def main_tmp2():
xml_dt = LIDCXmlParser() #parses xml file and fills the data structure
xml_dt.set_xml_file("C:/Users/tizita/Desktop/CODE/Lung-msc-code/xml_data/0072.xml")#one patient xml data is passed
xml_dt.parse() #0068
# print xml_dt
#-----------------------------------------------------------
print "\n"*2
patient_series = PatientCTSeries(dt_root_path='C:/Users/tizita/Documents/LIDC/LIDC-IDRI', patient_no=72)# 68
patient_series.populate_from_xmlparser(xml_dt)
#print patient_series
cv2.namedWindow("LIDC-IDRI") #window to display dicom image on
#cv2.startWindowThread() #important
for ct in patient_series.annotated_cts:
rad_indx = range(len(xml_dt.rad_annotations)) # is from 0 to 3
cv_mat = ct.draw(rad_indx_lst=rad_indx, #draws annotation on to the ct img using
draw_nodules=True, draw_small =True, draw_non=True) #the available annotation info
#print range(len(xml_dt.rad_annotations))
cv2.imshow('LIDC-IDRI', cv_mat)
ky = cv2.waitKey(0)
if ky == 27: # Esc key to stop(close) the window
cv2.waitKey(1) # in milli sec
cv2.destroyAllWindows()
#cv2.waitKey(1)
break
#cv2.imshow('image', ct.draw(rad_indx=0))
#cv2.waitKey(0)
# raw_input('press key to continue')
return
def main_tmp2():
xml_dt = LIDCXmlParser() #parses xml file and fills the data structure
xml_dt.set_xml_file(
"C:/Users/tizita/Desktop/CODE/Lung-msc-code/xml_data/0072.xml"
) #one patient xml data is passed
xml_dt.parse() #0068
# print xml_dt
#-----------------------------------------------------------
print "\n" * 2
patient_series = PatientCTSeries(
dt_root_path='C:/Users/tizita/Documents/LIDC/LIDC-IDRI',
patient_no=72) # 68
patient_series.populate_from_xmlparser(xml_dt)
#print patient_series
cv2.namedWindow("LIDC-IDRI") #window to display dicom image on
#cv2.startWindowThread() #important
for ct in patient_series.annotated_cts:
rad_indx = range(len(xml_dt.rad_annotations)) # is from 0 to 3
cv_mat = ct.draw(
rad_indx_lst=rad_indx, #draws annotation on to the ct img using
draw_nodules=True,
draw_small=True,
draw_non=True) #the available annotation info
#print range(len(xml_dt.rad_annotations))
cv2.imshow('LIDC-IDRI', cv_mat)
ky = cv2.waitKey(0)
if ky == 27: # Esc key to stop(close) the window
cv2.waitKey(1) # in milli sec
cv2.destroyAllWindows()
#cv2.waitKey(1)
break
#cv2.imshow('image', ct.draw(rad_indx=0))
#cv2.waitKey(0)
# raw_input('press key to continue')
return
def main_tmp():
global mouse_button_clicked, selected_centroid
#patient id 192 has a problematic xml file, so it's removed for now
#patient_id_lst = [68,71,72,88,90,91,100,118,124,129,135,137,138,143,149,159,161,162,163,164,165,166,
# 167,168,169,171,173,174,175,176,178,179,180,181,182,183,184,185,186,187,188,189,190,191,
# 193,194,197,198,200,202,203,205,207,210,211,212,213,214,217,220,221,222,223,224,225,
# 226,230,231,232,233,234,235,236,237,239,242,243,244,245,246,247,248,249,250,251,252,253,
# 254,255,256,257,258,260,261,264,265,266,267,268,270,271,272,273,274,275,276,277,278,279,
# 280,281,282,283,285,286,287,288,289,290,314,325,332,377,385,399,405,454,470,493,510,522,543,
# 559,562,568,568,576,580,610,624,766,771,772,811,818,875,921,924,939,965,994,1002,1004]
#patient_id_lst = [332,377,385,399,470,493,559,568,580,610,772,818,939,994,1004]
#patient_id_lst = [162,165,190,203,248,470]
#patient_id_lst = [165,176,178,180,198,202,231,243,266,285,818]
#patient_id_lst = [168,198,200,202,203,212,230,231,245,248,256,270,273,282,283,286,287,288,399,559,580,818]
gt_save_root_path = "C:/Users/tizita/Desktop/CODE/Lung-msc-code/gt/"
patient_id_lst = [72]
for patient_id in patient_id_lst:
print "\n\n Processing patient id %d" % patient_id
xml_dt = LIDCXmlParser(
('C:/Users/tizita/Desktop/CODE/Lung-msc-code/xml_data/%04d.xml') %
patient_id) #trial-xml.xml')
xml_dt.parse()
print xml_dt.xml_header
patient_ct_series = PatientCTSeries(
dt_root_path="C:/Users/tizita/Documents/LIDC/LIDC-IDRI/",
patient_no=patient_id)
patient_ct_series.populate_from_xmlparser(xml_dt)
cv2.namedWindow("LIDC-IDRI")
cv2.setMouseCallback("LIDC-IDRI", mouseClickCallback)
cv2.startWindowThread() #important
for trial in [1, 2]:
print "Round : ", trial
mouse_button_clicked = False
selected_centroid = []
for ct in patient_ct_series.annotated_cts:
if ct.no_consensus_annots() > 0: #if one or more rads agree
clusters = ct.get_nodule_clusters()
cv_mat = ct.draw(rad_indx_lst=range(
len(xml_dt.rad_annotations)),
draw_nodules=True,
draw_small=False,
draw_non=False)
for cluster in clusters:
cvx_hull = cluster.convex_hull_with_margin
#cv2.rectangle(img, pt1, pt2, color[, thickness[, lineType[, shift]]])#
cv2.rectangle(img=cv_mat,
pt1=cvx_hull[0],
pt2=cvx_hull[3],
color=(0, 255, 0),
thickness=1)
cv2.imshow('LIDC-IDRI', cv_mat)
ky = cv2.waitKey(0)
if ky == 27: #Esc key
cv2.waitKey(1)
cv2.destroyAllWindows()
#cv2.waitKey(1)
break
if (mouse_button_clicked):
#create a directory in the root path
dst_path = "%s/gt%04d/" % (gt_save_root_path, patient_id)
if not os.path.exists(dst_path):
os.makedirs(dst_path)
fo = open("%s/centroid.txt" % dst_path, "w")
fo.write("%d\n" % len(selected_centroid))
for (x, y) in selected_centroid:
fo.write("%d,%d\n" % (x, y))
fo.close()
print "[%d] cluster centroid(s) defined...processing data.." % len(
selected_centroid)
for indx, ct in enumerate(patient_ct_series.annotated_cts):
if ct.no_consensus_annots() > 0:
ct.save_nearest_cluster(selected_centroid, indx,
dst_path)
print "Finished processing patient id %d" % patient_id
def main_tmp():
global mouse_button_clicked,selected_centroid
#patient id 192 has a problematic xml file, so it's removed for now
#patient_id_lst = [68,71,72,88,90,91,100,118,124,129,135,137,138,143,149,159,161,162,163,164,165,166,
# 167,168,169,171,173,174,175,176,178,179,180,181,182,183,184,185,186,187,188,189,190,191,
# 193,194,197,198,200,202,203,205,207,210,211,212,213,214,217,220,221,222,223,224,225,
# 226,230,231,232,233,234,235,236,237,239,242,243,244,245,246,247,248,249,250,251,252,253,
# 254,255,256,257,258,260,261,264,265,266,267,268,270,271,272,273,274,275,276,277,278,279,
# 280,281,282,283,285,286,287,288,289,290,314,325,332,377,385,399,405,454,470,493,510,522,543,
# 559,562,568,568,576,580,610,624,766,771,772,811,818,875,921,924,939,965,994,1002,1004]
#patient_id_lst = [332,377,385,399,470,493,559,568,580,610,772,818,939,994,1004]
#patient_id_lst = [162,165,190,203,248,470]
#patient_id_lst = [165,176,178,180,198,202,231,243,266,285,818]
#patient_id_lst = [168,198,200,202,203,212,230,231,245,248,256,270,273,282,283,286,287,288,399,559,580,818]
gt_save_root_path = "C:/Users/tizita/Desktop/CODE/Lung-msc-code/gt/"
patient_id_lst = [72]
for patient_id in patient_id_lst:
print "\n\n Processing patient id %d"%patient_id
xml_dt = LIDCXmlParser(('C:/Users/tizita/Desktop/CODE/Lung-msc-code/xml_data/%04d.xml')%patient_id)#trial-xml.xml')
xml_dt.parse()
print xml_dt.xml_header
patient_ct_series = PatientCTSeries(dt_root_path="C:/Users/tizita/Documents/LIDC/LIDC-IDRI/",
patient_no = patient_id)
patient_ct_series.populate_from_xmlparser(xml_dt)
cv2.namedWindow("LIDC-IDRI")
cv2.setMouseCallback("LIDC-IDRI", mouseClickCallback)
cv2.startWindowThread() #important
for trial in [1,2]:
print "Round : ",trial
mouse_button_clicked = False
selected_centroid = []
for ct in patient_ct_series.annotated_cts:
if ct.no_consensus_annots() > 0: #if one or more rads agree
clusters = ct.get_nodule_clusters()
cv_mat = ct.draw(rad_indx_lst=range(len(xml_dt.rad_annotations)),
draw_nodules=True, draw_small=False, draw_non=False)
for cluster in clusters:
cvx_hull = cluster.convex_hull_with_margin
#cv2.rectangle(img, pt1, pt2, color[, thickness[, lineType[, shift]]])#
cv2.rectangle(img=cv_mat, pt1=cvx_hull[0], pt2=cvx_hull[3], color=(0,255,0), thickness=1)
cv2.imshow('LIDC-IDRI', cv_mat)
ky = cv2.waitKey(0)
if ky == 27: #Esc key
cv2.waitKey(1)
cv2.destroyAllWindows()
#cv2.waitKey(1)
break
if (mouse_button_clicked):
#create a directory in the root path
dst_path = "%s/gt%04d/"%(gt_save_root_path, patient_id)
if not os.path.exists(dst_path):
os.makedirs(dst_path)
fo = open("%s/centroid.txt"%dst_path, "w")
fo.write("%d\n"%len(selected_centroid))
for (x,y) in selected_centroid:
fo.write("%d,%d\n"%(x,y))
fo.close()
print "[%d] cluster centroid(s) defined...processing data.."%len(selected_centroid)
for indx,ct in enumerate(patient_ct_series.annotated_cts):
if ct.no_consensus_annots() > 0:
ct.save_nearest_cluster(selected_centroid, indx, dst_path)
print "Finished processing patient id %d"%patient_id
