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Sample usage of cubetools.py
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| import cubetools | |
| # https://gist.github.com/aditya95sriram/8d1fccbb91dae93c4edf31cd6a22510f | |
| # read_cube function reads in cube file as (numpy array, metadata) tuple | |
| data, meta = cubetools.read_cube('demo.cube') | |
| # volumetric data | |
| print data.shape | |
| # (8L, 8L, 8L) | |
| # metadata | |
| print meta['org'] # origin | |
| # [0.0, 0.0, 0.0] | |
| print meta['xvec'], meta['yvec'], meta['zvec'] | |
| # [0.151178, 0.0, 0.0] [0.0, 0.151178, 0.0] [0.0, 0.0, 0.151178] | |
| print meta['atoms'] | |
| # [(6, [6.0, 15.117809, 15.117809, 15.117809])] | |
| # write_cube function writes numpy array and metadata to file | |
| # size information is inferred from numpy array and | |
| # metadata doesn't contain size information | |
| cubetools.write_cube(data[:5,:5,:5], meta, 'new.cube') | |
| # read_imcube function reads in two cube files one containing real component | |
| # of volumetric data and the other containing imaginary component | |
| # as a (numpy complex128 array, metadata) tuple | |
| # retains metadata from file containing real component | |
| data, meta = cubetools.read_imcube('demo.cube', 'demo.cube') | |
| print data.dtype | |
| # complex128 | |
| print data.shape | |
| # (8L, 8L, 8L) | |
| # write_imcube function writes numpy complex128 array and metadata to file | |
| cubetools.write_imcube(data[:5,:5,:5], meta, 'new.real.cube', 'new.imag.cube') |
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| Cubefile created by cubetools.py | |
| source: none | |
| 1 0.000000 0.000000 0.000000 | |
| 8 0.151178 0.000000 0.000000 | |
| 8 0.000000 0.151178 0.000000 | |
| 8 0.000000 0.000000 0.151178 | |
| 6 6.000000 15.117809 15.117809 15.117809 | |
| -2.41160E+00 -1.82970E+00 -1.15690E+00 -1.74140E+00 -3.56050E+00 -5.66240E+00 | |
| -6.87530E+00 -6.41720E+00 | |
| -1.82970E+00 -1.45910E+00 -1.15950E+00 -1.97120E+00 -3.82710E+00 -5.84170E+00 | |
| -6.90200E+00 -6.33450E+00 | |
| -1.15690E+00 -1.15950E+00 -1.53610E+00 -2.74600E+00 -4.58800E+00 -6.29960E+00 | |
| -6.90680E+00 -6.07500E+00 | |
| -1.74140E+00 -1.97120E+00 -2.74600E+00 -4.08810E+00 -5.66240E+00 -6.78160E+00 | |
| -6.70550E+00 -5.64260E+00 | |
| -3.56050E+00 -3.82710E+00 -4.58800E+00 -5.66240E+00 -6.63160E+00 -6.88550E+00 | |
| -6.16260E+00 -5.12310E+00 | |
| -5.66240E+00 -5.84170E+00 -6.29960E+00 -6.78160E+00 -6.88550E+00 -6.33450E+00 | |
| -5.40370E+00 -4.64800E+00 | |
| -6.87530E+00 -6.90200E+00 -6.90680E+00 -6.70550E+00 -6.16260E+00 -5.40370E+00 | |
| -4.73750E+00 -4.24790E+00 | |
| -6.41720E+00 -6.33450E+00 -6.07500E+00 -5.64260E+00 -5.12310E+00 -4.64800E+00 | |
| -4.24790E+00 -3.85840E+00 | |
| -1.82970E+00 -1.45910E+00 -1.15950E+00 -1.97120E+00 -3.82710E+00 -5.84170E+00 | |
| -6.90200E+00 -6.33450E+00 | |
