VTKio 0.1.0.dev9__tar.gz → 0.1.0.dev11__tar.gz

{vtkio-0.1.0.dev9 → vtkio-0.1.0.dev11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: VTKio
-Version: 0.1.0.dev9
+Version: 0.1.0.dev11
 Summary: A simple package for converting data between VTK files (XML and HDF5) and NumPy arrays.
 Project-URL: Homepage, https://jpmorr.gitlab.io/vtkio
 Project-URL: Documentation, https://jpmorr.gitlab.io/vtkio

{vtkio-0.1.0.dev9 → vtkio-0.1.0.dev11}/examples/ImageData.py

@@ -1,267 +1,267 @@
-#!/usr/bin/env python
-"""
-VTK ImageDtata examples.
-
-Created at 20:22, 26 Apr, 2022
-"""
-
-__author__ = 'J.P. Morrissey'
-__copyright__ = 'Copyright 2022-2025'
-__maintainer__ = 'J.P. Morrissey'
-__email__ = 'morrissey.jp@gmail.com'
-__status__ = 'Development'
-
-# Standard Library
-
-# Imports
-import numpy as np
-
-# Local Sources
-from vtkio.writer import write_vti
-
-
-#%% Image data example
-print("Running ImageData Examples...")
-
-# write blank skeleton file
-write_vti('test_blank_vti_new', whole_extent=[0, 1, 0, 1, 0, 1], piece_extent=[0, 1, 0, 1, 0, 1],
-          spacing=[1, 1, 1], point_data=None, cell_data=None, field_data=None, encoding='ascii')
-
-# --8<-- [start:create_grid_data]
-
-# set numpy seed value so that all arrays contain repeatable numbers
-np.random.seed(77)
-
-# Grid Dimensions / Topology
-nx, ny, nz = 6, 6, 2
-ncells = nx * ny * nz
-npoints = (nx + 1) * (ny + 1) * (nz + 1)
-
-origin = np.array([0, 0, 0])
-num_cells = np.array([nx, ny, nz])
-spacing = np.array([1, 1, 1])
-max_extent = spacing * num_cells
-
-whole_extent = np.array([origin, max_extent]).T.flatten()
-piece_extent = np.array([origin, max_extent]).T.flatten()
-
-# Variables
-temp = np.random.random(npoints)
-multi_component2 = np.random.random((npoints, 2))
-multi_component3 = np.random.random((npoints, 3))
-multi_component4 = np.random.random((npoints, 4))
-force = np.random.random((npoints, 3)) * 20
-stress = np.random.random([npoints, 9]) * 1000
-norms = np.random.random([npoints, 3])
-norms /= np.linalg.norm(norms, axis=1)[:, np.newaxis]
-
-# data for writing for each point or cell is defined in a dict of dicts
-# where the keys represent the DataArray type and the nested keys the
-# DataArray name
-point_data = {"scalars": {"temp": temp,
-                          "2-components": multi_component2,
-                          "3-components": multi_component3,
-                          "4-components": multi_component4},
-              "vectors": {"force": force},
-              "tensors": {"stress": stress},
-              "normals": {"normals": norms},
-}
-
-pressure = np.arange(ncells)
-
-field_data = {'TimeValue': 0.122654987}
-
-# --8<-- [end:create_grid_data]
-
-
-## new version
-# --8<-- [start:write_imagedata_writer_ascii]
-from vtkio.writer.xml_writer import XMLImageDataWriter
-
-
-file = XMLImageDataWriter('test_uniform_image_data.vti',
-                          origin=origin, spacing=spacing,
-                          whole_extent=whole_extent,
-                          piece_extent=piece_extent,
-                          cell_data={"scalars": {"pressure": pressure}},
-                          field_data=field_data,
-                          point_data=point_data)
-
-file.write_xml_file()
-
-# --8<-- [end:write_imagedata_writer_ascii]
-
-# --8<-- [start:write_imagedata_writer_binary]
-
-file = XMLImageDataWriter('test_uniform_image_data.vti',
-                          origin=origin, spacing=spacing,
-                          whole_extent=whole_extent,
