simba-uw-tf-dev 5.4.9__tar.gz → 5.5.2__tar.gz

{simba_uw_tf_dev-5.4.9 → simba_uw_tf_dev-5.5.2}/.gitignore

@@ -1,45 +1,52 @@
-# Byte-compiled / optimized Python files
-__pycache__/
-*.py[cod]
-
-# Virtual environment
-venv/
-env/
-ENV/
-
-# IDE or editor specific files
-.idea/
-*.o
-*.pyc
-*.class
-.ipynb_checkpoints/
-.pytest_cache/
-simba/pose_configurations_archive/
-
-# Ignore PyPI build artifacts
-dist/
-build/
-runs/
-*.egg-info/
-*.egg
-*.tar.gz
-*.whl
-*.pt
-*.cursorrules
-
-# dev
-simba/sandbox
-
-#local docs build
-_build/html/
-docs/_build
-/docs/_build/
-/simba/sandbox/
-
-
-# ignore recent projects file anywhere
-**/.recent_projects.txt
-
-# Claude Code
-simba/.claude/
-.claude/
+# Byte-compiled / optimized Python files
+__pycache__/
+*.py[cod]
+
+# Virtual environment
+venv/
+env/
+ENV/
+
+# IDE or editor specific files
+.idea/
+*.o
+*.pyc
+*.class
+.ipynb_checkpoints/
+.pytest_cache/
+simba/pose_configurations_archive/
+
+# Ignore PyPI build artifacts
+dist/
+build/
+runs/
+*.egg-info/
+*.egg
+*.tar.gz
+*.whl
+*.pt
+*.cursorrules
+
+# dev
+simba/sandbox
+
+#local docs build
+_build/html/
+docs/_build
+/docs/_build/
+/simba/sandbox/
+
+
+# ignore recent projects file anywhere
+**/.recent_projects.txt
+
+# Claude Code
+simba/.claude/
+.claude/
+
+# runtime logs written by SimBA into project folders (incl. test fixtures)
+**/logs/project_log.log
+
+# macOS finder metadata
+.DS_Store
+**/.DS_Store

{simba_uw_tf_dev-5.4.9 → simba_uw_tf_dev-5.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: simba_uw_tf_dev
-Version: 5.4.9
+Version: 5.5.2
 Summary: Toolkit for computer classification and analysis of behaviors in experimental animals
 Home-page: https://github.com/sgoldenlab/simba
 Author: Simon Nilsson, Jia Jie Choong, Sophia Hwang

{simba_uw_tf_dev-5.4.9 → simba_uw_tf_dev-5.5.2}/README.md

@@ -20,7 +20,7 @@ SimBA is a toolkit for creating supervised machine-learning classifiers of anima
 **Pre-print: [Simple Behavioral Analysis (SimBA) – an open source toolkit for computer classification of complex social behaviors in experimental animals](https://www.biorxiv.org/content/10.1101/2020.04.19.049452v2)**
 
 <p align="center">
-<img src="https://github.com/sgoldenlab/simba/blob/master/images/landing_1.gif" />
+<img src="images/landing_1.webp" />
 </p>
 
 ## Quickstart
@@ -58,6 +58,12 @@ See **[Scenario 1](docs/Scenario1.md)** for a worked example that takes raw trac
     - *Movement & directionality:* distance plots, velocity/data line plots, directionality overlays (animal→animal, →body-part, →ROI).
     - *Assay-specific:* cue-light, light/dark box, spontaneous-alternation, circular/polar plots.
 
+<p align="center">
+<a href="https://simba-uw-tf-dev.readthedocs.io/en/latest/index.html"><img src="images/simba_splash.webp" width="900" alt="SimBA capabilities: 85 methods" /></a>
+<br>
+<a href="https://simba-uw-tf-dev.readthedocs.io/en/latest/index.html"><img src="https://img.shields.io/badge/MORE_INFORMATION_AT-readthedocs-21567a?style=for-the-badge&logo=readthedocs&logoColor=white" alt="More information at Read the Docs" /></a>
+</p>
+
 ##  Documentation: Scenario tutorials
 
 To faciliate the initial use of SimBA, we provide several use scenarios. We have created these scenarios around a hypothetical experiment that take a user from initial use (completely new start) all the way through analyzing a complete experiment and then adding additional experimental datasets to an initial project.

{simba_uw_tf_dev-5.4.9 → simba_uw_tf_dev-5.5.2}/setup.py

@@ -30,7 +30,7 @@ with open(GPU_REQUIREMENTS_PATH, "r") as f:
 # Setup configuration
 setuptools.setup(
     name="simba_uw_tf_dev",
-    version="5.4.9",
+    version="5.5.2",
     author="Simon Nilsson, Jia Jie Choong, Sophia Hwang",
     author_email="sronilsson@gmail.com",
     description="Toolkit for computer classification and analysis of behaviors in experimental animals",

simba_uw_tf_dev-5.5.2/simba/assets/.recent_projects.txt

@@ -0,0 +1,2 @@
+D:/troubleshooting/multi_animal_dlc_two_c57/project_folder/project_config.ini
+I:/mitra/nick_ressler/project_folder/project_config.ini

{simba_uw_tf_dev-5.4.9 → simba_uw_tf_dev-5.5.2}/simba/data_processors/circling_detector.py