| -1.45910E+00 -1.24750E+00 -1.23370E+00 -2.21890E+00 -4.08810E+00 -6.00790E+00 | |
| -6.91580E+00 -6.24940E+00 | |
| -1.15950E+00 -1.23370E+00 -1.74140E+00 -3.01770E+00 -4.82450E+00 -6.42450E+00 | |
| -6.88550E+00 -5.98700E+00 | |
| -1.97120E+00 -2.21890E+00 -3.01770E+00 -4.34230E+00 -5.84170E+00 -6.83530E+00 | |
| -6.64140E+00 -5.56060E+00 | |
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| -6.07510E+00 -5.06010E+00 | |
| -5.84170E+00 -6.00790E+00 -6.42450E+00 -6.83530E+00 -6.85380E+00 -6.24940E+00 | |
| -5.32940E+00 -4.60590E+00 | |
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| -4.69180E+00 -4.21580E+00 | |
| -6.33450E+00 -6.24940E+00 -5.98700E+00 -5.56060E+00 -5.06010E+00 -4.60590E+00 | |
| -4.21580E+00 -3.83050E+00 | |
| -1.15690E+00 -1.15950E+00 -1.53610E+00 -2.74600E+00 -4.58800E+00 -6.29960E+00 | |
| -6.90680E+00 -6.07500E+00 | |
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| -6.88550E+00 -5.98700E+00 | |
| -1.53610E+00 -1.74140E+00 -2.47840E+00 -3.82710E+00 -5.47050E+00 -6.71360E+00 | |
| -6.76310E+00 -5.72660E+00 | |
| -2.74600E+00 -3.01770E+00 -3.82710E+00 -5.05100E+00 -6.29960E+00 -6.91580E+00 | |
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| -4.56530E+00 -4.12230E+00 | |
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| -4.12230E+00 -3.74960E+00 | |
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| -6.70550E+00 -5.64260E+00 | |
| -1.97120E+00 -2.21890E+00 -3.01770E+00 -4.34230E+00 -5.84170E+00 -6.83530E+00 | |
| -6.64140E+00 -5.56060E+00 | |
| -2.74600E+00 -3.01770E+00 -3.82710E+00 -5.05100E+00 -6.29960E+00 -6.91580E+00 | |
| -6.41700E+00 -5.32930E+00 | |
| -4.08810E+00 -4.34230E+00 -5.05100E+00 -6.00770E+00 -6.78150E+00 -6.81270E+00 | |
| -5.98690E+00 -4.99990E+00 | |
| -5.66240E+00 -5.84170E+00 -6.29960E+00 -6.78150E+00 -6.88540E+00 -6.33440E+00 | |
| -5.40370E+00 -4.64810E+00 | |
| -6.78160E+00 -6.83530E+00 -6.91580E+00 -6.81270E+00 -6.33440E+00 -5.56060E+00 | |
| -4.83520E+00 -4.31310E+00 | |
| -6.70550E+00 -6.64140E+00 -6.41700E+00 -5.98690E+00 -5.40370E+00 -4.83520E+00 | |
| -4.38080E+00 -3.97250E+00 | |
| -5.64260E+00 -5.56060E+00 -5.32930E+00 -4.99990E+00 -4.64810E+00 -4.31310E+00 | |
| -3.97250E+00 -3.62310E+00 | |
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| -3.82710E+00 -4.08810E+00 -4.82450E+00 -5.84170E+00 -6.71350E+00 -6.85380E+00 | |
| -6.07510E+00 -5.06010E+00 | |
| -4.58800E+00 -4.82450E+00 -5.47050E+00 -6.29960E+00 -6.87530E+00 -6.70560E+00 | |
| -5.81230E+00 -4.88760E+00 | |
| -5.66240E+00 -5.84170E+00 -6.29960E+00 -6.78150E+00 -6.88540E+00 -6.33440E+00 | |
| -5.40370E+00 -4.64810E+00 | |
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| -4.94240E+00 -4.38080E+00 | |
| -6.88550E+00 -6.85380E+00 -6.70560E+00 -6.33440E+00 -5.72650E+00 -5.06010E+00 | |
| -4.52620E+00 -4.09160E+00 | |
