def __init__(self, user, project_id, stack_mirror_ids, x_min,
x_max, y_min, y_max, z_min, z_max, rotation_cw, zoom_level,
single_channel=False, output_path=None):
self.user = user
self.project_id = int(project_id)
self.project = get_object_or_404(Project, pk=project_id)
# Allow a single ID and a list
if isinstance(stack_mirror_ids, int):
self.stack_mirror_ids= [stack_mirror_ids]
else:
self.stack_mirror_ids = stack_mirror_ids
self.stack_mirrors = []
self.stack_tile_sources = {}
for sid in self.stack_mirror_ids:
stack_mirror = get_object_or_404(StackMirror, pk=sid)
self.stack_mirrors.append(stack_mirror)
tile_source = get_tile_source(stack_mirror.tile_source_type)
self.stack_tile_sources[stack_mirror.stack.id] = tile_source
# The reference stack is used to obtain e.g. resolution information
self.ref_stack = self.stack_mirrors[0].stack
self.x_min = float(x_min)
self.x_max = float(x_max)
self.y_min = float(y_min)
self.y_max = float(y_max)
self.z_min = float(z_min)
self.z_max = float(z_max)
self.zoom_level = int(zoom_level)
# Save a normalized version of the rotation angle
self.rotation_cw = rotation_cw % 360
# Create an output path if not already present
if output_path is None:
file_name = file_prefix + id_generator() + "." + file_extension
output_path = os.path.join(crop_output_path, file_name)
self.single_channel = single_channel
self.output_path = output_path
def __init__(self, user, project_id, stack_mirror_ids, x_min,
x_max, y_min, y_max, z_min, z_max, rotation_cw, zoom_level,
single_channel=False, output_path=None):
self.user = user
self.project_id = int(project_id)
self.project = get_object_or_404(Project, pk=project_id)
# Allow a single ID and a list
if isinstance(stack_mirror_ids, int):
self.stack_mirror_ids= [stack_mirror_ids]
else:
self.stack_mirror_ids = stack_mirror_ids
self.stack_mirrors:List = []
self.stack_tile_sources:Dict = {}
for sid in self.stack_mirror_ids:
stack_mirror = get_object_or_404(StackMirror, pk=sid)
self.stack_mirrors.append(stack_mirror)
tile_source = get_tile_source(stack_mirror.tile_source_type)
self.stack_tile_sources[stack_mirror.stack.id] = tile_source
# The reference stack is used to obtain e.g. resolution information
self.ref_stack = self.stack_mirrors[0].stack
self.x_min = float(x_min)
self.x_max = float(x_max)
self.y_min = float(y_min)
self.y_max = float(y_max)
self.z_min = float(z_min)
self.z_max = float(z_max)
self.zoom_level = int(zoom_level)
# Save a normalized version of the rotation angle
self.rotation_cw = rotation_cw % 360
# Create an output path if not already present
if output_path is None:
file_name = file_prefix + id_generator() + "." + file_extension
output_path = os.path.join(crop_output_path, file_name)
self.single_channel = single_channel
self.output_path = output_path
def crop(request: HttpRequest, project_id=None) -> JsonResponse:
""" Crops out the specified region of the stack. The region is expected to
be given in terms of real world units (e.g. nm).
"""
stack_ids = get_request_list(request.POST, "stack_ids", [], int)
x_min = float(request.POST['min_x'])
y_min = float(request.POST['min_y'])
z_min = float(request.POST['min_z'])
x_max = float(request.POST['max_x'])
y_max = float(request.POST['max_y'])
z_max = float(request.POST['max_z'])
zoom_level = float(request.POST['zoom_level'])
single_channel = get_request_bool(request.POST, 'single_channel', False)
rotation_cw = float(request.GET.get('rotationcw', 0.0))
# Make sure tmp dir exists and is writable
if not os.path.exists(crop_output_path) or not os.access(
crop_output_path, os.W_OK):
if request.user.is_superuser:
err_message = "Please make sure your output folder (%s) exists " \
"is writable." % crop_output_path
else:
err_message = "Sorry, the output path for the cropping tool " \
"isn't set up correctly. Please contact an administrator."
return json_error_response(err_message)
# Use first reachable stack mirrors
stack_mirror_ids = []
for sid in stack_ids:
stack_mirrors = StackMirror.objects.select_related('stack').filter(
stack_id=sid)
for sm in stack_mirrors:
# If mirror is reachable use it right away
tile_source = get_tile_source(sm.tile_source_type)
try:
req = requests.head(tile_source.get_canary_url(sm),
allow_redirects=True,
verify=verify_ssl)
reachable = req.status_code == 200
except Exception as e:
logger.error(e)
reachable = False
if reachable:
stack_mirror_ids.append(sm.id)
break
if not reachable:
raise ValueError(
"Can't find reachable stack mirror for stack {}".format(sid))
# Crate a new cropping job
job = CropJob(request.user, project_id, stack_mirror_ids, x_min, x_max,
y_min, y_max, z_min, z_max, rotation_cw, zoom_level,
single_channel)
# Parameter check
errors = sanity_check(job)
if len(errors) > 0:
err_message = "Some problems with the cropping parameters were found: "
for n, errtxt in enumerate(errors):
if n == 0:
err_message += str(n + 1) + ". " + errtxt
else:
err_message += ", " + str(n + 1) + ". " + errtxt
err_response = json_error_response(err_message)
return err_response
result = start_asynch_process(job)
return result
def crop(request, project_id=None):
""" Crops out the specified region of the stack. The region is expected to
be given in terms of real world units (e.g. nm).
"""
stack_ids = get_request_list(request.POST, "stack_ids", [], int)
x_min = float(request.POST['min_x'])
y_min = float(request.POST['min_y'])
z_min = float(request.POST['min_z'])
x_max = float(request.POST['max_x'])
y_max = float(request.POST['max_y'])
z_max = float(request.POST['max_z'])
zoom_level = float(request.POST['zoom_level'])
single_channel = request.POST['single_channel'] == 'true'
rotation_cw = float(request.GET.get('rotationcw', 0.0))
# Make sure tmp dir exists and is writable
if not os.path.exists( crop_output_path ) or not os.access( crop_output_path, os.W_OK ):
if request.user.is_superuser:
err_message = "Please make sure your output folder (%s) exists " \
"is writable." % crop_output_path
else:
err_message = "Sorry, the output path for the cropping tool " \
"isn't set up correctly. Please contact an administrator."
return json_error_response(err_message)
# Use first reachable stack mirrors
stack_mirror_ids = []
for sid in stack_ids:
stack_mirrors = StackMirror.objects.select_related('stack').filter(stack_id=sid);
for sm in stack_mirrors:
# If mirror is reachable use it right away
tile_source = get_tile_source(sm.tile_source_type)
try:
req = requests.head(tile_source.get_canaray_url(sm))
reachable = req.status_code == 200
except :
reachable = False
if reachable:
stack_mirror_ids.append(sm.id)
break
if not reachable:
raise ValueError("Can't find reachable stack mirror for stack {}".format(sid))
# Crate a new cropping job
job = CropJob(request.user, project_id, stack_mirror_ids, x_min, x_max,
y_min, y_max, z_min, z_max, rotation_cw, zoom_level, single_channel)
# Parameter check
errors = sanity_check( job )
if len(errors) > 0:
err_message = "Some problems with the cropping parameters were found: "
for n, e in enumerate( errors ):
if n == 0:
err_message += str( n+1 ) + ". " + e
else:
err_message += ", " + str( n+1 ) + ". " + e
err_response = json_error_response( err_message )
return err_response
result = start_asynch_process( job )
return result
