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Merged
merged 2 commits into from
May 19, 2016
Merged

connectivity for the bounding box added #73

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60ea08a
connectivity for the bounding box added
May 19, 2016
b330ef2
connectivity for the bounding box added
May 19, 2016
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50 changes: 24 additions & 26 deletions pygem/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,6 @@
import vtk
import numpy as np

# TODO: add the connectivity to the ffd control points to visualize the lattice.

def write_bounding_box(parameters, outfile, write_deformed=True):
"""
Method that writes a vtk file containing the FFD lattice. This method
Expand All @@ -31,7 +29,7 @@ def write_bounding_box(parameters, outfile, write_deformed=True):
aux_x = np.linspace(0, parameters.lenght_box_x, parameters.n_control_points[0])
aux_y = np.linspace(0, parameters.lenght_box_y, parameters.n_control_points[1])
aux_z = np.linspace(0, parameters.lenght_box_z, parameters.n_control_points[2])
lattice_y_coords, lattice_x_coords, lattice_z_coords = np.meshgrid(aux_y, aux_x, aux_z)
lattice_z_coords, lattice_y_coords, lattice_x_coords = np.meshgrid(aux_z, aux_y, aux_x)

if write_deformed:
box_points = np.array([lattice_x_coords.ravel() + parameters.array_mu_x.ravel() * parameters.lenght_box_x,\
Expand All @@ -40,43 +38,43 @@ def write_bounding_box(parameters, outfile, write_deformed=True):
else:
box_points = np.array([lattice_x_coords.ravel(), lattice_y_coords.ravel(), \
lattice_z_coords.ravel()])

n_rows = box_points.shape[1]

box_points = np.dot(parameters.rotation_matrix, box_points) + \
np.transpose(np.tile(parameters.origin_box, (n_rows, 1)))

_write_vtk_box(box_points, outfile)


def _write_vtk_box(box_points, filename):
_write_vtk_box(box_points, outfile, parameters.n_control_points)
def _write_vtk_box(box_points, filename, dimensions):
"""
Private method that writes a vtk file containing FFD control points.

:param numpy.ndarray box_points: coordinates of the FFD control points.
:param string filename: name of the output file.
:param list dimensions: dimension of the lattice in (x, y, z) directions.
"""
# setup points and vertices
points = vtk.vtkPoints()
vertices = vtk.vtkCellArray()


for index in range(0, box_points.shape[1]):
ind = points.InsertNextPoint(box_points[0, index], box_points[1, index], box_points[2, index])
vertices.InsertNextCell(1)
vertices.InsertCellPoint(ind)

polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.SetVerts(vertices)
polydata.Modified()

writer = vtk.vtkDataSetWriter()

grid = vtk.vtkStructuredGrid()

grid.SetPoints(points)
grid.SetDimensions(dimensions)
grid.Modified()

writer = vtk.vtkStructuredGridWriter()
writer.SetFileName(filename)

if vtk.VTK_MAJOR_VERSION <= 5:
polydata.Update()
writer.SetInput(polydata)
grid.Update()
writer.SetInput(grid)
else:
writer.SetInputData(polydata)

writer.SetInputData(grid)
writer.Write()

25 changes: 6 additions & 19 deletions tests/test_datasets/box_modified_test_sphere_true_version5.vtk
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,24 +1,11 @@
# vtk DataFile Version 3.0
vtk output
ASCII
DATASET POLYDATA
DATASET STRUCTURED_GRID
DIMENSIONS 3 2 2
POINTS 12 float
-20 -55 -45 -4.37166 -55 43.6327 -42.9398 31.9333 -40.9551
-27.3115 31.9333 47.6776 1.40315 -49.1766 -48.774 17.0315 -49.1766 39.8587
-21.5367 37.7568 -44.729 -5.90834 37.7568 43.9037 52.8929 -77.5023 -149.241
38.4346 -43.3531 36.0848 -0.133524 43.5802 -48.503 15.4948 43.5802 40.1297

VERTICES 12 24
1 0
1 1
1 2
1 3
1 4
1 5
1 6
1 7
1 8
1 9
1 10
1 11
-20 -55 -45 1.40315 -49.1766 -48.774 22.8063 -43.3531 -52.5479
-4.37166 -55 43.6327 17.0315 -49.1766 39.8587 38.4346 -43.3531 36.0848
-42.9398 31.9333 -40.9551 -21.5367 37.7568 -44.729 29.9531 9.431 -145.196
-27.3115 31.9333 47.6776 -5.90834 37.7568 43.9037 15.4948 43.5802 40.1297

