def DICOM2mha(self, path_rootFolder, img_folder, StudyID, AccessionN, DicomExamNumber, MorNMcase, finding_side):
# perform conversion
DicomDirectory = img_folder+os.sep+str(int(StudyID))+os.sep+AccessionN
if not os.path.exists(DicomDirectory):
DicomDirectory = img_folder+os.sep+str(int(StudyID))+os.sep+DicomExamNumber
DynSeries_id = MorNMcase['DynSeries_id']
T2Series_id = MorNMcase['T2Series_id']
### split bilateral series into left and right
[self.Left_pos_pat, self.Left_ori_pat, self.Right_pos_pat, self.Right_ori_pat] = processDicoms.get_LorR_from_bilateral(DicomDirectory, DynSeries_id, T2Series_id)
# get T2 position and orientation
[self.T2_pos_pat, self.T2_ori_pat, self.T2fatsat] = processDicoms.get_T2_pos_ori(DicomDirectory, T2Series_id)
# convert DynSeries_id
# Left
# cmd = path_rootFolder+os.sep+'dcm23d'+os.sep+'bin'+os.sep+'dcm23d.exe -i '+DicomDirectory+os.sep+DynSeries_id+os.sep+'Left'+' -o '+DicomDirectory+os.sep+'temp'
# print '\n---- Begin conversion of ' + DynSeries_id + 'Left to mha...' ;
# p1 = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True)
# p1.wait()
#
# os.chdir(DicomDirectory+os.sep+'temp')
# proc = subprocess.Popen('ls -a', stdout=subprocess.PIPE)
# output = proc.stdout.read()
# filetomove = output.split('\n')[2]
# os.chdir(DicomDirectory)
# proc = subprocess.Popen(['mv', 'temp'+os.sep+filetomove, DynSeries_id+'_Left.mha'], stdout=subprocess.PIPE)
# proc.wait()
#
# # Right
# cmd = path_rootFolder+os.sep+'dcm23d'+os.sep+'bin'+os.sep+'dcm23d.exe -i '+DicomDirectory+os.sep+DynSeries_id+os.sep+'Right'+' -o '+DicomDirectory+os.sep+'temp'
# print '\n---- Begin conversion of ' + DynSeries_id + 'Right to mha...' ;
# p1 = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True)
# p1.wait()
#
# os.chdir(DicomDirectory+os.sep+'temp')
# proc = subprocess.Popen('ls -a', stdout=subprocess.PIPE)
# output = proc.stdout.read()
# filetomove = output.split('\n')[2]
# os.chdir(DicomDirectory)
# proc = subprocess.Popen(['mv', 'temp'+os.sep+filetomove, DynSeries_id+'_Right.mha'], stdout=subprocess.PIPE)
# proc.wait()
#
# # convert T2Series_id
# cmd = path_rootFolder+os.sep+'dcm23d'+os.sep+'bin'+os.sep+'dcm23d.exe -i '+DicomDirectory+os.sep+T2Series_id+' -o '+DicomDirectory+os.sep+'temp'
# print '\n---- Begin conversion of ' + T2Series_id + ' to mha...' ;
# p1 = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True)
# p1.wait()
#
# os.chdir(DicomDirectory+os.sep+'temp')
# proc = subprocess.Popen('ls -a', stdout=subprocess.PIPE)
# output = proc.stdout.read()
# filetomove = output.split('\n')[2]
# os.chdir(DicomDirectory)
# proc = subprocess.Popen(['mv', 'temp'+os.sep+filetomove, T2Series_id+'.mha'], stdout=subprocess.PIPE)
# proc.wait()
#
# # remove temporal dirs, always when using processDicoms.get_LorR_from_bilateral(abspath_PhaseID) create auxiliary Left and Right dirs
# shutil.rmtree('temp')
shutil.rmtree(DicomDirectory+os.sep+DynSeries_id+os.sep+'Left')
shutil.rmtree(DicomDirectory+os.sep+DynSeries_id+os.sep+'Right')
mhaDirectory = DicomDirectory
moving_path = DicomDirectory+os.sep+DynSeries_id+'_'+finding_side+'.mha'
fixed_path = DicomDirectory+os.sep+T2Series_id+'.mha'
return mhaDirectory, fixed_path, moving_path
DicomDirectory = img_folder+os.sep+str(int(StudyID))+os.sep+AccessionN
if not os.path.exists(DicomDirectory):
DicomDirectory = img_folder+os.sep+str(int(StudyID))+os.sep+DicomExamNumber
DynSeries_id = MorNMcase['DynSeries_id']
T2Series_id = MorNMcase['T2Series_id']
mhaDirectory = DicomDirectory
fixed_path = DicomDirectory+os.sep+DynSeries_id+'_'+finding_side+'.mha'
moving_path = DicomDirectory+os.sep+T2Series_id+'.mha'
path_rootFolder = os.path.dirname(os.path.abspath(__file__))
print path_rootFolder
#[SendNew2DB.T2_pos_pat, SendNew2DB.T2_pos_pat] = SendNew2DB.DICOM2mha(path_rootFolder, img_folder, StudyID, AccessionN, DicomExamNumber, MorNMcase, finding_side)
[T2_pos_pat, T2_ori_pat] = processDicoms.get_T2_pos_ori(DicomDirectory, T2Series_id)
SendNew2DB.T2_pos_pat=T2_pos_pat#[-22.39, -150.9, 115]
SendNew2DB.T2_ori_pat=T2_ori_pat#[-0, 1, 0, -0, -0, -1]
ouput_warped_image_elastix = mhaDirectory+os.sep+T2Series_id+'_warped_elastix.mha'
#############################
###### 2) Check segmentation accuracy with annotations
#############################
print "\n Preload volumes and segmentation..."
[series_path, phases_series] = SendNew2DB.preloadSegment(img_folder, lesion_id, StudyID, AccessionN, DynSeries_id, pathSegment, nameSegment)
print "\n Visualize and load..."
SendNew2DB.loadSegment(pathSegment, nameSegment)