-                          piece_extent=piece_extent,
-                          cell_data={"scalars": {"pressure": pressure}},
-                          field_data=field_data,
-                          point_data=point_data,
-                          encoding='binary')
-
-file.write_xml_file()
-
-# --8<-- [end:write_imagedata_writer_binary]
-
-# --8<-- [start:write_imagedata_writer_appended_encoded]
-
-file = XMLImageDataWriter('test_uniform_image_data.vti',
-                          origin=origin, spacing=spacing,
-                          whole_extent=whole_extent,
-                          piece_extent=piece_extent,
-                          cell_data={"scalars": {"pressure": pressure}},
-                          field_data=field_data,
-                          point_data=point_data,
-                          encoding='appended')
-
-file.write_xml_file()
-
-# --8<-- [end:write_imagedata_writer_appended_encoded]
-
-# --8<-- [start:write_imagedata_writer_appended_raw]
-
-file = XMLImageDataWriter('test_uniform_image_data.vti', origin=origin, spacing=spacing,
-                          whole_extent=whole_extent,
-                          piece_extent=piece_extent,
-                          cell_data={"scalars": {"pressure": pressure}},
-                          field_data=field_data,
-                          point_data=point_data,
-                          encoding='appended',
-                          appended_encoding='raw')
-
-file.write_xml_file()
-
-# --8<-- [end:write_imagedata_writer_appended_raw]
-
-# --8<-- [start:write_grid_data_writer_api]
-from vtkio.writer import write_vti
-
-write_vti('test_image_data_grid_new',
-          whole_extent=whole_extent,
-          piece_extent=piece_extent,
-          origin=origin, spacing=spacing,
-          point_data=point_data,
-          cell_data={"scalars": {"pressure": pressure}},
-          field_data=None,
-          encoding='ascii')
-
-write_vti('test_image_data_grid_binary_new',
-          whole_extent=whole_extent,
-          piece_extent=piece_extent,
-          origin=origin, spacing=spacing,
-          point_data=point_data,
-          cell_data={"scalars": {"pressure": pressure}},
-          field_data=None,
-          encoding='binary')
-
-write_vti('test_image_data_grid_raw_appended_new',
-          whole_extent=whole_extent,
-          piece_extent=piece_extent,
-          origin=origin, spacing=spacing,
-          point_data=point_data,
-          cell_data={"scalars": {"pressure": pressure}},
-          field_data=None,
-          encoding='appended',
-          appended_encoding='raw')
-
-write_vti('test_image_data_grid_appended_new',
-          whole_extent=whole_extent,
-          piece_extent=piece_extent,
-          origin=origin, spacing=spacing,
-          point_data=point_data,
-          cell_data={"scalars": {"pressure": pressure}},
-          field_data=None, encoding='appended')
-
-# --8<-- [end:write_grid_data_writer_api]
-
-
-# --8<-- [start:write_grid_data_writer_api_vtkhdf]
-write_vti('test_image_data_grid_appended_new',
-          whole_extent=whole_extent,
-          origin=origin, spacing=spacing,
-          point_data=point_data,
-          cell_data={"scalars": {"pressure": pressure}},
-          field_data=None, file_format='vtkhdf')
-
-# --8<-- [end:write_grid_data_writer_api_vtkhdf]
-
-
-# --8<-- [start:write_grid_data_hl]
-from vtkio.simplified import uniform_grid
-
-uniform_grid('test_uniform_image_data',
