def anonymize(data_dir, save_dir, logger=None, i=None):
state = None
if i is not None and not i % 10:
print('Process: ', i)
num = 0
for root, _, files in os.walk(data_dir):
for f in files:
if os.path.splitext(f)[-1] not in EXTEN:
try:
src_path = os.path.join(root, f)
ds = pydicom.dcmread(src_path)
for tag, vr, v in ATTRIBUTE:
ds[tag] = pydicom.DataElement(tag, vr, v)
save_path = src_path.replace(data_dir, save_dir)
# save_path = os.path.join(save_dir, ds.PatientID, ds.StudyDate, ds.StudyInstanceUID, ds.SeriesInstanceUID, str(ds.InstanceNumber)+'.dcm')
if not os.path.exists(os.path.dirname(save_path)):
os.makedirs(os.path.dirname(save_path))
ds.save_as(save_path)
except Exception as e:
state = 'PT_DT_0001'
if logger is not None:
logger.info("\n")
logger.info(state + ": " + str(e))
logger.info("Error path: ", os.path.join(root, f))
# else:
# print("Error path: ", os.path.join(root, f))
return state
def test_RuleHandler() -> None:
ds = pydicom.Dataset()
tag = 0x00000001
ds[tag] = pydicom.DataElement(value=b"1", tag=tag, VR="CS")
handler = RuleHandler(lambda _: "x")
handler(ds, tag)
assert ds[tag].value == "x"
def diffcom(file1, file2):
"""Compare DICOM file1 with DICOM file2.
file1 is often the earlier, whereas file2 is the later.
"""
if not __check_file(file1):
return
if not __check_file(file2):
return
ds1 = pydicom.dcmread(file1)
ds2 = pydicom.dcmread(file2)
it1 = iter(ds1)
it2 = iter(ds2)
EOD = pydicom.DataElement(0xFFFFFFFF, 'PN', 'Guard')
elem1 = next(it1, EOD)
elem2 = next(it2, EOD)
while elem1 != EOD or elem2 != EOD:
if elem1.tag == elem2.tag:
__print_elem(elem1, elem2)
elem1 = next(it1, EOD)
elem2 = next(it2, EOD)
while elem1.tag < elem2.tag:
__print_elem(elem1)
elem1 = next(it1, EOD)
while elem1.tag > elem2.tag:
__print_elem(element2=elem2)
elem2 = next(it2, EOD)
def testRetrieve(self):
ds = pydicom.dcmread("tests/data/testDICOM_01.dcm")
self.assertEqual(retrieveFromDataset(["Modality"], ds), "MR")
self.assertEqual(retrieveFromDataset(["(0008, 0060)"], ds), "MR")
self.assertEqual(retrieveFromDataset(["ImageType"], ds),
['ORIGINAL', 'PRIMARY', 'M_FFE', 'M', 'FFE'])
self.assertEqual(retrieveFromDataset(["ImageType", "3"], ds), "M")
self.assertEqual(retrieveFromDataset(["(0008, 1111)",
"0",
"(0008, 0005)"], ds),
"ISO_IR 100")
self.assertIsNone(retrieveFromDataset(["ABC"],
ds,
fail_on_not_found=False))
self.assertIsNone(retrieveFromDataset(["ABC"],
ds,
fail_on_not_found=True,
fail_on_last_not_found=False))
with self.assertRaises(KeyError):
retrieveFromDataset(["ABC"], ds)
with self.assertRaises(KeyError):
retrieveFromDataset(["(0008, 1111)", "0", "ABC"], ds,
fail_on_not_found=True)
self.assertIsNone(retrieveFromDataset(["ImageType", "9"],
ds,
fail_on_not_found=False))
self.assertIsNone(retrieveFromDataset(["ImageType", "9"],
ds,
fail_on_not_found=True,
fail_on_last_not_found=False))
with self.assertRaises(KeyError):
retrieveFromDataset(["ImageType", "9"], ds)
exp = extractStruct(ds)
self.assertEqual(exp["ImageType"],
['ORIGINAL', 'PRIMARY', 'M_FFE', 'M', 'FFE'])
self.assertEqual(combineDateTime(ds, "Study"),
datetime(2001, 1, 1, 11, 33, 22))
self.assertIsNone(combineDateTime(ds, "Acquisition"))
ds.add(pydicom.DataElement("AcquisitionDateTime",
"DT",
"19920304112233"))
self.assertEqual(combineDateTime(ds, "Acquisition"),
datetime(1992, 3, 4, 11, 22, 33))
del ds["StudyTime"]