@@ -1,4 +1,5 @@
 import os
+from copy import deepcopy
 from typing import Optional, Union
 
 import numpy as np
@@ -111,6 +112,7 @@ class CirclingDetector(ConfigReader):
             save_file_path = os.path.join(self.save_dir, f'{video_name}.csv')
             df = read_df(file_path=file_path, file_type='csv').reset_index(drop=True)
             _, px_per_mm, fps = read_video_info(video_info_df=self.video_info_df, video_name=video_name)
+            original_cols = deepcopy(list(df.columns))
             df.columns = [str(x).lower() for x in df.columns]
             check_valid_dataframe(df=df, valid_dtypes=Formats.NUMERIC_DTYPES.value, required_fields=self.required_field)
 
@@ -129,6 +131,7 @@ class CirclingDetector(ConfigReader):
             circling_idx = np.argwhere(sliding_circular_range >= self.circular_range_threshold).astype(np.int32).flatten()
             movement_idx = np.argwhere(movement_sum >= self.movement_threshold).astype(np.int32).flatten()
             circling_idx = [x for x in movement_idx if x in circling_idx]
+            df.columns = original_cols
             df[f'Probability_{CIRCLING}'] = 0
             df[CIRCLING] = 0
             df.loc[circling_idx, CIRCLING] = 1
@@ -153,6 +156,10 @@ class CirclingDetector(ConfigReader):
         stdout_success(msg=f'Results saved in {self.save_dir} directory.')
 
 
+
+# detector = CirclingDetector(config_path=r"I:\mitra\nick_ressler\project_folder\project_config.ini")
+# detector.run()
+
 # detector = CirclingDetector(config_path=r"F:\troubleshooting\sam\sam\project_folder\project_config.ini")
 # detector.run()
 

{simba_uw_tf_dev-5.4.9 → simba_uw_tf_dev-5.5.2}/simba/data_processors/cuda/timeseries.py

@@ -1,6 +1,11 @@
 import math
 from time import perf_counter
-from typing import Literal, Optional
+from typing import Optional
+
+try:
+    from typing import Literal
+except:
+    from typing_extensions import Literal
 
 import numpy as np
 from numba import cuda, float64

{simba_uw_tf_dev-5.4.9 → simba_uw_tf_dev-5.5.2}/simba/data_processors/freezing_detector.py

@@ -1,4 +1,5 @@
 import os
+from copy import deepcopy
 from typing import Optional, Union
 
 import numpy as np
@@ -135,6 +136,7 @@ class FreezingDetector(ConfigReader):
             save_file_path = os.path.join(self.save_dir, f'{video_name}.csv')
             df = read_df(file_path=file_path, file_type='csv').reset_index(drop=True)
             _, px_per_mm, fps = read_video_info(vid_info_df=self.video_info_df, video_name=video_name)
+            original_cols = deepcopy(list(df.columns))
             df.columns = [str(x).lower() for x in df.columns]
             check_valid_dataframe(df=df, valid_dtypes=Formats.NUMERIC_DTYPES.value, required_fields=self.required_field)
             nose_shifted = FeatureExtractionMixin.create_shifted_df(df[self.nose_heads])
@@ -153,6 +155,7 @@ class FreezingDetector(ConfigReader):
             mean_movement = np.mean(movement, axis=1)
             mm_s = TimeseriesFeatureMixin.sliding_descriptive_statistics(data=mean_movement.astype(np.float32), window_sizes=np.array([1], dtype=np.float64), sample_rate=int(fps), statistics=typed.List(["sum"]))[0].flatten()
             freezing_idx = np.argwhere(mm_s <= self.movement_threshold).astype(np.int32).flatten()
+            df.columns = original_cols
             df[f'Probability_{FREEZING}'] = 0
             df[FREEZING] = 0
             df.loc[freezing_idx, FREEZING] = 1
@@ -173,6 +176,18 @@ class FreezingDetector(ConfigReader):
         agg_results.to_csv(agg_results_path)
         self.timer.stop_timer(); stdout_success(msg=f'Results saved in {self.save_dir} directory.', elapsed_time=self.timer.elapsed_time_str)
 
+
+# FreezingDetector(
+#     data_dir=r'I:\mitra\nick_ressler\project_folder\csv\outlier_corrected_movement_location',
+#     config_path=r"I:\mitra\nick_ressler\project_folder\project_config.ini",
+#     time_window=3,
+#     movement_threshold=3,
+#     shortest_bout=100
+# ).run()
+
+
+
+
 #
 # FreezingDetector(
 #     data_dir=r'G:\projects\jason_zhang\jason_project\project_folder\csv\outlier_corrected_movement_location',

{simba_uw_tf_dev-5.4.9 → simba_uw_tf_dev-5.5.2}/simba/data_processors/yolo_track_cleaner.py

@@ -14,7 +14,9 @@ from simba.utils.printing import SimbaTimer, stdout_success
 from simba.utils.read_write import (find_files_of_filetypes_in_directory,
                                     get_fn_ext, recursive_file_search)
 
-warnings.simplefilter(action='ignore', category=pd.errors.SettingWithCopyWarning)
+_SETTING_WITH_COPY_WARNING = getattr(pd.errors, 'SettingWithCopyWarning', None)   # absent in pandas < 1.0
+if _SETTING_WITH_COPY_WARNING is not None:
+    warnings.simplefilter(action='ignore', category=_SETTING_WITH_COPY_WARNING)
 
 FRAME = 'FRAME'
 CLASS_ID = 'CLASS_ID'

{simba_uw_tf_dev-5.4.9 → simba_uw_tf_dev-5.5.2}/simba/feature_extractors/amber_feature_extractor.py

@@ -105,6 +105,11 @@ class AmberFeatureExtractor(ConfigReader, FeatureExtractionMixin):
        :width: 400
        :align: center
 
+    ..  youtube:: yBS2_9it__I
+       :width: 640
+       :height: 480
+       :align: center
+
     :example:
 
     >>> AmberFeatureExtractor(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini')