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Change some matplotlib.tri calls to use scipy.spatial.Delaunay #649

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Change some matplotlib.tri calls to use scipy.spatial.Delaunay #649

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switch from matplotlib.tri to scipy.spatial.Delaunay for some of the …
David-Baddeley Nov 27, 2020
9d8d9db
Merge branch 'master' into tri-swap
David-Baddeley Apr 13, 2021
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32 changes: 20 additions & 12 deletions PYME/LMVis/visHelpers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -305,8 +305,12 @@ def rendGaussProd(x,y, sx, imageBounds, pixelSize):

def rendTri(T, imageBounds, pixelSize, c=None, im=None, geometric_mean=False):
from PYME.Analysis.points.SoftRend import drawTriang, drawTriangles
xs = T.x[T.triangles] # x posititions of vertices [nm], dimensions (# triangles, 3)
ys = T.y[T.triangles] # y posititions of vertices [nm], dimensions (# triangles, 3)
#xs = T.x[T.triangles] # x posititions of vertices [nm], dimensions (# triangles, 3)
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E265: block comment should start with '# '

#ys = T.y[T.triangles] # y posititions of vertices [nm], dimensions (# triangles, 3)
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E265: block comment should start with '# '


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W293: blank line contains whitespace

verts = T.points[T.simplices]
xs = verts[:,:,0]
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E231: missing whitespace after ','

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E231: missing whitespace after ','

ys = verts[:,:,1]

if c is None:
# We didn't pass anything in for c - use 1/ area of triangle
Expand Down Expand Up @@ -356,7 +360,7 @@ def rendTri(T, imageBounds, pixelSize, c=None, im=None, geometric_mean=False):


def rendJitTri(im, x, y, jsig, mcp, imageBounds, pixelSize, n=1, seed=None):
from matplotlib import tri
from scipy.spatial import Delaunay
np.random.seed(seed)

for i in range(int(n)):
Expand All @@ -367,7 +371,9 @@ def rendJitTri(im, x, y, jsig, mcp, imageBounds, pixelSize, n=1, seed=None):
jsig2 = jsig[Imc]
else:
jsig2 = float(jsig)
T = tri.Triangulation(x[Imc] + jsig2*np.random.randn(Imc.sum()), y[Imc] + jsig2*np.random.randn(Imc.sum()))

T = Delaunay(np.vstack([x[Imc] + jsig2*np.random.randn(Imc.sum()), y[Imc] + jsig2*np.random.randn(Imc.sum())]).T)


rendTri(T, imageBounds, pixelSize, im=im, geometric_mean=False)

Expand All @@ -378,7 +384,7 @@ def rendJitTri(im, x, y, jsig, mcp, imageBounds, pixelSize, n=1, seed=None):


def _rend_jit_tri_geometric(im, x, y, jsig, mcp, imageBounds, pixelSize, n=1, seed=None):
from matplotlib import tri
from scipy.spatial import Delaunay
np.random.seed(seed)

#im_ = numpy.zeros(im.shape, 'f')
Expand All @@ -394,8 +400,8 @@ def _rend_jit_tri_geometric(im, x, y, jsig, mcp, imageBounds, pixelSize, n=1, se
jsig2 = jsig[Imc]
else:
jsig2 = float(jsig)
T = tri.Triangulation(x[Imc] + jsig2 * np.random.randn(Imc.sum()), y[Imc] + jsig2 * np.random.randn(Imc.sum()))


T = Delaunay(np.vstack([x[Imc] + jsig2 * np.random.randn(Imc.sum()), y[Imc] + jsig2 * np.random.randn(Imc.sum())]).T)
rendTri(T, imageBounds, pixelSize, im=im, geometric_mean=True)

#im[:] = (im + (im_))# + 1e9*(im_ <=0)))[:]
Expand Down Expand Up @@ -540,8 +546,11 @@ def rendJitTriang(x,y,n,jsig, mcp, imageBounds, pixelSize, seeds=None, geometric

def rendTri2(T, imageBounds, pixelSize, c=None, im=None, im1=None):
from PYME.Analysis.points.SoftRend import drawTriang, drawTriangles
xs = T.x[T.triangles]
ys = T.y[T.triangles]
#xs = T.x[T.triangles]
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E265: block comment should start with '# '

#ys = T.y[T.triangles]
verts = T.points[T.simplices]
xs = verts[:,:,0]
ys = verts[:,:,1]

a = np.vstack((xs[:, 0] - xs[:, 1], ys[:, 0] - ys[:, 1])).T
b = np.vstack((xs[:, 0] - xs[:, 2], ys[:, 0] - ys[:, 2])).T
Expand Down Expand Up @@ -588,7 +597,7 @@ def rendTri2(T, imageBounds, pixelSize, c=None, im=None, im1=None):
return im, im1

def rendJitTri2(im, im1, x, y, jsig, mcp, imageBounds, pixelSize, n=1):
from matplotlib import tri
from scipy.spatial import Delaunay
np.random.seed()

for i in range(n):
Expand All @@ -601,8 +610,7 @@ def rendJitTri2(im, im1, x, y, jsig, mcp, imageBounds, pixelSize, n=1):
else:
jsig2 = float(jsig)

T = tri.Triangulation(x[Imc] + jsig2*np.random.randn(Imc.sum()), y[Imc] + jsig2*np.random.randn(Imc.sum()))

T = Delaunay(np.vstack([x[Imc] + jsig2*np.random.randn(Imc.sum()), y[Imc] + jsig2*np.random.randn(Imc.sum())]).T)
rendTri2(T, imageBounds, pixelSize, im=im, im1=im1)


Expand Down