def export_skeleton_as_nrrd_async(skeleton_id,
source_ref,
target_ref,
user_id,
mirror=True,
create_message=True):
result = export_skeleton_as_nrrd(skeleton_id, source_ref, target_ref,
user_id, mirror)
if create_message:
msg = Message()
msg.user = User.objects.get(pk=int(user_id))
msg.read = False
if result['errors']:
msg.title = "No NRRD file could be creaed for skeleton {}".format(
skeleton_id)
msg.text = "There was at least one error during the NRRD export: {}".format(
'\n'.join(result['errors']))
msg.action = ""
else:
url = urljoin(
urljoin(settings.MEDIA_URL,
settings.MEDIA_EXPORT_SUBDIRECTORY),
result['nrrd_name'])
msg.title = "Exported skeleton {} as NRRD file".format(skeleton_id)
msg.text = "The requested skeleton was exported as NRRD file. You " \
"can download it from this location: <a href='{}'>{}</a>".format(url, url)
msg.action = url
msg.save()
return "Errors: {}".format('\n'.join(
result['errors'])) if result['errors'] else result['nrrd_path']
def create_message(self, title, message, url):
msg = Message()
msg.user = User.objects.get(pk=int(self.job.user.id))
msg.read = False
msg.title = title
msg.text = message
msg.action = url
msg.save()
def create_message(self, title, message, url):
msg = Message()
msg.user = User.objects.get(pk=int(self.job.user.id))
msg.read = False
msg.title = title
msg.text = message
msg.action = url
msg.save()
def process_crop_job(job, create_message=True):
""" This method does the actual cropping. It controls the data extraction
and the creation of the sub-stack. It can be executed as Celery task.
"""
try:
# Create the sub-stack
cropped_stack = extract_substack(job)
# Create tho output image
outputImage = ImageList()
for img in cropped_stack:
outputImage.append(img)
# Save the resulting micro_stack to a temporary location
no_error_occured = True
error_message = ""
# Only produce an image if parts of stacks are within the output
if len(cropped_stack) > 0:
outputImage.writeImages(job.output_path.encode('ascii', 'ignore'))
# Add some meta data to the image
addMetaData(job.output_path, job, cropped_stack)
else:
no_error_occured = False
error_message = "A region outside the stack has been selected. " \
"Therefore, no image was produced."
except (IOError, OSError, ValueError) as e:
no_error_occured = False
error_message = str(e)
# Delete the file if parts of it have been written already
if os.path.exists(job.output_path):
os.remove(job.output_path)
if create_message:
# Create a notification message
bb_text = "( %s, %s, %s ) -> ( %s, %s, %s )" % (job.x_min, job.y_min, \
job.z_min, job.x_max, job.y_max, job.z_max)
msg = Message()
msg.user = User.objects.get(pk=int(job.user.id))
msg.read = False
if no_error_occured:
file_name = os.path.basename(job.output_path)
url = os.path.join(settings.CATMAID_URL,
"crop/download/" + file_name + "/")
msg.title = "Microstack finished"
msg.text = "The requested microstack %s is finished. You can " \
"download it from this location: <a href='%s'>%s</a>" % \
(bb_text, url, url)
msg.action = url
else:
msg.title = "Microstack could not be created"
msg.text = "The requested microstack %s could not be created due " \
"to an error while saving the result (%s)." % \
(bb_text, error_message)
msg.action = ""
msg.save()
return job.output_path if no_error_occured else error_message
def process_crop_job(job, create_message=True):
""" This method does the actual cropping. It controls the data extraction
and the creation of the sub-stack. It can be executed as Celery task.
"""
try:
# Create the sub-stack
cropped_stack = extract_substack(job)
# Create tho output image
outputImage = ImageList()
for img in cropped_stack:
outputImage.append( img )
# Save the resulting micro_stack to a temporary location
no_error_occured = True
error_message = ""
# Only produce an image if parts of stacks are within the output
if len( cropped_stack ) > 0:
outputImage.writeImages( job.output_path.encode('ascii', 'ignore') )
# Add some meta data to the image
addMetaData( job.output_path, job, cropped_stack )
else:
no_error_occured = False
error_message = "A region outside the stack has been selected. " \
"Therefore, no image was produced."
except (IOError, OSError, ValueError) as e:
no_error_occured = False
error_message = str(e)
# Delete the file if parts of it have been written already
if os.path.exists( job.output_path ):
os.remove( job.output_path )
if create_message:
# Create a notification message
bb_text = "( %s, %s, %s ) -> ( %s, %s, %s )" % (job.x_min, job.y_min, \
job.z_min, job.x_max, job.y_max, job.z_max)
msg = Message()
msg.user = User.objects.get(pk=int(job.user.id))
msg.read = False
if no_error_occured:
file_name = os.path.basename( job.output_path )
url = os.path.join( settings.CATMAID_URL, "crop/download/" + file_name + "/")
msg.title = "Microstack finished"
msg.text = "The requested microstack %s is finished. You can " \
"download it from this location: <a href='%s'>%s</a>" % \
(bb_text, url, url)
msg.action = url
else:
msg.title = "Microstack could not be created"
msg.text = "The requested microstack %s could not be created due " \
"to an error while saving the result (%s)." % \
(bb_text, error_message)
msg.action = ""
msg.save()
return job.output_path if no_error_occured else error_message
def process_crop_job(job: CropJob, create_message=True) -> str:
""" This method does the actual cropping. It controls the data extraction
and the creation of the sub-stack. It can be executed as Celery task.
