diff --git a/aliby/pipeline.py b/aliby/pipeline.py
index 7f02704b4d8ed8bbb912a1c4ae2218c3ee4bb575..be6936ed2b04e04c368177ede873d6b2e62d07b0 100644
--- a/aliby/pipeline.py
+++ b/aliby/pipeline.py
@@ -2,17 +2,14 @@
Pipeline and chaining elements.
"""
import logging
+import typing as t
import os
import re
import traceback
from copy import copy
from itertools import groupby
from pathlib import Path, PosixPath
-
-# from p_tqdm import p_map
from time import perf_counter
-
-# from abc import ABC, abstractmethod
from typing import Union
import h5py
@@ -54,6 +51,8 @@ logging.basicConfig(
class PipelineParameters(ParametersABC):
+ _pool_index = None
+
def __init__(
self, general, tiler, baby, extraction, postprocessing, reporting
):
@@ -72,7 +71,7 @@ class PipelineParameters(ParametersABC):
baby={},
extraction={},
postprocessing={},
- reporting={},
+ # reporting={},
):
"""
Load unit test experiment
@@ -137,14 +136,16 @@ class PipelineParameters(ParametersABC):
defaults["general"][k] = v
defaults["tiler"] = TilerParameters.default(**tiler).to_dict()
- defaults["baby"] = BabyParameters.default(**extraction).to_dict()
- defaults["extraction"] = exparams_from_meta(meta)
+ defaults["baby"] = BabyParameters.default(**baby).to_dict()
+ defaults["extraction"] = (
+ exparams_from_meta(meta)
+ or BabyParameters.default(**extraction).to_dict()
+ )
defaults["postprocessing"] = PostProcessorParameters.default(
**postprocessing
).to_dict()
defaults["reporting"] = {}
- # for k in defaults.keys():
- # exec("defaults[k].update(" + k + ")")
+
return cls(**{k: v for k, v in defaults.items()})
def load_logs(self):
@@ -161,12 +162,15 @@ class Pipeline(ProcessABC):
"""
iterative_steps = ["tiler", "baby", "extraction"]
+
step_sequence = [
"tiler",
"baby",
"extraction",
"postprocessing",
]
+
+ # Indicate groupings to perform special operations during step iteration
writer_groups = {
"tiler": ["trap_info"],
"baby": ["cell_info"],
@@ -244,7 +248,6 @@ class Pipeline(ProcessABC):
pipeline_parameters.general["directory"] = directory
pipeline_parameters.general["filter"] = Path(fpath).stem
- # Fix legacy postprocessing parameters
post_process_params = pipeline_parameters.postprocessing.get(
"parameters", None
)
@@ -322,13 +325,6 @@ class Pipeline(ProcessABC):
# position=0,
)
- # results = p_map(
- # lambda x: self.create_pipeline(*x),
- # [(k, i) for i, k in enumerate(image_ids.items())],
- # num_cpus=distributed,
- # position=0,
- # )
-
else: # Sequential
results = []
for k, v in tqdm(image_ids.items()):
@@ -338,142 +334,42 @@ class Pipeline(ProcessABC):
return results
def create_pipeline(self, image_id, index=None):
- config = self.parameters.to_dict()
- pparams = config
+ self._pool_index = index
name, image_id = image_id
- general_config = config["general"]
session = None
- earlystop = general_config.get("earlystop", None)
- process_from = {k: 0 for k in self.iterative_steps}
- steps = {}
- ow = {k: 0 for k in self.step_sequence}
-
- # check overwriting
- ow_id = general_config.get("overwrite", 0)
- ow = {step: True for step in self.step_sequence}
- if ow_id and ow_id != True:
- ow = {
- step: self.step_sequence.index(ow_id) < i
- for i, step in enumerate(self.step_sequence, 1)
- }
-
+ filename = None
+ run_kwargs = {"extraction": {"labels": None, "masks": None}}
try:
- # Set up
- directory = general_config["directory"]
+ (
+ filename,
+ meta,
+ config,
+ process_from,
+ tps,
+ steps,
+ earlystop,
+ session,
+ trackers_state,
+ ) = self._setup_pipeline(image_id)
+
+ loaded_writers = {
+ name: writer(filename)
+ for k in self.step_sequence
+ if k in self.writers
+ for name, writer in self.writers[k]
+ }
+ writer_ow_kwargs = {
+ "state": loaded_writers["state"].datatypes.keys(),
+ "baby": ["mother_assign"],
+ }
- image_wrapper = get_image_class(image_id)
+ # START PIPELINE
+ frac_clogged_traps = 0
