def test_rasterize_2d_coordinates_single_point_with_origin(self):
a = np.array([[109.99, 0.]])
b = np.array([[0., 109.99]])
a_rast = fpp.rasterized_2d_coordinates(a, 10, np.array([-0.5, -25]))
b_rast = fpp.rasterized_2d_coordinates(b, 10, np.array([-0.5, -25]))
nptest.assert_array_equal(a_rast, np.array([[11, 2]]))
nptest.assert_array_equal(b_rast, np.array([[0, 13]]))
def test_rasterize_2d_coordinates_single_point_with_origin(self):
a = np.array([[109.99, 0.]])
b = np.array([[0., 109.99]])
a_rast = fpp.rasterized_2d_coordinates(a, 10, np.array([-0.5, -25]))
b_rast = fpp.rasterized_2d_coordinates(b, 10, np.array([-0.5, -25]))
nptest.assert_array_equal(a_rast, np.array([[11, 2]]))
nptest.assert_array_equal(b_rast, np.array([[0, 13]]))
def test_rasterize_2d_coordinates_many_points_with_origin(self):
a = np.array([[100., 0.], [109.99, 0.], [110., 0.], [0., 100.],
[0., 109.99], [0., 110.]])
a_rast = fpp.rasterized_2d_coordinates(a, 10, np.array([-0.5, -25]))
nptest.assert_array_equal(
a_rast,
np.array([[10, 2], [11, 2], [11, 2], [0, 12], [0, 13], [0, 13]]))
def test_rasterize_2d_coordinates_many_points(self):
a = np.array([[100., 0.], [109.99, 0.], [110., 0.], [0., 100.],
[0., 109.99], [0., 110.]])
a_rast = fpp.rasterized_2d_coordinates(a, 10)
nptest.assert_array_equal(
a_rast,
np.array([[10, 0], [10, 0], [11, 0], [0, 10], [0, 10], [0, 11]]))
def test_rasterize_2d_coordinates_many_points_with_rotation2(self):
a = np.array([[100., 0.], [109.99, 0.], [110., 0.],
[0., 100.], [0., 109.99], [0., 110.]])
a_rast = fpp.rasterized_2d_coordinates(a, 10, rotate=-90)
print(a_rast)
nptest.assert_array_equal(a_rast, np.array(
[[0, 10], [0, 10], [0, 11], [-10, 0], [-11, 0], [-11, 0]]))
def test_rasterize_2d_coordinates_many_points_with_rotation_and_origin(self):
a = np.array([[100., 0.], [109.99, 0.], [110., 0.],
[0., 100.], [0., 109.99], [0., 110.]])
a_rast = fpp.rasterized_2d_coordinates(
a, 10, np.array([-0.5, -25]), rotate=-90)
print(a_rast)
nptest.assert_array_equal(a_rast, np.array(
[[0, 12], [0, 13], [0, 13], [-10, 2], [-11, 2], [-11, 2]]))
def update(self, _=None):
width = self.width.get()
rest = width % 10
if rest < 5:
self.width.set(width - rest)
else:
self.width.set(width - rest + 10)
proj = self.proj
# Offset
box = self.getBox()
# Rasterize the image
if self.showVres.get():
img, _ = proj.rasterize(self.dpi.get(),
box,
virtual_atoms=True,
rotate=self.inplane_rot.get(),
warn=False)
else:
img, _ = proj.rasterize(self.dpi.get(),
box,
virtual_atoms=True,
rotate=self.inplane_rot.get(),
virtual_residues=False,
warn=False)
img = fpp.to_rgb(img)
pilImg = Image.fromarray(img)
pilImg = pilImg.convert("RGB")
# Show stems
if self.showStems.get():
stemres = []
for s in self.cg.defines.keys():
if s[0] != "s":
continue
for pos in self.cg.define_residue_num_iterator(s):
stemres.append(proj.get_vres_by_position(pos))
stemres = np.array(stemres)
rast = fpp.rasterized_2d_coordinates(
stemres,
self.width.get() / self.dpi.get(),
origin=np.array([box[0], box[2]]),
rotate=self.inplane_rot.get())
for x, y in rast:
if 0 <= x < self.dpi.get() and 0 <= y < self.dpi.get():
pilImg.putpixel((int(y), int(x)), (100, 255, 0))
# Selected Nucleotide
x, y = self.getSelected()
if 0 <= x < self.dpi.get() and 0 <= y < self.dpi.get():
pilImg.putpixel((int(y), int(x)), (255, 0, 0))
# Zoom
zoom = int(self.zoom.get())
newsize = (self.dpi.get() * int(zoom), self.dpi.get() * int(zoom))
pilImg = pilImg.resize(newsize, Image.NEAREST)
# Show
tkImg = ImageTk.PhotoImage(pilImg)
self.imgDisplay.configure(image=tkImg)
self.image = tkImg # Keep a reference!
