curious.bio/planktoscope
curious.bio/planktoscope
9
0
Fork 0
Code Issues 10 Pull requests Packages Projects 7 Releases Wiki Activity

segmenter: fix missing parameters issue to segment_all call

Browse source
This commit is contained in:
Romain Bazile 2021-11-18 12:34:48 +01:00
parent 6698df4878
commit f2e41dc8b6
1 changed files with 18 additions and 19 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

31
scripts/planktoscope/segmenter/__init__.py
View file

@ -723,11 +723,13 @@ class SegmenterProcess(multiprocessing.Process):
# we're done free some mem
self.__flat = None
def segment_all(self, paths: list, force, ecotaxa_export):
def segment_all(self, paths: list, force=False, ecotaxa_export=True):
"""Starts the segmentation in all the folders given recursively
Args:
paths (list, optional): path list to recursively explore. Defaults to [self.__img_path].
paths (list): path list to recursively explore.
force (bool, optional): force the rework on all paths given. Defaults to False.
ecotaxa_export (bool, optional): generates ecotaxa export data. Defaults to True.
"""
img_paths = []
for path in paths:
@ -736,11 +738,13 @@ class SegmenterProcess(multiprocessing.Process):
img_paths.append(x[0])
self.segment_list(img_paths, force, ecotaxa_export)
def segment_list(self, path_list: list, force=True, ecotaxa_export=True):
def segment_list(self, path_list: list, force=False, ecotaxa_export=True):
"""Starts the segmentation in the folders given
Args:
path_list (list): [description]
paths (list): path list to recursively explore.
force (bool, optional): force the rework on all paths given. Defaults to False.
ecotaxa_export (bool, optional): generates ecotaxa export data. Defaults to True.
"""
logger.info(f"The pipeline will be run in {len(path_list)} directories")
logger.debug(f"Those are {path_list}")
@ -760,21 +764,16 @@ class SegmenterProcess(multiprocessing.Process):
logger.debug(f"{path}: Checking for the presence of metadata.json")
if os.path.exists(os.path.join(path, "metadata.json")):
# The file exists, let's check if we force or not
if force:
# forcing, let's gooooo
try:
self.segment_path(path, ecotaxa_export)
except Exception as e:
logger.error(f"There was an error while segmenting {path}")
exception = e
else:
# we need to check for the presence of done.txt in each folder
logger.debug(f"{path}: Checking for the presence of done.txt")
if os.path.exists(os.path.join(path, "done.txt")):
# we also need to check for the presence of done.txt in each folder
logger.debug(
f"{path}: Checking for the presence of done.txt or forcing({force})"
)
if os.path.exists(os.path.join(path, "done.txt")) and not force:
logger.debug(
f"Moving to the next folder, {path} has already been segmented"
)
else:
# forcing, let's gooooo
try:
self.segment_path(path, ecotaxa_export)
except Exception as e:
@ -957,7 +956,7 @@ class SegmenterProcess(multiprocessing.Process):
else:
self.segment_list(path, force, ecotaxa_export)
else:
self.segment_all(self.__img_path)
self.segment_all(self.__img_path, force, ecotaxa_export)
elif last_message["action"] == "stop":
logger.info("The segmentation has been interrupted.")