Source code for sleap.gui.learning.runners

Run training/inference in background process via CLI.
import abc
import attr
import os
import subprocess as sub
import tempfile
import time
from datetime import datetime
from typing import Any, Callable, Dict, List, Optional, Text, Tuple

from PySide2 import QtWidgets

from sleap import Labels, Video, LabeledFrame
from sleap.gui.learning.configs import ConfigFileInfo
from sleap.nn import training
from sleap.nn.config import TrainingJobConfig


[docs]@attr.s(auto_attribs=True) class ItemForInference(abc.ABC): """ Abstract base class for item on which we can run inference via CLI. Must have `path` and `cli_args` properties, used to build CLI call. """ @property @abc.abstractmethod def path(self) -> Text: pass @property @abc.abstractmethod def cli_args(self) -> List[Text]: pass
[docs]@attr.s(auto_attribs=True) class VideoItemForInference(ItemForInference): """ Encapsulate data about video on which inference should run. This allows for inference on an arbitrary list of frames from video. Attributes: video: the :py:class:`Video` object (which already stores its own path) frames: list of frames for inference; if None, then all frames are used use_absolute_path: whether to use absolute path for inference cli call """ video: Video frames: Optional[List[int]] = None use_absolute_path: bool = False @property def path(self): if self.use_absolute_path: return os.path.abspath( return @property def cli_args(self): arg_list = list() arg_list.append(self.path) # TODO: better support for video params if hasattr(, "dataset") and arg_list.extend(("--video.dataset", if ( hasattr(, "input_format") and ): arg_list.extend(("--video.input_format", # -Y represents endpoint of [X, Y) range but inference cli expects # [X, Y-1] range (so add 1 since negative). frame_int_list = [i + 1 if i < 0 else i for i in self.frames] arg_list.extend(("--frames", ",".join(map(str, frame_int_list)))) return arg_list
[docs]@attr.s(auto_attribs=True) class DatasetItemForInference(ItemForInference): """ Encapsulate data about frame selection based on dataset data. Attributes: labels_path: path to the saved :py:class:`Labels` dataset. frame_filter: which subset of frames to get from dataset, supports * "user" * "suggested" use_absolute_path: whether to use absolute path for inference cli call. """ labels_path: str frame_filter: str = "user" use_absolute_path: bool = False @property def path(self): if self.use_absolute_path: return os.path.abspath(self.labels_path) return self.labels_path @property def cli_args(self): args_list = ["--labels", self.path] if self.frame_filter == "user": args_list.append("--only-labeled-frames") elif self.frame_filter == "suggested": args_list.append("--only-suggested-frames") return args_list
[docs]@attr.s(auto_attribs=True) class ItemsForInference: """Encapsulates list of items for inference.""" items: List[ItemForInference] total_frame_count: int def __len__(self): return len(self.items) @classmethod def from_video_frames_dict( cls, video_frames_dict: Dict[Video, List[int]], total_frame_count: int ): items = [] for video, frames in video_frames_dict.items(): if frames: items.append(VideoItemForInference(video=video, frames=frames)) return cls(items=items, total_frame_count=total_frame_count)
[docs]@attr.s(auto_attribs=True) class InferenceTask: """Encapsulates all data needed for running inference via CLI.""" trained_job_paths: List[str] inference_params: Dict[str, Any] = attr.ib(default=attr.Factory(dict)) labels: Optional[Labels] = None labels_filename: Optional[str] = None results: List[LabeledFrame] = attr.ib(default=attr.Factory(list))
[docs] def make_predict_cli_call( self, item_for_inference: ItemForInference, output_path: Optional[str] = None ) -> List[Text]: """Makes list of CLI arguments needed for running inference.""" cli_args = ["sleap-track"] cli_args.extend(item_for_inference.cli_args) # TODO: encapsulate in inference item class if ( not self.trained_job_paths and "tracking.tracker" in self.inference_params and self.labels_filename ): # No models so we must want to re-track previous predictions cli_args.extend(("--labels", self.labels_filename)) # Make path where we'll save predictions (if not specified) if output_path is None: if self.labels_filename: # Make a predictions directory next to the labels dataset file predictions_dir = os.path.join( os.path.dirname(self.labels_filename), "predictions" ) os.makedirs(predictions_dir, exist_ok=True) else: # Dataset filename wasn't given, so save predictions in same dir # as the video predictions_dir = os.path.dirname( # Build filename with video name and timestamp timestamp ="%y%m%d_%H%M%S") output_path = os.path.join( predictions_dir, f"{os.path.basename(item_for_inference.path)}.