def build(self):
main_scroll = ScrollView(do_scroll_x=False)
main_grid = GridLayout(cols=1,
spacing=100,
padding=[0, 50, 0, 50],
size_hint_y=None)
main_grid.bind(minimum_height=main_grid.setter('height'))
main_scroll.add_widget(main_grid)
scroll_count = 4
for _ in range(scroll_count):
scroll = ScrollView(size_hint_y=None,
height=300,
do_scroll_y=False)
grid = GridLayout(rows=1, spacing=1, size_hint=(None, 1))
grid.bind(minimum_width=grid.setter('width'))
scroll.add_widget(grid)
for r in range(0, 50):
bt = Button(text='Button ' + str(r),
size_hint_x=None,
width=cm(2))
bt.bind(on_press=self.print_btn)
grid.add_widget(bt)
main_grid.add_widget(scroll)
return main_scroll
border_width=3,
border_radius=10,
font_kwargs={"bold": True, "italic": True},
dest=(0.1, 0.1, 0.1, 0.1), # position within parent
on_click=lambda self, event: self.run_hook("NAVIGATE_TO", "level_select"),
),
ScrollView(
dest=(0.6, 0.1, 0.35, 0.4),
canvas_size_factors=(1.0, 3.0),
border_width=3,
aspect_ratio=1,
children=[
View(bg_color=GREEN, dest=(0.1, 0.0, 0.2, 1.0), margins=(0, 10, 0, 10)),
Button(bg_color=RED, dest=(0.4, 0.1, 0.2, 0.2), text="!", on_click=lambda s, e: print("HI")),
View(bg_color=BLUE, dest=(0.4, 0.4, 0.2, 0.2)),
View(bg_color=MAGENTA, dest=(0.8, 0.6, 0.2, 0.2)),
ScrollView(
border_width=1,
dest=(0.4, 0.7, 0.3, 0.2),
canvas_size_factors=(2.0, 2.0),
children=[
Image(image=test_image_source)
]
)
]
),
ScrollView(
dest=(0.1, 0.7, 0.4, 0.2),
canvas_size_factors=(2.0, 1.0),
border_width=3,
children=[
Text(
itk_image_opr = sitk.ReadImage(opr_image_path)
image_array_opr = sitk.GetArrayFromImage(itk_image_opr)
pr_image_path = os.path.join(patient, 'prostaat.mhd')
itk_image_pr = sitk.ReadImage(pr_image_path)
image_array_pr = sitk.GetArrayFromImage(itk_image_pr)
mr_image_path = os.path.join(patient, 'mr_bffe.mhd')
itk_image_mr = sitk.ReadImage(mr_image_path)
image_array_mr = sitk.GetArrayFromImage(itk_image_mr)
overlay = image_array_mr - 7000 * image_array_pr
fig, (ax1, ax2, ax3, ax4, ax5) = plt.subplots(1, 5, figsize=(25, 5))
ScrollView(image_array_unseen).plot(ax1, cmap='gray')
ScrollView(overlay).plot(ax2, cmap='gray')
ax1.set_title('Unseen')
ax2.set_title('Prostate overlay')
# Define a new elastix object 'el' with the correct path to elastix
el = elastix.ElastixInterface(elastix_path=ELASTIX_PATH)
# Execute the registration. Make sure the paths below are correct, and
# that the results folder exists from where you are running this script
el.register(fixed_image=unseen_image_path,
moving_image=mr_image_path,
parameters=[
os.path.join('parameterfiles', 'parameters_affine.txt'),
os.path.join('parameterfiles', 'parameters_bspline142.txt')
],
#path_to_transformed_image = T.transform_image(im1, output_dir='results')
#
## Get the Jacobian matrix
#path_to_jacobian_matrix = T.jacobian_matrix(output_dir='results')
#
## Get the Jacobian determinant
#path_to_jacobian_determinant = T.jacobian_determinant(output_dir='results')
#
## Get the full deformation field
#path_to_deformation_field = T.deformation_field(output_dir='results')
#
from scrollview import ScrollView
#image = np.load('path/to/image')
#aspect_ratio = [2.3, 0.95, 0.95] # i.e. the ElementSpacing
aspect_ratio = [2.3, 2.3, 2.3] # i.e. the ElementSpacing
# Define viewers for every axis
viewer1 = ScrollView(im_arr1)
viewer2 = ScrollView(im_arr2)
viewer3 = ScrollView(im_arrres)
#viewer2 = ScrollView(im.transpose(1, 0, 2))
#viewer3 = ScrollView(im.transpose(2, 0, 1))
