def _get_truth_db_rois(subimg_path_base, filename_base, db_path_base=None):
"""Get ROIs from a truth database.
Args:
subimg_path_base (str): Base path with sub-image.
filename_base (str): Base path without sub-image to find the
experiment, used only if an experiment cannot be found based on
``subimg_path_base``.
db_path_base (str): Path to database to load; defaults to None
to use :attr:`config.truth_db`.
Returns:
str, list[:class:`sqlite3.Row`]: Found experiment name and
list of database ROI rows in that experiment, or None for each
if the ROIs are not found.
"""
name = None
exp_rois = None
if db_path_base:
# load truth DB
_logger.debug("Loading truth db for verifications from '%s'",
db_path_base)
sqlite.load_truth_db(db_path_base)
if config.truth_db is not None:
# load experiment and ROIs from truth DB using the sub-image-based
# name; series not included in exp name since in ROI
name = sqlite.get_exp_name(subimg_path_base)
_logger.debug("Loading truth ROIs from experiment '%s'", name)
exp_rois = config.truth_db.get_rois(name)
if exp_rois is None:
# exp may have been named without sub-image
old_name = name
name = sqlite.get_exp_name(filename_base)
_logger.debug(
"'%s' experiment name not found, will try without any "
"sub-image offset/size: '%s'", old_name, name)
exp_rois = config.truth_db.get_rois(name)
if exp_rois is None:
# exp may differ from image name all together
_logger.debug(
"'%s' experiment name not found, will try first "
"available experiment", name)
exps = config.truth_db.select_experiment()
if exps:
name = exps[0]["name"]
_logger.debug(
"Loading ROIs from first available experiment: '%s'", name)
exp_rois = config.truth_db.get_rois(name)
if not exp_rois:
_logger.warn("No matching experiments found in the truth database")
return name, exp_rois
def _get_truth_db_rois(subimg_path_base, filename_base, db_path_base=None):
"""Get ROIs from a truth database.
Args:
subimg_path_base (str): Base path with sub-image.
filename_base (str): Base path without sub-image to find the
experiment, used only if an experiment cannot be found based on
``subimg_path_base``.
db_path_base (str): Path to database to load; defaults to None
to use :attr:`config.truth_db`.
Returns:
str, list[:class:`sqlite3.Row`]: Found experiment name and
list of database ROI rows in that experiment, or None for each
if the ROIs are not found.
"""
name = None
exp_rois = None
if db_path_base:
# load truth DB
print("Loading truth db for verifications from", db_path_base)
sqlite.load_truth_db(db_path_base)
if config.truth_db is not None:
# load experiment and ROIs from truth DB using the sub-image-based
# name; series not included in exp name since in ROI
name = sqlite.get_exp_name(subimg_path_base)
print("Loading truth ROIs from experiment:", name)
exp_rois = config.truth_db.get_rois(name)
if exp_rois is None:
# exp may have been named without sub-image
print("{} experiment name not found, will try without "
"sub-image offset/size".format(name))
name = sqlite.get_exp_name(filename_base)
exp_rois = config.truth_db.get_rois(name)
return name, exp_rois
def make_density_images_mp(img_paths,
scale=None,
shape=None,
suffix=None,
channel=None):
"""Make density images for a list of files as a multiprocessing
wrapper for :func:``make_density_image``
Args:
img_paths (List[str]): Sequence of image paths, which will be used to
indentify the blob files.
scale (int, float): Rescaling factor as a scalar value. If set,
the corresponding image for this factor will be opened. If None,
the full size image will be used. Defaults to None.
shape (List[int]): Sequence of target shape defining the voxels for
the density map; defaults to None.
suffix (str): Modifier to append to end of ``img_path`` basename for
registered image files that were output to a modified name;
defaults to None.
channel (List[int]): Sequence of channels to include in density image;
defaults to None to use all channels.
"""
start_time = time()
pool = chunking.get_mp_pool()
pool_results = []
for img_path in img_paths:
print("Making density image from blobs related to:", img_path)
if config.channel:
# get blob matches for the given channels if available; must load
# from db outside of multiprocessing to avoid MemoryError
matches = colocalizer.select_matches(
config.db,
config.channel,
exp_name=sqlite.get_exp_name(img_path))
else:
matches = None
pool_results.append(
pool.apply_async(make_density_image,
args=(img_path, scale, shape, suffix, None,
channel, matches, config.atlas_profile)))
for result in pool_results:
_, path = result.get()
print("finished {}".format(path))
pool.close()
pool.join()
print("time elapsed for making density images:", time() - start_time)
def _get_roi_id(db, offset, shape, exp_name=None):
"""Get database ROI ID for the given ROI position within the main image5d.
Args:
db (:obj:`sqlite.ClrDB`): Database object.
offset (List[int]): ROI offset in z,y,x.
shape (List[int]): ROI shape in z,y,x.
exp_name (str): Name of experiment; defaults to None to attempt
discovery through any image loaded to :attr:`config.img5d`.
Returns:
int: ROI ID or found or inserted ROI.
"""
if exp_name is None:
exp_name = sqlite.get_exp_name(
config.img5d.path_img if config.img5d else None)
exp_id = sqlite.select_or_insert_experiment(
db.conn, db.cur, exp_name, None)
roi_id = sqlite.select_or_insert_roi(
db.conn, db.cur, exp_id, config.series, offset, shape)[0]
return roi_id