def cmktest_inputs3(self):
from pysnptools.pstreader import PstData
np.random.seed(0)
row_property=None
col_property=None
pstdata = PstData(row=[[1.0,2.0],[3,4],[6,7]],
col=np.array([]),
val = [[],[],[]],
row_property=row_property,
col_property=col_property,
name="test_read")
assert pstdata.row_to_index([[3,4]])[0] == 1
assert np.array_equal(pstdata[1:,:2].row_property,pstdata.row_property[1:])
assert np.array_equal(pstdata[1:,:2].col_property,pstdata.col_property[:2])
logging.info("done with test")
def test_inputs3(self):
from pysnptools.pstreader import PstData
np.random.seed(0)
row_property=None
col_property=None
pstdata = PstData(row=[[1.0,2.0],[3,4],[6,7]],
col=np.array([]),
val = [[],[],[]],
row_property=row_property,
col_property=col_property,
name="test_read")
assert pstdata.row_to_index([[3,4]])[0] == 1
assert np.array_equal(pstdata[1:,:2].row_property,pstdata.row_property[1:])
assert np.array_equal(pstdata[1:,:2].col_property,pstdata.col_property[:2])
logging.info("done with test")
def cmktest_inputs2(self):
from pysnptools.pstreader import PstData
np.random.seed(0)
row_property=None
col_property=None
pstdata = PstData(row=np.array([1.0,3,6]),
col=np.array(["Aa","Bb"]),
val = np.random.normal(.5,2,size=(3,2)),
row_property=row_property,
col_property=col_property,
name="test_read")
assert pstdata.row_to_index([3])[0] == 1
assert pstdata.col_to_index(["Aa"])[0] == 0
assert np.array_equal(pstdata[1:,:2].row_property,pstdata.row_property[1:])
assert np.array_equal(pstdata[1:,:2].col_property,pstdata.col_property[:2])
logging.info("done with test")
def test_inputs2(self):
from pysnptools.pstreader import PstData
np.random.seed(0)
row_property=None
col_property=None
pstdata = PstData(row=np.array([1.0,3,6]),
col=np.array(["Aa","Bb"]),
val = np.random.normal(.5,2,size=(3,2)),
row_property=row_property,
col_property=col_property,
name="test_read")
assert pstdata.row_to_index([3])[0] == 1
assert pstdata.col_to_index(["Aa"])[0] == 0
assert np.array_equal(pstdata[1:,:2].row_property,pstdata.row_property[1:])
assert np.array_equal(pstdata[1:,:2].col_property,pstdata.col_property[:2])
logging.info("done with test")
def test_read(self):
np.random.seed(0)
row_property=np.array([[1.0,2,2.5],[3,4,4.5],[5,6,6.5]])
col_property=np.array([[1.0,2,2.5,1],[3,4,4.5,3]])
pstdata = PstData(row=np.array([[1.0,2],[3,4],[5,6]]),
col=np.array([["A","a"],["B","b"]]),
val = np.random.normal(.5,2,size=(3,2)),
row_property=row_property,
col_property=col_property,
name="test_read")
assert pstdata.row_to_index([np.array([3.0,4])])[0] == 1
assert pstdata.col_to_index([np.array(["A","a"])])[0] == 0
assert np.array_equal(pstdata[1:,:2].row_property,row_property[1:])
assert np.array_equal(pstdata[1:,:2].col_property,col_property[:2])
pstdata2 = pstdata[:2,:2].read()
from pysnptools.kernelreader.test import _fortesting_JustCheckExists
_fortesting_JustCheckExists().input(pstdata)
_fortesting_JustCheckExists().input(pstdata2)
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata3 = pstdata[[],:].read()
assert pstdata3.val.shape[0] == 0 and pstdata3.val.shape[1]==2
pstdata.val = pstdata.val.copy(order='F')
pstdata2 = pstdata[:2,:2].read()
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata2 = pstdata[:2,:2].read(order='F')
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata2 = pstdata[:2,:2].read(order='A')
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata2 = pstdata[:2,:2].read(force_python_only=True,dtype=None,order='C')
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata2 = pstdata[:2,:2].read(force_python_only=True,dtype='float32',order='C')
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2].astype(dtype='float32'), decimal=10)
pstdata2 = pstdata[:2,:2].read(force_python_only=True,dtype='float32',order=None)
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2].astype(dtype='float32'), decimal=10)
pstdata2 = pstdata[:2,:2].read(force_python_only=True,dtype=None,order='F')
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata4 = pstdata[::,::].read(force_python_only=True)
np.testing.assert_array_almost_equal(pstdata4.val, pstdata.val, decimal=10)
logging.info("done with test")
def test_read(self):
np.random.seed(0)
row_property=np.array([[1.0,2,2.5],[3,4,4.5],[5,6,6.5]])
col_property=np.array([[1.0,2,2.5,1],[3,4,4.5,3]])
pstdata = PstData(row=np.array([[1.0,2],[3,4],[5,6]]),
col=np.array([["A","a"],["B","b"]]),
val = np.random.normal(.5,2,size=(3,2)),
row_property=row_property,
col_property=col_property,
name="test_read")
assert pstdata.row_to_index([np.array([3.0,4])])[0] == 1
assert pstdata.col_to_index([np.array(["A","a"])])[0] == 0
assert np.array_equal(pstdata[1:,:2].row_property,row_property[1:])
assert np.array_equal(pstdata[1:,:2].col_property,col_property[:2])
pstdata2 = pstdata[:2,:2].read()
from pysnptools.kernelreader.test import _fortesting_JustCheckExists
_fortesting_JustCheckExists().input(pstdata)
_fortesting_JustCheckExists().input(pstdata2)
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata3 = pstdata[[],:].read()
assert pstdata3.val.shape[0] == 0 and pstdata3.val.shape[1]==2
pstdata.val = pstdata.val.copy(order='F')
pstdata2 = pstdata[:2,:2].read()
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata2 = pstdata[:2,:2].read(order='F')
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata2 = pstdata[:2,:2].read(order='A')
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata2 = pstdata[:2,:2].read(force_python_only=True,dtype=None,order='C')
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata2 = pstdata[:2,:2].read(force_python_only=True,dtype='float32',order='C')
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2].astype(dtype='float32'), decimal=10)
pstdata2 = pstdata[:2,:2].read(force_python_only=True,dtype='float32',order=None)
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2].astype(dtype='float32'), decimal=10)
pstdata2 = pstdata[:2,:2].read(force_python_only=True,dtype=None,order='F')
np.testing.assert_array_almost_equal(pstdata2.val, pstdata.val[:2,:2], decimal=10)
pstdata4 = pstdata[::,::].read(force_python_only=True)
np.testing.assert_array_almost_equal(pstdata4.val, pstdata.val, decimal=10)
logging.info("done with test")