def test_L1Norm_2D(self):
model = 12 # select a model number from the library
N = 400 # set dimension of the phantom
path = os.path.dirname(tomophantom.__file__)
path_library2D = os.path.join(path, "Phantom2DLibrary.dat")
phantom_2D = TomoP2D.Model(model, N, path_library2D)
# data = ImageData(phantom_2D)
ig = ImageGeometry(voxel_num_x=N, voxel_num_y=N)
data = ig.allocate(None)
data.fill(phantom_2D)
# Create acquisition data and geometry
detectors = N
angles = np.linspace(0, 180, 120, dtype=np.float32)
ag = AcquisitionGeometry.create_Parallel2D()\
.set_angles(angles, angle_unit=AcquisitionGeometry.DEGREE)\
.set_panel(detectors)
sin = ag.allocate(None)
sino = TomoP2D.ModelSino(model, detectors, detectors, angles, path_library2D)
sin.fill(sino)
sin_stripe = sin.copy()
# sin_stripe = sin
tmp = sin_stripe.as_array()
tmp[:,::27]=tmp[:,::28]
sin_stripe.fill(tmp)
ring_recon = RingRemover(20, "db15", 21, info = True)(sin_stripe)
error = (ring_recon - sin).abs().as_array().mean()
print ("L1Norm ", error)
np.testing.assert_almost_equal(error, 83.20592, 4)
def Phantom(self, model, size):
model = model
sizeN = size
#This will generate 256x256 phantom from the model
self.phantom = TomoP2D.Model(
model, sizeN,
'/home/sohila/Documents/BIO-MATERIALS/Third-Year/Second-Term/MRI/Task2-MRI/phantoms/TomoPhantom/PhantomLibrary/models/Phantom2DLibrary.dat'
)
angles_num = int(sizeN) # angles number
self.angles = np.linspace(0, 180, angles_num, dtype='float32')
angles_rad = self.angles * (np.pi / 180)
P = int(np.sqrt(2) * sizeN) #detectors
#This will generate a sinogram of the model
sino_an = TomoP2D.ModelSino(
model, sizeN, P, self.angles,
'/home/sohila/Documents/BIO-MATERIALS/Third-Year/Second-Term/MRI/Task2-MRI/phantoms/TomoPhantom/PhantomLibrary/models/Phantom2DLibrary.dat'
)
# pp = {'Obj': TomoP2D.Objects2D.RECTANGLE,
# 'C0': 9.00,
# 'x0': 0.3,
# 'y0': -0.25,
# 'a': 0.5,
# 'b': 0.8,
# 'phi': 90.0}
# G=TomoP2D.Object(256, pp)
return self.phantom
def generateImage():
model = 6 # selecting a model
N_size = 256
#specify a full path to the parameters file
pathTP = 'Phantom2DLibrary.dat'
#This will generate a N_size x N_size phantom (2D)
phantom_2D = TomoP2D.Model(model, N_size, pathTP)
Labels = []
Labels_array = []
Images = []
shapeTypes = [TomoP2D.Objects2D.RECTANGLE, TomoP2D.Objects2D.ELLIPSE]
for a in range(0, 1, 1):
num_back_shapes = np.random.randint(200, 400)
back_temp = np.zeros((256, 256), dtype=np.uint8)
for i in range(0, num_back_shapes, 1):
shapeRand = np.random.randint(2)
shape = TomoP2D.Object(256, genTomoShape(shapeTypes[shapeRand]))
back_temp = back_temp + shape
scaler = np.amax(back_temp)
back_temp = np.divide(back_temp, scaler)
num_shapes = np.random.randint(5, 20)
image_temp = np.zeros((256, 256), dtype=np.uint8)
for i in range(0, num_shapes, 1):
#Random pick of shape type
shapeRand = np.random.randint(2)
#Generate shape
shape = TomoP2D.Object(256, genTomoShape(shapeTypes[shapeRand]))
#add the shape to the image and take away the original to get the positions where a new shape has been added.
