class TestDensityMapReader(test.Case):
def setUp(self):
super(TestDensityMapReader, self).setUp()
self.file = self.config.getTestFile('1C3W_10.mrc')
self.reader = DensityMapReader(self.file)
self.rawheader = None
with open(self.file, 'rb') as stream:
self.rawheader = self.reader._rawheader(stream)
def testReadRawHeader(self):
self.assertEqual(len(self.rawheader), DensityMapReader.HEADER_SIZE)
def testReadHeader(self):
density = self.reader.read_header()
self.assertEqual(density.data, None)
self.assertEqual(density.header, self.rawheader)
self.assertEqual(density.origin, [-36.0, -36.0, -36.0])
self.assertEqual(density.shape, (72, 72, 72))
self.assertEqual(density.spacing, (1.0, 1.0, 1.0))
def testRead(self):
density = self.reader.read()
self.assertNotEqual(density.data, None)
self.assertEqual(density.header, self.rawheader)
self.assertEqual(density.origin, [-36.0, -36.0, -36.0])
self.assertEqual(density.shape, (72, 72, 72))
self.assertEqual(density.spacing, (1.0, 1.0, 1.0))
class TestDensityMapWriter(test.Case):
def setUp(self):
super(TestDensityMapWriter, self).setUp()
self.file = self.config.getTestFile('1C3W_10.mrc')
self.writer = DensityMapWriter()
self.reader = DensityMapReader(self.file)
self.density = self.reader.read()
def testWriteDensity(self):
with self.config.getTempStream(mode='b') as temp:
with open(self.file, 'rb') as source:
self.writer.write(temp, self.density)
temp.flush()
if temp.content() != source.read():
self.fail('binary strings differ')
def testReconstructHeader(self):
raw = self.density.header
self.density.header = None
new = self.writer.reconstruct_header(self.density)
original = self.reader._inspect(raw, ByteOrder.NATIVE)
generated = self.reader._inspect(new, ByteOrder.NATIVE)
for o, g in zip(original, generated):
self.assertAlmostEqual(o, g, places=4)
def setUp(self):
super(TestDensityMapWriter, self).setUp()
self.file = self.config.getTestFile('1C3W_10.mrc')
self.writer = DensityMapWriter()
self.reader = DensityMapReader(self.file)
self.density = self.reader.read()
def setUp(self):
super(TestDensityMapReader, self).setUp()
self.file = self.config.getTestFile('1C3W_10.mrc')
self.reader = DensityMapReader(self.file)
self.rawheader = None
with open(self.file, 'rb') as stream:
self.rawheader = self.reader._rawheader(stream)
def run(self):
writer = DensityMapWriter()
self.log('Reading input density map...')
try:
input = DensityMapReader(self.args.mapfile).read()
embd = Deconvolution(input.data, self.args.psf_size)
except DensityMapFormatError as e:
msg = 'Error reading input MRC file: {0}'.format(e)
DeconvolutionApp.exit(msg, code=ExitCodes.INVALID_DATA)
self.log('Running {0} iterations...'.format(self.args.iterations))
self.log(' Iteration Loss Correlation Output')
for i in range(1, self.args.iterations + 1):
embd.run_once()
if i % self.args.output_frequency == 0:
output = OutputPathBuilder(self.args, i)
density = DensityInfo(embd.data,
None,
None,
header=input.header)
writer.write_file(output.fullpath, density)
self.log('{0:>9}. {1:15.2f} {2:10.4f} {3}'.format(
i, embd.loss, embd.correlation, output.filename))
self.log('Done: {0}.'.format(output.fullpath))