+ min_process_from = min(process_from.values())
- with image_wrapper(
+ with get_image_class(image_id)(
image_id, **self.general.get("server_info", {})
) as image:
- filename = f"{directory}/{image.name}.h5"
- meta = MetaData(directory, filename)
-
- from_start = True
- trackers_state = None
- if Path(filename).exists(): # If no previous segmentation
-
- if not ow["tiler"]: # Try to load config from file
- try:
- with h5py.File(filename, "r") as f:
- steps["tiler"] = Tiler.from_hdf5(
- image, filename
- )
-
- legacy_get_last_tp = { # Function to support seg in ver < 0.24
- "tiler": lambda f: f[
- "trap_info/drifts"
- ].shape[0]
- - 1,
- "baby": lambda f: f["cell_info/timepoint"][
- -1
- ],
- "extraction": lambda f: f[
- "extraction/general/None/area/timepoint"
- ][-1],
- }
- for k, v in process_from.items():
- if not ow[k]:
- process_from[k] = legacy_get_last_tp[
- k
- ](f)
- # process_from[k] = f[
- # self.writer_groups[k][-1]
- # ].attrs.get(
- # "last_processed",
- # legacy_get_last_tp[k](f),
- # )
- process_from[k] += 1
- # get state array
- if not ow["baby"]:
- trackers_state = StateReader(
- filename
- ).get_formatted_states()
-
- config["tiler"] = steps[
- "tiler"
- ].parameters.to_dict()
- if not np.any(ow.values()):
- from_start = False
- print(
- f"Existing file {filename} will be used."
- )
- except Exception as e:
- print(e)
-
- # Delete datasets to overwrite and update pipeline data
- with h5py.File(filename, "r") as f:
- pparams = PipelineParameters.from_yaml(
- f.attrs["parameters"]
- ).to_dict()
-
- with h5py.File(filename, "a") as f:
- for k, v in ow.items():
- if v:
- for gname in self.writer_groups[k]:
- if gname in f:
- del f[gname]
-
- pparams[k] = config[k]
- meta.add_fields(
- {
- "parameters": PipelineParameters.from_dict(
- pparams
- ).to_yaml()
- },
- overwrite=True,
- )
-
- if from_start: # New experiment or overwriting
- if config.get("overwrite", False) == True or np.all(
- list(ow.values())
- ):
- if Path(filename).exists():
- os.remove(filename)
- meta.run()
- meta.add_fields( # Add non-logfile metadata
- {
- "omero_id,": config["general"]["id"],
- "image_id": image_id,
- "parameters": PipelineParameters.from_dict(
- pparams
- ).to_yaml(),
- }
- )
-
- tps = min(general_config["tps"], image.data.shape[0])
-
- run_kwargs = {"extraction": {"labels": None, "masks": None}}
- loaded_writers = {
- name: writer(filename)
- for k in self.step_sequence
- if k in self.writers
- for name, writer in self.writers[k]
- }
- writer_ow_kwargs = {
- "state": loaded_writers["state"].datatypes.keys(),
- "baby": ["mother_assign"],
- }
# Initialise Steps
if "tiler" not in steps:
@@ -508,7 +404,7 @@ class Pipeline(ProcessABC):
[c + "_bgsub" for c in config["extraction"]["sub_bg"]]
)
tmp = copy(config["extraction"]["multichannel_ops"])
- for op, (input_ch, op_id, red_ext) in tmp.items():
+ for op, (input_ch, _, _) in tmp.items():
if not set(input_ch).issubset(av_channels_wsub):
del config["extraction"]["multichannel_ops"][op]
@@ -518,112 +414,101 @@ class Pipeline(ProcessABC):
steps["extraction"] = Extractor.from_tiler(
exparams, store=filename, tiler=steps["tiler"]
)
+ pbar = tqdm(
+ range(min_process_from, tps),
+ desc=image.name,
+ initial=min_process_from,
+ total=tps,
+ # position=index + 1,
+ )
+ for i in pbar:
- # RUN
- # Adjust tps based on how many tps are available on the server
- frac_clogged_traps = 0
- # print(f"Processing from {process_from}")
- min_process_from = min(process_from.values())
- pbar = tqdm(
- range(min_process_from, tps),
- desc=image.name,
- initial=min_process_from,
- total=tps,
- # position=index + 1,
- )
- for i in pbar:
-
- if (
- frac_clogged_traps < earlystop["thresh_pos_clogged"]
- or i < earlystop["min_tp"]
- ):
-
- for step in self.iterative_steps:
- if i >= process_from[step]:
- t = perf_counter()
