root / ase / test / vtk_data.py @ 13
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#!/usr/bin/env python
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from ase.visualize.vtk import requirevtk, probe_vtk_kilobyte |
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requirevtk() |
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vtk_kilobyte = probe_vtk_kilobyte(1024)
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import numpy as np |
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import sys, unittest, gc |
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from ase.test import CustomTestCase, CustomTextTestRunner |
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from ase.utils.memory import MemoryStatistics, MemorySingleton, shapeopt |
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from vtk import vtkDataArray |
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from ase.visualize.vtk.data import vtkFloatArrayFromNumPyArray, \ |
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vtkDoubleArrayFromNumPyArray, \
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vtkFloatArrayFromNumPyMultiArray, \
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vtkDoubleArrayFromNumPyMultiArray
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# -------------------------------------------------------------------
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class UTConversionDataArrayNumPy(CustomTestCase): |
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"""
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Abstract class with test cases for VTK/NumPy data conversion.
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Leak tests the six possible permutations of deletion order for the
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objects involved in conversion between VTK and NumPy data formats.
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Objects:
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conv: instance of vtkDataArrayFromNumPyBuffer of subclass thereof
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The object in charge of the conversion
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data: NumPy array
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NumPy data with a specific memory footprint
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vtk_da: instance of vtkDataArray of subclass thereof
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VTK data array with a similar memory footprint
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Permutations:
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Case A: 012 i.e. deletion order is conv, data, vtk_da
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Case B: 021 i.e. deletion order is conv, vtk_da, data
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Case C: 102 i.e. deletion order is data, conv, vtk_da
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Case D: 120 i.e. deletion order is data, vtk_da, conv
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Case E: 201 i.e. deletion order is vtk_da, conv, data
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Case F: 210 i.e. deletion order is vtk_da, data, conv
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"""
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footprint = 100*1024**2 |
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dtype = None
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verbose = 0
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gc_threshold = (300,5,5) #default is (700,10,10) |
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gc_flags = gc.DEBUG_LEAK # | gc.DEBUG_STATS
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ctol = -7 #10MB |
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etol = -7 #10MB |
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def setUp(self): |
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self.mem_ini = MemorySingleton(self.verbose-1) |
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self.mem_ref = MemoryStatistics(self.verbose-1) |
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self.mem_cur = self.mem_ref.copy() |
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self.gc_threshold_old = gc.get_threshold()
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self.gc_flags_old = gc.get_debug()
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gc.set_threshold(*self.gc_threshold)
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gc.set_debug(self.gc_flags)
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# Try to obtain a clean slate
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gc.collect() |
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self.gc_count = len(gc.garbage) |
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del gc.garbage[:]
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def tearDown(self): |
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gc.collect() |
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self.assertEqual(len(gc.garbage), self.gc_count) |
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if len(gc.garbage)>0: |
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if self.verbose>1: print gc.get_objects() |
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#TODO be pedantic and fail?
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del gc.garbage[:]
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gc.set_threshold(*self.gc_threshold_old)
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gc.set_debug(self.gc_flags_old)
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def assertAlmostConsumed(self, bytes, digits=0, key='VmSize'): |
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self.mem_cur.update()
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dm = self.mem_cur-self.mem_ref |
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self.assertAlmostEqual(dm[key], bytes, digits) |
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def assertAlmostExceeded(self, bytes, digits=0, key='VmPeak'): |
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self.mem_cur.update()
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dm = self.mem_cur-self.mem_ini |
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#self.assertAlmostEqual(dm[key], bytes, digits) #TODO what really?
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#self.assertAlmostEqual(max(0, dm[key]-bytes), 0, digits) #TODO ???
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#dm = 200 MB, bytes = 100MB ok
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#dm = 101 MB, bytes = 100MB ok
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#dm = 0 MB, bytes = 100MB bad
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def convert_to_vtk_array(self, data): |
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"""Convert an ndarray to a VTK data array.
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data: NumPy array
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NumPy data with a specific memory footprint
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"""
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raise RuntimeError('Virtual member function.') |
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def get_leaktest_scenario(self): |
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"""Construct the necessary conversion objects for leak testing.
