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segmenter: fix morphocut error with objects files in img folder

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This commit is contained in:
Romain Bazile 2020-10-21 00:37:12 +02:00
parent 5fb9d510dc
commit 06d9facb3d
1 changed files with 29 additions and 10 deletions
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39
scripts/planktoscope/segmenter.py
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@ -63,16 +63,22 @@ class SegmenterProcess(multiprocessing.Process):
self.stop_event = event
self.__pipe = None
self.segmenter_client = None
self.__img_path = "/home/pi/data/img"
self.__export_path = "/home/pi/data/export"
self.__img_path = "/home/pi/data/img/"
self.__export_path = "/home/pi/data/export/"
self.__objects_base_path = "/home/pi/data/objects/"
self.__ecotaxa_path = os.path.join(self.__export_path, "ecotaxa")
self.__global_metadata = None
self.__working_path = ""
self.__working_obj_path = ""
self.__archive_fn = ""
if not os.path.exists(self.__ecotaxa_path):
# create the path!
os.makedirs(self.__ecotaxa_path)
if not os.path.exists(self.__objects_base_path):
# create the path!
os.makedirs(self.__objects_base_path)
# Morphocut's pipeline will be created at runtime otherwise shit ensues
logger.success("planktoscope.segmenter is initialised and ready to go!")
@ -85,7 +91,7 @@ class SegmenterProcess(multiprocessing.Process):
# TODO wrap morphocut.Call(logger.debug()) in something that allows it not to be added to the pipeline
# if the logger.level is not debug. Might not be as easy as it sounds.
# Recursively find .jpg files in import_path.
# Sort to get consective frames.
# Sort to get consecutive frames.
abs_path = morphocut.file.Find(
self.__working_path, [".jpg"], sort=True, verbose=True
)
@ -174,7 +180,7 @@ class SegmenterProcess(multiprocessing.Process):
# Define the name of each object
object_fn = morphocut.str.Format(
os.path.join(self.__working_path, "objects", "{name}.jpg"),
os.path.join(self.__working_obj_path, "{name}.jpg"),
name=object_id,
)
@ -215,7 +221,7 @@ class SegmenterProcess(multiprocessing.Process):
)
id_json = morphocut.str.Format(
'{"object_id":"{object_id}"}', object_id=object_id
'{{"object_id":"{object_id}"}}', object_id=object_id
)
# Publish the object_id to via MQTT to Node-RED
@ -248,9 +254,9 @@ class SegmenterProcess(multiprocessing.Process):
)
img_paths = [x[0] for x in os.walk(self.__img_path)]
logger.info(f"The pipeline will be run in {len(img_paths)} directories")
logger.debug(f"The pipeline will be run in these directories {img_paths}")
logger.debug(f"Those are {img_paths}")
for path in img_paths:
logger.info("Checking for the presence of metadata.json")
logger.info(f"{path}: Checking for the presence of metadata.json")
if os.path.exists(os.path.join(path, "metadata.json")):
# The file exists, let's run the pipe!
logger.info(f"Loading the metadata file for {path}")
@ -272,10 +278,23 @@ class SegmenterProcess(multiprocessing.Process):
self.__working_path = path
# recreate the subfolder img architecture of this folder inside objects
# when we split the working path with the base img path, we get the date/sample architecture back
# "/home/pi/data/img/2020-10-17/5/5".split("/home/pi/data/img/")[1] => '2020-10-17/5/5'
sample_path = self.__working_path.split(self.__img_path)[1].strip()
logger.debug(f"base obj path is {self.__objects_base_path}")
logger.debug(f"sample path is {sample_path}")
self.__working_obj_path = os.path.join(
self.__objects_base_path, sample_path
)
logger.debug(
f"The working objects path is {self.__working_obj_path}"
)
# Create the objects path
if not os.path.exists(os.path.join(self.__working_path, "objects")):
if not os.path.exists(self.__working_obj_path):
# create the path!
os.makedirs(os.path.join(self.__working_path, "objects"))
os.makedirs(self.__working_obj_path)
logger.debug(f"The archive folder is {self.__archive_fn}")
@ -290,7 +309,7 @@ class SegmenterProcess(multiprocessing.Process):
logger.exception(f"There was an error in the pipeline {e}")
logger.info(f"Pipeline has been run for {path}")
else:
logger.info("Moving to the next folder, this one's empty")
logger.info(f"Moving to the next folder, {path} is empty")
# remove directory
# shutil.rmtree(import_path)