fit = ((image_temp + shape) - image_temp) > 0
#update the pixel values where the shape has been added, do no tjust add the pixel values together but replace them so the overlap is smooth
image_temp[fit] = shape[fit]
noise = np.random.uniform(low=0,
high=np.amax(image_temp),
size=(256, 256))
nos = (image_temp * 1.0) + (noise * 1.0) + (back_temp * 1.0)
nos = np.divide(nos, np.amax(nos))
Images.append(nos)
Labels_array.append(np.array(image_temp))
#%%
return np.array(Images), np.array(Labels_array)
ab_min,
ab_max,
N_size,
tot_objects,
object_type='mix')
plt.figure()
plt.imshow(Objfoam2D, vmin=0, vmax=0.3, cmap="gray")
# Generate a sinogram
angles_num = int(0.5 * np.pi * N_size)
# angles number
angles = np.linspace(0, 180, angles_num, dtype='float32')
angles_rad = angles * (np.pi / 180)
P = int(np.sqrt(2) * N_size) #detectors
sino_Objfoam2D = TomoP2D.ObjectSino(N_size, P, angles, myObjects)
plt.figure()
plt.imshow(sino_Objfoam2D, cmap="gray")
#%%
# 3D example
print("Generating 3D random phantom")
(Objfoam3D, myObjects) = foam3D(x0min,
x0max,
y0min,
y0max,
z0min,
z0max,
c0min,
c0max,
ab_min,
def get_ImageData(num_model, geometry):
'''Returns an ImageData relative to geometry with the model num_model from tomophantom
:param num_model: model number
:type num_model: int
:param geometry: geometrical info that describes the phantom
:type geometry: ImageGeometry
Example usage:
.. code-block:: python
ndim = 2
N=128
angles = np.linspace(0, 360, 50, True, dtype=np.float32)
offset = 0.4
channels = 3
if ndim == 2:
ag = AcquisitionGeometry.create_Cone2D((offset,-100), (offset,100))
ag.set_panel(N)
else:
ag = AcquisitionGeometry.create_Cone3D((offset,-100, 0), (offset,100,0))
ag.set_panel((N,N-2))
ag.set_channels(channels)
ag.set_angles(angles, angle_unit=AcquisitionGeometry.DEGREE)
ig = ag.get_ImageGeometry()
num_model = 1
phantom = TomoPhantom.get_ImageData(num_model=num_model, geometry=ig)
'''
ig = geometry.copy()
ig.set_labels(DataOrder.TOMOPHANTOM_IG_LABELS)
num_dims = len(ig.dimension_labels)
if ImageGeometry.CHANNEL in ig.dimension_labels:
if not is_model_temporal(num_model):
raise ValueError('Selected model {} is not a temporal model, please change your selection'.format(num_model))
if num_dims == 4:
# 3D+time for tomophantom
# output dimensions channel and then spatial,
# e.g. [ 'channel', 'vertical', 'horizontal_y', 'horizontal_x' ]
num_model = num_model
shape = tuple(ig.shape[1:])
phantom_arr = TomoP3D.ModelTemporal(num_model, shape, path_library3D)
elif num_dims == 3:
# 2D+time for tomophantom
# output dimensions channel and then spatial,
# e.g. [ 'channel', 'horizontal_y', 'horizontal_x' ]
N = ig.shape[1]
num_model = num_model
phantom_arr = TomoP2D.ModelTemporal(num_model, ig.shape[1], path_library2D)
else:
raise ValueError('Wrong ImageGeometry')
if ig.channels != phantom_arr.shape[0]:
raise ValueError('The required model {} has {} channels. The ImageGeometry you passed has {}. Please update your ImageGeometry.'\
.format(num_model, ig.channels, phantom_arr.shape[0]))
else:
if num_dims == 3:
# 3D
num_model = num_model
phantom_arr = TomoP3D.Model(num_model, ig.shape, path_library3D)
elif num_dims == 2:
# 2D
if ig.shape[0] != ig.shape[1]:
raise ValueError('Can only handle square ImageData, got shape'.format(ig.shape))
N = ig.shape[0]
num_model = num_model
phantom_arr = TomoP2D.Model(num_model, N, path_library2D)
else:
raise ValueError('Wrong ImageGeometry')
im_data = ImageData(phantom_arr, geometry=ig, suppress_warning=True)
im_data.reorder(list(geometry.dimension_labels))
return im_data
@author: Daniil Kazantsev
"""
import numpy as np
import matplotlib.pyplot as plt
import os
import tomophantom
from tomophantom import TomoP2D
model = 102 # note that the selected model is temporal (2D + time)
N_size = 512 # set dimension of the phantom
# one can specify an exact path to the parameters file
# path_library2D = '../../../PhantomLibrary/models/Phantom2DLibrary.dat'
path = os.path.dirname(tomophantom.__file__)