-             num_cells=num_cells, spacing=spacing,
-             cell_data={"scalars": {"pressure": pressure}},
-             point_data=point_data)
-
-uniform_grid('test_uniform_image_data_binary',
-             num_cells=num_cells, spacing=spacing,
-             cell_data={"scalars": {"pressure": pressure}},
-             point_data=point_data, encoding='binary')
-
-uniform_grid('test_uniform_image_data_appended',
-             num_cells=num_cells, spacing=spacing,
-             cell_data={"scalars": {"pressure": pressure}},
-             point_data=point_data, encoding='appended')
-
-uniform_grid('test_uniform_image_data_2',
-             num_cells=num_cells, spacing=spacing * 0.45,
-             origin=origin + 0.7312,
-             cell_data={"scalars": {"pressure": pressure}},
-             point_data=point_data,
-             field_data=field_data)
-
-# --8<-- [end:write_grid_data_hl]
-
-#%% test vtkhdf writing with writer
-
-# --8<-- [start:write_imagedata_writer_vtkhdf]
-from vtkio.writer.vtkhdf import VTKHDFImageDataWriter
-
-imagedata_test = VTKHDFImageDataWriter('test_image_data_grid_hdf5',
-                                       whole_extent=whole_extent,
-                                       origin=origin, spacing=spacing,
-                                       field_data=field_data,
-                                       point_data=point_data,
-                                       cell_data={"scalars": {"pressure": pressure}})
-
-imagedata_test.write_vtkhdf_file()
-# --8<-- [end:write_imagedata_writer_vtkhdf]
-
-#%% test vtkhdf writing with hl api
-
-# whole_extent = [0, 3, 0, 3, 0, 3]
-# origin = [0, 0, 0]
-# spacing = [0.1, 0.1, 0.1]
-# direction = [1, 0, 0, 0, 1, 0, 0, 0, 1]
-
-write_vti('test_uniform_image_data_2', whole_extent, origin=origin+0.7312, spacing=spacing*0.45,
-                 cell_data={"scalars": {"pressure": pressure}}, point_data=point_data, field_data=field_data)
-
-#%% VTKHDFImageDataWriter example
-imagedata_test = VTKHDFImageDataWriter('test_image_data_grid_hdf5_new', whole_extent=whole_extent, origin=origin,
-                                       spacing=spacing, field_data=None, point_data=point_data,
-                                       cell_data={"scalars": {"pressure": pressure}})
-
-imagedata_test.write_vtkhdf_file()
-
-
-#%% write vtkhdf file with additional metadata
-from vtkio.reader import read_vtkxml_data
-
-regular_grid_example_data = read_vtkxml_data('../TestData/vti/regular_grid_example.vti')
-structured_points_data = read_vtkxml_data('../TestData/vti/structured_points.vti')
-vase_data = read_vtkxml_data('../TestData/vti/vase.vti')
-
-# --8<-- [start:write_points_writer_api_vtkhdf_additional_metadata]
-from vtkio.writer.vtkhdf import VTKHDFMultiBlockWriter
-
-blocks = {'block1': regular_grid_example_data, 'block2': structured_points_data, 'block3': vase_data,}
-
-writer = VTKHDFMultiBlockWriter('hdf_multiblock_test_imagedata', blocks)
-writer.write_vtkhdf_file()
-
-# --8<-- [end:write_points_writer_api_vtkhdf_additional_metadata]
+#!/usr/bin/env python
+"""
+VTK ImageDtata examples.
+
+Created at 20:22, 26 Apr, 2022
+"""
+
+__author__ = 'J.P. Morrissey'
+__copyright__ = 'Copyright 2022-2025'
+__maintainer__ = 'J.P. Morrissey'
+__email__ = 'morrissey.jp@gmail.com'
+__status__ = 'Development'
+
+# Standard Library
+
+# Imports
+import numpy as np
+
+# Local Sources
+from vtkio.writer import write_vti
+
+
+#%% Image data example
+print("Running ImageData Examples...")
