Hi all, I have slicer version 4.7.0-2017-07-07 r26146 installed. I am trying to convert a numpy 3d array into a new volume. I tried the following as listed in the nightly documentation: resultVolumeNode = getNode(‘fixed’) resultVtkArray = vtk.util.numpy_support.numpy_to_vtk(a, deep=True, arra…

Hi Hailey - If you are creating a new volume from scratch you need to create and initialize the vtkImageData as well as the vtkMRML nodes. Here’s a fully worked out example in this postNRRD method which starts from a nrrd file in memory but it should give you the info you need to adapt to your use…

I’ve added better numpy array adapter methods and added working examples to the wiki: https://www.slicer.org/wiki/Documentation/Nightly/Developers/Python_scripting#Accessing_Volume_data_as_numpy_array The new methods will be available in tomorrow’s nightly build. If you don’t want to wait till the…

import numpy as np import math def some_func(x, y, z): return 0.01*x*x + 0.01*y*y + 0.01*z*z a = np.fromfunction(some_func,(512,512,512)) volumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLScalarVolumeNode') volumeNode.CreateDefaultDisplayNodes() updateVolumeFromArray(volumeNode, a) setSli…

Do you have any question related to this?

[image] Improve the resolution of segment for "import a model" Development What I am doing is to have a boolean opertation between two cylinder created by MakerupToModel. But the segment resolution seems not very well even after “crop volume wih 0.01 spacing scale” just a…

See the script repository for an example how to create a new volume: https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Create_a_new_volume In recent Slicer nightly builds, there is a feature introduced exactly for this, as explained in this post: Improve the resolution of segment …

This is not thread safe, I have tried to process several volumes independently at the same time but it does not work. The linear code works good but when trying to use some parallelization technique the calls to slicer.mrmlScene.AddNewNodeByClass(“vtkMRMLScalarVolumeNode”, nodeName) breaks the flow …

[image] Alex_Vergara: This is not thread safe Yes, of course it is not thread-safe. Thread safety has enormous overhead in complexity of development and also has significant performance impact, so no software component is ever developed thread-safe unless there is a strong reason to do so. Yo…

I dont need synchronization/communication in my problem, I just want to modify one volume with some calculations, then the next, and so on. Therefore there are no interactions between them. Basically this is parallelization, not multi-threading. Slicer should be able to handle this, I mean several c…

[image] Alex_Vergara: Basically this is parallelization, not multi-threading. Multi-threading is parallelization. Read up a bit more on this here . [image] Alex_Vergara: I just want to modify one volume with some calculations, then the next, and so on. Therefore there are no interactions …

Creating Volume from Numpy

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Creating Volume from Numpy

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