<div dir="ltr"><div>Quentan,</div><div><br></div><div>Great, I'm glad that part is solved.</div><div><br></div>Sorry, I don't know why the seemingly odd transpose arguments are needed that way. Maybe someone with more experience converting numpy arrays to VTK arrays can chime in.<div><br></div><div>Thanks,</div><div>Cory</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jul 21, 2015 at 3:58 AM, Quentan Qi <span dir="ltr"><<a href="mailto:quentan@gmail.com" target="_blank">quentan@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Dear Cory,<div><br></div><div>Thank you so much for your explanation! My problem is solved!</div><div><br></div><div>One more thing is the array order in the conversion from numpy array to vtkArray, which should change to [2, 0, 1] instead of [2, 1, 0]. It guarantees the rendering result will not be up-side-down or with other disordered results.</div><div><br></div><div><font face="Courier New">```Python</font></div><div><div><font face="Courier New">vtk_array = numpy_support.numpy_to_vtk(</font></div><div><font face="Courier New"> num_array=quadric_2.transpose(2, 0, 1).ravel(), # was (2, 1, 0)</font></div><div><font face="Courier New"> deep=True,</font></div><div><font face="Courier New"> array_type=vtk.VTK_FLOAT)</font></div></div><div><font face="Courier New">```</font></div><div><br></div><div>It confused me actually that numpy has opposite array order against VTK, but here it seems not. What happened?</div><div><br></div><div>Cheers,</div><div>Quentan</div><div><div class="h5"><div><br></div><div><br><div><blockquote type="cite"><div>On 21 Jul 2015, at 04:07, Cory Quammen <<a href="mailto:cory.quammen@kitware.com" target="_blank">cory.quammen@kitware.com</a>> wrote:</div><br><div><div dir="ltr">Quentan,<div><br></div><div>Thank you for posting the excellent code sample. With it, I could see what the problem was right away.</div><div><br></div><div>The problem is that vtkImageData has the notion of an origin, and you are not setting it. By default, vtkImageData have a corner at (0, 0, 0), but your function in numpy starts at (-1, -1, -1). By not setting the origin to (-1, -1, -1), you are accidentally shifting your data. You'll need to set the origin in your vtk_image_data via</div><div><br></div><div>vtk_image_data.SetOrigin(-1, -1, -1)</div><div><br></div><div>You'll also need to figure out your vtk_image_data's spacing. For the x-component, this can be computed with</div><div><br></div><div>(x_max - x_min) / (x_dim - 1)</div><div><br></div><div>where x_{max, min} are the maximum and minimum x coordinate and x_dim is the number of voxels in the x direction.</div><div><br></div><div>I hope that helps,</div><div>Cory</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Jul 19, 2015 at 1:40 PM, Quentan Qi <span dir="ltr"><<a href="mailto:quentan@gmail.com" target="_blank">quentan@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Dear Cory,<div><br></div><div>I may fail to explain my problem, so I made <a href="https://github.com/quentan/Test_ImageData" target="_blank">an example</a> to show what I want to express, as you suggested. <a href="https://github.com/quentan/Test_ImageData" target="_blank">https://github.com/quentan/Test_ImageData</a></div><div><br></div><div>This example generates a quadric with its implicit form: <font face="Courier New">F(x,y,z) = a0*x^2 + a1*y^2 + a2*z^2 + a3*x*y + a4*y*z + a5*x*z + a6*x + a7*y + a8*z + a9</font> </div><div><br></div><div>The left viewport renders the quadric with vtkQuadric, which works perfectly.</div><div><br></div><div>The right viewport renders the same quadric with a meshgrid generated with numpy. The meshgrid is converted to vtkFloatArray then to vtkImageData. Its shape is right, but locates at wrong position, which seems like it was scaled to some positive values. </div><div><br></div><div>Note the small perpendicular coordinate lines in the corner.</div><div><br></div><div>I guess the issue raises around line 120 - 123. If any other wrongs happen, point it for me, please.