def test_iterRows(self):
print("Checking iterRows...")
dataFile = testfile('star', 'refine3d', 'run_it016_data.star')
table = Table(fileName=dataFile, tableName='particles')
# Let's open again the same file for iteration
with open(dataFile) as f:
tableReader = Table.Reader(f, tableName='particles')
for c1, c2 in zip(table.getColumns(), tableReader.getColumns()):
self.assertEqual(c1, c2, "Column c1 (%s) differs from c2 (%s)"
% (c1, c2))
for r1, r2 in zip(table, tableReader):
self.assertEqual(r1, r2)
# Now try directly with iterRows function
for r1, r2 in zip(table,
Table.iterRows(dataFile, tableName='particles')):
self.assertEqual(r1, r2)
defocusSorted = sorted(float(r.rlnDefocusU) for r in table)
for d1, row in zip(defocusSorted,
Table.iterRows(dataFile,
tableName='particles',
key=lambda r: r.rlnDefocusU)):
self.assertAlmostEqual(d1, row.rlnDefocusU)
# Test sorting by imageName column, also using getColumnValues and sort()
imageIds = table.getColumnValues('rlnImageName')
imageIds.sort()
# Check sorted iteration give the total amount of rows
rows = [r for r in Table.iterRows(dataFile,
tableName='particles',
key='rlnImageName')]
self.assertEqual(len(imageIds), len(rows))
for id1, row in zip(imageIds,
Table.iterRows(dataFile,
tableName='particles',
key='rlnImageName')):
self.assertEqual(id1, row.rlnImageName)
def getIter():
""" Test a function to get an iterator. """
return Table.iterRows(dataFile,
tableName='particles', key='rlnImageName')
iterByIds = getIter()
for id1, row in zip(imageIds, iterByIds):
self.assertEqual(id1, row.rlnImageName)
def test_read_blocks(self):
"""
Read an star file with several blocks
"""
print("Reading micrograph star file...")
t1 = Table()
f1 = StringIO(one_micrograph_mc)
# This is a single-row table (different text format key, value)
print("\tread data_general ..")
t1.readStar(f1, tableName='general')
goldValues = [('rlnImageSizeX', 3710),
('rlnImageSizeY', 3838),
('rlnImageSizeZ', 24),
('rlnMicrographMovieName', 'Movies/20170629_00027_frameImage.tiff'),
('rlnMicrographGainName', 'Movies/gain.mrc'),
('rlnMicrographBinning', 1.000000),
('rlnMicrographOriginalPixelSize', 0.885000),
('rlnMicrographDoseRate', 1.277000),
('rlnMicrographPreExposure', 0.000000),
('rlnVoltage', 200.000000),
('rlnMicrographStartFrame', 1),
('rlnMotionModelVersion', 1)
]
self._checkColumns(t1, [k for k, v in goldValues])
row = t1[0]
for k, v in goldValues:
self.assertEqual(getattr(row, k), v, "data_general table check failed!")
print("\tread data_global_shift ..")
t1.readStar(f1, tableName='global_shift')
cols = t1.getColumns()
self.assertEqual(len(t1), 24, "Number of rows check failed!")
self._checkColumns(t1, ['rlnMicrographFrameNumber',
'rlnMicrographShiftX',
'rlnMicrographShiftY'])
print("\tread data_local_motion_model ..")
t1.readStar(f1, tableName='local_motion_model')
self.assertEqual(len(t1), 36, "Number of rows check failed!")
self._checkColumns(t1, ['rlnMotionModelCoeffsIdx',
'rlnMotionModelCoeff'])
coeffs = [int(v) for v in t1.getColumnValues('rlnMotionModelCoeffsIdx')]
self.assertEqual(coeffs, list(range(36)), "rlnMotionModelCoeffsIdx check failed")
f1.close()
def test_read_particles(self):
"""
Read from a particles .star file
"""
print("Reading particles star file...")
t1 = Table()
f1 = StringIO(particles_3d_classify)
t1.readStar(f1)
cols = t1.getColumns()
self.assertEqual(len(t1), 16, "Number of rows check failed!")
self.assertEqual(len(cols), 25, "Number of columns check failed!")
# Check that all rlnOpticsGroup is 1 and rlnImageName file is the same
for i, row in enumerate(t1):
self.assertEqual(row.rlnOpticsGroup, 1, "rlnOpticsGroup check failed!")
self.assertEqual(row.rlnImageName.split("@")[1], "Extract/job012/Movies/20170629_00021_frameImage.mrcs",
"rlnImageId check failed!")
f1.close()