self.pilImage = pilImg # For saving
def getSelected(self):
box = self.getBox()
selected = int(self.nucleotidePosition.get())
nucPos = self.proj.get_vres_by_position(selected)
x, y = fpp.rasterized_2d_coordinates(np.array([[nucPos[0], nucPos[1]]]),
self.width.get() / self.dpi.get(),
origin=np.array([box[0], box[2]]),
rotate=self.inplane_rot.get())[0]
return x, y
def test_rasterize_2d_coordinates_many_points_with_rotation2(self):
a = np.array([[100., 0.], [109.99, 0.], [110., 0.], [0., 100.],
[0., 109.99], [0., 110.]])
a_rast = fpp.rasterized_2d_coordinates(a, 10, rotate=-90)
print(a_rast)
nptest.assert_array_equal(
a_rast,
np.array([[0, 10], [0, 10], [0, 11], [-10, 0], [-11, 0], [-11,
0]]))
def getSelected(self):
box = self.getBox()
selected = int(self.nucleotidePosition.get())
nucPos = self.proj.get_vres_by_position(selected)
x, y = fpp.rasterized_2d_coordinates(np.array([[nucPos[0],nucPos[1]]]),
self.width.get()/self.dpi.get(),
origin = np.array([box[0],box[2]]),
rotate = self.inplane_rot.get())[0]
return x,y
def update(self, _=None):
width = self.width.get()
rest = width % 10
if rest < 5:
self.width.set(width - rest)
else:
self.width.set(width - rest + 10)
proj = self.proj
# Offset
box = self.getBox()
# Rasterize the image
if self.showVres.get():
img, _ = proj.rasterize(self.dpi.get(), box, virtual_atoms=True,
rotate=self.inplane_rot.get(), warn=False)
else:
img, _ = proj.rasterize(self.dpi.get(), box, virtual_atoms=True,
rotate=self.inplane_rot.get(),
virtual_residues=False, warn=False)
img = fpp.to_rgb(img)
pilImg = Image.fromarray(img)
pilImg = pilImg.convert("RGB")
# Show stems
if self.showStems.get():
stemres = []
for s in self.cg.defines.keys():
if s[0] != "s":
continue
for pos in self.cg.define_residue_num_iterator(s):
stemres.append(proj.get_vres_by_position(pos))
stemres = np.array(stemres)
rast = fpp.rasterized_2d_coordinates(stemres, self.width.get() / self.dpi.get(),
origin=np.array(
[box[0], box[2]]),
rotate=self.inplane_rot.get())
for x, y in rast:
if 0 <= x < self.dpi.get() and 0 <= y < self.dpi.get():
pilImg.putpixel((int(y), int(x)), (100, 255, 0))
# Selected Nucleotide
x, y = self.getSelected()
if 0 <= x < self.dpi.get() and 0 <= y < self.dpi.get():
pilImg.putpixel((int(y), int(x)), (255, 0, 0))
# Zoom
zoom = int(self.zoom.get())
newsize = (self.dpi.get() * int(zoom), self.dpi.get() * int(zoom))
pilImg = pilImg.resize(newsize, Image.NEAREST)
# Show
tkImg = ImageTk.PhotoImage(pilImg)
self.imgDisplay.configure(image=tkImg)
self.image = tkImg # Keep a reference!
self.pilImage = pilImg # For saving
def test_rasterize_2d_coordinates_single_point_Y3(self):
a = np.array([[0., 110.]])
a_rast = fpp.rasterized_2d_coordinates(a, 10)
nptest.assert_array_equal(a_rast, np.array([[0, 11]]))
def test_rasterize_2d_coordinates_single_point_X2(self):
a = np.array([[109.99, 0.]])
a_rast = fpp.rasterized_2d_coordinates(a, 10)
nptest.assert_array_equal(a_rast, np.array([[10, 0]]))
def test_rasterize_2d_coordinates_many_points(self):
a = np.array([[100., 0.], [109.99, 0.], [110., 0.],
[0., 100.], [0., 109.99], [0., 110.]])
a_rast = fpp.rasterized_2d_coordinates(a, 10)
nptest.assert_array_equal(a_rast, np.array(
[[10, 0], [10, 0], [11, 0], [0, 10], [0, 10], [0, 11]]))
def test_rasterize_2d_coordinates_single_point_Y3(self):
a = np.array([[0., 110.]])
a_rast = fpp.rasterized_2d_coordinates(a, 10)
nptest.assert_array_equal(a_rast, np.array([[0, 11]]))
def test_rasterize_2d_coordinates_single_point_X2(self):
a = np.array([[109.99, 0.]])
a_rast = fpp.rasterized_2d_coordinates(a, 10)
nptest.assert_array_equal(a_rast, np.array([[10, 0]]))