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Returns tuple of the form (conv, data, vtk_da,) where:
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conv: instance of vtkDataArrayFromNumPyBuffer of subclass thereof
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The object in charge of the conversion
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data: NumPy array
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NumPy data with a specific memory footprint
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vtk_da: instance of vtkDataArray of subclass thereof
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VTK data array with a similar memory footprint
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"""
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raise RuntimeError('Virtual member function.') |
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# =================================
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def test_deletion_case_a(self): |
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# Case A: 012 i.e. deletion order is conv, data, vtk_da
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(conv, data, vtk_da,) = self.get_leaktest_scenario()
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# Conversion cleanup
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del conv
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self.assertAlmostConsumed(2*self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'Conversion cleanup=', self.mem_cur-self.mem_ref |
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# NumPy cleanup
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del data
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self.assertAlmostConsumed(self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'NumPy cleanup=', self.mem_cur-self.mem_ref |
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# VTK cleanup
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del vtk_da
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self.assertAlmostConsumed(0, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'VTK cleanup=', self.mem_cur-self.mem_ref |
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def test_deletion_case_b(self): |
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# Case B: 021 i.e. deletion order is conv, vtk_da, data
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(conv, data, vtk_da,) = self.get_leaktest_scenario()
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# Conversion cleanup
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del conv
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self.assertAlmostConsumed(2*self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'Conversion cleanup=', self.mem_cur-self.mem_ref |
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# VTK cleanup
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del vtk_da
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self.assertAlmostConsumed(self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'VTK cleanup=', self.mem_cur-self.mem_ref |
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# Numpy cleanup
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del data
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self.assertAlmostConsumed(0, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'NumPy cleanup=', self.mem_cur-self.mem_ref |
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def test_deletion_case_c(self): |
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# Case C: 102 i.e. deletion order is data, conv, vtk_da
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(conv, data, vtk_da,) = self.get_leaktest_scenario()
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# NumPy cleanup
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del data
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self.assertAlmostConsumed(self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'NumPy cleanup=', self.mem_cur-self.mem_ref |
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# Conversion cleanup
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del conv
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self.assertAlmostConsumed(self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'Conversion cleanup=', self.mem_cur-self.mem_ref |
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# VTK cleanup
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del vtk_da
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self.assertAlmostConsumed(0, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'VTK cleanup=', self.mem_cur-self.mem_ref |
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def test_deletion_case_d(self): |
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# Case D: 120 i.e. deletion order is data, vtk_da, conv
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(conv, data, vtk_da,) = self.get_leaktest_scenario()
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# NumPy cleanup
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del data
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self.assertAlmostConsumed(self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'NumPy cleanup=', self.mem_cur-self.mem_ref |
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# VTK cleanup
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del vtk_da
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self.assertAlmostConsumed(self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'VTK cleanup=', self.mem_cur-self.mem_ref |
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# Conversion cleanup
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del conv
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self.assertAlmostConsumed(0, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'Conversion cleanup=', self.mem_cur-self.mem_ref |
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def test_deletion_case_e(self): |
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# Case E: 201 i.e. deletion order is vtk_da, conv, data
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(conv, data, vtk_da,) = self.get_leaktest_scenario()
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# VTK cleanup
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del vtk_da
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self.assertAlmostConsumed(2*self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'VTK cleanup=', self.mem_cur-self.mem_ref |
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# Conversion cleanup
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del conv
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self.assertAlmostConsumed(self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'Conversion cleanup=', self.mem_cur-self.mem_ref |
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# NumPy cleanup
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del data
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self.assertAlmostConsumed(0, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'NumPy cleanup=', self.mem_cur-self.mem_ref |
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def test_deletion_case_f(self): |
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# Case F: 210 i.e. deletion order is vtk_da, data, conv
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(conv, data, vtk_da,) = self.get_leaktest_scenario()
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# VTK cleanup
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del vtk_da
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self.assertAlmostConsumed(2*self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'VTK cleanup=', self.mem_cur-self.mem_ref |
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# NumPy cleanup
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del data
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self.assertAlmostConsumed(self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'NumPy cleanup=', self.mem_cur-self.mem_ref |
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# Conversion cleanup
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del conv
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self.assertAlmostConsumed(0, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'Conversion cleanup=', self.mem_cur-self.mem_ref |
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# -------------------------------------------------------------------
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# class UTDataArrayFromNumPyBuffer(...): TODO
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# -------------------------------------------------------------------
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class UTDataArrayFromNumPyArray_Scalar(UTConversionDataArrayNumPy): |
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"""
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Test cases for memory leaks during VTK/NumPy data conversion.