path_library2D = os.path.join(path, "Phantom2DLibrary.dat")
#This will generate a N_size x N_size x Time frames phantom (2D + time)
phantom_2Dt = TomoP2D.ModelTemporal(model, N_size, path_library2D)
plt.close('all')
plt.figure(1)
plt.rcParams.update({'font.size': 21})
plt.title('{}''{}'.format('2D+t phantom using model no.',model))
for sl in range(0,np.shape(phantom_2Dt)[0]):
im = phantom_2Dt[sl,:,:]
plt.imshow(im, vmin=0, vmax=1)
plt.pause(.1)
plt.draw
# create sinogram analytically
angles_num = int(0.5*np.pi*N_size); # angles number
angles = np.linspace(0,180,angles_num,dtype='float32')
angles_rad = angles*(np.pi/180)
b_el3 = random.uniform(b_el3_min, b_el3_max)
phi_min = 0.0
phi_max = 90.0
phi = random.uniform(phi_min, phi_max)
el3 = {
'Obj': Objects2D.RECTANGLE,
'C0': C_0,
'x0': 0.0,
'y0': 0.0,
'a': a_el3,
'b': b_el3,
'phi': phi
}
GROUND_TRUTH = TomoP2D.Object(N_size, [el1, el2, el3])
plt.close('all')
plt.figure(1)
plt.rcParams.update({'font.size': 21})
plt.imshow(GROUND_TRUTH, vmin=0, vmax=1, cmap="BuPu")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('{}'.format('Ground Truth Object'))
#%%
# define all objects bellow:
el1 = {
'Obj': Objects2D.ELLIPSE,
'C0': 0.7,
'x0': 0.0,
'y0': 0.0,
import os, sys
import tomophantom
from tomophantom import TomoP2D
# user supplied input
if len(sys.argv) > 1:
which_noise = int(sys.argv[1])
else:
which_noise = 0
model = 1 # select a model number from the library
N = 128 # set dimension of the phantom
path = os.path.dirname(tomophantom.__file__)
path_library2D = os.path.join(path, "Phantom2DLibrary.dat")
phantom_2D = TomoP2D.Model(model, N, path_library2D)
data = ImageData(phantom_2D)
ig = ImageGeometry(voxel_num_x=N, voxel_num_y=N)
# Create acquisition data and geometry
detectors = N
angles = np.linspace(0, np.pi, 180)
ag = AcquisitionGeometry('parallel', '2D', angles, detectors)
# Select device
device = input('Available device: GPU==1 / CPU==0 ')
if device == '1':
dev = 'gpu'
else:
dev = 'cpu'
def generateImage():
model = 6 # selecting a model
N_size = 256
#specify a full path to the parameters file
pathTP = 'Phantom2DLibrary.dat'
#This will generate a N_size x N_size phantom (2D)
phantom_2D = TomoP2D.Model(model, N_size, pathTP)
Labels = []
Labels_array = []
Images = []
shapeTypes = [TomoP2D.Objects2D.RECTANGLE, TomoP2D.Objects2D.ELLIPSE]
insertImage = np.asarray(PIL.Image.open('2.jpg').convert('L'))
# print(inssertImage.shape)
# insertImage = np.append(insertImage,insertImage, axis=0)
# insertImage = np.append(insertImage,insertImage, axis=0)
# insertImage = np.append(insertImage,insertImage, axis=0)
# print(insertImage.shape)
insertImage.setflags(write=1)
insertImage = [insertImage[:256, :256], insertImage[:256, :256]]
for a in range(0, 1, 1):
objects = []
background = []
array_label = []
num_back_shapes = np.random.randint(200, 400)
for i in range(0, num_back_shapes, 1):
shapeRand = np.random.randint(2)
background.append(genTomoShape(shapeTypes[shapeRand]))
num_shapes = np.random.randint(5, 20)
num_shapes = 5
label_temp = np.zeros((256, 256), dtype=np.uint8)
image_temp = np.zeros((256, 256), dtype=np.uint8)
pattern = np.random.randint(len(insertImage))
for i in range(0, num_shapes, 1):
#Generate tomoshape
#Random pick of shape type
shapeRand = np.random.randint(2)
#Generate shape
shape = TomoP2D.Object(256, genTomoShape(shapeTypes[shapeRand]))
#add the shape to the laebl image and take away the original to get the positions where a new shape has been added.
fit = ((label_temp + shape) - image_temp) > 0
#update the pixel values where the shape has been added, do no tjust add the pixel values together but replace them so the overlap is smooth
label_temp[fit] = shape[fit]
#filter looking for where the shape is
shapeFilter = shape >= 0.5
#for those positions where the shape exists set those values to the value in the image pattern
shape[shapeFilter] = insertImage[pattern][shapeFilter]
#add the shape to the image and take away the original to get the positions where a new shape has been added.