- result = steps[step].run_tp(
- i, **run_kwargs.get(step, {})
- )
- logging.debug(
- f"Timing:{step}:{perf_counter() - t}s"
- )
- if step in loaded_writers:
+ if (
+ frac_clogged_traps
+ < earlystop["thresh_pos_clogged"]
+ or i < earlystop["min_tp"]
+ ):
+
+ for step in self.iterative_steps:
+ if i >= process_from[step]:
t = perf_counter()
- loaded_writers[step].write(
- data=result,
- overwrite=writer_ow_kwargs.get(
- step, []
- ),
- tp=i,
- meta={"last_processed": i},
+ result = steps[step].run_tp(
+ i, **run_kwargs.get(step, {})
)
logging.debug(
- f"Timing:Writing-{step}:{perf_counter() - t}s"
+ f"Timing:{step}:{perf_counter() - t}s"
)
+ if step in loaded_writers:
+ t = perf_counter()
+ loaded_writers[step].write(
+ data=result,
+ overwrite=writer_ow_kwargs.get(
+ step, []
+ ),
+ tp=i,
+ meta={"last_processed": i},
+ )
+ logging.debug(
+ f"Timing:Writing-{step}:{perf_counter() - t}s"
+ )
- # Step-specific actions
-
- if step == "tiler":
- if i == min_process_from:
+ # Step-specific actions
+ if (
+ step == "tiler"
+ and i == min_process_from
+ ):
print(
f"Found {steps['tiler'].n_traps} traps in {image.name}"
)
- elif (
- step == "baby"
- ): # Write state and pass info to ext
- loaded_writers["state"].write(
- data=steps[
- step
- ].crawler.tracker_states,
- overwrite=loaded_writers[
- "state"
- ].datatypes.keys(),
- tp=i,
- )
- labels, masks = groupby_traps(
- result["trap"],
- result["cell_label"],
- result["edgemasks"],
- steps["tiler"].n_traps,
- )
-
- elif (
- step == "extraction"
- ): # Remove mask/label after ext
- for k in ["masks", "labels"]:
- run_kwargs[step][k] = None
-
- frac_clogged_traps = self.check_earlystop(
- filename, earlystop, steps["tiler"].tile_size
- )
- logging.debug(
- f"Quality:Clogged_traps:{frac_clogged_traps}"
- )
-
- frac = np.round(frac_clogged_traps * 100)
- pbar.set_postfix_str(f"{frac} Clogged")
- else: # Stop if more than X% traps are clogged
- logging.debug(
- f"EarlyStop:{earlystop['thresh_pos_clogged']*100}% traps clogged at time point {i}"
- )
- print(
- f"Stopping analysis at time {i} with {frac_clogged_traps} clogged traps"
- )
- meta.add_fields({"end_status": "Clogged"})
- break
-
- meta.add_fields({"last_processed": i})
- # Run post processing
-
- meta.add_fields({"end_status": "Success"})
- post_proc_params = PostProcessorParameters.from_dict(
- config["postprocessing"]
- )
- PostProcessor(filename, post_proc_params).run()
+ elif (
+ step == "baby"
+ ): # Write state and pass info to ext
+ loaded_writers["state"].write(
+ data=steps[
+ step
+ ].crawler.tracker_states,
+ overwrite=loaded_writers[
+ "state"
+ ].datatypes.keys(),
+ tp=i,
+ )
+ elif (
+ step == "extraction"
+ ): # Remove mask/label after ext
+ for k in ["masks", "labels"]:
+ run_kwargs[step][k] = None
+
+ frac_clogged_traps = self.check_earlystop(
+ filename, earlystop, steps["tiler"].tile_size
+ )
+ logging.debug(
+ f"Quality:Clogged_traps:{frac_clogged_traps}"
+ )
+
+ frac = np.round(frac_clogged_traps * 100)
+ pbar.set_postfix_str(f"{frac} Clogged")
+ else: # Stop if more than X% traps are clogged
+ logging.debug(
+ f"EarlyStop:{earlystop['thresh_pos_clogged']*100}% traps clogged at time point {i}"
+ )
+ print(
+ f"Stopping analysis at time {i} with {frac_clogged_traps} clogged traps"
+ )
+ meta.add_fields({"end_status": "Clogged"})
+ break
+
+ meta.add_fields({"last_processed": i})
+ # Run post processing
+
+ meta.add_fields({"end_status": "Success"})
+ post_proc_params = PostProcessorParameters.from_dict(
+ config["postprocessing"]
+ )
+ PostProcessor(filename, post_proc_params).run()
- # return 1
+ return 1
- except Exception as e: # bug in the trap getting
+ except Exception as e: # bug during setup or runtime
logging.exception(
f"Caught exception in worker thread (x = {name}):",
exc_info=True,
@@ -632,11 +517,9 @@ class Pipeline(ProcessABC):