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Conversion of 1D NumPy array to VTK data array using buffers."""
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def setUp(self): |
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UTConversionDataArrayNumPy.setUp(self)
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self.shape = self.footprint//np.nbytes[self.dtype] |
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def get_leaktest_scenario(self): |
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self.assertAlmostEqual(np.prod(self.shape)*np.nbytes[self.dtype], \ |
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self.footprint, -2) #100B |
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# Update memory reference
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self.mem_ref.update()
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# NumPy allocation
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data = np.empty(self.shape, self.dtype) |
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self.assertAlmostConsumed(self.footprint, self.ctol) |
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self.assertAlmostExceeded(self.footprint, self.etol) |
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if self.verbose>=1: print 'NumPy allocation=', self.mem_cur-self.mem_ref |
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# NumPy to VTK conversion
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np2da = self.convert_to_vtk_array(data)
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self.assertAlmostConsumed(2*self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'Conversion=', self.mem_cur-self.mem_ref |
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# VTK retrieval
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vtk_da = np2da.get_output() |
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self.assertTrue(isinstance(vtk_da, vtkDataArray)) |
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self.assertAlmostEqual(vtk_da.GetActualMemorySize()*vtk_kilobyte, \
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self.footprint, -3) #1kB |
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if self.verbose>=1: print 'VTK retrieval=', self.mem_cur-self.mem_ref |
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return (np2da, data, vtk_da,)
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class UTFloatArrayFromNumPyArray_Scalar(UTDataArrayFromNumPyArray_Scalar): |
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__doc__ = UTDataArrayFromNumPyArray_Scalar.__doc__ |
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dtype = np.float32 |
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convert_to_vtk_array = vtkFloatArrayFromNumPyArray |
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class UTDoubleArrayFromNumPyArray_Scalar(UTDataArrayFromNumPyArray_Scalar): |
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__doc__ = UTDataArrayFromNumPyArray_Scalar.__doc__ |
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dtype = np.float64 |
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convert_to_vtk_array = vtkDoubleArrayFromNumPyArray |
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class UTDataArrayFromNumPyArray_Vector(UTConversionDataArrayNumPy): |
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"""
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Test cases for memory leaks during VTK/NumPy data conversion.
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Conversion of 2D NumPy array to VTK data array using buffers."""
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def setUp(self): |
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UTConversionDataArrayNumPy.setUp(self)
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size = self.footprint//np.nbytes[self.dtype] |
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self.shape = (size//3, 3) |
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def get_leaktest_scenario(self): |
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self.assertAlmostEqual(np.prod(self.shape)*np.nbytes[self.dtype], \ |
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self.footprint, -2) #100B |
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# Update memory reference
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self.mem_ref.update()
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# NumPy allocation
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data = np.empty(self.shape, self.dtype) |
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self.assertAlmostConsumed(self.footprint, self.ctol) |
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self.assertAlmostExceeded(self.footprint, self.etol) |
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if self.verbose>=1: print 'NumPy allocation=', self.mem_cur-self.mem_ref |
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# NumPy to VTK conversion
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np2da = self.convert_to_vtk_array(data)
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self.assertAlmostConsumed(2*self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'Conversion=', self.mem_cur-self.mem_ref |
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# VTK retrieval
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vtk_da = np2da.get_output() |
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self.assertTrue(isinstance(vtk_da, vtkDataArray)) |
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self.assertAlmostEqual(vtk_da.GetActualMemorySize()*vtk_kilobyte, \
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self.footprint, -3) #1kB |
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if self.verbose>=1: print 'VTK retrieval=', self.mem_cur-self.mem_ref |
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return (np2da, data, vtk_da,)
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class UTFloatArrayFromNumPyArray_Vector(UTDataArrayFromNumPyArray_Vector): |
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__doc__ = UTDataArrayFromNumPyArray_Vector.__doc__ |
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dtype = np.float32 |
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convert_to_vtk_array = vtkFloatArrayFromNumPyArray |
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class UTDoubleArrayFromNumPyArray_Vector(UTDataArrayFromNumPyArray_Vector): |
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__doc__ = UTDataArrayFromNumPyArray_Vector.__doc__ |
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dtype = np.float64 |
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convert_to_vtk_array = vtkDoubleArrayFromNumPyArray |
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# -------------------------------------------------------------------
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class UTDataArrayFromNumPyMultiArray_Scalar(UTConversionDataArrayNumPy): |
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"""
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Test cases for memory leaks during VTK/NumPy data conversion.