fit = ((image_temp + shape) - image_temp) > 0
#update the pixel values where the shape has been added, do no tjust add the pixel values together but replace them so the overlap is smooth
image_temp[fit] = shape[fit]
array_temp = np.zeros(len(insertImage))
array_temp[pattern] = int(1)
array_label.append(array_temp)
noise = np.random.uniform(low=0,
high=np.amax(image_temp) * 0.1,
size=(256, 256))
nos = (image_temp * 1.0) + (noise * 1.0)
plt.imshow(nos)
Images.append(nos)
#%%
# fig = plt.figure(figsize=(15, 15))
# fig.subplots_adjust(bottom=0.15, top=0.95, hspace=0.2,left=0.1, right=0.95, wspace=0.2)
# #plt.figure(1)
# #plt.rcParams.update({'font.size': 21})
## NOISY_IMAGES = np.array(NOISY_IMAGE)
## IMAGE = np.array(IMAGE)
## np.save('TM_Images.npy', NOISY_IMAGES)
## np.save('TM_Labels.npy', IMAGE)
# ax_heat = fig.add_subplot(121)
#
# ax_heat.imshow(NOISY_IMAGE[0], cmap="BuPu")
# ax_heat = fig.add_subplot(122)
#
# ax_heat.imshow(IMAGE[0], cmap="BuPu")
#
# plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
# plt.title('{}''{}'.format('2D Phantom using model no.',model))
# plt.show()
return np.array([Labels, Images])
This demo demonstrates frequent inaccuracies which are accosiated with X-ray imaging:
zingers, rings and noise
@author: Daniil Kazantsev
"""
import numpy as np
import matplotlib.pyplot as plt
from tomophantom import TomoP2D
model = 4 # select a model
N_size = 512
#specify a full path to the parameters file
pathTP = '../../functions/models/Phantom2DLibrary.dat'
#objlist = modelfile2Dtolist(pathTP, model) # one can extract parameters
#This will generate a N_size x N_size phantom (2D)
phantom_2D = TomoP2D.Model(model, N_size, pathTP)
plt.close('all')
plt.figure(1)
plt.rcParams.update({'font.size': 21})
plt.imshow(phantom_2D, vmin=0, vmax=1, cmap="gray")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('{}' '{}'.format('2D Phantom using model no.', model))
# create sinogram analytically
angles_num = int(0.5 * np.pi * N_size)
# angles number
angles = np.linspace(0, 180, angles_num, dtype='float32')
angles_rad = angles * (np.pi / 180)
P = int(np.sqrt(2) * N_size) #detectors
'b': 0.3,
'phi': -30.0
}
pp1 = {
'Obj': Objects2D.RECTANGLE,
'C0': 1.00,
'x0': -0.2,
'y0': 0.2,
'a': 0.25,
'b': 0.4,
'phi': 60.0
}
myObjects = [pp, pp1] # dictionary of objects
Object1 = TomoP2D.Object(N_size, myObjects)
plt.close('all')
plt.figure(1)
plt.rcParams.update({'font.size': 21})
plt.imshow(Object1, vmin=0, vmax=1, cmap="BuPu")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('{}'.format('2D Object'))
# create sinogram analytically without using the parameters file
angles_num = int(0.5 * np.pi * N_size)
# angles number
angles = np.linspace(0, 180, angles_num, dtype='float32')
angles_rad = angles * (np.pi / 180)
P = int(np.sqrt(2) * N_size) #detectors
def generateImage():
model = 6 # selecting a model
N_size = 256
#specify a full path to the parameters file
pathTP = 'Phantom2DLibrary.dat'
#This will generate a N_size x N_size phantom (2D)
phantom_2D = TomoP2D.Model(model, N_size, pathTP)
IMAGE = []
NOISY_IMAGE = []
flowers = ((np.asarray(Image.open('flowers.png').convert('L')))/255)*0.9
for a in range(0,1,1):
pps = []
back = []
num_back_rectangles = np.random.randint(200, 400)
for i in range(0,num_back_rectangles,1):
pp = {'Obj': TomoP2D.Objects2D.RECTANGLE,
'C0' : float(np.random.uniform(low=0.5, high=0.9, size =1)),
'x0' : float(np.random.uniform(low=-1.0, high=1.0, size =1)),
'y0' : float(np.random.uniform(low=-1.0, high=1.0, size =1)),
'a' : float(np.random.uniform(low=0.02, high=0.3, size = 1)),
'b' : float(np.random.uniform(low=0.02, high=0.3, size=1)),
'phi': float(np.random.uniform(low=0, high=180, size=1))}
bb = {'Obj': TomoP2D.Objects2D.ELLIPSE,
'C0' : float(np.random.uniform(low=0.1, high=0.5, size =1)),
'x0' : float(np.random.uniform(low=-1.0, high=1.0, size =1)),
'y0' : float(np.random.uniform(low=-1.0, high=1.0, size =1)),
'a' : float(np.random.uniform(low=0.02, high=0.3, size = 1)),
'b' : float(np.random.uniform(low=0.02, high=0.3, size=1)),
'phi': float(np.random.uniform(low=0, high=180, size=1))}
cc = {'Obj': TomoP2D.Objects2D.RECTANGLE,
'C0' : float(np.random.uniform(low=0.5, high=0.9, size =1)),
