adds vtkhdf and updates ve #29

pyVEs/bareVE.yml

@@ -9,18 +9,24 @@ name: bareVE
 channels:
   - conda-forge #pyside6
 dependencies:
-  - python=3.10
-  #- python=3.11
   #- python=3.8
+  #- python=3.9
+  #- python=3.10
+  - python=3.11
   - pip
   - pip:
      ### VERSIONS of pyside6: https://pypi.org/project/PySide6/#history
      - pyside6>=6.4.2
      ### VERSIONS of VTK https://gitlab.kitware.com/vtk/vtk/-/tags
+     #- vtk>=9.0.3
+     #- vtk>=9.2.0
      #- vtk>=9.2.5
      - vtk>=9.3.0
      ### VERSIONS of opencv-contrib-python-headless  https://pypi.org/project/opencv-contrib-python-headless/#history
      - opencv-contrib-python-headless>=4.7.0.68
+     #
+     - h5py
+     #- pyvista #https://pypi.org/project/pyvista/#history #https://github.com/pyvista/pyvista/tags
      #- qimage2ndarray
      #- notebook
      #- pandas

vtk/vtkhdf/README.md

@@ -0,0 +1,28 @@
+# VTKHDF files
+https://www.kitware.com/how-to-write-time-dependent-data-in-vtkhdf-files/
+>  October 27, 2023; Lucas Givord and Julien Fausty
+> It can be read into VTK or ParaView master at the moment and will be available in the next release of both : VTK 9.3.0 and ParaView 5.12.0.
+
+## Application
+python vtkpython.py 
+
+## issues
+* python=3.10 with vtk>=9.3.0 in bareVE.yaml; 
+* python=3.11 with vtk>=9.3.0 in bareVE.yaml; 
+* python=3.9 with vtk>=9.3.0 in bareVE.yaml; 
+* python=3.9 with  - vtk>=9.2.5 in bareVE.yaml; 
+* python=3.9 with  - vtk>=9.2.0 in bareVE.yaml; 
+* python=3.8 with  - vtk>=9.2.0 in bareVE.yaml; 
+
+
+```
+Traceback (most recent call last):
+  File "/home/mxochicale/repositories/mxochicale/code/vtk/vtkhdf/vtkpython.py", line 3, in <module>
+    from vtkmodules.vtkFiltersGeneral import (vtkGroupDataSetsFilter,
+ImportError: cannot import name 'vtkSpatioTemporalHarmonicsAttribute' from 'vtkmodules.vtkFiltersGeneral' (/home/mxochicale/mambaforge/envs/bareVE/lib/python3.10/site-packages/vtkmodules/vtkFiltersGeneral.cpython-310-x86_64-linux-gnu.so)
+ImportError: cannot import name 'vtkSpatioTemporalHarmonicsAttribute' from 'vtkmodules.vtkFiltersGeneral' (/home/mxochicale/mambaforge/envs/bareVE/lib/python3.9/site-packages/vtkmodules/vtkFiltersGeneral.cpython-39-x86_64-linux-gnu.so)
+ImportError: cannot import name 'vtkSpatioTemporalHarmonicsAttribute' from 'vtkmodules.vtkFiltersGeneral' (/home/mxochicale/mambaforge/envs/bareVE/lib/python3.9/site-packages/vtkmodules/vtkFiltersGeneral.cpython-39-x86_64-linux-gnu.so)
+ImportError: cannot import name 'vtkSpatioTemporalHarmonicsAttribute' from 'vtkmodules.vtkFiltersGeneral' (/home/mxochicale/mambaforge/envs/bareVE/lib/python3.11/site-packages/vtkmodules/vtkFiltersGeneral.cpython-311-x86_64-linux-gnu.so)
+```
+
+

vtk/vtkhdf/vtkpython.py

@@ -0,0 +1,68 @@
+import numpy as np
+import h5py as h5
+
+from vtkmodules.vtkCommonDataModel import (vtkDataObject,
+                                            vtkPartitionedDataSet,
+                                            vtkPolyData)
+from vtkmodules.vtkFiltersGeneral import vtkGroupDataSetsFilter
+from vtkmodules.vtkFiltersGeneral import vtkWarpScalar
+
+from vtkmodules.vtkFiltersGeneral import vtkSpatioTemporalHarmonicsAttribute
+#https://gitlab.kitware.com/vtk/vtk/-/blob/master/Filters/General/vtkSpatioTemporalHarmonicsAttribute.h
+
+from vtkmodules.vtkFiltersHybrid import vtkGenerateTimeSteps
+from vtkmodules.vtkFiltersSources import vtkSphereSource
+from vtkmodules.util.numpy_support import vtk_to_numpy
+
+
+
+sphere0 = vtkSphereSource()
+sphere0.SetPhiResolution(30)
+sphere0.SetThetaResolution(30)
+sphere0.SetRadius(10)
+
+sphere1 = vtkSphereSource()
+sphere1.SetPhiResolution(30)
+sphere1.SetThetaResolution(30)
+sphere1.SetRadius(10)
+sphere1.SetCenter(15, 15, 15)
+
+# store the spheres in a single partitioned data set
+groupDataSets = vtkGroupDataSetsFilter()
+groupDataSets.AddInputConnection(sphere0.GetOutputPort())
+groupDataSets.AddInputConnection(sphere1.GetOutputPort())
+groupDataSets.SetOutputTypeToPartitionedDataSet()
+
+# generate time steps
+timeSteps = vtkGenerateTimeSteps()
+timeSteps.SetInputConnection(groupDataSets.GetOutputPort())
+timeValues = np.linspace(0.0, 2*np.pi, 100, endpoint=False)
+timeSteps.SetTimeStepValues(100, timeValues)
+
+# generate fields
+addFields = vtkSpatioTemporalHarmonicsAttribute()
+harmonics = np.array([
+ 	[1.0, 1.0, 0.6283, 0.6283, 0.6283, 0.0],
+ 	[3.0, 1.0, 0.6283, 0.0, 0.0, 1.5708],
+ 	[2.0, 2.0, 0.0, 0.6283, 0.0, 3.1416],
+ 	[1.0, 3.0, 0.0, 0.0, 0.6283, 4.7124]
+ 	])
+for iH in range(harmonics.shape[0]):
+	addFields.AddHarmonic(harmonics[iH, 0],
+                      	harmonics[iH, 1],
+                      	harmonics[iH, 2],
+                      	harmonics[iH, 3],
+                      	harmonics[iH, 4],
+                      	harmonics[iH, 5])
+
+addFields.SetInputConnection(timeSteps.GetOutputPort())
+
+# warp spheres
+warp = vtkWarpScalar()
+warp.SetInputConnection(addFields.GetOutputPort())
+warp.SetInputArrayToProcess(0, 0, 0,
+                        	vtkDataObject.FIELD_ASSOCIATION_POINTS,
+                        	'SpatioTemporalHarmonics')
+
+# update the entire thing
+warp.Update()