def load(filename):
''' Initate TrackEdit/ZStackEdit object and load object to database.
Send specific attributes of the object to the .js file.
'''
start = timeit.default_timer()
current_app.logger.info('Loading track at %s', filename)
folders = re.split('__', filename)
filename = folders[len(folders) - 1]
subfolders = folders[2:len(folders) - 1]
subfolders = '/'.join(subfolders)
full_path = os.path.join(subfolders, filename)
input_bucket = folders[0]
output_bucket = folders[1]
# arg is 'false' which gets parsed to True if casting to bool
rgb = request.args.get('rgb', default='false', type=str)
rgb = bool(distutils.util.strtobool(rgb))
if not is_trk_file(filename) and not is_npz_file(filename):
error = {
'error':
'invalid file extension: {}'.format(
os.path.splitext(filename)[-1])
}
return jsonify(error), 400
# Initate Edit object and entry in database
caliban_file = CalibanFile(filename, input_bucket, full_path)
edit = get_edit(caliban_file, output_bucket, rgb)
project = Project.create_project(filename, edit, subfolders)
if is_trk_file(filename):
current_app.logger.debug('Loaded trk file "%s" in %s s.', filename,
timeit.default_timer() - start)
# Send attributes to .js file
return jsonify({
'max_frames': caliban_file.max_frames,
'tracks': caliban_file.readable_tracks,
'dimensions': (caliban_file.width, caliban_file.height),
'project_id': project.id,
'screen_scale': edit.scale_factor
})
if is_npz_file(filename):
current_app.logger.debug('Loaded npz file "%s" in %s s.', filename,
timeit.default_timer() - start)
# Send attributes to .js file
return jsonify({
'max_frames': caliban_file.max_frames,
'channel_max': caliban_file.channel_max,
'feature_max': caliban_file.feature_max,
'tracks': caliban_file.readable_tracks,
'dimensions': (caliban_file.width, caliban_file.height),
'project_id': project.id
})
def upload_file(project_id):
'''Upload .trk/.npz data file to AWS S3 bucket.'''
start = timeit.default_timer()
# Use id to grab appropriate TrackEdit/ZStackEdit object from database
project = Project.get_project_by_id(project_id)
if not project:
return jsonify({'error': 'project_id not found'}), 404
state = load_project_state(project)
filename = state.file.filename
# Call function in caliban.py to save data file and send to S3 bucket
if is_trk_file(filename):
state.action_save_track()
elif is_npz_file(filename):
state.action_save_zstack()
# add "finished" timestamp and null out state longblob
Project.finish_project(project)
current_app.logger.debug('Uploaded file "%s" for project "%s" in %s s.',
filename, project_id,
timeit.default_timer() - start)
return redirect('/')
def test_is_npz_file():
assert helpers.is_npz_file('test.npz')
assert helpers.is_npz_file('test.NpZ')
assert not helpers.is_npz_file('test.pdf')
assert not helpers.is_npz_file('test.trk')
assert not helpers.is_npz_file('this is just a string')
assert not helpers.is_npz_file(1234)
assert not helpers.is_npz_file(None)
assert not helpers.is_npz_file(dict())
def load(filename):
''' Initate TrackReview/ZStackReview object and load object to database.
Send specific attributes of the object to the .js file.
'''
conn = create_connection("caliban.db")
print(f"Loading track at {filename}", file=sys.stderr)
folders = re.split('__', filename)
filename = folders[len(folders) - 1]
subfolders = folders[2:len(folders)]
subfolders = '/'.join(subfolders)
input_bucket = folders[0]
output_bucket = folders[1]
if is_trk_file(filename):
# Initate TrackReview object and entry in database
track_review = TrackReview(filename, input_bucket, output_bucket,
subfolders)
project_id = create_project(conn, filename, track_review)
conn.commit()
conn.close()
# Send attributes to .js file
return jsonify({
"max_frames": track_review.max_frames,
"tracks": track_review.readable_tracks,
"dimensions": track_review.dimensions,
"project_id": project_id,
"screen_scale": track_review.scale_factor
})
if is_npz_file(filename):
# Initate ZStackReview object and entry in database
zstack_review = ZStackReview(filename, input_bucket, output_bucket,
subfolders)
project_id = create_project(conn, filename, zstack_review)
conn.commit()
conn.close()
# Send attributes to .js file
return jsonify({
"max_frames": zstack_review.max_frames,
"channel_max": zstack_review.channel_max,
"feature_max": zstack_review.feature_max,
"tracks": zstack_review.readable_tracks,
"dimensions": zstack_review.dimensions,
"project_id": project_id,
"screen_scale": zstack_review.scale_factor
})
conn.close()
error = {
'error':
'invalid file extension: {}'.format(os.path.splitext(filename)[-1])
}
return jsonify(error), 400
def get_edit(file_, output_bucket, rgb):
"""Factory for Edit objects"""
if is_npz_file(file_.filename):
return ZStackEdit(file_, output_bucket, rgb)
elif is_trk_file(file_.filename):
# don't use RGB mode with track files
return TrackEdit(file_, output_bucket)
return BaseEdit(file_, output_bucket)
def tool():
''' Request HTML caliban tool page to be rendered after user inputs
filename in the landing page.
