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dicoms_to_vtk.py
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import sys
import os
import os.path as osp
import argparse
import numpy as np
import pyvista as pv
from tqdm import tqdm
import re
import utils as ut
#-----------------------------------------------------------------------------------------------------------------------
## Options
parser = argparse.ArgumentParser()
parser.add_argument('--data_dir', type=str, default='', help='Directory containing dicom images', required=True)
parser.add_argument('--save_dir', type=str, default='', help='Output directory', required=True)
parser.add_argument('--subject_id', type=str, default='TEST_CASE', help='ID assigned to subject')
parser.add_argument('--venc', default=(0, 0, 0), nargs='+', help='Velocity encoding. If all zeros, automatic detection')
parser.add_argument('--flip_x', action='store_true', help='Flip image volume wrt the x-direction')
parser.add_argument('--flip_y', action='store_true', help='Flip image volume wrt the y-direction')
parser.add_argument('--flip_z', action='store_true', help='Flip image volume wrt the z-direction')
parser.add_argument('--minus_u', action='store_true', help='Invert the sign of the x-component of the velocity vector')
parser.add_argument('--minus_v', action='store_true', help='Invert the sign of the y-component of the velocity vector')
parser.add_argument('--minus_w', action='store_true', help='Invert the sign of the z-component of the velocity vector')
parser.add_argument('--write_pcmra', action='store_true')
parser.add_argument('--phase_coeff', type=float, default=1.0, help='Phase coefficient for PCMRA')
parser.add_argument('--mag_coeff', type=float, default=1.0, help='Magnitude coefficient for PCMRA')
args = parser.parse_args()
#-----------------------------------------------------------------------------------------------------------------------
## Read dicom files and create numpy arrays
data, meta = ut.read_acquisition(args.data_dir)
if args.venc == (0,0,0):
args.venc = meta['venc']
arrayData = ut.seriesData_to_arrayData(data, meta)
#-----------------------------------------------------------------------------------------------------------------------
## Automatic detection of magnitude series
meansArr = [np.mean(x) for x in arrayData]
dist0 = []
dist1 = []
dist2 = []
dist3 = []
for i in [1, 2, 3]:
dist0.append(np.abs(meansArr[0] - meansArr[i]))
for i in [0, 2, 3]:
dist1.append(np.abs(meansArr[1] - meansArr[i]))
for i in [0, 1, 3]:
dist2.append(np.abs(meansArr[2] - meansArr[i]))
for i in [0, 1, 2]:
dist3.append(np.abs(meansArr[3] - meansArr[i]))
allmean = [np.mean(d) for d in [dist0, dist1, dist2, dist3]]
magId = np.argmax(allmean)
magTemp = arrayData[magId]
arrayData.pop(magId)
velTemp = np.zeros((meta['num_rows'], meta['num_cols'], meta['num_slices'], meta['num_frames'], 3))
for i in range(3):
velTemp[:, :, :, :, i] = arrayData[i][:]
#-----------------------------------------------------------------------------------------------------------------------
## Velocity adjustment
print('Adjusting units.')
if re.search('GE', meta['vendor'], re.IGNORECASE):
velTemp *= 0.001 # m/s
elif re.search('siemens', meta['vendor'], re.IGNORECASE) or re.search('philips', meta['vendor'], re.IGNORECASE):
levels = 2**meta['HighBit']-1
for d in range(3):
velTemp[:, :, :, :, d] = (velTemp[:, :, :, :, d] - levels) * args.venc[d] / levels
velTemp *= 0.01 # m/s
else:
print('Manufacturer not found. Exiting.')
sys.exit()
if meta['position'] == 'FFS':
velTemp[:, :, :, :, 2] *= -1
if meta['position'] == 'HFS':
velTemp[:, :, :, :, 0] *= -1
velTemp[:, :, :, :, 1] *= -1
velTemp = np.flip(velTemp, 0)
magTemp = np.flip(magTemp, 0)
velTemp = np.flip(velTemp, 2)
magTemp = np.flip(magTemp, 2)
magTemp = np.swapaxes(magTemp, 0, 2)
velTemp = np.swapaxes(velTemp, 0, 2)
if args.flip_x:
velTemp = np.flip(velTemp, 0)
magTemp = np.flip(magTemp, 0)
if args.flip_y:
velTemp = np.flip(velTemp, 1)
magTemp = np.flip(magTemp, 1)
if args.flip_z:
velTemp = np.flip(velTemp, 2)
magTemp = np.flip(magTemp, 2)
if args.minus_u:
velTemp[:, :, :, :, 0] *= -1
if args.minus_v:
velTemp[:, :, :, :, 1] *= -1
if args.minus_w:
velTemp[:, :, :, :, 2] *= -1
#-----------------------------------------------------------------------------------------------------------------------
## Create vtk grids
os.makedirs(osp.join(args.save_dir, 'flow'), exist_ok=True)
print('Creating grids and writing to file.')
for f in tqdm(range(meta['num_frames']), desc='Processing and saving frames'):
mag = magTemp[:, :, :, f]
u = velTemp[:, :, :, f, 0]
v = velTemp[:, :, :, f, 1]
w = velTemp[:, :, :, f, 2]
grid = pv.ImageData()
grid.dimensions = np.array(mag.shape)
grid.origin = meta['origin']
grid.spacing = meta['spacing'][::-1]
grid['MagnitudeSequence'] = mag.flatten(order='F')
grid['Velocity'] = np.transpose(np.vstack((u.flatten(order='F'),
v.flatten(order='F'),
w.flatten(order='F'))))
grid.save(osp.join(args.save_dir, 'flow', args.subject_id + '_{:02d}'.format(f) + '.vtk'), binary=True)
if args.write_pcmra:
print('Writing PCMRA image.')
pcmra = np.zeros((magTemp.shape[0], magTemp.shape[1], magTemp.shape[2]))
for i in range(meta['num_frames']):
mag = magTemp[:, :, :, i]
phase1 = velTemp[:, :, :, i, 0]
phase2 = velTemp[:, :, :, i, 1]
phase3 = velTemp[:, :, :, i, 2]
pcmra += (args.mag_coeff * mag) ** 2 * (
(args.phase_coeff * phase1) ** 2 + (args.phase_coeff * phase2) ** 2 + (args.phase_coeff * phase3) ** 2)
pcmra /= meta['num_frames']
pcmra = pcmra ** 0.5
# save pcmra image
pcmravtk = pv.wrap(pcmra)
pcmravtk.SetSpacing(meta['spacing'][::-1])
pcmravtk.save(os.path.join(args.save_dir, args.subject_id + '_pcmra.vtk'))
fout = osp.join(args.save_dir, 'meta.txt')
fo = open(fout, "w")
for k, v in meta.items():
fo.write(str(k) + ': '+ str(v) + '\n')
fo.close()
print('\nFiles written to: ', osp.abspath(args.save_dir))