segmenter: ecotaxa export, check that there are objects to export
(cherry picked from commit 31b8c83aa6f0db59c64a62f4caf73cf3974da4f6)
This commit is contained in:
Romain Bazile
Romain Bazile
parent
86c322ccbe
commit
36eccd43f2
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@ -507,7 +507,7 @@ class SegmenterProcess(multiprocessing.Process):
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)
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return (object_number, len(regionprops))
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def _pipe(self):
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def _pipe(self, ecotaxa_export):
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logger.info("Finding images")
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images_list = self._find_files(
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self.__working_path, ("JPG", "jpg", "JPEG", "jpeg")
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@ -638,18 +638,27 @@ class SegmenterProcess(multiprocessing.Process):
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f"We also found {total_objects} objects, or an average of {total_objects / (total_duration * 60)}objects per second"
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)
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planktoscope.segmenter.ecotaxa.ecotaxa_export(
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self.__archive_fn,
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self.__global_metadata,
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self.__working_obj_path,
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keep_files=True,
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)
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if ecotaxa_export:
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if "objects" in self.__global_metadata:
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if planktoscope.segmenter.ecotaxa.ecotaxa_export(
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self.__archive_fn,
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self.__global_metadata,
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self.__working_obj_path,
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keep_files=True,
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):
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logger.error("The ecotaxa export could not be completed")
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else:
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logger.succes("Ecotaxa archive export completed for this folder")
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else:
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logger.info("There are no objects to export")
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else:
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logger.info("We are not creating the ecotaxa output archive for this folder")
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# cleanup
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# we're done free some mem
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self.__flat = None
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def segment_all(self, paths: list):
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def segment_all(self, paths: list, force, ecotaxa_export):
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"""Starts the segmentation in all the folders given recursively
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Args:
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@ -660,9 +669,9 @@ class SegmenterProcess(multiprocessing.Process):
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for x in os.walk(path):
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if x[0] not in img_paths:
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img_paths.append(x[0])
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self.segment_list(img_paths)
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self.segment_list(img_paths, force, ecotaxa_export)
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def segment_list(self, path_list: list, force=True):
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def segment_list(self, path_list: list, force=True, ecotaxa_export=True):
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"""Starts the segmentation in the folders given
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Args:
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@ -676,7 +685,7 @@ class SegmenterProcess(multiprocessing.Process):
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# The file exists, let's check if we force or not
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if force:
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# forcing, let's gooooo
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if not self.segment_path(path):
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if not self.segment_path(path, ecotaxa_export):
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logger.error(f"There was en error while segmenting {path}")
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else:
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# we need to check for the presence of done.txt in each folder
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@ -686,14 +695,14 @@ class SegmenterProcess(multiprocessing.Process):
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f"Moving to the next folder, {path} has already been segmented"
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)
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else:
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if not self.segment_path(path):
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if not self.segment_path(path, ecotaxa_export):
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logger.error(f"There was en error while segmenting {path}")
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else:
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logger.debug(f"Moving to the next folder, {path} has no metadata.json")
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# Publish the status "Done" to via MQTT to Node-RED
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self.segmenter_client.client.publish("status/segmenter", '{"status":"Done"}')
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def segment_path(self, path):
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def segment_path(self, path, ecotaxa_export):
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"""Starts the segmentation in the given path
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Args:
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@ -755,7 +764,7 @@ class SegmenterProcess(multiprocessing.Process):
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logger.info(f"Starting the pipeline in {path}")
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try:
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self._pipe()
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self._pipe(ecotaxa_export)
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except Exception as e:
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logger.exception(f"There was an error in the pipeline {e}")
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return False
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@ -781,6 +790,7 @@ class SegmenterProcess(multiprocessing.Process):
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path = None
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recursive = True
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force = False
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ecotaxa_export = True
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# {"action":"segment"}
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if "settings" in last_message:
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if "force" in last_message["settings"]:
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@ -789,6 +799,9 @@ class SegmenterProcess(multiprocessing.Process):
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if "recursive" in last_message["settings"]:
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# parse folders recursively starting from the given parameter
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recursive = last_message["settings"]["recursive"]
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if "ecotaxa" in last_message["settings"]:
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# generate ecotaxa output archive
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ecotaxa_export = last_message["settings"]["ecotaxa"]
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# TODO eventually add customisation to segmenter parameters here
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if "path" in last_message:
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@ -800,9 +813,9 @@ class SegmenterProcess(multiprocessing.Process):
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)
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if path:
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if recursive:
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self.segment_all(path)
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self.segment_all(path, force, ecotaxa_export)
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else:
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self.segment_list(path)
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self.segment_list(path, force, ecotaxa_export)
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else:
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self.segment_all(self.__img_path)
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@ -199,7 +199,11 @@ def ecotaxa_export(archive_filepath, metadata, image_base_path, keep_files=False
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# empty table, one line per object
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tsv_content = []
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object_list = metadata.pop("objects")
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if "objects" in metadata:
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object_list = metadata.pop("objects")
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else:
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logger.error("No objects metadata recorded, cannot continue the export")
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return 0
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# fix crappy old camera resolution that was not exported as string
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if type(metadata["acq_camera_resolution"]) != str:
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@ -248,3 +252,4 @@ def ecotaxa_export(archive_filepath, metadata, image_base_path, keep_files=False
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path_or_buf=tsv_file, sep="\t", encoding="utf-8", index=False
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)
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logger.success("Ecotaxa archive is ready!")
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return 1
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