{timestamp}.predictions.slp", ) for job_path in self.trained_job_paths: cli_args.extend(("-m", job_path)) optional_items_as_nones = ( "tracking.target_instance_count", "tracking.kf_init_frame_count", ) for key in optional_items_as_nones: if key in self.inference_params and self.inference_params[key] is None: del self.inference_params[key] # --tracking.kf_init_frame_count enables the kalman filter tracking # so if not set, then remove other (unused) args if "tracking.kf_init_frame_count" not in self.inference_params: if "tracking.kf_node_indices" in self.inference_params: del self.inference_params["tracking.kf_node_indices"] bool_items_as_ints = ( "tracking.pre_cull_to_target", "tracking.post_connect_single_breaks", ) for key in bool_items_as_ints: if key in self.inference_params: self.inference_params[key] = int(self.inference_params[key]) for key, val in self.inference_params.items(): if not key.startswith(("_", "outputs.", "model.", "data.")): cli_args.extend((f"--{key}", str(val))) cli_args.extend(("-o", output_path)) return cli_args, output_path
[docs] def predict_subprocess( self, item_for_inference: ItemForInference, append_results: bool = False, waiting_callback: Optional[Callable] = None, ) -> Tuple[Text, bool]: """Runs inference in a subprocess.""" cli_args, output_path = self.make_predict_cli_call(item_for_inference) print("Command line call:") print(" \\\n".join(cli_args)) print() with sub.Popen(cli_args) as proc: while proc.poll() is None: if waiting_callback is not None: if waiting_callback() == -1: # -1 signals user cancellation return "", False time.sleep(0.1) print(f"Process return code: {proc.returncode}") success = proc.returncode == 0 if success and append_results: # Load frames from inference into results list new_inference_labels = Labels.load_file(output_path, match_to=self.labels) self.results.extend(new_inference_labels.labeled_frames) return output_path, success
[docs] def merge_results(self): """Merges result frames into labels dataset.""" # Remove any frames without instances new_lfs = list(filter(lambda lf: len(lf.instances), self.results)) # Merge predictions into current labels dataset _, _, new_conflicts = Labels.complex_merge_between( self.labels, new_labels=Labels(new_lfs), unify=False, # since we used match_to when loading predictions file ) # new predictions should replace old ones Labels.finish_complex_merge(self.labels, new_conflicts)
[docs]def write_pipeline_files( output_dir: str, labels_filename: str, config_info_list: List[ConfigFileInfo], inference_params: Dict[str, Any], items_for_inference: ItemsForInference, ): """Writes the config files and scripts for manually running pipeline.""" # Use absolute path for all files that aren't contained in the output dir. labels_filename = os.path.abspath(labels_filename) # Preserve current working directory and change working directory to the # output directory, so we can set local paths relative to that. old_cwd = os.getcwd() os.chdir(output_dir) new_cfg_filenames = [] train_script = "#!/bin/bash\n" for cfg_info in config_info_list: if cfg_info.dont_retrain: # Use full absolute path to already training model trained_path = os.path.normpath(os.path.join(old_cwd, cfg_info.path)) new_cfg_filenames.append(trained_path) else: # We're training this model, so save config file... # First we want to set the run folder so that we know where to find # the model after it's trained. # We'll use local path to the output directory (cwd). # Note that setup_new_run_folder does things relative to cwd which # is the main reason we're setting it to the output directory rather # than just using normpath. cfg_info.config.outputs.runs_folder = "" training.setup_new_run_folder(cfg_info.config.outputs) # Now we set the filename for the training config file new_cfg_filename = f"{cfg_info.head_name}.json" # Save the config file cfg_info.config.save_json(new_cfg_filename) # Keep track of the path where we'll find the trained model new_cfg_filenames.append(cfg_info.config.outputs.run_name) # Add a line to the script for training this model train_script += f"sleap-train {new_cfg_filename} {labels_filename}\n" # Write the script to train the models which need to be trained with open(os.path.join(output_dir, ""), "w") as f: f.write(train_script) # Build the script for running inference inference_script = "#!