def mod_primary(composite, mod_id, algorithm):
# paths
template = composite.templates.get(name="source") # SOURCE TEMPLATE
# channel
channel, channel_created = composite.channels.get_or_create(name="-primary")
# iterate
for t in range(composite.series.ts):
print(t)
# get markers
markers = composite.experiment.markers.filter(t=t)
primary = np.zeros(composite.series.shape(d=2))
for marker in markers:
primary[marker.r - 3 : marker.r + 2, marker.c - 3 : marker.c + 2] = 255
# make blank image and print dots
gon = composite.gons.create(
experiment=composite.experiment, series=composite.series, channel=channel, template=template
)
gon.id_token = generate_id_token("img", "Gon")
gon.set_origin(0, 0, 0, t)
gon.set_extent(composite.series.rs, composite.series.cs, 1)
gon.array = primary.copy()
gon.save_array(composite.experiment.composite_path, template)
gon.save()
def compose(self):
# composite
composite, composite_created = self.composites.get_or_create(experiment=self.experiment, id_token=generate_id_token('img', 'Composite'))
# templates
for template in self.experiment.templates.all():
composite_template, composite_template_created = composite.templates.get_or_create(name=template.name)
if composite_template_created:
composite_template.rx = template.rx
composite_template.rv = template.rv
composite_template.save()
# iterate over paths
for channel in self.experiment.channels.all():
composite_channel, composite_channel_created = composite.channels.get_or_create(name=channel.name)
for t in range(self.ts):
# path set
path_set = self.paths.filter(channel=channel, t=t)
# if the total number of paths is less than a great gon, do not make one. Save only individual gons.
if path_set.count()==self.zs:
# gon
gon, gon_created = self.gons.get_or_create(experiment=self.experiment, composite=composite, channel=composite_channel, t=t)
if gon_created:
gon.set_origin(0,0,0,t)
gon.set_extent(self.rs, self.cs, self.zs)
for z in range(self.zs):
# path
path = path_set.get(channel=channel, t=t, z=z)
template = composite.templates.get(name=path.template.name)
gon.template = template
gon.paths.get_or_create(composite=composite, channel=composite_channel, template=template, url=path.url, file_name=path.file_name, t=t, z=z)
# sub gon
sub_gon, sub_gon_created = self.gons.get_or_create(experiment=self.experiment, gon=gon, channel=composite_channel, template=template, t=t, z=z)
E = z==self.zs-1 and t==self.ts-1
if sub_gon_created:
# print('step01 | composing {} series {}... channel {} t{} z{}... created.{}'.format(self.experiment.name, self.name, channel.name, t, z, spacer), end='\n' if E else '\r')
sub_gon.set_origin(0,0,z,t)
sub_gon.set_extent(self.rs, self.cs, 1)
sub_gon.paths.create(composite=composite, channel=composite_channel, template=template, url=path.url, file_name=path.file_name, t=t, z=z)
else:
pass
# print('step01 | composing {} series {}... channel {} t{} z{}... already exists.{}'.format(self.experiment.name, self.name, channel.name, t, z, spacer), end='\n' if E else '\r')
sub_gon.save()
gon.save()
else: # disfuse gon structure (reduced, regions)
L = len(path_set) - 1
for i, path in enumerate(path_set):
E = i==L and t==self.ts-1
# print('step01 | composing {} series {}... channel {} t{} z{}... created diffuse.{}'.format(self.experiment.name, self.name, channel.name, t, path.z, spacer), end='\n' if E else '\r')
template = composite.templates.get(name=path.template.name)
gon, gon_created = self.gons.get_or_create(experiment=self.experiment, composite=composite, channel=composite_channel, template=template, t=t, z=path.z)
if gon_created:
gon.set_origin(0,0,path.z,t)
gon.set_extent(self.rs, self.cs, 1)
gon.paths.create(composite=composite, channel=composite_channel, template=template, url=path.url, file_name=path.file_name, t=t, z=path.z)
gon.save()
composite.save()