"""
try:
# Create the sub-stack
cropped_stack = extract_substack(job)
# Save the resulting micro_stack to a temporary location
no_error_occured = True
error_message = ""
# Only produce an image if parts of stacks are within the output
if len(cropped_stack) > 0:
metadata = job.create_tiff_metadata(len(cropped_stack))
cropped_stack[0].save(job.output_path, compression="raw", save_all=True,
append_images=cropped_stack[1:], tiffinfo=metadata)
else:
no_error_occured = False
error_message = "A region outside the stack has been selected. " \
"Therefore, no image was produced."
except (IOError, OSError, ValueError) as e:
no_error_occured = False
error_message = str(e)
# Delete the file if parts of it have been written already
if os.path.exists( job.output_path ):
os.remove( job.output_path )
if create_message:
# Create a notification message
bb_text = "( %s, %s, %s ) -> ( %s, %s, %s )" % (job.x_min, job.y_min, \
job.z_min, job.x_max, job.y_max, job.z_max)
user = User.objects.get(pk=int(job.user.id))
msg = Message()
msg.user = user
msg.read = False
if no_error_occured:
file_name = os.path.basename( job.output_path )
url = os.path.join( settings.CATMAID_URL, "crop/download/" + file_name + "/")
msg.title = "Microstack finished"
msg.text = "The requested microstack %s is finished. You can " \
"download it from this location: <a href='%s'>%s</a>" % \
(bb_text, url, url)
msg.action = url
else:
msg.title = "Microstack could not be created"
msg.text = "The requested microstack %s could not be created due " \
"to an error while saving the result (%s)." % \
(bb_text, error_message)
msg.action = ""
msg.save()
notify_user(user.id, msg.id, msg.title)
return job.output_path if no_error_occured else error_message
def export_skeleton_as_nrrd_async(skeleton_id, source_ref, target_ref, user_id,
mirror=True, create_message=True):
result = export_skeleton_as_nrrd(skeleton_id, source_ref, target_ref,
user_id, mirror)
if create_message:
msg = Message()
msg.user = User.objects.get(pk=int(user_id))
msg.read = False
if result['errors']:
msg.title = "No NRRD file could be creaed for skeleton {}".format(skeleton_id)
msg.text = "There was at least one error during the NRRD export: {}".format('\n'.join(result['errors']))
msg.action = ""
else:
url = urljoin(urljoin(settings.MEDIA_URL, settings.MEDIA_EXPORT_SUBDIRECTORY), result['nrrd_name'])
msg.title = "Exported skeleton {} as NRRD file".format(skeleton_id)
msg.text = "The requested skeleton was exported as NRRD file. You " \
"can download it from this location: <a href='{}'>{}</a>".format(url, url)
msg.action = url
msg.save()
return "Errors: {}".format('\n'.join(result['errors'])) if result['errors'] else result['nrrd_path']
msg.read = False
if no_error_occured:
file_name = os.path.basename( job.output_path )
url = os.path.join( settings.CATMAID_URL, "crop/download/" + file_name + "/")
msg.title = "Microstack finished"
msg.text = "The requested microstack %s is finished. You can " \
"download it from this location: <a href='%s'>%s</a>" % \
(bb_text, url, url)
msg.action = url
else:
msg.title = "Microstack could not be created"
msg.text = "The requested microstack %s could not be created due " \
"to an error while saving the result (%s)." % \
(bb_text, error_message)
msg.action = ""
msg.save()
return None if no_error_occured else error_message
def start_asynch_process( job ):
""" It launches the data extraction and sub-stack building as a seperate process.
This process uses the addmessage command with manage.py to write a message for the
user into the data base once the process is done.
"""
result = process_crop_job.delay( job )
# Create closing response
closingResponse = HttpResponse(json.dumps(""), content_type="application/json")
return closingResponse
if no_error_occured:
file_name = os.path.basename(job.output_path)
url = os.path.join(settings.CATMAID_URL,
"crop/download/" + file_name + "/")
msg.title = "Microstack finished"
msg.text = "The requested microstack %s is finished. You can " \
"download it from this location: <a href='%s'>%s</a>" % \
(bb_text, url, url)
msg.action = url
else:
msg.title = "Microstack could not be created"
msg.text = "The requested microstack %s could not be created due " \
"to an error while saving the result (%s)." % \
(bb_text, error_message)
msg.action = ""
msg.save()
return None if no_error_occured else error_message
def start_asynch_process(job):
""" It launches the data extraction and sub-stack building as a seperate process.
This process uses the addmessage command with manage.py to write a message for the
user into the data base once the process is done.
"""
result = process_crop_job.delay(job)
# Create closing response
closingResponse = HttpResponse(json.dumps(""),
content_type="application/json")
