def write(self, em: EmitterSet, ix_low: int, ix_high: int):
"""Write emitter chunk to file."""
if self._last_index == 'including':
ix = f'_{ix_low}_{ix_high}'
elif self._last_index == 'excluding':
ix = f'_{ix_low}_{ix_high - 1}'
else:
raise ValueError
fname = self._path / (self._name + ix + self._suffix)
em.save(fname)
def test_sanity_check(self):
"""Test correct shape of 1D tensors in EmitterSet"""
xyz = torch.rand((10, 3))
phot = torch.rand((10, 1))
frame_ix = torch.rand(10)
with pytest.raises(ValueError):
EmitterSet(xyz, phot, frame_ix)
"""Test correct number of el. in EmitterSet."""
xyz = torch.rand((10, 3))
phot = torch.rand((11, 1))
frame_ix = torch.rand(10)
with pytest.raises(ValueError):
EmitterSet(xyz, phot, frame_ix)
def test_split_in_frames(self, em2d, em3d):
splits = em2d.split_in_frames(None, None)
assert splits.__len__() == 1
splits = em3d.split_in_frames(None, None)
assert em3d.frame_ix.max() - em3d.frame_ix.min() + 1 == len(splits)
"""Test negative numbers in Frame ix."""
neg_frames = EmitterSet(torch.rand((3, 3)), torch.rand(3),
torch.tensor([-1, 0, 1]))
splits = neg_frames.split_in_frames(None, None)
assert splits.__len__() == 3
splits = neg_frames.split_in_frames(0, None)
assert splits.__len__() == 2
def forward(self, output: emitter.EmitterSet, target: emitter.EmitterSet):
"""Setup split in frames. Determine the frame range automatically so as to cover everything."""
if len(output) >= 1 and len(target) >= 1:
frame_low = output.frame_ix.min() if output.frame_ix.min(
) < target.frame_ix.min() else target.frame_ix.min()
frame_high = output.frame_ix.max() if output.frame_ix.max(
) > target.frame_ix.max() else target.frame_ix.max()
elif len(output) >= 1:
frame_low = output.frame_ix.min()
frame_high = output.frame_ix.max()
elif len(target) >= 1:
frame_low = target.frame_ix.min()
frame_high = target.frame_ix.max()
else:
return (emitter.EmptyEmitterSet(xy_unit=target.xyz,
px_size=target.px_size), ) * 4
out_pframe = output.split_in_frames(frame_low.item(),
frame_high.item())
tar_pframe = target.split_in_frames(frame_low.item(),
frame_high.item())
tpl, fpl, fnl, tpml = [], [], [], [
] # true positive list, false positive list, false neg. ...
"""Match the emitters framewise"""
for out_f, tar_f in zip(out_pframe, tar_pframe):
filter_mask = self.filter(out_f.xyz_nm,
tar_f.xyz_nm) # batch implemented
tp_ix, tp_match_ix, tp_ix_bool, tp_match_ix_bool = self._match_kernel(
out_f.xyz_nm, tar_f.xyz_nm, filter_mask) # non batch impl.
tpl.append(out_f[tp_ix])
tpml.append(tar_f[tp_match_ix])
fpl.append(out_f[~tp_ix_bool])
fnl.append(tar_f[~tp_match_ix_bool])
"""Concat them back"""
tp = emitter.EmitterSet.cat(tpl)
fp = emitter.EmitterSet.cat(fpl)
fn = emitter.EmitterSet.cat(fnl)
tp_match = emitter.EmitterSet.cat(tpml)
"""Let tp and tp_match share the same id's. IDs of ground truth are copied to true positives."""
if (tp_match.id == -1).all().item():
tp_match.id = torch.arange(len(tp_match)).type(tp_match.id.dtype)
tp.id = tp_match.id.type(tp.id.dtype)
return self._return_match(tp=tp, fp=fp, fn=fn, tp_match=tp_match)
def test_to_dict(self):
em = RandomEmitterSet(100, xy_unit='nm', px_size=(100., 200.))