+
+# write blank skeleton file
+write_vti('test_blank_vti_new', whole_extent=[0, 1, 0, 1, 0, 1], piece_extent=[0, 1, 0, 1, 0, 1],
+          spacing=[1, 1, 1], point_data=None, cell_data=None, field_data=None, encoding='ascii')
+
+# --8<-- [start:create_grid_data]
+
+# set numpy seed value so that all arrays contain repeatable numbers
+np.random.seed(77)
+
+# Grid Dimensions / Topology
+nx, ny, nz = 6, 6, 2
+ncells = nx * ny * nz
+npoints = (nx + 1) * (ny + 1) * (nz + 1)
+
+origin = np.array([0, 0, 0])
+num_cells = np.array([nx, ny, nz])
+spacing = np.array([1, 1, 1])
+max_extent = spacing * num_cells
+
+whole_extent = np.array([origin, max_extent]).T.flatten()
+piece_extent = np.array([origin, max_extent]).T.flatten()
+
+# Variables
+temp = np.random.random(npoints)
+multi_component2 = np.random.random((npoints, 2))
+multi_component3 = np.random.random((npoints, 3))
+multi_component4 = np.random.random((npoints, 4))
+force = np.random.random((npoints, 3)) * 20
+stress = np.random.random([npoints, 9]) * 1000
+norms = np.random.random([npoints, 3])
+norms /= np.linalg.norm(norms, axis=1)[:, np.newaxis]
+
+# data for writing for each point or cell is defined in a dict of dicts
+# where the keys represent the DataArray type and the nested keys the
+# DataArray name
+point_data = {"scalars": {"temp": temp,
+                          "2-components": multi_component2,
+                          "3-components": multi_component3,
+                          "4-components": multi_component4},
+              "vectors": {"force": force},
+              "tensors": {"stress": stress},
+              "normals": {"normals": norms},
+}
+
+pressure = np.arange(ncells)
+
+field_data = {'TimeValue': 0.122654987}
+
+# --8<-- [end:create_grid_data]
+
+
+## new version
+# --8<-- [start:write_imagedata_writer_ascii]
+from vtkio.writer.xml_writer import XMLImageDataWriter
+
+
+file = XMLImageDataWriter('test_uniform_image_data.vti',
+                          origin=origin, spacing=spacing,
+                          whole_extent=whole_extent,
+                          piece_extent=piece_extent,
+                          cell_data={"scalars": {"pressure": pressure}},
+                          field_data=field_data,
+                          point_data=point_data)
+
+file.write_xml_file()
+
+# --8<-- [end:write_imagedata_writer_ascii]
+
+# --8<-- [start:write_imagedata_writer_binary]
+
+file = XMLImageDataWriter('test_uniform_image_data.vti',
+                          origin=origin, spacing=spacing,
+                          whole_extent=whole_extent,
+                          piece_extent=piece_extent,
+                          cell_data={"scalars": {"pressure": pressure}},
+                          field_data=field_data,
+                          point_data=point_data,
+                          encoding='binary')
+
+file.write_xml_file()
+
+# --8<-- [end:write_imagedata_writer_binary]
+
+# --8<-- [start:write_imagedata_writer_appended_encoded]
+
+file = XMLImageDataWriter('test_uniform_image_data.vti',
+                          origin=origin, spacing=spacing,
+                          whole_extent=whole_extent,
+                          piece_extent=piece_extent,
+                          cell_data={"scalars": {"pressure": pressure}},
+                          field_data=field_data,
+                          point_data=point_data,
+                          encoding='appended')
+
+file.write_xml_file()
+
+# --8<-- [end:write_imagedata_writer_appended_encoded]
+
+# --8<-- [start:write_imagedata_writer_appended_raw]
+
+file = XMLImageDataWriter('test_uniform_image_data.vti', origin=origin, spacing=spacing,
+                          whole_extent=whole_extent,
+                          piece_extent=piece_extent,
+                          cell_data={"scalars": {"pressure": pressure}},
+                          field_data=field_data,
+                          point_data=point_data,
+                          encoding='appended',
+                          appended_encoding='raw')
+
+file.write_xml_file()
+
+# --8<-- [end:write_imagedata_writer_appended_raw]
+
+# --8<-- [start:write_grid_data_writer_api]
+from vtkio.writer import write_vti
+
+write_vti('test_image_data_grid_new',
+          whole_extent=whole_extent,
+          piece_extent=piece_extent,
+          origin=origin, spacing=spacing,
+          point_data=point_data,
+          cell_data={"scalars": {"pressure": pressure}},
+          field_data=None,
+          encoding='ascii')
+
+write_vti('test_image_data_grid_binary_new',
