def setUp(self):
f_path = os.path.dirname(os.path.realpath(__file__))
cell_list = load(
os.path.join(f_path, 'test_data', 'test_synth_cell_storm.hdf5'))
icp = IterCellPlot(cell_list)
# Padding
self.cell_list = icp.cell_list
self.icp = IterCellPlot(self.cell_list, pad=False)
self.num = len(self.cell_list)
self.num_st = [
len(cell.data.data_dict['storm']) for cell in self.cell_list
]
self.num_poles = []
self.num_05 = []
for c in self.cell_list:
st_x, st_y = c.data.data_dict['storm']['x'], c.data.data_dict[
'storm']['y']
l, r, phi = c.coords.transform(st_x, st_y)
self.num_poles.append((l == 0).sum() + (l == c.length).sum())
self.num_05.append(
((l > 0.25 * c.length) * (l < 0.75 * c.length)).sum())
self.num_full = np.array(self.num_st) - np.array(self.num_poles)
def setUp(self):
f_path = os.path.dirname(os.path.realpath(__file__))
self.cell_list = load(
os.path.join(f_path, 'test_data', 'test_synth_cell_storm.hdf5'))
self.cell = self.cell_list[0]
data = Data()
data.add_data(self.cell.data.binary_img, 'binary')
self.empty_cell = Cell(data)
def setUp(self):
self.data = load_testdata('ds1')
f_path = os.path.dirname(os.path.realpath(__file__))
self.storm_cells_1 = load(
os.path.join(f_path, 'test_data/test_single_spot_storm.hdf5'))
self.storm_cells_2 = load(
os.path.join(f_path, 'test_data/test_double_spot_storm.hdf5'))
cells_no_flu = []
for c in self.storm_cells_2:
d = Data()
d.add_data(c.data.binary_img, 'binary')
d.add_data(c.data.data_dict['storm_1'], 'storm', 'storm_1')
d.add_data(c.data.data_dict['storm_2'], 'storm', 'storm_2')
cell = Cell(d)
cells_no_flu.append(cell)
self.storm_cells_2_no_flu = CellList(cells_no_flu)
def setUp(self):
f_path = os.path.dirname(os.path.realpath(__file__))
self.cell_list = load(
os.path.join(f_path, 'test_data', 'test_synth_cell_storm.hdf5'))
self.cell = self.cell_list[0]
x = np.arange(20)
y = np.exp(-x / 5)
img_3d = self.cell.data.data_dict['fluorescence'][
np.newaxis, :, :] * y[:, np.newaxis, np.newaxis]
self.cell.data.add_data(img_3d, 'fluorescence', 'flu_3d')
data = Data()
data.add_data(self.cell.data.binary_img, 'binary')
self.empty_cell = Cell(data)
def setUp(self):
f_path = os.path.dirname(os.path.realpath(__file__))
self.cell_list = load(os.path.join(f_path, 'test_data', 'test_synth_cell_storm.hdf5'))
self.num = len(self.cell_list)
self.num_st = np.sum([len(cell.data.data_dict['storm']) for cell in self.cell_list])
self.clp = CellListPlot(self.cell_list)
self.num_poles = 0
self.num_05 = 0
for c in self.cell_list:
st_x, st_y = c.data.data_dict['storm']['x'], c.data.data_dict['storm']['y']
l, r, phi = c.coords.transform(st_x, st_y)
self.num_poles += ((l == 0).sum() + (l == c.length).sum())
self.num_05 += np.sum((l > 0.25 * c.length) * (l < 0.75 * c.length))
self.num_full = self.num_st - self.num_poles
self.model_cell = SynthCell(50, 8, 1e-10)
def test_save_load_cell_list(self):
save('temp_save_celllist.hdf5', self.cell_list)
cell_list_load = load('temp_save_celllist.hdf5')
os.remove('temp_save_celllist.hdf5')
self.assertEqual(len(self.cell_list), len(cell_list_load))
for ci, co in zip(self.cell_list, cell_list_load):
for item in ['r', 'xl', 'xr']:
self.assertEqual(getattr(ci.coords, item),
getattr(co.coords, item))
self.assertEqual(ci.name, co.name)
for p1, p2 in zip(ci.coords.coeff, co.coords.coeff):
self.assertEqual(p1, p2)
self.assertArrayEqual(ci.data.binary_img, co.data.binary_img)
self.assertArrayEqual(ci.data.flu_fluorescence,
co.data.flu_fluorescence)
def test_save_load_cells(self):
save('temp_save.hdf5', self.cell_obj)
cell_obj_load = load('temp_save.hdf5')
os.remove('temp_save.hdf5')
for item in ['r', 'xl', 'xr']:
self.assertEqual(getattr(self.cell_obj.coords, item),
getattr(cell_obj_load.coords, item))
self.assertEqual(self.cell_obj.name, cell_obj_load.name)
for p1, p2 in zip(self.cell_obj.coords.coeff,
cell_obj_load.coords.coeff):
self.assertEqual(p1, p2)
self.assertEqual(self.cell_obj.coords.shape,
cell_obj_load.coords.shape)
self.assertArrayEqual(self.cell_obj.data.binary_img,
cell_obj_load.data.binary_img)
self.assertArrayEqual(self.cell_obj.data.flu_fluorescence,
cell_obj_load.data.flu_fluorescence)
def setUp(self):
f_path = os.path.dirname(os.path.realpath(__file__))
self.cells = load(os.path.join(f_path, 'test_data', 'test_cells.hdf5'))
self.memory = Memory(verbose=0)
self.de_kwargs = {'popsize': 10, 'seed': 42}
def setUp(self):
self.data = load_testdata('ds1')
f_path = os.path.dirname(os.path.realpath(__file__))
self.cells = load(
os.path.join(f_path, 'test_data/test_synth_cell_storm.hdf5'))
self.cell = self.cells[0]
def setUp(self):
f_path = os.path.dirname(os.path.realpath(__file__))
self.cells = load(
os.path.join(f_path, 'test_data', 'test_synth_cell_storm.hdf5'))
def setUp(self):
f_path = os.path.dirname(os.path.realpath(__file__))
self.cells = load(os.path.join(f_path, 'test_data', 'test_cells.hdf5'))
self.de_kwargs = {'popsize': 10, 'recombination': 0.9, 'seed': 42}