/bin/bash\n" # Object with settings for inference inference_task = InferenceTask( labels_filename=labels_filename, trained_job_paths=new_cfg_filenames, inference_params=inference_params, ) for item_for_inference in items_for_inference.items: # We want to save predictions in output dir so use local path prediction_output_path = ( f"{os.path.basename(item_for_inference.path)}.predictions.slp" ) # Use absolute path to video item_for_inference.use_absolute_path = True # Get list of cli args cli_args, _ = inference_task.make_predict_cli_call( item_for_inference=item_for_inference, output_path=prediction_output_path, ) # And join them into a single call to inference inference_script += " ".join(cli_args) + "\n" # And write it with open(os.path.join(output_dir, ""), "w") as f: f.write(inference_script) # Restore the working directory os.chdir(old_cwd)
[docs]def run_learning_pipeline( labels_filename: str, labels: Labels, config_info_list: List[ConfigFileInfo], inference_params: Dict[str, Any], items_for_inference: ItemsForInference, ) -> int: """Runs training (as needed) and inference. Args: labels_filename: Path to already saved current labels object. labels: The current labels object; results will be added to this. config_info_list: List of ConfigFileInfo with configs for training and inference. inference_params: Parameters to pass to inference. frames_to_predict: Dict that gives list of frame indices for each video. Returns: Number of new frames added to labels. """ save_viz = inference_params.get("_save_viz", False) # Train the TrainingJobs trained_job_paths = run_gui_training( labels_filename=labels_filename, labels=labels, config_info_list=config_info_list, gui=True, save_viz=save_viz, ) # Check that all the models were trained if None in trained_job_paths.values(): return -1 inference_task = InferenceTask( labels=labels, labels_filename=labels_filename, trained_job_paths=list(trained_job_paths.values()), inference_params=inference_params, ) # Run the Predictor for suggested frames new_labeled_frame_count = run_gui_inference(inference_task, items_for_inference) return new_labeled_frame_count
[docs]def run_gui_training( labels_filename: str, labels: Labels, config_info_list: List[ConfigFileInfo], gui: bool = True, save_viz: bool = False, ) -> Dict[Text, Text]: """ Runs training for each training job. Args: labels: Labels object from which we'll get training data. config_info_list: List of ConfigFileInfo with configs for training. gui: Whether to show gui windows and process gui events. save_viz: Whether to save visualizations from training. Returns: Dictionary, keys are head name, values are path to trained config. """ trained_job_paths = dict() if gui: from sleap.nn.monitor import LossViewer from sleap.gui.widgets.imagedir import QtImageDirectoryWidget # open training monitor window win = LossViewer() win.resize(600, 400) for config_info in config_info_list: if config_info.dont_retrain: if not config_info.has_trained_model: raise ValueError( f"Config is set to not retrain but no trained model found: {config_info.path}" ) print( f"Using already trained model for {config_info.head_name}: {config_info.path}" ) trained_job_paths[config_info.head_name] = config_info.path else: job = config_info.config model_type = config_info.head_name # We'll pass along the list of paths we actually used for loading # the videos so that we don't have to rely on the paths currently # saved in the labels file for finding videos. video_path_list = [video.filename for video in labels.videos] # Update save dir and run name for job we're about to train # so we have access to them here (rather than letting # train_subprocess update them). # training.Trainer.set_run_name(job, labels_filename) job.outputs.runs_folder = os.path.join( os.path.dirname(labels_filename), "models" ) training.setup_new_run_folder( job.outputs, base_run_name=f"{model_type}.