25 changes: 6 additions & 19 deletions tests/test_datasets/box_modified_test_sphere_true_version6.vtk
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,24 +1,11 @@
# vtk DataFile Version 4.0
vtk output
ASCII
DATASET POLYDATA
DATASET STRUCTURED_GRID
DIMENSIONS 3 2 2
POINTS 12 float
-20 -55 -45 -4.37166 -55 43.6327 -42.9398 31.9333 -40.9551
-27.3115 31.9333 47.6776 1.40315 -49.1766 -48.774 17.0315 -49.1766 39.8587
-21.5367 37.7568 -44.729 -5.90834 37.7568 43.9037 52.8929 -77.5023 -149.241
38.4346 -43.3531 36.0848 -0.133524 43.5802 -48.503 15.4948 43.5802 40.1297

VERTICES 12 24
1 0
1 1
1 2
1 3
1 4
1 5
1 6
1 7
1 8
1 9
1 10
1 11
-20 -55 -45 1.40315 -49.1766 -48.774 22.8063 -43.3531 -52.5479
-4.37166 -55 43.6327 17.0315 -49.1766 39.8587 38.4346 -43.3531 36.0848
-42.9398 31.9333 -40.9551 -21.5367 37.7568 -44.729 29.9531 9.431 -145.196
-27.3115 31.9333 47.6776 -5.90834 37.7568 43.9037 15.4948 43.5802 40.1297

25 changes: 6 additions & 19 deletions tests/test_datasets/box_test_sphere_true_version5.vtk
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,24 +1,11 @@
# vtk DataFile Version 3.0
vtk output
ASCII
DATASET POLYDATA
DATASET STRUCTURED_GRID
DIMENSIONS 3 2 2
POINTS 12 float
-20 -55 -45 -4.37166 -55 43.6327 -42.9398 31.9333 -40.9551
-27.3115 31.9333 47.6776 1.40315 -49.1766 -48.774 17.0315 -49.1766 39.8587
-21.5367 37.7568 -44.729 -5.90834 37.7568 43.9037 22.8063 -43.3531 -52.5479
38.4346 -43.3531 36.0848 -0.133524 43.5802 -48.503 15.4948 43.5802 40.1297

VERTICES 12 24
1 0
1 1
1 2
1 3
1 4
1 5
1 6
1 7
1 8
1 9
1 10
1 11
-20 -55 -45 1.40315 -49.1766 -48.774 22.8063 -43.3531 -52.5479
-4.37166 -55 43.6327 17.0315 -49.1766 39.8587 38.4346 -43.3531 36.0848
-42.9398 31.9333 -40.9551 -21.5367 37.7568 -44.729 -0.133524 43.5802 -48.503
-27.3115 31.9333 47.6776 -5.90834 37.7568 43.9037 15.4948 43.5802 40.1297

25 changes: 6 additions & 19 deletions tests/test_datasets/box_test_sphere_true_version6.vtk
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,24 +1,11 @@
# vtk DataFile Version 4.0
vtk output
ASCII
DATASET POLYDATA
DATASET STRUCTURED_GRID
DIMENSIONS 3 2 2
POINTS 12 float
-20 -55 -45 -4.37166 -55 43.6327 -42.9398 31.9333 -40.9551
-27.3115 31.9333 47.6776 1.40315 -49.1766 -48.774 17.0315 -49.1766 39.8587
-21.5367 37.7568 -44.729 -5.90834 37.7568 43.9037 22.8063 -43.3531 -52.5479
38.4346 -43.3531 36.0848 -0.133524 43.5802 -48.503 15.4948 43.5802 40.1297

VERTICES 12 24
1 0
1 1
1 2
1 3
1 4
1 5
1 6
1 7
1 8
1 9
1 10
1 11
-20 -55 -45 1.40315 -49.1766 -48.774 22.8063 -43.3531 -52.5479
-4.37166 -55 43.6327 17.0315 -49.1766 39.8587 38.4346 -43.3531 36.0848
-42.9398 31.9333 -40.9551 -21.5367 37.7568 -44.729 -0.133524 43.5802 -48.503
-27.3115 31.9333 47.6776 -5.90834 37.7568 43.9037 15.4948 43.5802 40.1297