self.assertIsNone(combineDateTime(ds, "Study"))
def insertTag(dataset, tag, value, type):
if tag in dataset:
dataset[tag].value = value
else:
dataset[tag] = pydicom.DataElement(tag, type, value)
bits = m_.flatten()
padded_bits = _sdiv(len(bits), 8) * 8
if len(bits) < padded_bits:
bits = np.append(
bits, np.zeros((padded_bits - len(bits), ),
dtype=np.uint8))
if slice_.is_little_endian:
bits = np.reshape(bits, (-1, 8))
bits = np.fliplr(bits)
bytes_ = np.packbits(bits)
# set new seriesinstanceuid
slice_[0x0020, 0x000e] = pydicom.DataElement((0x0020, 0x000e),
"UI", uid_gen)
slice_[0x0008, 0x0018] = pydicom.DataElement(
(0x0008, 0x0018), "UI", pydicom.uid.generate_uid())
# update series description
slice_[0x0008, 0x103e].value = str(
slice_[0x0008, 0x103e].value) + " (Volumetrie)"
# set DICOM elements
# TODO check if overlay exists
if (0x6000, 0x3000) in slice_:
print("Warning: Overwriting existing overlay!")
overlay_data = pydicom.DataElement((0x6000, 0x3000), "OW",
bytes_.tobytes())
slice_[0x6000, 0x3000] = overlay_data
def process_plan(filename,fig):
dataset = pydicom.dcmread(filename)
source_dataset=[]
xs=[]
ys=[]
zs=[]
ts=[]
print(dataset[0x300a, 0x004]) #<-- example of nested tag access
print(dataset[0x300a, 0x006]) #<-- example of nested tag access
print(dataset[0x300a, 0x007]) #<-- example of nested tag access
print(dataset[0x0008, 0x0018]) #<-- example of nested tag access
dataset[0x0020,0x0011].value="9"
#dataset[0x0020,0x000d].value=str(rand.randint(1,10000))
instance_rand=str(rand.randint(1,10000))
dataset[0x0020,0x000e].value=instance_rand # <-- creating a new random series instance
dataset[0x300c,0x0002][0][0x0008,0x1155].value=instance_rand # <-- replacing the reference value
new_UID=str(rand.randint(1,10000))
dataset[0x0008, 0x0018].value=new_UID #<-- creating a new random SOP instance UID
print('Maximum number of catheters in dataset =',dataset[0x300a, 0x0230][0][0x300a, 0x0280].VM) # prints the number of catheters
while True: # example of infinite loops using try and except to catch only numbers
line = input('Please enter the catheter number> ')
try:
# if line == 'done':
# break
catnum = int(line.lower())
if catnum >= 1 and catnum <= dataset[0x300a, 0x0230][0][0x300a, 0x0280].VM:
break
else:
print('Please select a value between 1 and the max number of catheters:')
except:
print('Please select a value between 1 and the max number of catheters:')
catheter=dataset[0x300a, 0x0230][0][0x300a, 0x0280][catnum-1]
tipcat = np.asarray(catheter[0x1001,0x1080][0][0x1001,0x1083].value) # this variable holds the tip of the catheter
print('tip catheter=',tipcat)
#print('Coordinates of the first point=',catheter[0x300a, 0x02d0][0][0x300a, 0x02d4].value)
xoffset=dataset[0x300a, 0x0230][0][0x300a, 0x0280][catnum-1][0x300a, 0x02d0][0][0x300a, 0x02d4].value[0]
yoffset=dataset[0x300a, 0x0230][0][0x300a, 0x0280][catnum-1][0x300a, 0x02d0][0][0x300a, 0x02d4].value[1]
print('xoffset=',xoffset)
print('yoffset=',yoffset)
source_dataset=[]
xs=[]
ys=[]
zs=[]
ts=[]
for pos in dataset[0x300a, 0x0230][0][0x300a, 0x0280][catnum-1][0x300a, 0x02d0]:
# print(pos[0x300a, 0x02d4]) # position (x,y,z)
# print(pos[0x300a, 0x02d6]) # weight time
# print(pos[0x300a, 0x0112]) # control point index
# source_dataset.append([ elem[0x300a, 0x0282].value, elem[0x300a, 0x0284].value, elem[0x300a, 0x0286].value, pos[0x300a, 0x02d4].value, pos[0x300a, 0x02d6].value])
x, y, z = pos[0x300a, 0x02d4].value