# This prints the type, value, and stack trace of the
# current exception being handled.
traceback.print_exc()
- print()
raise e
finally:
- if session:
- session.close()
+ _close_session(session)
# try:
# compiler = ExperimentCompiler(None, filepath)
@@ -666,6 +549,146 @@ class Pipeline(ProcessABC):
return (traps_above_nthresh & traps_above_athresh).mean()
+ def _load_config_from_file(
+ self,
+ filename: PosixPath,
+ process_from: t.Dict[str, int],
+ trackers_state: t.List,
+ overwrite: t.Dict[str, bool],
+ ):
+ with h5py.File(filename, "r") as f:
+ for k in process_from.keys():
+ if not overwrite[k]:
+ process_from[k] = self.legacy_get_last_tp[k](f)
+ process_from[k] += 1
+ return process_from, trackers_state, overwrite
+
+ @staticmethod
+ def legacy_get_last_tp(step: str) -> t.Callable:
+ """Get last time-point in different ways depending
+ on which step we are using
+
+ To support segmentation in aliby < v0.24
+ TODO Deprecate and replace with State method
+ """
+ switch_case = {
+ "tiler": lambda f: f["trap_info/drifts"].shape[0] - 1,
+ "baby": lambda f: f["cell_info/timepoint"][-1],
+ "extraction": lambda f: f[
+ "extraction/general/None/area/timepoint"
+ ][-1],
+ }
+ return switch_case[step]
+
+ def _setup_pipeline(self, image_id: int):
+ config = self.parameters.to_dict()
+ pparams = config
+ image_id = image_id
+ general_config = config["general"]
+ session = None
+ earlystop = general_config.get("earlystop", None)
+ process_from = {k: 0 for k in self.iterative_steps}
+ steps = {}
+ ow = {k: 0 for k in self.step_sequence}
+
+ # check overwriting
+ ow_id = general_config.get("overwrite", 0)
+ ow = {step: True for step in self.step_sequence}
+ if ow_id and ow_id is not True:
+ ow = {
+ step: self.step_sequence.index(ow_id) < i
+ for i, step in enumerate(self.step_sequence, 1)
+ }
+
+ # Set up
+ directory = general_config["directory"]
+
+ with get_image_class(image_id)(
+ image_id, **self.general.get("server_info", {})
+ ) as image:
+ filename = Path(f"{directory}/{image.name}.h5")
+ meta = MetaData(directory, filename)
+
+ from_start = False if np.any(ow.values()) else True
+ trackers_state = []
+ # If no previous segmentation and keep tiler
+ if filename.exists():
+ if not ow["tiler"]:
+ steps["tiler"] = Tiler.from_hdf5(image, filename)
+ try:
+ (
+ process_from,
+ trackers_state,
+ ow,
+ ) = self._load_config_from_file(
+ filename, process_from, trackers_state, ow
+ )
+ # get state array
+ trackers_state = (
+ []
+ if ow["baby"]
+ else StateReader(filename).get_formatted_states()
+ )
+
+ config["tiler"] = steps["tiler"].parameters.to_dict()
+ except Exception:
+ pass
+
+ # Delete datasets to overwrite and update pipeline data
+ # Use existing parameters
+ with h5py.File(filename, "a") as f:
+ pparams = PipelineParameters.from_yaml(
+ f.attrs["parameters"]
+ ).to_dict()
+
+ for k, v in ow.items():
+ if v:
+ for gname in self.writer_groups[k]:
+ if gname in f:
+ del f[gname]
+
+ pparams[k] = config[k]
+ meta.add_fields(
+ {
+ "parameters": PipelineParameters.from_dict(
+ pparams
+ ).to_yaml()
+ },
+ overwrite=True,
+ )
+
+ if from_start: # New experiment or overwriting
+ if (
+ config.get("overwrite", False) is True
+ or np.all(list(ow.values()))
+ ) and filename.exists():
+ os.remove(filename)
+
+ meta.run()
+ meta.add_fields( # Add non-logfile metadata
+ {
+ "omero_id,": config["general"]["id"],
+ "image_id": image_id,
+ "parameters": PipelineParameters.from_dict(
+ pparams
+ ).to_yaml(),
+ }
+ )
+
+ tps = min(general_config["tps"], image.data.shape[0])
+
+ return (
+ filename,
+ meta,
+ config,
+ process_from,
+ tps,
+ steps,
+ earlystop,
+ session,
+ trackers_state,
+ )
+
def groupby_traps(traps, labels, edgemasks, ntraps):
# Group data by traps to pass onto extractor without re-reading hdf5
@@ -685,3 +708,8 @@ def groupby_traps(traps, labels, edgemasks, ntraps):
masks = {i: mask_d.get(i, []) for i in range(ntraps)}
return labels, masks
+
+
+def _close_session(session):
+ if session:
+ session.close()