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segmenter: fix missing parameters issue to segment_all call

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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
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37
scripts/planktoscope/segmenter/__init__.py
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@ -723,11 +723,13 @@ class SegmenterProcess(multiprocessing.Process):
# we're done free some mem # we're done free some mem
self.__flat = None 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 """Starts the segmentation in all the folders given recursively
Args: 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 = [] img_paths = []
for path in paths: for path in paths:
@ -736,11 +738,13 @@ class SegmenterProcess(multiprocessing.Process):
img_paths.append(x[0]) img_paths.append(x[0])
self.segment_list(img_paths, force, ecotaxa_export) 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 """Starts the segmentation in the folders given
Args: 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.info(f"The pipeline will be run in {len(path_list)} directories")
logger.debug(f"Those are {path_list}") logger.debug(f"Those are {path_list}")
@ -760,26 +764,21 @@ class SegmenterProcess(multiprocessing.Process):
logger.debug(f"{path}: Checking for the presence of metadata.json") logger.debug(f"{path}: Checking for the presence of metadata.json")
if os.path.exists(os.path.join(path, "metadata.json")): if os.path.exists(os.path.join(path, "metadata.json")):
# The file exists, let's check if we force or not # The file exists, let's check if we force or not
if force: # 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 # forcing, let's gooooo
try: try:
self.segment_path(path, ecotaxa_export) self.segment_path(path, ecotaxa_export)
except Exception as e: except Exception as e:
logger.error(f"There was an error while segmenting {path}") logger.error(f"There was an error while segmenting {path}")
exception = e 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")):
logger.debug(
f"Moving to the next folder, {path} has already been segmented"
)
else:
try:
self.segment_path(path, ecotaxa_export)
except Exception as e:
logger.error(f"There was an error while segmenting {path}")
exception = e
else: else:
logger.debug(f"Moving to the next folder, {path} has no metadata.json") logger.debug(f"Moving to the next folder, {path} has no metadata.json")
if exception is None: if exception is None:
@ -957,7 +956,7 @@ class SegmenterProcess(multiprocessing.Process):
else: else:
self.segment_list(path, force, ecotaxa_export) self.segment_list(path, force, ecotaxa_export)
else: else:
self.segment_all(self.__img_path) self.segment_all(self.__img_path, force, ecotaxa_export)
elif last_message["action"] == "stop": elif last_message["action"] == "stop":
logger.info("The segmentation has been interrupted.") logger.info("The segmentation has been interrupted.")