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Conversion of NumPy grid scalars to VTK data array using buffers."""
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def setUp(self): |
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UTConversionDataArrayNumPy.setUp(self)
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size = self.footprint//np.nbytes[self.dtype] |
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digits, shape = shapeopt(1000, size, ndims=3, ecc=0.3) |
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if self.verbose>=1: print 'digits=%8.3f, shape=%s' % (digits,shape) |
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self.shape = shape + (1,) |
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self.assertAlmostEqual(np.prod(self.shape)*np.nbytes[self.dtype], \ |
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self.footprint, -4) #10kB |
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def get_leaktest_scenario(self): |
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# Update memory reference
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self.mem_ref.update()
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# NumPy allocation
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data = np.empty(self.shape, self.dtype) |
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self.assertAlmostConsumed(self.footprint, self.ctol) |
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self.assertAlmostExceeded(self.footprint, self.etol) |
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if self.verbose>=1: print 'NumPy allocation=', self.mem_cur-self.mem_ref |
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# NumPy to VTK conversion
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np2da = self.convert_to_vtk_array(data)
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self.assertAlmostConsumed(2*self.footprint, self.ctol) |
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self.assertAlmostExceeded(2*self.footprint, self.etol) |
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if self.verbose>=1: print 'Conversion=', self.mem_cur-self.mem_ref |
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# VTK retrieval
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vtk_da = np2da.get_output() |
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self.assertTrue(isinstance(vtk_da, vtkDataArray)) |
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self.assertAlmostEqual(vtk_da.GetActualMemorySize()*vtk_kilobyte, \
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self.footprint, -4) #10kB |
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if self.verbose>=1: print 'VTK retrieval=', self.mem_cur-self.mem_ref |
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return (np2da, data, vtk_da,)
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class UTFloatArrayFromNumPyMultiArray_Scalar(UTDataArrayFromNumPyMultiArray_Scalar): |
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__doc__ = UTDataArrayFromNumPyMultiArray_Scalar.__doc__ |
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dtype = np.float32 |
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convert_to_vtk_array = vtkFloatArrayFromNumPyMultiArray |
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class UTDoubleArrayFromNumPyMultiArray_Scalar(UTDataArrayFromNumPyMultiArray_Scalar): |
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__doc__ = UTDataArrayFromNumPyMultiArray_Scalar.__doc__ |
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dtype = np.float64 |
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convert_to_vtk_array = vtkDoubleArrayFromNumPyMultiArray |
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class UTDataArrayFromNumPyMultiArray_Vector(UTConversionDataArrayNumPy): |
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"""
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Test cases for memory leaks during VTK/NumPy data conversion.
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Conversion of NumPy grid vectors to VTK data array using buffers."""
