def VesselTubeToNumPyTest(tubes, baseline_array):
import numpy as np
from tubetk.numpy import tubes_from_file
array = tubes_from_file(tubes)
print(array.dtype)
print(array)
baseline = np.load(baseline_array)
all_fields_close = True
for field in baseline.dtype.fields.iterkeys():
if not np.allclose(array[field], baseline[field]):
all_fields_close = False
print('The array field: ' + field + ' does not match!')
return all_fields_close
def VesselTubeToNumPyTest(tubes, baseline_array):
import numpy as np
from tubetk.numpy import tubes_from_file
array = tubes_from_file(tubes)
print(array.dtype)
print(array)
baseline = np.load(baseline_array)
all_fields_close = True
for field in baseline.dtype.fields.iterkeys():
if not np.allclose(array[field], baseline[field]):
all_fields_close = False
print('The array field: ' + field + ' does not match!')
return all_fields_close
def VesselTubeToNumPyTest(tubes, baseline_array):
import numpy as np
from tubetk.numpy import tubes_from_file
print('Reading file: ' + tubes)
array = tubes_from_file(tubes)
print(array.dtype)
print(array)
baseline = np.load(baseline_array)
all_fields_close = True
for field in baseline.dtype.fields.keys():
print("Testing field = " + field)
if not np.allclose(array[field], baseline[field]):
all_fields_close = False
print('The array field: ' + field + ' does not match!')
print('array = ' + str(array[field]))
print('baseline = ' + str(baseline[field]))
return all_fields_close
def PyQtGraphTubesAsCirclesTest(tube_file, screenshot):
import pyqtgraph as pg
import pyqtgraph.opengl as gl
from tubetk.numpy import tubes_from_file
from tubetk.pyqtgraph import tubes_as_circles
tubes = tubes_from_file(tube_file)
subsample = 30
tubes = tubes[::subsample]
# Setup QApplication
qapp = pg.mkQApp()
view = gl.GLViewWidget()
view.setCameraPosition(distance=200)
view.orbit(0., 20.)
view.setWindowTitle('PyQtGraphTubePointsTest')
view.show()
x_grid = gl.GLGridItem()
grid_scale = 20
x_grid.rotate(90, 0, 1, 0)
x_grid.translate(-10 * grid_scale, 0, 0)
y_grid = gl.GLGridItem()
y_grid.rotate(90, 1, 0, 0)
y_grid.translate(0, -10 * grid_scale, 0)
z_grid = gl.GLGridItem()
z_grid.translate(0, 0, -10 * grid_scale)
for grid in x_grid, y_grid, z_grid:
grid.scale(grid_scale, grid_scale, grid_scale)
view.addItem(grid)
circles = tubes_as_circles(tubes)
circles_mesh = gl.GLMeshItem(meshdata=circles, smooth=False)
view.addItem(circles_mesh)
#return qapp.exec_()
view.paintGL()
framebuffer = view.grabFrameBuffer()
return framebuffer.save(screenshot)
def PyQtGraphTubesAsCirclesTest(tube_file, screenshot):
import pyqtgraph as pg
import pyqtgraph.opengl as gl
from tubetk.numpy import tubes_from_file
from tubetk.pyqtgraph import tubes_as_circles
tubes = tubes_from_file(tube_file)
subsample = 30
tubes = tubes[::subsample]
# Setup QApplication
qapp = pg.mkQApp()
view = gl.GLViewWidget()
view.setCameraPosition(distance=200)
view.orbit(0., 20.)
view.setWindowTitle('PyQtGraphTubePointsTest')
view.show()
x_grid = gl.GLGridItem()
grid_scale = 20
x_grid.rotate(90, 0, 1, 0)
x_grid.translate(-10 * grid_scale, 0, 0)
y_grid = gl.GLGridItem()
y_grid.rotate(90, 1, 0, 0)
y_grid.translate(0, -10 * grid_scale, 0)
z_grid = gl.GLGridItem()
z_grid.translate(0, 0, -10 * grid_scale)
for grid in x_grid, y_grid, z_grid:
grid.scale(grid_scale, grid_scale, grid_scale)
view.addItem(grid)
circles = tubes_as_circles(tubes)
circles_mesh = gl.GLMeshItem(meshdata=circles, smooth=False)
view.addItem(circles_mesh)
#return qapp.exec_()
view.paintGL()
framebuffer = view.grabFrameBuffer()
return framebuffer.save(screenshot)
def add_tubes(self):
"""Add the transformed tubes for the visualization."""
memory = 4
target_iterations = tuple(range(self.logic.iteration,
self.logic.iteration - memory,
-1))
for it in target_iterations:
if it >= 0 and it <= self.logic.number_of_iterations:
alpha = np.exp(0.8*(it - self.logic.iteration))
center_color = (0.8, 0.1, 0.25, alpha)
center = self.logic.tubes_center
if self.logic.progression != None:
parameters = self.logic.progression[it]['Parameters']
else:
parameters = (0.0, 0.0, 0.0, 0.0, 0.0, 0.0)
tubes = tubes_from_file(self.logic.subsampled_tubes)
#tubes_color = (0.2, 0.25, 0.75, alpha)
if 'TubePointWeightsFile' in self.config and \
os.path.exists(self.config['TubePointWeightsFile']):
with open(self.config['TubePointWeightsFile'], 'r') as fp:
tube_weights = json.load(fp)['TubePointWeights']
tube_weights = np.array(tube_weights)
else:
tube_weights = 2./(1. + np.exp(-2 * tubes['Radius']))
tube_weights = tube_weights - tube_weights.min()
tube_weights = tube_weights / tube_weights.max()
tubes_colors = matplotlib.cm.PuBuGn(tube_weights)
tubes_colors[:, 3] = tube_weights**0.5 * alpha
circles = tubes_as_circles(tubes, point_colors=tubes_colors)
circles_mesh = gl.GLMeshItem(meshdata=circles,
glOptions='translucent',
smooth=False)
if self.logic.progression != None:
# TODO: need to verify that this is correct
circles_mesh.translate(-center[0],
-center[1],
-center[2])
r2d = 180. / np.pi
circles_mesh.rotate(parameters[0] * r2d, 1, 0, 0,
local=False)
circles_mesh.rotate(parameters[1] * r2d, 0, 1, 0,
local=False)
circles_mesh.rotate(parameters[2] * r2d, 0, 0, 1,
local=False)
circles_mesh.translate(center[0] + parameters[3],
center[1] + parameters[4],
center[2] + parameters[5])
if it in self.tubes_circles:
self.removeItem(self.tubes_circles[it][1])
self.addItem(circles_mesh)
sphere = gl.MeshData.sphere(rows=10,
cols=20,
radius=1.0)
center_mesh = gl.GLMeshItem(meshdata=sphere,
smooth=False,
color=center_color,
glOptions='translucent')
center_mesh.translate(center[0] + parameters[3],
center[1] + parameters[4],
center[2] + parameters[5])
if it in self.tubes_circles:
self.removeItem(self.tubes_circles[it][2])
self.addItem(center_mesh)
self.tubes_circles[it] = [circles,
circles_mesh,
center_mesh]
for it, circs in self.tubes_circles.items():
if not it in target_iterations:
self.removeItem(circs[1])
self.removeItem(circs[2])
self.tubes_circles.pop(it)