source_dataset.append([catheter[0x300a, 0x0282].value, catheter[0x300a, 0x0284].value, catheter[0x300a, 0x0286].value,
pos[0x300a, 0x0112].value, x, y, z, pos[0x300a, 0x02d6].value])
source_dataset = np.asarray(source_dataset)
coords=np.transpose(source_dataset[:,4:7])
for i in range(1, source_dataset.shape[0], 2):
x = source_dataset[i, 4]
y = source_dataset[i, 5]
z = source_dataset[i, 6]
tw = source_dataset[i, 7] - source_dataset[i - 1, 7]
xs.append(x)
ys.append(y)
zs.append(z)
ts.append(tw / 100 * source_dataset[i, 2])
#for matplotlib3d
ax.scatter(xs, ys, zs, s=ts, label='Catheter(o)='+str(catnum))
# print(ts)
while True: # example of infinite loops using try and except to catch only numbers
line = input('Please enter the offset value in the z direction [cm]> ')
try:
# if line == 'done':
# break
offset = float(line.lower())
break
except:
print('Please enter a valid option:')
zoffset=(offset - tipcat[2]) #the point offset in the z direction is the value of the offset minus the tip of the catheter location
coords_offset=np.zeros_like(coords)
coords_offset[0,:]=coords[0,:]-xoffset
coords_offset[1,:]=coords[1,:]-yoffset
coords_offset[2,:]=coords[2,:]+zoffset
# preparing the catheter for rotation
tipcat_offset = np.zeros_like(tipcat)
tipcat_offset[0] = tipcat[0] - xoffset
tipcat_offset[1] = tipcat[1] - yoffset
tipcat_offset[2] = tipcat[2] + zoffset
print('zoffset=',zoffset)
#here we update the catheter values where the bending occurs
needle=catheter[0x1001,0x1080]
# catheter[0x300a, 0x0291].value='M117X0004-CAT' # changing the type of catheter from virtual
# dataset[0x1001, 0x10af][0][0x1001,0x10c2].value=-10 #testing this value
# print(catheter[0x300a, 0x0291])
x_dup,y_dup,z_dup=needle[0][0x10011083].value #we extract these coordinates from the tip and create another set located at the point where the catheter bends
dup_elem=pydicom.Dataset()#creating a point where the catheter bends
dup_elem.add_new(0x10010010,'LO',needle[0][0x1001,0x0010].value)
dup_elem.add_new(0x10011081,'SL',needle[0][0x1001,0x1081].value+1)
dup_elem.add_new(0x10011082,'SL',0)
# dup_elem.add_new(0x10011083,'DS',[x_dup,y_dup,z_dup-zoffset])
dup_elem.add_new(0x10011083,'DS',[x_dup,y_dup,-zoffset])
print('elbow point z value=',-zoffset)
seq_needle=pydicom.DataElement(0x10011080,'SQ',[needle[0],dup_elem,needle[1],needle[2],needle[3]])
for needle_point in seq_needle[2:]:
needle_point[0x1001,0x1081].value=needle_point[0x1001,0x1081].value+1
# needle_point[0x1001,0x1082].value=needle_point[0x1001,0x1082].value+1
dataset[0x300a, 0x0230][0][0x300a, 0x0280][catnum-1][0x1001,0x1080]=seq_needle
# del(dataset[0x300c,0x0080]) #deleting the dose dependency (not necessary in a live catheter from Oncentra)
#print('needle=',*dataset[0x300a, 0x0230][0][0x300a, 0x0280][catnum-1][0x1001,0x1080],sep='\n')
while True: # example of infinite loops using try and except to catch only numbers
line = input('Please enter the theta value [deg]> ')
try:
# if line == 'done':
# break
theta = float(line.lower())
break
except:
print('Please enter a valid option:')
r1 = R.from_euler('x', theta, degrees=True)
coords_rot1=np.matmul(np.asarray(r1.as_dcm()),coords_offset)
tipcatrot1=np.matmul(np.asarray(r1.as_dcm()),tipcat_offset)