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def setUp(self): |
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UTConversionDataArrayNumPy.setUp(self)
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size = self.footprint//np.nbytes[self.dtype] |
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digits, shape = shapeopt(1000, size//3, ndims=3, ecc=0.3) |
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if self.verbose>=1: print 'digits=%8.3f, shape=%s' % (digits,shape) |
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self.shape = shape + (3,) |
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self.assertAlmostEqual(np.prod(self.shape)*np.nbytes[self.dtype], \ |
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self.footprint, -4) #10kB |
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|
| 419 |
def get_leaktest_scenario(self): |
| 420 |
|
| 421 |
# Update memory reference
|
| 422 |
self.mem_ref.update()
|
| 423 |
|
| 424 |
# NumPy allocation
|
| 425 |
data = np.empty(self.shape, self.dtype) |
| 426 |
self.assertAlmostConsumed(self.footprint, self.ctol) |
| 427 |
self.assertAlmostExceeded(self.footprint, self.etol) |
| 428 |
if self.verbose>=1: print 'NumPy allocation=', self.mem_cur-self.mem_ref |
| 429 |
|
| 430 |
# NumPy to VTK conversion
|
| 431 |
np2da = self.convert_to_vtk_array(data)
|
| 432 |
self.assertAlmostConsumed(2*self.footprint, self.ctol) |
| 433 |
self.assertAlmostExceeded(2*self.footprint, self.etol) |
| 434 |
if self.verbose>=1: print 'Conversion=', self.mem_cur-self.mem_ref |
| 435 |
|
| 436 |
# VTK retrieval
|
| 437 |
vtk_da = np2da.get_output() |
| 438 |
self.assertTrue(isinstance(vtk_da, vtkDataArray)) |
| 439 |
self.assertAlmostEqual(vtk_da.GetActualMemorySize()*vtk_kilobyte, \
|
| 440 |
self.footprint, -4) #10kB |
| 441 |
if self.verbose>=1: print 'VTK retrieval=', self.mem_cur-self.mem_ref |
| 442 |
|
| 443 |
return (np2da, data, vtk_da,)
|
| 444 |
|
| 445 |
class UTFloatArrayFromNumPyMultiArray_Vector(UTDataArrayFromNumPyMultiArray_Vector): |
| 446 |
__doc__ = UTDataArrayFromNumPyMultiArray_Vector.__doc__ |
| 447 |
dtype = np.float32 |
| 448 |
convert_to_vtk_array = vtkFloatArrayFromNumPyMultiArray |
| 449 |
|
| 450 |
class UTDoubleArrayFromNumPyMultiArray_Vector(UTDataArrayFromNumPyMultiArray_Vector): |
| 451 |
__doc__ = UTDataArrayFromNumPyMultiArray_Vector.__doc__ |
| 452 |
dtype = np.float64 |
| 453 |
convert_to_vtk_array = vtkDoubleArrayFromNumPyMultiArray |
| 454 |
|
| 455 |
# -------------------------------------------------------------------
|
| 456 |
|
| 457 |
if __name__ in ['__main__', '__builtin__']: |
| 458 |
# We may have been imported by test.py, if so we should redirect to logfile
|
| 459 |
if __name__ == '__builtin__': |
| 460 |
testrunner = CustomTextTestRunner('vtk_data.log', verbosity=2) |
| 461 |
else:
|
| 462 |
testrunner = unittest.TextTestRunner(stream=sys.stdout, verbosity=2)
|
| 463 |
|
| 464 |
testcases = [UTFloatArrayFromNumPyArray_Scalar, \ |
| 465 |
UTDoubleArrayFromNumPyArray_Scalar, \ |
| 466 |
UTFloatArrayFromNumPyArray_Vector, \ |
| 467 |
UTDoubleArrayFromNumPyArray_Vector, \ |
| 468 |
UTFloatArrayFromNumPyMultiArray_Scalar, \ |
| 469 |
UTDoubleArrayFromNumPyMultiArray_Scalar, \ |
| 470 |
UTFloatArrayFromNumPyMultiArray_Vector, \ |
| 471 |
UTDoubleArrayFromNumPyMultiArray_Vector] |
| 472 |
|
| 473 |
for test in testcases: |
| 474 |
info = '\n' + test.__name__ + '\n' + test.__doc__.strip('\n') + '\n' |
| 475 |
testsuite = unittest.defaultTestLoader.loadTestsFromTestCase(test) |
| 476 |
testrunner.stream.writeln(info) |
| 477 |
testresult = testrunner.run(testsuite) |
| 478 |
# Provide feedback on failed tests if imported by test.py
|
| 479 |
if __name__ == '__builtin__' and not testresult.wasSuccessful(): |
| 480 |
raise SystemExit('Test failed. Check vtk_data.log for details.') |
| 481 |
|