{len(labels)}" ) if gui: print("Resetting monitor window.") win.reset(what=str(model_type)) win.setWindowTitle(f"Training Model - {str(model_type)}") win.set_message(f"Preparing to run training...") if save_viz: viz_window = QtImageDirectoryWidget.make_training_vizualizer( job.outputs.run_path ) viz_window.move(win.x() + win.width() + 20, win.y()) win.on_epoch.connect(viz_window.poll) print(f"Start training {str(model_type)}...") def waiting(): if gui: QtWidgets.QApplication.instance().processEvents() # Run training trained_job_path, success = train_subprocess( job_config=job, labels_filename=labels_filename, video_paths=video_path_list, waiting_callback=waiting, save_viz=save_viz, ) if success: # get the path to the resulting TrainingJob file trained_job_paths[model_type] = trained_job_path print(f"Finished training {str(model_type)}.") else: if gui: win.close() QtWidgets.QMessageBox( text=f"An error occurred while training {str(model_type)}. Your command line terminal may have more information about the error." ).exec_() trained_job_paths[model_type] = None if gui: # close training monitor window win.close() return trained_job_paths
[docs]def run_gui_inference( inference_task: InferenceTask, items_for_inference: ItemsForInference, gui: bool = True, ) -> int: """Run inference on specified frames using models from training_jobs. Args: inference_task: Encapsulates information needed for running inference, such as labels dataset and models. items_for_inference: Encapsulates information about the videos (etc.) on which we're running inference. gui: Whether to show gui windows and process gui events. Returns: Number of new frames added to labels. """ if gui: # show message while running inference progress = QtWidgets.QProgressDialog( f"Running inference on {len(items_for_inference)} videos...", "Cancel", 0, len(items_for_inference), ) QtWidgets.QApplication.instance().processEvents() # Make callback to process events while running inference def waiting(done_count): if gui: QtWidgets.QApplication.instance().processEvents() progress.setValue(done_count) if progress.wasCanceled(): return -1 for i, item_for_inference in enumerate(items_for_inference.items): # Run inference for desired frames in this video predictions_path, success = inference_task.predict_subprocess( item_for_inference, append_results=True, waiting_callback=lambda: waiting(i) ) if not success: if gui: progress.close() QtWidgets.QMessageBox( text=f"An error occcured during inference. Your command line terminal may have more information about the error." ).exec_() return -1 inference_task.merge_results() # close message window if gui: progress.close() # return total_new_lf_count return len(inference_task.results)
[docs]def train_subprocess( job_config: TrainingJobConfig, labels_filename: str, video_paths: Optional[List[Text]] = None, waiting_callback: Optional[Callable] = None, save_viz: bool = False, ): """Runs training inside subprocess.""" # run_name = job_config.outputs.run_name run_path = job_config.outputs.run_path success = False with tempfile.TemporaryDirectory() as temp_dir: # Write a temporary file of the TrainingJob so that we can respect # any changed made to the job attributes after it was loaded. temp_filename ="%y%m%d_%H%M%S") + "_training_job.json" training_job_path = os.path.join(temp_dir, temp_filename) job_config.save_json(training_job_path) # Build CLI arguments for training cli_args = [ "sleap-train", training_job_path, labels_filename, "--zmq", ] if save_viz: cli_args.append("--save_viz") # Use cli arg since cli ignores setting in config if job_config.outputs.tensorboard.write_logs: cli_args.append("--tensorboard") # Add list of video paths so we can find video even if paths in saved # labels dataset file are incorrect. if video_paths: cli_args.extend(("--video-paths", ",".join(video_paths))) print(cli_args) if not SKIP_TRAINING: # Run training in a subprocess with sub.Popen(cli_args) as proc: # Wait till training is done, calling a callback if given. while proc.poll() is None: if waiting_callback is not None: if waiting_callback() == -1: # -1 signals user cancellation return "", False time.sleep(0.1) success = proc.returncode == 0 print("Run Path:", run_path) return run_path, success