print('coords_offset=',coords_offset,'r1=',r1)
exit(0)
while True: # example of infinite loops using try and except to catch only numbers
line = input('Please enter the phi value [deg]> ')
try:
# if line == 'done':
# break
phi = float(line.lower())
break
except:
print('Please enter a valid option:')
r2 = R.from_euler('z', phi, degrees=True)
coords_rot2 = np.matmul(np.asarray(r2.as_dcm()), coords_rot1)
tipcatrot2 = np.matmul(np.asarray(r2.as_dcm()), tipcatrot1)
coords_f=coords # creating the array from the initial coordinates in order to "bend" the needle from a certain offset
for i in range(0,np.shape(coords)[1]):
if coords_f[2,i]>tipcat[2]-zoffset:
coords_f[0,i]=coords_rot2[0,i]+xoffset
coords_f[1,i]=coords_rot2[1,i]+yoffset
coords_f[2,i]=coords_rot2[2,i]-zoffset
tipcat_f = np.zeros_like(tipcat)
tipcat_f[0] = tipcatrot2[0] + xoffset
tipcat_f[1] = tipcatrot2[1] + yoffset
tipcat_f[2] = tipcatrot2[2] - zoffset
catheter[0x1001, 0x1080][0][0x1001, 0x1083].value = [tipcat_f[0], tipcat_f[1], tipcat_f[2]]
print('theta=',theta,'phi=',phi)
print('post-transformation',coords_f)
print(tipcat, tipcatrot1,tipcat_f)
# exit(0)
# print(ts)
ax.scatter(coords_f[0,:], coords_f[1,:], coords_f[2,:], s=ts,label='Catheter(m)='+str(catnum))
ax.legend()
k=0
for pos in dataset[0x300a, 0x0230][0][0x300a, 0x0280][catnum-1][0x300a, 0x02d0]:
# print(pos[0x300a, 0x02d4]) # position (x,y,z)
#print('after transformation=',pos[0x300a, 0x02d6]) # weight time
# print(pos[0x300a, 0x0112]) # control point index
# source_dataset.append([ elem[0x300a, 0x0282].value, elem[0x300a, 0x0284].value, elem[0x300a, 0x0286].value, pos[0x300a, 0x02d4].value, pos[0x300a, 0x02d6].value])
pos[0x300a, 0x02d4].value=[coords_f[0,k],coords_f[1,k],coords_f[2,k]]
k=k+1
while True: # example of infinite loops using try and except to catch only numbers
line = input('Please enter a comment for the output file> ')
try:
# if line == 'done':
# break
desc = str(line.lower())
break
except:
print('Please enter a valid option:')
date=dt.date.today().strftime('%Y%m%d')
now=dt.datetime.now().strftime('%H%M%S')
dataset[0x300a, 0x004].value=desc
dataset[0x300a, 0x006].value=date
dataset[0x300a, 0x007].value=now
dirname = os.path.dirname(filename)
dataset.save_as(dirname+'/mod-plan.dcm')
def name(self) -> str:
try:
return pydicom.DataElement(self.tag, "US", None).name
except Exception:
return "Unnamed"
def clean_meta(dcm):
dcm.add(dicom.DataElement((0x0008, 0x0023), 'DA', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0008, 0x0033), 'TM', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0008, 0x1050), 'PN', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0008, 0x1070), 'PN', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0010, 0x0030), 'DA', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0010, 0x1000), 'LO', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0010, 0x1040), 'LO', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0010, 0x2154), 'SH', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0010, 0x2160), 'SH', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0010, 0x2180), 'SH', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0010, 0x21b0), 'LT', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0010, 0x21f0), 'LO', EMPTY_VALUE))
dcm.add(dicom.DataElement((0x0038, 0x0500), 'LO', EMPTY_VALUE))
return dcm