+          whole_extent=whole_extent,
+          piece_extent=piece_extent,
+          origin=origin, spacing=spacing,
+          point_data=point_data,
+          cell_data={"scalars": {"pressure": pressure}},
+          field_data=None,
+          encoding='binary')
+
+write_vti('test_image_data_grid_raw_appended_new',
+          whole_extent=whole_extent,
+          piece_extent=piece_extent,
+          origin=origin, spacing=spacing,
+          point_data=point_data,
+          cell_data={"scalars": {"pressure": pressure}},
+          field_data=None,
+          encoding='appended',
+          appended_encoding='raw')
+
+write_vti('test_image_data_grid_appended_new',
+          whole_extent=whole_extent,
+          piece_extent=piece_extent,
+          origin=origin, spacing=spacing,
+          point_data=point_data,
+          cell_data={"scalars": {"pressure": pressure}},
+          field_data=None, encoding='appended')
+
+# --8<-- [end:write_grid_data_writer_api]
+
+
+# --8<-- [start:write_grid_data_writer_api_vtkhdf]
+write_vti('test_image_data_grid_appended_new',
+          whole_extent=whole_extent,
+          origin=origin, spacing=spacing,
+          point_data=point_data,
+          cell_data={"scalars": {"pressure": pressure}},
+          field_data=None, file_format='vtkhdf')
+
+# --8<-- [end:write_grid_data_writer_api_vtkhdf]
+
+
+# --8<-- [start:write_grid_data_hl]
+from vtkio.simplified import uniform_grid
+
+uniform_grid('test_uniform_image_data',
+             num_cells=num_cells, spacing=spacing,
+             cell_data={"scalars": {"pressure": pressure}},
+             point_data=point_data)
+
+uniform_grid('test_uniform_image_data_binary',
+             num_cells=num_cells, spacing=spacing,
+             cell_data={"scalars": {"pressure": pressure}},
+             point_data=point_data, encoding='binary')
+
+uniform_grid('test_uniform_image_data_appended',
+             num_cells=num_cells, spacing=spacing,
+             cell_data={"scalars": {"pressure": pressure}},
+             point_data=point_data, encoding='appended')
+
+uniform_grid('test_uniform_image_data_2',
+             num_cells=num_cells, spacing=spacing * 0.45,
+             origin=origin + 0.7312,
+             cell_data={"scalars": {"pressure": pressure}},
+             point_data=point_data,
+             field_data=field_data)
+
+# --8<-- [end:write_grid_data_hl]
+
+#%% test vtkhdf writing with writer
+
+# --8<-- [start:write_imagedata_writer_vtkhdf]
+from vtkio.writer.vtkhdf import VTKHDFImageDataWriter
+
+imagedata_test = VTKHDFImageDataWriter('test_image_data_grid_hdf5',
+                                       whole_extent=whole_extent,
+                                       origin=origin, spacing=spacing,
+                                       field_data=field_data,
+                                       point_data=point_data,
+                                       cell_data={"scalars": {"pressure": pressure}})
+
+imagedata_test.write_vtkhdf_file()
+# --8<-- [end:write_imagedata_writer_vtkhdf]
+
+#%% test vtkhdf writing with hl api
+
+# whole_extent = [0, 3, 0, 3, 0, 3]
+# origin = [0, 0, 0]
+# spacing = [0.1, 0.1, 0.1]
+# direction = [1, 0, 0, 0, 1, 0, 0, 0, 1]
+
+write_vti('test_uniform_image_data_2', whole_extent, origin=origin+0.7312, spacing=spacing*0.45,
+                 cell_data={"scalars": {"pressure": pressure}}, point_data=point_data, field_data=field_data)
+
+#%% VTKHDFImageDataWriter example
+imagedata_test = VTKHDFImageDataWriter('test_image_data_grid_hdf5_new', whole_extent=whole_extent, origin=origin,
+                                       spacing=spacing, field_data=None, point_data=point_data,
+                                       cell_data={"scalars": {"pressure": pressure}})
+
+imagedata_test.write_vtkhdf_file()
+
+
+#%% write vtkhdf file with additional metadata
+from vtkio.reader import read_vtkxml_data
+
+regular_grid_example_data = read_vtkxml_data('../TestData/vti/regular_grid_example.vti')
+structured_points_data = read_vtkxml_data('../TestData/vti/structured_points.vti')
+vase_data = read_vtkxml_data('../TestData/vti/vase.vti')
+
+# --8<-- [start:write_points_writer_api_vtkhdf_additional_metadata]
+from vtkio.writer.vtkhdf import VTKHDFMultiBlockWriter
+
+blocks = {'block1': regular_grid_example_data, 'block2': structured_points_data, 'block3': vase_data,}
+
+writer = VTKHDFMultiBlockWriter('hdf_multiblock_test_imagedata', blocks)
+writer.write_vtkhdf_file()
+
+# --8<-- [end:write_points_writer_api_vtkhdf_additional_metadata]