"""Check whether doing one round of to_dict and back works"""
em_clone = em.clone()
em_dict = EmitterSet(**em.to_dict())
assert em_clone == em_dict
def test_save_load(self, format, tmpdir):
em = RandomEmitterSet(1000, xy_unit='nm', px_size=(100., 100.))
p = Path(tmpdir / f'em{format}')
em.save(p)
em_load = EmitterSet.load(p)
assert em == em_load, "Reloaded emitterset is not equivalent to inital one."
def em3d():
"""Most basic (i.e. all necessary fields) 3D EmitterSet"""
frames = torch.arange(25, dtype=torch.long)
frames[[0, 1, 2]] = 1
return EmitterSet(xyz=torch.rand((25, 3)),
phot=torch.rand(25),
frame_ix=frames)
def forward(self, features: torch.Tensor):
"""
Forward the feature map through the post processing and return an EmitterSet or a list of EmitterSets.
For the input features we use the following convention:
0 - Detection channel
1 - Photon channel
2 - 'x' channel
3 - 'y' channel
4 - 'z' channel
5 - Background channel
Expecting x and y channels in nano-metres.
Args:
features (torch.Tensor): Features of size :math:`(N, C, H, W)`
Returns:
EmitterSet or list of EmitterSets: Specified by return_format argument, EmitterSet in nano metres.
"""
if self.skip_if(features):
return EmptyEmitterSet(xy_unit=self.xy_unit, px_size=self.px_size)
if features.dim() != 4:
raise ValueError(
"Wrong dimensionality. Needs to be N x C x H x W.")
features = features[:, self.
pphotxyzbg_mapping] # change channel order if needed
p = features[:, [0], :, :]
features = features[:, 1:, :, :] # phot, x, y, z, bg
p_out, feat_out = self._forward_raw_impl(p, features)
feature_list, prob_final, frame_ix = self._frame2emitter(
p_out, feat_out)
frame_ix = frame_ix.squeeze()
return EmitterSet(xyz=feature_list[:, 1:4],
phot=feature_list[:, 0],
frame_ix=frame_ix,
prob=prob_final,
bg=feature_list[:, 4],
xy_unit=self.xy_unit,
px_size=self.px_size)
def test_cat_emittersets(self):
sets = [RandomEmitterSet(50), RandomEmitterSet(20)]
cat_sets = EmitterSet.cat(sets, None, 1)
assert 70 == len(cat_sets)
assert 0 == cat_sets.frame_ix[0]
assert 1 == cat_sets.frame_ix[50]
sets = [RandomEmitterSet(50), RandomEmitterSet(20)]
cat_sets = EmitterSet.cat(sets, torch.tensor([5, 50]), None)
assert 70 == len(cat_sets)
assert 5 == cat_sets.frame_ix[0]
assert 50 == cat_sets.frame_ix[50]
# test correctness of px size and xy unit
sets = [
RandomEmitterSet(50, xy_unit='px', px_size=(100., 200.)),
RandomEmitterSet(20)
]
em = EmitterSet.cat(sets)
assert em.xy_unit == 'px'
assert (em.px_size == torch.tensor([100., 200.])).all()
def em3d_full(em3d):
return EmitterSet(xyz=em3d.xyz,
phot=em3d.phot,
bg=torch.rand_like(em3d.phot) * 100,
frame_ix=em3d.frame_ix,
id=em3d.id,
xyz_sig=torch.rand_like(em3d.xyz),
phot_sig=torch.rand_like(em3d.phot) * em3d.phot.sqrt(),
xyz_cr=torch.rand_like(em3d.xyz)**2,
phot_cr=torch.rand_like(em3d.phot) * em3d.phot.sqrt() *
1.5,
bg_cr=torch.rand_like(em3d.phot),
xy_unit='nm',
px_size=(100., 200.))
def test_chunk(self):
big_em = RandomEmitterSet(100000)
splits = big_em.chunks(10000)
re_merged = EmitterSet.cat(splits)
assert sum([len(e) for e in splits]) == len(big_em)
assert re_merged == big_em
# test not evenly splittable number
em = RandomEmitterSet(7)
splits = em.chunks(3)
assert len(splits[0]) == 3
assert len(splits[1]) == 2
assert len(splits[-1]) == 2
def transform_emitter(em: emitter.EmitterSet,
trafo: dict) -> emitter.EmitterSet:
"""
Transform a set of emitters specified by a transformation dictionary. Returns transformed emitterset.
