def fromString(stringValue):
""" Create an OpticsGroups from string content (STAR format)
"""
f = io.StringIO(stringValue)
t = Table()
t.readStar(f, tableName='optics')
return OpticsGroups(t)
def test_write_singleRow(self):
fn = '/tmp/test-single-row.star'
print("Writing a single row to %s..." % fn)
t = Table()
f1 = StringIO(one_micrograph_mc)
t.readStar(f1, tableName='global_shift')
t.writeStar(sys.stdout, tableName='global_shift', singleRow=True)
t = Table(columns=['rlnImageSizeX',
'rlnImageSizeY',
'rlnMicrographMovieName'])
t.addRow(3710, 3838, 'Movies/14sep05c_00024sq_00003hl_00002es.frames.out.mrc')
with open(fn, 'w') as f:
t.writeStar(f, singleRow=True)
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()
def test_types(self):
""" Tests when providing types dict instead of guessing the type. """
def _checkCols(goldValues, t):
""" Check expected columns and their types. """
for colName, colType in goldValues.items():
col = t.getColumn(colName)
self.assertIsNotNone(col)
self.assertEqual(colType, col.getType())
# Replace the micName to get a number value for that column
micsStr = corrected_micrographs_mc
micsStr = micsStr.replace('MotionCorr/job002/Movies/20170629_000', '')
micsStr = micsStr.replace('_frameImage.mrc', '')
f = StringIO(micsStr)
t = Table()
t.readStar(f, tableName='micrographs')
goldValues = {'rlnCtfPowerSpectrum': str,
'rlnMicrographName': int, # should be integer after replace
'rlnMicrographMetadata': str,
'rlnOpticsGroup': int,
'rlnAccumMotionTotal': float,
'rlnAccumMotionEarly': float,
'rlnAccumMotionLate': float
}
_checkCols(goldValues, t)
# Now parse again the table but force some columns to be str
types = {'rlnMicrographName': str,
'rlnOpticsGroup': str
}
f = StringIO(micsStr)
t.readStar(f, tableName='micrographs', types=types)
goldValues.update(types)
_checkCols(goldValues, t)
def test_addRows(self):
print("Checking addRows...")
t1 = Table()
f1 = StringIO(particles_3d_classify)
t1.readStar(f1)
nRows = len(t1)
lastRow = t1[-1]
values = [378.000000, 2826.000000, 5.360625, 4, -87.35289,
"000100@Extract/job012/Movies/20170629_00021_frameImage.mrcs",
"MotionCorr/job002/Movies/20170629_00021_frameImage.mrc",
1, 4.809192, 0.131159, 10864.146484, 10575.793945, 77.995003, 0.000000,
1.000000, 0.000000, 1, 81.264321, 138.043147, 4.959233, -2.12077,
0.798727, 10937.130965, 0.998434, 5
]
for i in range(1, 4):
values[4] = nRows + 1
t1.addRow(*values)
self.assertEqual(nRows + 3, len(t1))
newLastRow = t1[-1]
self.assertEqual(len(lastRow), len(newLastRow))
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()
