Update model.PoseEstimation to infer_output_dir

CHANGELOG.md

@@ -3,9 +3,13 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and 
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
-## [0.2.11] - 2023-11-28
+## [0.2.11] - 2023-01-04
 
-+ Fix - Modify training to update init_weights path in pose_cfg.yaml
++ Fix - docstring typo
++ Fix - `dj.config()` setup moved to `tutorial_pipeline.py` instead of `__init__.py`
++ Bugfix - Resolved AttributeError from the latest update of the YAML dependency
++ Update - Flowchart images to increase consistency with other DataJoint Elements
++ Update - Elements installed directly from GitHub instead of PyPI
 
 ## [0.2.10] - 2023-11-20
 

docs/src/.overrides/assets/stylesheets/extra.css

@@ -92,7 +92,6 @@ html a[title="YouTube"].md-social__link svg {
     /* --md-footer-fg-color: var(--dj-white); */
 }
 
-[data-md-color-scheme="slate"] td,
-th {
+[data-md-color-scheme="slate"] .jupyter-wrapper .Table Td {
     color: var(--dj-black)
 }

element_deeplabcut/__init__.py

@@ -1,21 +1 @@
-import os
-import datajoint as dj
 
-if "custom" not in dj.config:
-    dj.config["custom"] = {}
-
-# overwrite dj.config['custom'] values with environment variables if available
-
-dj.config["custom"]["database.prefix"] = os.getenv(
-    "DATABASE_PREFIX", dj.config["custom"].get("database.prefix", "")
-)
-
-dj.config["custom"]["dlc_root_data_dir"] = os.getenv(
-    "DLC_ROOT_DATA_DIR", dj.config["custom"].get("dlc_root_data_dir", "")
-)
-
-dj.config["custom"]["dlc_processed_data_dir"] = os.getenv(
-    "DLC_PROCESSED_DATA_DIR", dj.config["custom"].get("dlc_processed_data_dir", "")
-)
-
-db_prefix = dj.config["custom"].get("database.prefix", "")

element_deeplabcut/model.py

@@ -7,7 +7,7 @@
 import os
 import cv2
 import csv
-import yaml
+from ruamel.yaml import YAML
 import inspect
 import importlib
 import numpy as np
@@ -239,8 +239,9 @@ def extract_new_body_parts(cls, dlc_config: dict, verbose: bool = True):
                 ".yaml",
             ), f"dlc_config is neither dict nor filepath\n Check: {dlc_config_fp}"
             if dlc_config_fp.suffix in (".yml", ".yaml"):
+                yaml = YAML(typ="safe", pure=True)
                 with open(dlc_config_fp, "rb") as f:
-                    dlc_config = yaml.safe_load(f)
+                    dlc_config = yaml.load(f)
         # -- Check and insert new BodyPart --
         assert "bodyparts" in dlc_config, f"Found no bodyparts section in {dlc_config}"
         tracked_body_parts = cls.fetch("body_part")
@@ -307,7 +308,7 @@ class Model(dj.Manual):
         config_template (longblob): Dictionary of the config for analyze_videos().
         project_path ( varchar(255) ): DLC's project_path in config relative to root.
         model_prefix ( varchar(32) ): Optional. Prefix for model files.
-        model_description ( varchar(1000) ): Optional. User-entered description.
+        model_description ( varchar(300) ): Optional. User-entered description.
         TrainingParamSet (foreign key): Optional. Training parameters primary key.
 
     Note:
@@ -381,8 +382,9 @@ def insert_new_model(
             "dlc_config is not a filepath" + f"\n Check: {dlc_config_fp}"
         )
         if dlc_config_fp.suffix in (".yml", ".yaml"):
+            yaml = YAML(typ="safe", pure=True)
             with open(dlc_config_fp, "rb") as f:
-                dlc_config = yaml.safe_load(f)
+                dlc_config = yaml.load(f)
         if isinstance(params, dict):
             dlc_config.update(params)
 
@@ -704,7 +706,14 @@ def make(self, key):
         task_mode, output_dir = (PoseEstimationTask & key).fetch1(
             "task_mode", "pose_estimation_output_dir"
         )
-
+        if not output_dir:
+            output_dir = PoseEstimationTask.infer_output_dir(
+                key, relative=True, mkdir=True
+            )
+            # update pose_estimation_output_dir
+            PoseEstimationTask.update1(
+                {**key, "pose_estimation_output_dir": output_dir.as_posix()}
+            )
         output_dir = find_full_path(get_dlc_root_data_dir(), output_dir)
 
         # Triger PoseEstimation

element_deeplabcut/readers/dlc_reader.py

@@ -4,7 +4,7 @@
 import pandas as pd
 from pathlib import Path
 import pickle
-import ruamel.yaml as yaml
+from ruamel.yaml import YAML
 from element_interface.utils import find_root_directory, dict_to_uuid
 from .. import model
 from ..model import get_dlc_root_data_dir
@@ -145,7 +145,8 @@ def yml(self):
         """json-structured config.yaml file contents"""
         if self._yml is None:
             with open(self.yml_path, "rb") as f:
-                self._yml = yaml.safe_load(f)
+                yaml = YAML(typ="safe", pure=True)
+                self._yml = yaml.load(f)
         return self._yml
 
     @property