Args:
em: emitterset to be transformed
trafo: transformation specs
"""
mod_em = em.clone()
"""Set Px Size"""
mod_em.px_size = torch.tensor(
trafo['px_size']) if trafo['px_size'] is not None else mod_em.px_size
"""Modify proper attributes"""
if trafo['xyz_axis'] is not None:
mod_em.xyz = mod_em.xyz[:, trafo['xyz_axis']]
mod_em.xyz_cr = mod_em.xyz_cr[:, trafo['xyz_axis']]
mod_em.xyz_sig = mod_em.xyz_sig[:, trafo['xyz_axis']]
if trafo['xyz_nm_factor'] is not None:
mod_em.xyz_nm *= torch.tensor(trafo['xyz_nm_factor'])
if trafo['xyz_nm_shift'] is not None:
mod_em.xyz_nm += torch.tensor(trafo['xyz_nm_shift'])
if trafo['xyz_px_factor'] is not None:
mod_em.xyz_px *= torch.tensor(trafo['xyz_px_factor'])
if trafo['xyz_px_shift'] is not None:
mod_em.xyz_px += torch.tensor(trafo['xyz_px_shift'])
if trafo['frame_ix_shift'] is not None:
mod_em.frame_ix += torch.tensor(trafo['frame_ix_shift'])
"""Modify unit in which emitter is stored and possibly set px size'"""
if trafo['xy_unit'] is not None:
if trafo['xy_unit'] == 'nm':
mod_em.xyz_nm = mod_em.xyz_nm
elif trafo['xy_unit'] == 'px':
mod_em.xyz_px = mod_em.xyz_px
else:
raise ValueError(f"Unsupported unit ({trafo['xy_unit']}).")
return mod_em
def test_split_cat(self):
"""
Tests whether split and cat (and sort by ID) returns the same result as the original starting.
"""
em = RandomEmitterSet(1000)
em.id = torch.arange(len(em))
em.frame_ix = torch.randint_like(em.frame_ix, 10000)
"""Run"""
em_split = em.split_in_frames(0, 9999)
em_re_merged = EmitterSet.cat(em_split)
"""Assertions"""
# sort both by id
ix = torch.argsort(em.id)
ix_re = torch.argsort(em_re_merged.id)
assert em[ix] == em_re_merged[ix_re]
def forward(self, x: torch.Tensor) -> EmitterSet:
"""
Forward model output tensor through post-processing and return EmitterSet. Will include sigma values in
EmitterSet if mapping was provided initially.
Args:
x: model output
Returns:
EmitterSet
"""
"""Reorder features channel-wise."""
x_mapped = x[:, self.pphotxyzbg_mapping]
"""Filter"""
active_px = self._filter(x_mapped[:,
0]) # 0th ch. is detection channel
prob = x_mapped[:, 0][active_px]
"""Look-Up in channels"""
frame_ix, features = self._lookup_features(x_mapped[:, 1:], active_px)
"""Return EmitterSet"""
xyz = features[1:4].transpose(0, 1)
"""If sigma mapping is present, get those values as well."""
if self.photxyz_sigma_mapping is not None:
sigma = x[:, self.photxyz_sigma_mapping]
_, features_sigma = self._lookup_features(sigma, active_px)
xyz_sigma = features_sigma[1:4].transpose(0, 1).cpu()
phot_sigma = features_sigma[0].cpu()
else:
xyz_sigma = None
phot_sigma = None
return EmitterSet(
xyz=xyz.cpu(),
frame_ix=frame_ix.cpu(),
phot=features[0, :].cpu(),
xyz_sig=xyz_sigma,
phot_sig=phot_sigma,
bg_sig=None,
bg=features[4, :].cpu() if features.size(0) == 5 else None,
prob=prob.cpu(),
xy_unit=self.xy_unit,
px_size=self.px_size)
def test_adjacent_frame_split(self):
xyz = torch.rand((500, 3))
phot = torch.rand_like(xyz[:, 0])
frame_ix = torch.randint_like(xyz[:, 0], low=-1, high=2).int()
em = EmitterSet(xyz, phot, frame_ix)
em_split = em.split_in_frames(-1, 1)
assert (em_split[0].frame_ix == -1).all()
assert (em_split[1].frame_ix == 0).all()
assert (em_split[2].frame_ix == 1).all()
em_split = em.split_in_frames(0, 0)
assert em_split.__len__() == 1
assert (em_split[0].frame_ix == 0).all()
em_split = em.split_in_frames(-1, -1)
assert em_split.__len__() == 1
assert (em_split[0].frame_ix == -1).all()
em_split = em.split_in_frames(1, 1)
assert em_split.__len__() == 1
assert (em_split[0].frame_ix == 1).all()
def em2d():
"""Effectively 2D EmitterSet"""
return EmitterSet(xyz=torch.rand((25, 2)),
phot=torch.rand(25),
frame_ix=torch.zeros(25, dtype=torch.long))