'x0' : float(np.random.uniform(low=-1.0, high=1.0, size =1)),
'y0' : float(np.random.uniform(low=-1.0, high=1.0, size =1)),
'a' : float(np.random.uniform(low=0.02, high=0.3, size = 1)),
'b' : float(np.random.uniform(low=0.02, high=0.3, size=1)),
'phi': float(np.random.uniform(low=0, high=180, size=1))}
dd = {'Obj': TomoP2D.Objects2D.ELLIPSE,
'C0' : float(np.random.uniform(low=0.5, high=0.9, size =1)),
'x0' : float(np.random.uniform(low=-1.0, high=1.0, size =1)),
'y0' : float(np.random.uniform(low=-1.0, high=1.0, size =1)),
'a' : float(np.random.uniform(low=0.02, high=0.3, size = 1)),
'b' : float(np.random.uniform(low=0.02, high=0.3, size=1)),
'phi': float(np.random.uniform(low=0, high=180, size=1))}
back.append(pp)
back.append(bb)
back.append(cc)
back.append(dd)
back.append(bb)
num_rectangles = np.random.randint(5, 20)
print(a)
for i in range(0,num_rectangles,1):
pp = {'Obj': TomoP2D.Objects2D.RECTANGLE,
'C0' : float(np.random.uniform(low=0.7, high=0.9, size =1)),
'x0' : float(np.random.uniform(low=-0.5, high=1.0, size =1)),
'y0' : float(np.random.uniform(low=-1.0, high=0.5, size =1)),
'a' : float(np.random.uniform(low=0.02, high=0.3, size = 1)),
'b' : float(np.random.uniform(low=0.02, high=0.3, size=1)),
'phi': float(np.random.uniform(low=0, high=180, size=1))}
bb = {'Obj': TomoP2D.Objects2D.ELLIPSE,
'C0' : float(np.random.uniform(low=0.7, high=0.9, size =1)),
'x0' : float(np.random.uniform(low=-1.0, high=1.0, size =1)),
'y0' : float(np.random.uniform(low=-1.0, high=0.5, size =1)),
'a' : float(np.random.uniform(low=0.02, high=0.3, size = 1)),
'b' : float(np.random.uniform(low=0.02, high=0.3, size=1)),
'phi': float(np.random.uniform(low=0, high=180, size=1))}
cc = {'Obj': TomoP2D.Objects2D.RECTANGLE,
'C0' : float(np.random.uniform(low=0.7, high=0.9, size =1)),
'x0' : float(np.random.uniform(low=-1.0, high=1.0, size =1)),
'y0' : float(np.random.uniform(low=-1.0, high=0.5, size =1)),
'a' : float(np.random.uniform(low=0.02, high=0.3, size = 1)),
'b' : float(np.random.uniform(low=0.02, high=0.3, size=1)),
'phi': float(np.random.uniform(low=0, high=180, size=1))}
dd = {'Obj': TomoP2D.Objects2D.ELLIPSE,
'C0' : float(np.random.uniform(low=0.7, high=0.9, size =1)),
'x0' : float(np.random.uniform(low=-1.0, high=1.0, size =1)),
'y0' : float(np.random.uniform(low=-1.0, high=0.5, size =1)),
'a' : float(np.random.uniform(low=0.02, high=0.3, size = 1)),
'b' : float(np.random.uniform(low=0.02, high=0.3, size=1)),
'phi': float(np.random.uniform(low=0, high=180, size=1))}
pps.append(pp)
pps.append(bb)
pps.append(cc)
pps.append(dd)
plt.close('all')
shapes = np.zeros((256, 256), dtype=np.uint8)
background = np.zeros((256, 256), dtype=np.uint8)
for i in range(0,num_back_rectangles,1):
phantom_2D = (TomoP2D.Object(256,back[i]))
background = (background + phantom_2D)
for i in range(0,num_rectangles,1):
phantom_2D = (TomoP2D.Object(256,pps[i]))
shapes = (shapes + phantom_2D)
noise = np.random.uniform(low=0,high=1, size=(256, 256))
filter1 = shapes >1
shapes[filter1] = 1
filter2 = background >1
background[filter1] = 1
IMAGE.append(shapes)
nos = (background*0.2)+(noise*1.0)+(shapes*1)
scaler = np.amax(nos)
nos = nos / scaler
NOISY_IMAGE.append(nos)
#%%
#plt.figure(1)
#plt.rcParams.update({'font.size': 21})
# NOISY_IMAGES = np.array(NOISY_IMAGE)
# IMAGE = np.array(IMAGE)
# np.save('TM_Images.npy', NOISY_IMAGES)
# np.save('TM_Labels.npy', IMAGE)
plt.imshow(NOISY_IMAGES[0], cmap="BuPu")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('{}''{}'.format('2D Phantom using model no.',model))
plt.show()
return np.array([NOISY_IMAGES[0],IMAGES[0]])
def process_frames(self, data):
# print "The input data shape is", data[0].shape
if (self.out_shape_sino[1] == 1):
# create a 2D phantom
model = TomoP2D.Model(self.model, self.dims, self.path_library2D)
# create a 2D sinogram
projdata_clean = TomoP2D.ModelSino(self.model, self.dims,
self.detectors_num, self.angles,
self.path_library2D)
# Adding artifacts and noise
# forming dictionaries with artifact types
_noise_ = {
'type': self.parameters['artifacts_noise_type'],
'sigma': self.parameters['artifacts_noise_sigma'],
'seed': 0,
'prelog': False
}
