def test_base_row_column(self):
self.assertEqual(BioPlateMatrix._base_row_column("A1"), ("1", "A"))
self.assertEqual(BioPlateMatrix._base_row_column("A[2,5]"),
("[2,5]", "A"))
self.assertEqual(BioPlateMatrix._base_row_column("1[A-C]"),
("1", "[A-C]"))
self.assertEqual(BioPlateMatrix._base_row_column("A-B[1-6]"),
("1-6", "A-B"))
def __getitem__(
self, index: Tuple[Union[int, slice], Union[int, slice], int, str]
) -> np.ndarray:
if isinstance(index, str):
well = BioPlateMatrix(index)
return self[well.row, well.column]
return super(Array, self).__getitem__(index)
def __getitem__(self, index):
if isinstance(index, tuple):
if any(isinstance(i, str) for i in index):
ind = {"top": 0, "bot": 1, "0": 0, "1": 1, 0: 0, 1: 1}
plt = self[ind[index[0]]]
if isinstance(index[1], str):
well = BioPlateMatrix(index[1])
return plt[well.row, well.column]
return super(Inserts, self).__getitem__(index)
def __setitem__(self, index, value):
if isinstance(index, tuple):
if any(isinstance(i, str) for i in index):
ind = {"top": 0, "bot": 1, 0: 0, 1: 1}
plt = self[ind[index[0]]]
if isinstance(index[1], str):
well = BioPlateMatrix(index[1])
plt[index[1]] = value
return
super(Inserts, self).__setitem__(index, value)
def test_general(self):
self.assertEqual(BioPlateMatrix("A2"), bpu.EL("W", 1, 2))
self.assertEqual(BioPlateMatrix("5G"), bpu.EL("W", 7, 5))
self.assertEqual(BioPlateMatrix("B[2,8]"),
bpu.EL("R", 2, slice(2, 9, 1)))
self.assertEqual(BioPlateMatrix("2[B-G]"),
bpu.EL("C", slice(2, 8, 1), 2))
self.assertEqual(BioPlateMatrix("A-G[1-8]"),
bpu.EL("R", slice(1, 8, 1), slice(1, 9, 1)))
self.assertEqual(BioPlateMatrix("1-8[A-G]"),
bpu.EL("C", slice(1, 8, 1), slice(1, 9, 1)))
self.assertEqual(BioPlateMatrix("C"), bpu.EL("R", 3, slice(1, None)))
self.assertEqual(BioPlateMatrix("12"), bpu.EL("C", slice(1, None), 12))
def test_index_row_column(self):
self.assertEqual(BioPlateMatrix._index_row_column("A", "1"),
bpu.EL("W", 1, 1))
self.assertEqual(BioPlateMatrix._index_row_column("D", "10"),
bpu.EL("W", 4, 10))
self.assertEqual(
BioPlateMatrix._index_row_column("D-G", "10"),
bpu.EL("C", slice(4, 8, 1), 10),
)
self.assertEqual(
BioPlateMatrix._index_row_column("G-I", "5-8"),
bpu.EL("R", slice(7, 10, 1), slice(5, 9, 1)),
)
self.assertEqual(BioPlateMatrix._index_row_column("G", "5-8"),
bpu.EL("R", 7, slice(5, 9, 1)))
self.assertEqual(BioPlateMatrix._index_row_column("B-E", "5"),
bpu.EL("C", slice(2, 6, 1), 5))
def __setitem__(
self,
index: Tuple[Union[int, slice], Union[int, slice]],
value: Union[List[int], List[str], int, str],
) -> None:
if isinstance(index, str):
well = BioPlateMatrix(index)
if isinstance(value, list):
plate_shape = self[well.row, well.column].shape
len_plate_shape = len(plate_shape)
if len_plate_shape > 1:
if well.pos == "R":
resh_val = np.reshape(value, (plate_shape[0], 1))
else:
resh_val = value
self[well.row, well.column] = resh_val
return
else:
self[well.row, well.column][: len(value)] = value
return
else:
self[well.row, well.column] = value
return
super(Array, self).__setitem__(index, value)
def test_all_row_column(self):
self.assertEqual(BioPlateMatrix._all_row_column("A"),
bpu.EL("R", 1, slice(1, None)))
self.assertEqual(BioPlateMatrix._all_row_column(3),
bpu.EL("C", slice(1, None), 3))
def test_well_letter_index(self):
self.assertEqual(BioPlateMatrix._well_letter_index("A"), 1)
self.assertEqual(BioPlateMatrix._well_letter_index("G"), 7)
def test_multi_row_column(self):
self.assertEqual(BioPlateMatrix._multi_row_column("A-B"), ("A", "B"))
self.assertEqual(BioPlateMatrix._multi_row_column("C,G"), ("C", "G"))
self.assertEqual(BioPlateMatrix._multi_row_column("U,D"), ("D", "U"))
def test__test_row_or_column(self):
self.assertTrue(BioPlateMatrix._test_row_or_column("A"))
self.assertTrue(BioPlateMatrix._test_row_or_column("12"))
self.assertTrue(BioPlateMatrix._test_row_or_column(10))
def set(self, *args, merge=False):
"""Main entry point to assign value on plate
Parameters
----------
well : dict or str
- if dict, well must contain well identifier as key and value to assign as value.eg : {"A2" : "value", "A[3-6]" : 42}
- if string, well is only a well identifier eg : "G5"
value : list or str or int or float
- if list, value should be presented with multiple well identifer "B-D[2-5]", ["value1", "value2", "value3"]
merge : bool (by default False)
Value on well are not overide but added
Returns
-------
BioPlate : BioPlate
return instance of plate
Exemples
--------
see :ref:`Set-values-on-plate`
"""
well, value = self._args_analyse(*args)
if not isinstance(well, str) and isinstance(well, Iterable):
generator = well.items() if isinstance(well, dict) else well
for key, val in generator:
if merge:
self.set(key, val, merge=True)
else:
self.set(key, val)
return self
well = BioPlateMatrix(str(well))
if isinstance(value, list):
plate_shape = self[well.row, well.column].shape
len_plate_shape = len(plate_shape)
if len_plate_shape > 1:
if well.pos == "R":
resh_val = np.reshape(value, (plate_shape[0], 1))
else:
resh_val = value
if merge:
self[well.row,
well.column] = ncd.add(self[well.row, well.column],
resh_val)
return self
self[well.row, well.column] = resh_val
return self
else:
if merge:
self[well.row, well.column][:len(value)] = ncd.add(
self[well.row, well.column][:len(value)], value)
return self
self[well.row, well.column][:len(value)] = value
return self
if merge:
self[well.row, well.column] = ncd.add(self[well.row, well.column],
value)
return self
self[well.row, well.column] = value
return self