From f2e41dc8b68e7506eff31925c0d3f2b4954b48e1 Mon Sep 17 00:00:00 2001 From: Romain Bazile Date: Thu, 18 Nov 2021 12:34:48 +0100 Subject: [PATCH] segmenter: fix missing parameters issue to segment_all call --- scripts/planktoscope/segmenter/__init__.py | 37 +++++++++++----------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/scripts/planktoscope/segmenter/__init__.py b/scripts/planktoscope/segmenter/__init__.py index cf5f83a..814e2ea 100644 --- a/scripts/planktoscope/segmenter/__init__.py +++ b/scripts/planktoscope/segmenter/__init__.py @@ -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}") @@ -760,26 +764,21 @@ 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: + # 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: 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")): - 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: logger.debug(f"Moving to the next folder, {path} has no metadata.json") if exception is None: @@ -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.")