# misalignment dictionary
_sinoshifts_ = {}
if self.parameters[
'artifacts_misalignment_maxamplitude'] is not None:
_sinoshifts_ = {
'maxamplitude':
self.parameters['artifacts_misalignment_maxamplitude']
}
# adding zingers and stripes
_zingers_ = {}
if self.parameters['artifacts_zingers_percentage'] is not None:
_zingers_ = {
'percentage':
self.parameters['artifacts_zingers_percentage'],
'modulus': 10
}
_stripes_ = {}
if self.parameters['artifacts_stripes_percentage'] is not None:
_stripes_ = {
'percentage':
self.parameters['artifacts_stripes_percentage'],
'maxthickness':
self.parameters['artifacts_stripes_maxthickness'],
'intensity':
self.parameters['artifacts_stripes_intensity'],
'type':
self.parameters['artifacts_stripes_type'],
'variability':
self.parameters['artifacts_stripes_variability']
}
if self.parameters[
'artifacts_misalignment_maxamplitude'] is not None:
[projdata,
shifts] = _Artifacts_(projdata_clean, _noise_, _zingers_,
_stripes_, _sinoshifts_)
else:
projdata = _Artifacts_(projdata_clean, _noise_, _zingers_,
_stripes_, _sinoshifts_)
else:
# create a 3D phantom
frame_idx = self.out_pData[0].get_current_frame_idx()[0]
model = TomoP3D.ModelSub(self.model, self.dims,
(frame_idx, frame_idx + 1),
self.path_library3D)
model = np.swapaxes(model, 0, 1)
model = np.flipud(model[:, 0, :])
# create a 3D projection data
projdata_clean = TomoP3D.ModelSinoSub(
self.model, self.dims, self.detectors_num, self.dims,
(frame_idx, frame_idx + 1), self.angles, self.path_library3D)
# Adding artifacts and noise
# forming dictionaries with artifact types
_noise_ = {
'type': self.parameters['artifacts_noise_type'],
'sigma': self.parameters['artifacts_noise_sigma'],
'seed': 0,
'prelog': False
}
# misalignment dictionary
_sinoshifts_ = {}
if self.parameters[
'artifacts_misalignment_maxamplitude'] is not None:
_sinoshifts_ = {
'maxamplitude':
self.parameters['artifacts_misalignment_maxamplitude']
}
# adding zingers and stripes
_zingers_ = {}
if self.parameters['artifacts_zingers_percentage'] is not None:
_zingers_ = {
'percentage':
self.parameters['artifacts_zingers_percentage'],
'modulus': 10
}
_stripes_ = {}
if self.parameters['artifacts_stripes_percentage'] is not None:
_stripes_ = {
'percentage':
self.parameters['artifacts_stripes_percentage'],
'maxthickness':
self.parameters['artifacts_stripes_maxthickness'],
'intensity':
self.parameters['artifacts_stripes_intensity'],
'type':
self.parameters['artifacts_stripes_type'],
'variability':
self.parameters['artifacts_stripes_variability']
}
if self.parameters[
'artifacts_misalignment_maxamplitude'] is not None:
[projdata,
shifts] = _Artifacts_(projdata_clean, _noise_, _zingers_,
_stripes_, _sinoshifts_)
else:
projdata = _Artifacts_(projdata_clean, _noise_, _zingers_,
_stripes_, _sinoshifts_)
projdata = np.swapaxes(projdata, 0, 1)
return [projdata, model]
def generateImage():
model = 6 # selecting a model
N_size = 256
#specify a full path to the parameters file
pathTP = 'Phantom2DLibrary.dat'
#This will generate a N_size x N_size phantom (2D)
phantom_2D = TomoP2D.Model(model, N_size, pathTP)
Labels = []
Labels_array = []
Images = []
shapeTypes = [TomoP2D.Objects2D.RECTANGLE, TomoP2D.Objects2D.ELLIPSE]
for a in range(0, 1, 1):
objects = []
background = []
array_label = []
num_back_shapes = np.random.randint(200, 400)
for i in range(0, num_back_shapes, 1):
shapeRand = np.random.randint(2)
background.append(genTomoShape(shapeTypes[shapeRand]))
num_shapes = np.random.randint(5, 20)
num_shapes = 5
insertImage = loadSimpleImg()
label_temp = np.zeros((256, 256), dtype=np.uint8)
image_temp = np.zeros((256, 256), dtype=np.uint8)
temp_label_array = []
for i in range(0, len(insertImage)):
temp_label_array.append(label_temp)
temp_label_array = np.array(temp_label_array)
for i in range(0, num_shapes, 1):
patternType = np.random.randint((insertImage.shape[0]))
pattern = np.random.randint((insertImage[patternType].shape[0]))
#Random pick of shape type
shapeRand = np.random.randint(2)
#Generate shape
shape = TomoP2D.Object(256, genTomoShape(shapeTypes[shapeRand]))
#add the shape to the laebl image and take away the original to get the positions where a new shape has been added.