</div><div><br></div><div>Cheers,</div><div>Quentan</div><div><br></div><div><br><div><blockquote type="cite"><div><div><div>On 18 Jul 2015, at 15:09, Cory Quammen <<a href="mailto:cory.quammen@kitware.com" target="_blank">cory.quammen@kitware.com</a>> wrote:</div><br></div></div><div><div><div><div dir="ltr">Quentan,<div><br></div><div>vtkImageData is in fact a subclass of vtkDataSet, so no conversion is needed. You said, "<span style="font-size:12.8000001907349px">vtkImageData scales all points to positive integer values", but this should not be the case. Something strange is going on.</span></div><div><span style="font-size:12.8000001907349px"><br></span></div><div><span style="font-size:12.8000001907349px">Could you expand the code above into a complete example that can be run through vtkpython? That will make it easier to take a look. In particular, please add a part that shows the vtkImageData are being scaled to positive integers. It's fine if you fill the array with random values.</span></div><div><span style="font-size:12.8000001907349px"><br></span></div><div><span style="font-size:12.8000001907349px">Thanks,</span></div><div><span style="font-size:12.8000001907349px">Cory</span></div><div><br></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Sat, Jul 18, 2015 at 6:08 AM, Quentan Qi <span dir="ltr"><<a href="mailto:quentan@gmail.com" target="_blank">quentan@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div style="word-wrap:break-word">Hi there,<div><br></div><div>I am going to read a set of discrete 3D points (<font face="Courier New">float</font> value, not <font face="Courier New">int</font> value) and show both the points and the fitting surface via VTK’s implicit functions, say vtkImplicitVolume or vtkImplicitDataSet.</div><div><br></div><div>It works fine of the numpy arrary to vtkImageData conversion in the following code, but is out of my mind how to convert it to vtkDataSet, which is my requirement.</div><div><br></div><div><font face="Courier New">```Python</font></div><div><div><font face="Courier New"> # Convert numpy array to VTK array (vtkFloatArray)</font></div></div><div><font face="Courier New"> vtk_data_array = numpy_support.numpy_to_vtk(</font></div><div><div><font face="Courier New"> num_array=ndarray.transpose(2, 1, 0).ravel(), # ndarray contains the fitting result from the points. It is a 3D array</font></div><div><font face="Courier New"> deep=True,</font></div><div><font face="Courier New"> array_type=vtk.VTK_FLOAT)</font></div><div><font face="Courier New"><br></font></div><div><font face="Courier New"> # Convert the VTK array to vtkImageData</font></div><div><font face="Courier New"> img_vtk = vtk.vtkImageData()</font></div><div><font face="Courier New"> img_vtk.SetDimensions(ndarray.shape)</font></div><div><font face="Courier New"> img_vtk.SetSpacing(spacing[::-1])</font></div><div><font face="Courier New"> img_vtk.GetPointData().SetScalars(vtk_data_array)</font></div></div><div><font face="Courier New"><br></font></div><div><font face="Courier New"> # …</font></div><div><font face="Courier New"><div> implicit_volume = vtk.vtkImplicitVolume() # I want a vtkImplicitDataSet, whose input is a vtkDataSet</div><div> implicit_volume.SetVolume(img_vtk)</div></font></div><div><font face="Courier New">```</font></div><div><br></div><div>Because vtkImageData scales all points to positive integer values so that the rendering result mismatches the original points, I deem vtkDataSet or its subclass can do it. Anybody knows how to convert?</div><div><br></div><div>Cheers,</div><div>Quentan</div></div><br>_______________________________________________<br></div></div>
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<br></span></blockquote></div><span><br><br clear="all"><div><br></div>-- <br><div>Cory Quammen<br>R&D Engineer<br>Kitware, Inc.</div>
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</div></blockquote></div><br></div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div>Cory Quammen<br>R&D Engineer<br>Kitware, Inc.</div>
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</div></blockquote></div><br></div></div></div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature">Cory Quammen<br>R&D Engineer<br>Kitware, Inc.</div>
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