def OnCompute(self, event):
global tex_data
global tex2
global omega
global kappa
global offset_matrix
global shadowsetting
global tex_shadow
global tex_noshad
global noshad_data
global tex
omega = self.widget[0].GetValue()
kappa = self.widget[1].GetValue()
offset_matrix = [
self.widget[2].GetValue(),
self.widget[3].GetValue(),
self.widget[4].GetValue(),
]
newshadow = shadowmapper.Shadow(
shadowmapper.day2_coords,
filename,
DET_ANGLE,
d,
detector_origin,
fast_axis,
slow_axis,
)
[
tex_data,
tex,
tex2,
tex_shadow,
tex_noshad,
noshad_data,
] = newshadow.shadow_texture(kappa=kappa,
omega=omega,
blank=blanksetting)
pixels = newshadow.affected_pixels(kappa=kappa,
omega=omega,
blank=blanksetting)[1]
shadowsetting = self.shadowcheck.GetValue()
if shadowsetting is True:
print("At these goniometer angles, the shadow affects", pixels,
"pixels.")
self.Destroy()
app.MainLoop()
def OnPlot(self, event):
myshadow = shadowmapper.Shadow(
shadowmapper.day2_coords,
filename,
DET_ANGLE,
d,
detector_origin,
fast_axis,
slow_axis,
)
myshadow.pixel_plotter(num_points=self.points.GetValue())
self.Destroy()
def __init__(self, filename):
self.newimage = analyser.Image(filename)
(
origin,
fast,
slow,
dimensions,
pix,
dist,
res,
) = self.newimage.detector_parameters()
self.newshadow = shadowmapper.Shadow(shadowmapper.day2_coords,
filename, det_angle, dist, origin,
fast, slow)
def view_experiment(
filename, sample_x_length=4.0, sample_y_length=0.5, sample_z_length=8.0
):
"""
Read a cbf image and display a 3D model of the experiment.
This function is intended to be used by the block of code at the
end of the module. This will start the program with a dialog box
allowing the user to select a file.
Arguments:
filename -- the name of the cbf image to be read. Must include the
.cbf extension.
sample_x,y,z_length -- the dimensions of the sample in mm.
The model can be rotated by clicking and dragging the mouse, and
zoomed with the mousewheel. The model is displayed in a wxPython
based OpenGLCanvas.
Note that the default sample dimensions are much larger than the
true dimensions; however for the purposes of the program it is best
to have a crystal large enough to be visible.
"""
myimage = analyser.Image(filename)
viewer.B = myimage.find_beam_direction()
(
viewer.detector_origin,
viewer.fast_axis,
viewer.slow_axis,
viewer.dimensions,
viewer.pix,
viewer.d,
res,
) = myimage.detector_parameters()
((i, j, k), (alpha, beta, gamma), viewer.R) = myimage.get_sample_orientation()
viewer.sample_angles = (alpha, beta, gamma)
viewer.img_array = myimage.image_to_array()
mysample = modeller.Sample(sample_x_length, sample_y_length, sample_z_length)
viewer.r_f = mysample.rotate(i, j, k)
for i in range(viewer.num_panels):
det.append(modeller.Panel(viewer.dimensions[i, 0], viewer.dimensions[i, 1]))
viewer.d_r_f[i] = det[i].get_coords(
viewer.detector_origin[i], viewer.fast_axis[i], viewer.slow_axis[i]
)
myshadow = shadowmapper.Shadow(
shadowmapper.day2_coords,
filename,
viewer.DET_ANGLE,
viewer.d,
viewer.detector_origin,
viewer.fast_axis,
viewer.slow_axis,
)
viewer.filename, viewer.shadowsetting, viewer.blanksetting = (
filename,
False,
False,
)
(viewer.kappa, viewer.omega, viewer.offset_matrix, viewer.sample_x) = (
-180.0,
90.0,
np.zeros(3),
0.0,
)
(
viewer.tex_data,
viewer.tex,