| -6.16260E+00 -6.07510E+00 -5.81230E+00 -5.40370E+00 -4.94240E+00 -4.52620E+00 | |
| -4.15310E+00 -3.77630E+00 | |
| -5.12310E+00 -5.06010E+00 -4.88760E+00 -4.64810E+00 -4.38080E+00 -4.09160E+00 | |
| -3.77630E+00 -3.46350E+00 | |
| -5.66240E+00 -5.84170E+00 -6.29960E+00 -6.78160E+00 -6.88550E+00 -6.33450E+00 | |
| -5.40370E+00 -4.64800E+00 | |
| -5.84170E+00 -6.00790E+00 -6.42450E+00 -6.83530E+00 -6.85380E+00 -6.24940E+00 | |
| -5.32940E+00 -4.60590E+00 | |
| -6.29960E+00 -6.42450E+00 -6.71360E+00 -6.91580E+00 -6.70560E+00 -5.98700E+00 | |
| -5.12300E+00 -4.48830E+00 | |
| -6.78160E+00 -6.83530E+00 -6.91580E+00 -6.81270E+00 -6.33440E+00 -5.56060E+00 | |
| -4.83520E+00 -4.31310E+00 | |
| -6.88550E+00 -6.85380E+00 -6.70560E+00 -6.33440E+00 -5.72650E+00 -5.06010E+00 | |
| -4.52620E+00 -4.09160E+00 | |
| -6.33450E+00 -6.24940E+00 -5.98700E+00 -5.56060E+00 -5.06010E+00 -4.60580E+00 | |
| -4.21570E+00 -3.83050E+00 | |
| -5.40370E+00 -5.32940E+00 -5.12300E+00 -4.83520E+00 -4.52620E+00 -4.21570E+00 | |
| -3.88620E+00 -3.55230E+00 | |
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| -3.55230E+00 -3.28300E+00 | |
| -6.87530E+00 -6.90200E+00 -6.90680E+00 -6.70550E+00 -6.16260E+00 -5.40370E+00 | |
| -4.73750E+00 -4.24790E+00 | |
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| -4.69180E+00 -4.21580E+00 | |
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| -4.56530E+00 -4.12230E+00 | |
| -6.70550E+00 -6.64140E+00 -6.41700E+00 -5.98690E+00 -5.40370E+00 -4.83520E+00 | |
| -4.38080E+00 -3.97250E+00 | |
| -6.16260E+00 -6.07510E+00 -5.81230E+00 -5.40370E+00 -4.94240E+00 -4.52620E+00 | |
| -4.15310E+00 -3.77630E+00 | |
| -5.40370E+00 -5.32940E+00 -5.12300E+00 -4.83520E+00 -4.52620E+00 -4.21570E+00 | |
| -3.88620E+00 -3.55230E+00 | |
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| -3.59910E+00 -3.32130E+00 | |
| -4.24790E+00 -4.21580E+00 -4.12230E+00 -3.97250E+00 -3.77630E+00 -3.55230E+00 | |
| -3.32130E+00 -3.08730E+00 | |
| -6.41720E+00 -6.33450E+00 -6.07500E+00 -5.64260E+00 -5.12310E+00 -4.64800E+00 | |
| -4.24790E+00 -3.85840E+00 | |
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| -4.21580E+00 -3.83050E+00 | |
| -6.07500E+00 -5.98700E+00 -5.72660E+00 -5.32930E+00 -4.88760E+00 -4.48830E+00 | |
| -4.12230E+00 -3.74960E+00 | |
| -5.64260E+00 -5.56060E+00 -5.32930E+00 -4.99990E+00 -4.64810E+00 -4.31310E+00 | |
| -3.97250E+00 -3.62310E+00 | |
| -5.12310E+00 -5.06010E+00 -4.88760E+00 -4.64810E+00 -4.38080E+00 -4.09160E+00 | |
| -3.77630E+00 -3.46350E+00 | |
| -4.64800E+00 -4.60590E+00 -4.48830E+00 -4.31310E+00 -4.09160E+00 -3.83050E+00 | |
| -3.55230E+00 -3.28300E+00 | |
| -4.24790E+00 -4.21580E+00 -4.12230E+00 -3.97250E+00 -3.77630E+00 -3.55230E+00 | |
| -3.32130E+00 -3.08730E+00 | |
| -3.85840E+00 -3.83050E+00 -3.74960E+00 -3.62310E+00 -3.46350E+00 -3.28300E+00 | |
| -3.08730E+00 -2.87920E+00 |
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