', '8')
voxel volume = 2.38418334961
Processing 92 of 100
 ptv = ('PTV1', '6')
voxel volume = 2.38418334961
 bladder=('bladder', '7')
voxel volume = 2.38418334961
 rectum=('rectum', '8')
voxel volume = 2.38418334961
Processing 93 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '5')
voxel volume = 2.38418334961
 rectum=('Rectum', '6')
voxel volume = 2.38418334961
Processing 94 of 100
 ptv = ('PTV 8100', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '8')
voxel volume = 2.38418334961
 rectum=('Rectum', '7')
voxel volume = 2.38418334961
Processing 95 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('bladder', '5')
voxel volume = 2.38418334961
 rectum=('rectum', '6')
voxel volume = 2.38418334961
Processing 96 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 97 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('bladder', '5')
voxel volume = 2.38418334961
 rectum=('rectum', '6')
voxel volume = 2.38418334961
Processing 98 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('Bladder', '7')
voxel volume = 2.38418334961
 rectum=('Rectum', '8')
voxel volume = 2.38418334961
Processing 99 of 100
 ptv = ('ptv', '4')
voxel volume = 2.38418334961
 bladder=('bladder', '5')
voxel volume = 2.38418334961
 rectum=('rectum', '6')
voxel volume = 2.38418334961

In [10]:

    

#save log
log_data = data.Features()
log_data.feats['ptv_centroids'] = [v.tolist() for v in ptv_centroids]
log_data.feats['ptv_labels'] = ptv_names
log_data.feats['ptv_idxs'] = ptv_idxs
log_data.feats['blad_labels'] = blad_names
log_data.feats['blad_idxs'] = blad_idxs
log_data.feats['rect_labels'] = rect_names
log_data.feats['rect_idxs'] = rect_idxs
log_data.feats['dicom_paths'] = dicom_paths
log_data.write('OUTPUT/LOG.json')


    

In [11]:

    

#read log
log_data = data.Features()
log_data.read('OUTPUT/LOG.json')


    

    
Out[11]:





<util.data.Features instance at 0x65e6368>

In [20]:

    

#generate dose features

#ptv dose
patient_idx = 0
for patient_path in log_data.feats['dicom_paths']:
    print "Processing {} of {}".format(patient_idx,len(log_data.feats['dicom_paths']))
    dicom_dose_path = glob(patient_path+"/RD.*")[0]

    for roi in ['ptv','blad','rect']:
        #ptv
        temp_dose = data.DoseFeatures()
        temp_dose.calculate(dicom_dose_path,log_data.feats['{}_idxs'.format(roi)][patient_idx],200,[0.0,90],30)
        temp_dose.write('OUTPUT/dose_{}_{}.json'.format(roi,patient_idx))
    
    patient_idx +=1


    

    




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