fit = ((temp_label_array[patternType] + shape) -
temp_label_array[patternType]) > 0
#update the pixel values where the shape has been added, do no tjust add the pixel values together but replace them so the overlap is smooth
temp_label_array[patternType][fit] = shape[fit]
#filter looking for where the shape is
shapeFilter = shape >= 0.5
#for those positions where the shape exists set those values to the value in the image pattern
shape[shapeFilter] = insertImage[patternType][pattern][shapeFilter]
#add the shape to the image and take away the original to get the positions where a new shape has been added.
fit = ((image_temp + shape) - image_temp) > 0
#update the pixel values where the shape has been added, do no tjust add the pixel values together but replace them so the overlap is smooth
image_temp[fit] = shape[fit]
noise = np.random.uniform(low=0,
high=np.amax(image_temp) * 1.0,
size=(256, 256))
nos = (image_temp * 1.0) + (noise * 0.2)
Images.append(nos)
Labels_array.append(np.array(temp_label_array))
#%%
item = []
item.append(Images)
item.append(Labels_array)
item = np.array(item)
return np.array(nos), np.array(temp_label_array)
#f,l = generateImage()
#fig = plt.figure()
#ax = fig.add_subplot(121)
#ax.imshow(f)
#ax = fig.add_subplot(122)
#print(l.shape)
#ax.imshow(l[1])
#plt.show()
x = np.random.rand() * 2
y = np.random.rand() * 2
max_length = R - (x**2 + y**2) ** 0.5
max_length *= 4/(2**0.5)
long_length = np.random.rand() * max_length
short_length = np.random.rand() * long_length
rot = np.random.randint(0, 360)
ob = {'Obj': shape,
'C0' : density,
'x0' : x,
'y0' : y,
'a' : long_length,
'b' : short_length,
'phi': rot}
ob_list[ob_index] = ob
#make these choices
phantom = TomoP2D.Object(1499, ob_list)
vol_geom = astra.creators.create_vol_geom(1499, 1499, -256, 256, -256, 256)
proj_geom = astra.creators.create_proj_geom('parallel',1,
512, np.linspace(0, np.pi, 512, False))
proj_id = astra.create_projector("cuda",proj_geom,vol_geom)
vol_geom_rec = astra.create_vol_geom(512,512)
sino_id, sinogram = astra.create_sino(phantom,proj_id, gpuIndex=1)
np.save(os.path.join(phantoms_folder, phantom_name.format(i)), phantom)
np.save(os.path.join(sinogram_folder, sino_name.format(i)), sinogram)
import matplotlib.pyplot as plt
from tomophantom import TomoP2D
model = 1 # selecting a model
N_size = 512
#specify a full path to the parameters file
pathTP = r'C:\Users\zyv57124\Documents\TomoPhantom-master\TomoPhantom-master\functions\models\Phantom2DLibrary.dat'
#objlist = modelfile2Dtolist(pathTP, model) # one can extract parameters
#This will generate a N_size x N_size phantom (2D)
phantom_2D = TomoP2D.Model(model, N_size, pathTP)
plt.close('all')
plt.figure(1)
plt.rcParams.update({'font.size': 21})
plt.imshow(phantom_2D, vmin=0, vmax=1, cmap="BuPu")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('{}' '{}'.format('2D Phantom using model no.', model))
#Components : 01;
#TimeSteps : 1;
#Object : rectangle 1.00 -0.15 0.2 0.4 0.3 45;
import numpy as np
import matplotlib.pyplot as plt
from tomophantom import TomoP2D
import PIL
from PIL import Image
model = 6 # selecting a model
N_size = 256
#specify a full path to the parameters file
pathTP = r'C:\Users\zyv57124\Documents\TomoPhantom-master\TomoPhantom-master\functions\models\Phantom2DLibrary.dat'
#This will generate a N_size x N_size phantom (2D)
phantom_2D = TomoP2D.Model(model, N_size, pathTP)
IMAGE = []
NOISY_IMAGE = []
for a in range(0, 1, 1):
pps = []
num_rectangles = np.random.randint(1, 11)
for i in range(0, num_rectangles, 1):
pp = {
'Obj': TomoP2D.Objects2D.RECTANGLE,
'C0': 1.0,
'x0': float(np.random.uniform(low=-0.5, high=0.5, size=1)),
'y0': float(np.random.uniform(low=-0.5, high=0.5, size=1)),
'a': float(np.random.uniform(low=0.1, high=1.3, size=1)),
'b': float(np.random.uniform(low=0.02, high=0.05, size=1)),
if device=='1':
dev = 'gpu'
else:
dev = 'cpu'
# Create phantom for TV 2D dynamic tomography
model = 102 # note that the selected model is temporal (2D + time)