'''
if 'filename' not in request.form:
return redirect('/')
filename = request.form['filename']
current_app.logger.info('%s is filename', filename)
# TODO: better name template?
new_filename = 'caliban-input__caliban-output__test__{}'.format(filename)
# if no options passed (how this route will be for now),
# still want to pass in default settings
rgb = request.args.get('rgb', default='false', type=str)
pixel_only = request.args.get('pixel_only', default='false', type=str)
label_only = request.args.get('label_only', default='false', type=str)
# Using distutils to cast string arguments to bools
settings = {
'rgb': bool(distutils.util.strtobool(rgb)),
'pixel_only': bool(distutils.util.strtobool(pixel_only)),
'label_only': bool(distutils.util.strtobool(label_only))
}
if is_trk_file(new_filename):
filetype = 'track'
title = 'Tracking Tool'
elif is_npz_file(new_filename):
filetype = 'zstack'
title = 'Z-Stack Tool'
else:
# TODO: render an error template instead of JSON.
error = {
'error':
'invalid file extension: {}'.format(
os.path.splitext(filename)[-1])
}
return jsonify(error), 400
return render_template('tool.html',
filetype=filetype,
title=title,
filename=new_filename,
settings=settings)
def shortcut(filename):
''' Request HTML caliban tool page to be rendered if user makes a URL
request to access a specific data file that has been preloaded to the
input S3 bucket (ex. http://127.0.0.1:5000/test.npz).
'''
if is_trk_file(filename):
return render_template('index_track.html', filename=filename)
if is_npz_file(filename):
return render_template('index_zstack.html', filename=filename)
error = {
'error':
'invalid file extension: {}'.format(os.path.splitext(filename)[-1])
}
return jsonify(error), 400
def tool():
''' Request HTML caliban tool page to be rendered after user inputs
filename in the landing page.
'''
filename = request.form['filename']
print(f"{filename} is filename", file=sys.stderr)
new_filename = 'caliban-input__caliban-output__test__{}'.format(
str(filename))
if is_trk_file(new_filename):
return render_template('index_track.html', filename=new_filename)
if is_npz_file(new_filename):
return render_template('index_zstack.html', filename=new_filename)
error = {
'error':
'invalid file extension: {}'.format(os.path.splitext(filename)[-1])
}
return jsonify(error), 400
def shortcut(filename):
''' Request HTML caliban tool page to be rendered if user makes a URL
request to access a specific data file that has been preloaded to the
input S3 bucket (ex. http://127.0.0.1:5000/test.npz).
'''
rgb = request.args.get('rgb', default='false', type=str)
pixel_only = request.args.get('pixel_only', default='false', type=str)
label_only = request.args.get('label_only', default='false', type=str)
settings = {
'rgb': bool(distutils.util.strtobool(rgb)),
'pixel_only': bool(distutils.util.strtobool(pixel_only)),
'label_only': bool(distutils.util.strtobool(label_only))
}
if is_trk_file(filename):
filetype = 'track'
title = 'Tracking Tool'
elif is_npz_file(filename):
filetype = 'zstack'
title = 'Z-Stack Tool'
else:
# TODO: render an error template instead of JSON.
error = {
'error':
'invalid file extension: {}'.format(
os.path.splitext(filename)[-1])
}
return jsonify(error), 400
return render_template('tool.html',
filetype=filetype,
title=title,
filename=filename,
settings=settings)
def upload_file(project_id):
''' Upload .trk/.npz data file to AWS S3 bucket.
'''
conn = create_connection("caliban.db")
# Use id to grab appropriate TrackReview/ZStackReview object from database
id_exists = get_project(conn, project_id)
if id_exists is None:
conn.close()
return jsonify({'error': 'project_id not found'}), 404
state = pickle.loads(id_exists[2])
# Call function in caliban.py to save data file and send to S3 bucket
if is_trk_file(id_exists[1]):
state.action_save_track()
elif is_npz_file(id_exists[1]):
state.action_save_zstack()
# Delete id and object from database
delete_project(conn, project_id)
conn.close()
return redirect("/")