From 3757d3fcca94d75525fdc5e9296952344e388b8b Mon Sep 17 00:00:00 2001 From: sronilsson Date: Fri, 17 Jan 2025 20:41:03 +0000 Subject: [PATCH] cleaned --- simba/data_processors/cuda/statistics.py | 6 ++++-- simba/data_processors/movement_calculator.py | 8 +++++--- simba/roi_tools/ROI_analyzer.py | 10 ++++++---- 3 files changed, 15 insertions(+), 9 deletions(-) diff --git a/simba/data_processors/cuda/statistics.py b/simba/data_processors/cuda/statistics.py index 3d81100e3..200cd016b 100644 --- a/simba/data_processors/cuda/statistics.py +++ b/simba/data_processors/cuda/statistics.py @@ -9,15 +9,17 @@ import numpy as np from numba import cuda from scipy.spatial import ConvexHull -from simba.utils.read_write import read_df, get_unique_values_in_iterable + +from simba.utils.read_write import get_unique_values_in_iterable, read_df from simba.utils.warnings import GPUToolsWarning + try: import cupy as cp from cupyx.scipy.spatial.distance import cdist except: GPUToolsWarning(msg='GPU tools not detected, reverting to CPU') - from scipy.spatial.distance import cdist import numpy as cp + from scipy.spatial.distance import cdist try: from cuml.cluster import KMeans diff --git a/simba/data_processors/movement_calculator.py b/simba/data_processors/movement_calculator.py index 908b11ff5..eb021178e 100644 --- a/simba/data_processors/movement_calculator.py +++ b/simba/data_processors/movement_calculator.py @@ -7,14 +7,16 @@ import numpy as np import pandas as pd -from simba.mixins.feature_extraction_supplement_mixin import FeatureExtractionSupplemental from simba.feature_extractors.perimeter_jit import jitted_centroid from simba.mixins.config_reader import ConfigReader from simba.mixins.feature_extraction_mixin import FeatureExtractionMixin -from simba.utils.checks import (check_if_filepath_list_is_empty,check_that_column_exist, check_valid_array, check_float) +from simba.mixins.feature_extraction_supplement_mixin import \ + FeatureExtractionSupplemental +from simba.utils.checks import (check_float, check_if_filepath_list_is_empty, + check_that_column_exist, check_valid_array) +from simba.utils.enums import Formats from simba.utils.printing import stdout_success from simba.utils.read_write import get_fn_ext, read_df -from simba.utils.enums import Formats class MovementCalculator(ConfigReader, FeatureExtractionMixin): diff --git a/simba/roi_tools/ROI_analyzer.py b/simba/roi_tools/ROI_analyzer.py index 1f18425f1..e01a6fa91 100644 --- a/simba/roi_tools/ROI_analyzer.py +++ b/simba/roi_tools/ROI_analyzer.py @@ -1,26 +1,28 @@ __author__ = "Simon Nilsson" import os -from typing import List, Optional, Union, Tuple - +from typing import List, Optional, Tuple, Union import numpy as np import pandas as pd from simba.mixins.config_reader import ConfigReader from simba.mixins.feature_extraction_mixin import FeatureExtractionMixin -from simba.mixins.feature_extraction_supplement_mixin import FeatureExtractionSupplemental +from simba.mixins.feature_extraction_supplement_mixin import \ + FeatureExtractionSupplemental from simba.utils.checks import ( check_all_file_names_are_represented_in_video_log, check_file_exist_and_readable, check_float, check_that_column_exist, check_valid_lst) from simba.utils.data import detect_bouts, slice_roi_dict_for_video from simba.utils.enums import Keys -from simba.utils.errors import (CountError, MissingColumnsError, ROICoordinatesNotFoundError) +from simba.utils.errors import (CountError, MissingColumnsError, + ROICoordinatesNotFoundError) from simba.utils.printing import stdout_success from simba.utils.read_write import get_fn_ext, read_data_paths, read_df from simba.utils.warnings import NoDataFoundWarning + class ROIAnalyzer(ConfigReader, FeatureExtractionMixin): """ Analyze movements, entries, exits, and time-spent-in user-defined ROIs. Results are stored in the