N = 50 # set dimension of the phantom
# one can specify an exact path to the parameters file
# path_library2D = '../../../PhantomLibrary/models/Phantom2DLibrary.dat'
path = os.path.dirname(tomophantom.__file__)
path_library2D = os.path.join(path, "Phantom2DLibrary.dat")
#This will generate a N_size x N_size x Time frames phantom (2D + time)
phantom_2Dt = TomoP2D.ModelTemporal(model, N, path_library2D)[0:-1:2]
fig = plt.figure()
ims1 = []
for sl in range(0,np.shape(phantom_2Dt)[0]):
im1 = plt.imshow(phantom_2Dt[sl,:,:], animated=True, vmin=0, vmax=1)
ims1.append([im1])
ani1 = animation.ArtistAnimation(fig, ims1, interval=500,repeat_delay=10)
plt.show()
ig = ImageGeometry(voxel_num_x = N, voxel_num_y = N, channels = np.shape(phantom_2Dt)[0])
data = ImageData(phantom_2Dt, geometry=ig)
detectors = N
@author: Daniil Kazantsev
"""
import numpy as np
import matplotlib.pyplot as plt
from tomophantom import TomoP2D
import os
import tomophantom
from tomophantom.supp.qualitymetrics import QualityTools
model = 4 # select a model
N_size = 512 # set dimension of the phantom
# one can specify an exact path to the parameters file
# path_library2D = '../../../PhantomLibrary/models/Phantom2DLibrary.dat'
path = os.path.dirname(tomophantom.__file__)
path_library2D = os.path.join(path, "Phantom2DLibrary.dat")
phantom_2D = TomoP2D.Model(model, N_size, path_library2D)
plt.close('all')
plt.figure(1)
plt.rcParams.update({'font.size': 21})
plt.imshow(phantom_2D, vmin=0, vmax=1, cmap="gray")
plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical')
plt.title('{}''{}'.format('2D Phantom using model no.',model))
# create sinogram analytically
angles_num = int(0.5*np.pi*N_size); # angles number
angles = np.linspace(0.0,179.9,angles_num,dtype='float32')
angles_rad = angles*(np.pi/180.0)
P = int(np.sqrt(2)*N_size) #detectors
sino_an = TomoP2D.ModelSino(model, N_size, P, angles, path_library2D)
def foam2D(x0min, x0max, y0min, y0max, c0min, c0max, ab_min, ab_max, N_size,
tot_objects, object_type):
import numpy as np
import math
import random
#2D functions
from tomophantom import TomoP2D
from tomophantom.TomoP2D import Objects2D
attemptsNo = 2000 # the number of attempts to fit the object
# objects accepted: 'ellipse', 'parabola', 'gaussian', 'mix'
mix_objects = False
if (object_type == 'ellipse'):
object_type = Objects2D.ELLIPSE
elif (object_type == 'parabola'):
object_type = Objects2D.PARABOLA
elif (object_type == 'gaussian'):
object_type = Objects2D.GAUSSIAN
elif (object_type == 'mix'):
mix_objects = True
else:
raise TypeError(
'object_type can be only ellipse, parabola, gaussian or mix')
X0 = np.float32(np.zeros(tot_objects))
Y0 = np.float32(np.zeros(tot_objects))
AB = np.float32(np.zeros(tot_objects))
C0_var = np.float32(np.zeros(tot_objects))
for i in range(0, tot_objects):
(x0, y0, c0, ab) = rand_init2D(x0min, x0max, y0min, y0max, c0min,
c0max, ab_min, ab_max)
if (i > 0):
breakj = False
for j in range(0, attemptsNo):
if (breakj == True):
(x0, y0, c0, ab) = rand_init2D(x0min, x0max, y0min, y0max,
c0min, c0max, ab_min,
ab_max)
breakj = False
else:
for l in range(
0, i
): # checks consistency with previously created objects
dist = math.sqrt((X0[l] - x0)**2 + (Y0[l] - y0)**2)
if (dist < (ab + AB[l])) or ((abs(x0) + ab)**2 +
(abs(y0) + ab)**2 > 1.0):
breakj = True
break
if (breakj == False
): # re-initialise if doesn't fit the criteria
X0[i] = x0
Y0[i] = y0
AB[i] = ab
C0_var[i] = c0
break
if (AB[i] == 0.0):
X0[i] = x0
Y0[i] = y0
AB[i] = 0.0001
C0_var[i] = c0
myObjects = [] # dictionary of objects
for obj in range(0, len(X0)):
if (mix_objects == True):
rand_obj = random.randint(0, 2)
if (rand_obj == 0):
object_type = Objects2D.ELLIPSE
if (rand_obj == 1):
object_type = Objects2D.PARABOLA
if (rand_obj == 2):
object_type = Objects2D.GAUSSIAN
curr_obj = {
'Obj': object_type,
'C0': C0_var[obj],
'x0': X0[obj],
'y0': Y0[obj],
'a': AB[obj],
'b': AB[obj],
'phi': 0.0
}
myObjects.append(curr_obj)
Object = TomoP2D.Object(N_size, myObjects)
return (Object, myObjects)
