mirror of
https://gitlab.kitware.com/vtk/vtk-m
synced 2024-09-08 13:23:51 +00:00
There are numerous scripts and configuration files defined in the CI setup and elsewhere that were missing the copyright statement. Add more types of files to check in the CopyrightStatement test, and update the files with the appropriate statement.
162 lines
6.0 KiB
Python
Executable File
162 lines
6.0 KiB
Python
Executable File
#!/usr/bin/env python3
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##=============================================================================
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##
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## Copyright (c) Kitware, Inc.
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## All rights reserved.
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## See LICENSE.txt for details.
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##
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## This software is distributed WITHOUT ANY WARRANTY; without even
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## the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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## PURPOSE. See the above copyright notice for more information.
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##
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##=============================================================================
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import numpy as np
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import math
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import os
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import sys
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# For readBOV
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from functools import reduce
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import operator
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try:
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import h5py
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USE_HDF = True
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except:
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USE_HDF = False
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def read_file(fn):
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"""
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Read a 3D plain text file from disk into a NumPy array
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"""
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data = np.fromfile(fn, dtype=float, sep=" ")
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data = data[3:].reshape((int(data[2]),int(data[0]),int(data[1])))
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return data
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def readBOV(filename):
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"""
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Read data from a VisIt BOV file
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"""
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with open(filename, 'r') as f:
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header = dict([(lambda x: (x[0].strip().lower(), x[1].strip()))(l.strip().split(':')) for l in f.readlines()])
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if 'data_endian' in header:
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if header['data_endian'].lower() != sys.byteorder:
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print('Unsopported endianess ' + eader['data_endian'].lower())
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return None
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shape = tuple([int(x) for x in header['data_size'].split(' ')])
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count = reduce(operator.mul, shape, 1)
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dtype_map = { 'float': 'float32', 'double': 'float64', 'char': 'uint8' }
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dtype = np.dtype(dtype_map[header['data_format'].lower()])
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dataname = os.path.realpath(os.path.join(os.path.dirname(filename), header['data_file']))
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if 'variable' not in header:
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header['variable'] = 'val'
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return (header['variable'], header['centering'].lower(), np.fromfile(dataname, dtype, count).reshape(tuple(reversed(shape))))
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return None
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def save_piece(fn, array, offset, n_blocks, block_index, size):
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"""
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Save a block from a 3D NumPy array to disk.
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Python order is slice, row, col
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TXT file order is row, col, slice
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offset and size are in file order
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Args:
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fn (str): filename
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array (np.array) : Array with the full data
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offset (tuple) : Tuple of int offsets
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n_blocks (tuple) : Tuple of ints with the number of blocks per dimension
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block_index (tuple) : Tuple of ints with index of the block
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size (tuple) : Tuple of ints with the size of the block in each dimension
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"""
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with open(fn, 'w') as f:
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perm = [1, 2, 0]
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f.write('#GLOBAL_EXTENTS ' + ' '.join(map(str, [array.shape[i] for i in perm])) + '\n')
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f.write('#OFFSET ' + ' '.join(map(str, offset))+'\n')
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f.write('#BLOCKS_PER_DIM ' + ' '.join(map(str, n_blocks))+'\n')
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f.write('#BLOCK_INDEX ' + ' '.join(map(str, block_index))+'\n')
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f.write(' '.join(map(str, size)) + '\n')
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if fn[-5:]=='.bdem':
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array[offset[2]:offset[2]+size[2],offset[0]:offset[0]+size[0],offset[1]:offset[1]+size[1]].astype(np.double).tofile(f)
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else:
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for s in range(offset[2], offset[2]+size[2]):
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np.savetxt(f, array[s, offset[0]:offset[0]+size[0],offset[1]:offset[1]+size[1]], fmt='%.16g')
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f.write('\n')
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def split_points(shape, nblocks):
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"""
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Compute split points for splitting into n blocks:
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Args:
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shape (int): Length of the axis
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nblocks (int): Number of blocks to split the axis into
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Return:
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List of split points along the axis
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"""
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dx = float(shape-1) / nblocks
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return [ math.floor(i*dx) for i in range(nblocks)] + [ shape - 1 ]
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def save_hdf(filename, data, **kwargs):
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"""
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Save the data to HDF5.
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The axes of the data will be transposed and reorded to match the order of save_piece function.
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Args:
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filename (str) : Name fo the HDF5 file
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data (np.array): 3D array with the data
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kwargs (dict) : Dict with keyword arguments for the h5py create_dataset function
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"""
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f = h5py.File(filename, 'w')
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f.create_dataset(name='data', data=np.swapaxes(np.transpose(data), 0, 1), **kwargs)
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if __name__ == '__main__':
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if len(sys.argv) < 2:
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print("Error: Usage split_data_3d.py <filename> <outfilepattern> [<n_blocks_per_axis>|<n_blocks_x> <n_blocks_y> <n_blocks_z>]", file=sys.stderr)
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sys.exit(1)
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# Parse parameters
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in_filename = sys.argv[1]
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name, ext = os.path.splitext(in_filename)
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#out_filename_pattern = name + '_split_%d.txt'
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out_filename_pattern = sys.argv[2]
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n_blocks = (2, 2, 2)
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if len(sys.argv) > 3:
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if len(sys.argv) >= 6:
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n_blocks = (int(sys.argv[3]), int(sys.argv[4]), int(sys.argv[5]))
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else:
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n_blocks = (int(sys.argv[3]), int(sys.argv[3]), int(sys.argv[3]))
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# Read data
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if ext == '.bov':
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data = readBOV(in_filename)[2]
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else:
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data = read_file(in_filename)
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# export to hdf5 as well
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if USE_HDF:
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save_hdf((out_filename_pattern % 0).replace('.txt', '.h5'), data)
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# Python order is slice, row, col
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# Compute split points
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split_points_s = split_points(data.shape[0], n_blocks[2])
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split_points_r = split_points(data.shape[1], n_blocks[0])
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split_points_c = split_points(data.shape[2], n_blocks[1])
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# Create the file that records the slice values
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slice_filename = name + '_slices.txt'
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# Save blocks
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block_no = 0
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for block_index_s, (s_start, s_stop) in enumerate(zip(split_points_s, split_points_s[1:])):
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for block_index_r, (r_start, r_stop) in enumerate(zip(split_points_r, split_points_r[1:])):
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for block_index_c, (c_start, c_stop) in enumerate(zip(split_points_c, split_points_c[1:])):
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n_s = s_stop - s_start + 1
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n_r = r_stop - r_start + 1
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n_c = c_stop - c_start + 1
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save_piece(out_filename_pattern % block_no, data, (r_start, c_start, s_start), n_blocks, (block_index_r, block_index_c, block_index_s), (n_r, n_c, n_s))
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block_no += 1
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