# Make three Matplotlib supblots, and populate them with the viewers objects
# The aspect ratios of the different axes need to be defined here as well.
fig, ax = plt.subplots(1, 3)
viewer1.plot(ax[0], cmap='gray', aspect=aspect_ratio[1] / aspect_ratio[2])
viewer2.plot(ax[1], cmap='gray', aspect=aspect_ratio[0] / aspect_ratio[2])
viewer3.plot(ax[2], cmap='gray', aspect=aspect_ratio[0] / aspect_ratio[1])
plt.show()
num_rows = NUM_LEVELS // LEVELS_PER_ROW
level_select_layout = [
level_select_buttons[row * LEVELS_PER_ROW:(row + 1) * LEVELS_PER_ROW]
for row in range(NUM_LEVELS // LEVELS_PER_ROW)
]
level_select_screen = View(children=[
Text(LEVELS_PER_ROW,
0.5,
text="Levels",
dest=(0.25, 0.0, 0.5, 0.1),
**menu_h2_style),
# TODO: some sort of border or bg-color change to differentiate this region
ScrollView(
children=[GridView(level_select_layout, margins=(12, 0) * 2)],
canvas_size_factors=(1.0, 2.0),
dest=(0.1, 0.1, 0.8, 0.7),
),
Button(text="Back",
dest=(0.4, 0.85, 0.2, 0.1),
on_click=lambda self, event: self.run_hook("NAVIGATE_BACK"),
**menu_button_style)
])
# --- Settings Screen --- #
# TODO
# --- Credits Screen --- #
# TODO
hoster = Hoster(
patients2 = ['p116', 'p117', 'p119', 'p120', 'p125']
patients3 = ['p127', 'p128', 'p129', 'p133', 'p135']
# load images and masks
images_org = [
sitk.GetArrayFromImage(sitk.ReadImage(os.path.join(patient,
"mr_bffe.mhd")))
for patient in patients1
]
# normalize images
images_norm = normalization(images_org)
fig, (ax1, ax2, ax3, ax4, ax5) = plt.subplots(1, 5, figsize=(25, 5))
ScrollView(images_norm[0]).plot(ax1, cmap='gray')
ScrollView(images_norm[1]).plot(ax2, cmap='gray')
ScrollView(images_norm[2]).plot(ax3, cmap='gray')
ScrollView(images_norm[3]).plot(ax4, cmap='gray')
ScrollView(images_norm[4]).plot(ax5, cmap='gray')
ax3.set_title("genormaliseerd")
fig, (ax6, ax7, ax8, ax9, ax10) = plt.subplots(1, 5, figsize=(25, 5))
ScrollView(images_org[0]).plot(ax6, cmap='gray')
ScrollView(images_org[1]).plot(ax7, cmap='gray')
ScrollView(images_org[2]).plot(ax8, cmap='gray')
ScrollView(images_org[3]).plot(ax9, cmap='gray')
ScrollView(images_org[4]).plot(ax10, cmap='gray')
ax8.set_title("origineel")
plt.show()
import matplotlib.pyplot as plt
import numpy as np
import imageio
import os
import SimpleITK as sitk
from scrollview import ScrollView
#image = sitk.ReadImage(r'C:\Users\s166646\Downloads\Capita Selecta\results2\result.0.mhd')
image = sitk.ReadImage(
r'C:\Users\s166646\Downloads\TrainingData\TrainingData\p102\mr_bffe.mhd')
#image = sitk.ReadImage(r'C:\Users\s166646\Downloads\TrainingData\TrainingData\p102\prostaat.mhd')
image_array = sitk.GetArrayFromImage(image)
#print(image_array)
#print(np.max(image_array))
fig, ax = plt.subplots()
ScrollView(image_array).plot(ax)
#fixed_image = sitk.ReadImage(r'C:\Users\s166646\Downloads\ImagesforPractical\ImagesforPractical\chest_xrays\fixed_image.mhd')
#moving_image = sitk.ReadImage(r'C:\Users\s166646\Downloads\ImagesforPractical\ImagesforPractical\chest_xrays\moving_image.mhd')
#fixed_image_path = sitk.GetArrayFromImage(fixed_image)
#moving_image_path = sitk.GetArrayFromImage(moving_image)
#fig, ax = plt.subplots(1, 3, figsize=(20, 5))
#ax[0].imshow(fixed_image_path)
#ax[1].imshow(moving_image_path)
#ax[2].imshow(image_array[24], cmap='gray')
plt.show()
ax.scatter(pos_fixed[0], pos_fixed[1], pos_fixed[2], c='black')
ax.set_title('Fixed')
ax = fig.add_subplot(1, 3, 2, projection='3d')
ax.scatter(pos_moving[0], pos_moving[1], pos_moving[2], c='black')
ax.set_title('Moving')
ax = fig.add_subplot(1, 3, 3, projection='3d')
ax.scatter(pos_transformed[0],
pos_transformed[1],
pos_transformed[2],
c='black')
ax.set_title('Transformed')
plt.show()
'''
#3d beeld test
fig, ax = plt.subplots()
ScrollView(fixed_img).plot(ax)
#resultaat geeft maar een beeld waarmee niet doorheen te scrollen is met touchpad
plt.show()
'''
###################################################################################################
#quantifying the results
#using dice score
dice2 = ((2.0 * np.sum(np.logical_and(t_seg_img, fixed_mask))) /
(np.sum(t_seg_img) + np.sum(fixed_mask)))
print('Dice similarity score 2 is {}'.format(dice2))