def insert_stack(self):
s = Stack()
s.title = "Example Stack"
s.image_base = "http://incf.ini.uzh.ch/image-stack-fib/"
s.trakem2_project = False
s.dimension = Integer3D(x=2048, y=1536, z=460)
s.resolution = Double3D(x=5.0001, y=5.0002, z=9.0003)
s.num_zoom_levels = -1
s.file_extension = 'jpg'
s.tile_width = 256
s.tile_height = 256
s.tile_source_type = 1
s.save()
return s
def insert_stack(self):
s = Stack()
s.title = "Example Stack"
s.dimension = Integer3D(x=2048, y=1536, z=460)
s.resolution = Double3D(x=5.0001, y=5.0002, z=9.0003)
s.save()
sm = StackMirror()
sm.stack = s
sm.image_base = "http://incf.ini.uzh.ch/image-stack-fib/"
sm.file_extension = 'jpg'
sm.tile_width = 256
sm.tile_height = 256
sm.tile_source_type = 1
sm.save()
return s
def handle(self, *args, **options):
if not options['user_id']:
raise CommandError("You must specify a user ID with --user")
user = User.objects.get(pk=options['user_id'])
projects: Dict[str, Dict] = {
'Default Project': {
'stacks': []
},
'Evaluation data set': {
'stacks': []
},
'Focussed Ion Beam (FIB)': {
'stacks': []
},
}
# Define the details of a stack for two of these projects:
projects['Default Project']['stacks'].append({
'title':
'Original data.',
'dimension':
Integer3D(4096, 4096, 16),
'resolution':
Double3D(3.2614000000000001, 3.2614000000000001, 60),
'comment':
'''<p>©2007 by Stephan Saalfeld.</p>
<p>Rendered with <a href="http://www.povray.org/">POV-Ray v3.6</a>
using this <a href="http://fly.mpi-cbg.de/~saalfeld/download/volume.tar.bz2">scene-file</a>.</p>''',
'mirrors': [{
'title':
'Public copy',
'image_base':
'http://fly.mpi-cbg.de/map/evaluation/original/',
}]
})
projects['Focussed Ion Beam (FIB)']['stacks'].append({
'title':
'Focussed Ion Beam (FIB) stack of Rat Striatum',
'dimension':
Integer3D(2048, 1536, 460),
'resolution':
Double3D(5, 5, 9),
'comment':
'''
<p>©2009 <a href="http://people.epfl.ch/graham.knott">Graham Knott</a>.</p>
<p>Public INCF data set available at the
<a href="http://www.incf.org/about/nodes/switzerland/data">Swiss INCF Node</a>.</p>''',
'mirrors': [{
'title':
'FIB Public copy',
'image_base':
'http://incf.ini.uzh.ch/image-stack-fib/',
}]
})
# Make sure that each project and its stacks exist, and are
# linked via ProjectStack:
for project_title in projects:
project_object, _ = Project.objects.get_or_create(
title=project_title)
for stack_dict in projects[project_title]['stacks']:
stack, _ = Stack.objects.get_or_create(
title=stack_dict['title'],
defaults={
'dimension': stack_dict['dimension'],
'resolution': stack_dict['resolution'],
})
mirrors = list(StackMirror.objects.filter(stack=stack))
if not mirrors:
for m in stack_dict['mirrors']:
mirrors.append(
StackMirror.objects.create(
stack=stack,
title=m['title'],
image_base=m['image_base']))
ProjectStack.objects.get_or_create(project=project_object,
stack=stack)
projects[project_title]['project_object'] = project_object
# Also set up the FIB project for tracing with treelines:
tracing_project = projects['Focussed Ion Beam (FIB)']['project_object']
call_command('catmaid_setup_tracing_for_project', '--project_id',
str(tracing_project.id), '--user', str(user.id))