viewer.tex2,
viewer.tex_shadow,
viewer.tex_noshad,
viewer.noshad_data,
) = myshadow.shadow_texture()
viewer.app = wx.App()
viewer.frame = viewer.MainWindow()
viewer.app.MainLoop()
def OnCompute(self, event):
alpha = -np.deg2rad(self.angle[0].GetValue())
beta = np.deg2rad(self.angle[1].GetValue())
gamma = np.deg2rad(self.angle[2].GetValue())
# rotation matrices for each axis
r_x = np.array(
[
[1.0, 0.0, 0.0],
[0.0, np.cos(alpha), -np.sin(alpha)],
[0.0, np.sin(alpha), np.cos(alpha)],
],
float,
)
r_y = np.array(
[
[np.cos(beta), 0.0, np.sin(beta)],
[0.0, 1.0, 0.0],
[-np.sin(beta), 0.0, np.cos(beta)],
],
float,
)
r_z = np.array(
[
[np.cos(gamma), -np.sin(gamma), 0.0],
[np.sin(gamma), np.cos(gamma), 0.0],
[0.0, 0.0, 1.0],
],
float,
)
# r_tot = matrix representing the total rotation
r_tot = np.dot(r_z, np.dot(r_y, r_x))
newSample = modeller.Sample()
r_f = newSample.rotate(r_tot[0], r_tot[1], r_tot[2])
sample_x = 0.0
if self.rb2.GetValue() is True:
sample_x = 6.4
elif self.rb3.GetValue() is True:
sample_x = -6.4
new_origin = deepcopy(detector_origin)
new_origin[0, 0] += sample_x
newDet = []
for i in range(num_panels):
newDet.append(modeller.Panel(dimensions[i, 0], dimensions[i, 1]))
d_r_f[i] = newDet[i].get_coords(new_origin, fast_axis[i],
slow_axis[i])
print(
"The new alpha, beta, and gamma angles are, respectively, ",
np.rad2deg(alpha),
", ",
np.rad2deg(beta),
"and ",
np.rad2deg(gamma),
"degrees",
)
newshadow = shadowmapper.Shadow(
shadowmapper.day2_coords,
filename,
DET_ANGLE,
d,
detector_origin,
fast_axis,
slow_axis,
)
[
tex_data,
tex,
tex2,
tex_shadow,
tex_noshad,
noshad_data,
] = newshadow.shadow_texture(kappa=kappa,
omega=omega,
blank=blanksetting)
pixels = newshadow.affected_pixels(kappa=kappa,
omega=omega,
blank=blanksetting)[1]
if shadowsetting is True:
print("At these goniometer angles, the shadow affects", pixels,
"pixels.")
self.Destroy()
app.MainLoop()
def OnAdjust(self, event):
global d
global DET_ANGLE
global tex_data
global tex2
global tex_noshad
global noshad_data
global blanksetting
global tex
global tex_shadow
# angle = angular displacement
angle = np.deg2rad(self.angles.GetValue() - DET_ANGLE)
displacement = self.dist.GetValue() - d
# Rotation matrix
r_x = np.array(
[
[1.0, 0.0, 0.0],
[0.0, np.cos(angle), -np.sin(angle)],
[0.0, np.sin(angle), np.cos(angle)],
],
float,
)
det = []
for i in range(num_panels):
det.append(modeller.Panel(dimensions[i, 0], dimensions[i, 1]))
detector_origin[
i] = detector_origin[i] + displacement * detector_normal
detector_origin[i] = np.dot(r_x, detector_origin[i])
fast_axis[i] = np.dot(r_x, fast_axis[i])
slow_axis[i] = np.dot(r_x, slow_axis[i])
d_r_f[i] = det[i].get_coords(detector_origin[i], fast_axis[i],
slow_axis[i])
d = self.dist.GetValue()
DET_ANGLE = self.angles.GetValue()
blanksetting = not self.detcheck.GetValue()
newshadow = shadowmapper.Shadow(
shadowmapper.day2_coords,
filename,
DET_ANGLE,
d,
detector_origin,
fast_axis,
slow_axis,
)
[
tex_data,
tex,
tex2,
tex_shadow,
tex_noshad,
noshad_data,
] = newshadow.shadow_texture(kappa=kappa,
omega=omega,
blank=blanksetting)
pixels = newshadow.affected_pixels(kappa=kappa,
omega=omega,
blank=blanksetting)[1]
if shadowsetting is True:
print("At these goniometer angles, the shadow affects", pixels,
"pixels.")
self.Destroy()
app.MainLoop()