__author__ = "Simon Nilsson; sronilsson@gmail.com"
import os
from typing import Optional, Union
import pandas as pd
from simba.mixins.config_reader import ConfigReader
from simba.roi_tools.roi_utils import (get_circle_df_headers,
get_polygon_df_headers,
get_rectangle_df_headers)
from simba.utils.checks import (check_file_exist_and_readable,
check_valid_boolean)
from simba.utils.enums import Keys
from simba.utils.errors import InvalidInputError
from simba.utils.printing import stdout_success
from simba.utils.read_write import find_all_videos_in_directory
from simba.utils.warnings import MissingFileWarning, NoFileFoundWarning
VIDEO = 'Video'
EXPECTED_RECT_COLS = ['Video', 'Shape_type', 'Name', 'Color name', 'Color BGR', 'Thickness', 'Center_X', 'Center_Y', 'topLeftX', 'topLeftY', 'Bottom_right_X', 'Bottom_right_Y', 'width', 'height', 'width_cm', 'height_cm', 'area_cm','Tags', 'Ear_tag_size']
EXPECTED_CIRC_COLS = ['Video', 'Shape_type', 'Name', 'Color name', 'Color BGR', 'Thickness', 'centerX', 'centerY', 'radius', 'radius_cm', 'area_cm', 'Tags', 'Ear_tag_size', 'Center_X', 'Center_Y']
EXPECTED_POLY_COLS = ['Video', 'Shape_type', 'Name', 'Color name', 'Color BGR', 'Thickness', 'Center_X', 'Center_Y', 'vertices', 'center', 'area', 'max_vertice_distance', 'area_cm', 'Tags', 'Ear_tag_size']
#EXPECTED_RECT_COLS, EXPECTED_CIRC_COLS, EXPECTED_POLY_COLS = get_rectangle_df_headers(), get_circle_df_headers(), get_polygon_df_headers()
[docs]class ROIDefinitionsCSVImporter(ConfigReader):
"""
Import ROI definitions from CSV files into SimBA H5 format.
Converts human-readable CSV files containing ROI definitions (rectangles, circles, and/or polygons)
into SimBA's native H5 format for use in ROI analysis workflows. At least one CSV file path
(rectangles, circles, or polygons) must be provided.
.. note::
ROI CSV files can be created from existing SimBA H5 ROI definitions using :func:`simba.utils.data.convert_roi_definitions`.
:param Union[str, os.PathLike] config_path: Path to SimBA project config file in Configparser format.
:param Optional[Union[str, os.PathLike]] rectangles_path: Path to CSV file containing rectangle ROI definitions. If None, no rectangles will be imported.
:param Optional[Union[str, os.PathLike]] circles_path: Path to CSV file containing circle ROI definitions. If None, no circles will be imported.
:param Optional[Union[str, os.PathLike]] polygon_path: Path to CSV file containing polygon ROI definitions. If None, no polygons will be imported.
:param bool append: If True, append ROI definitions to existing ROI_definitions.h5 file. If False, overwrite existing file. Default: False.
:example:
>>> importer = ROIDefinitionsCSVImporter(
... config_path=r"project_folder/project_config.ini",
... rectangles_path=r"logs/measures/rectangles_20251122110043.csv",
... circles_path=r"logs/measures/circles_20251122110043.csv",
... polygon_path=r"logs/measures/polygons_20251122110043.csv",
... append=False
... )
>>> importer.run()
:example:
>>> importer = ROIDefinitionsCSVImporter(
... config_path=r"C:\troubleshooting\mouse_open_field\project_folder\project_config.ini",
... circles_path=r"C:\troubleshooting\mouse_open_field\project_folder\logs\measures\circles_20251122110043.csv",
... rectangles_path=r"C:\troubleshooting\mouse_open_field\project_folder\logs\measures\rectangles_20251122110043.csv",
... polygon_path=r"C:\troubleshooting\mouse_open_field\project_folder\logs\measures\polygons_20251122110043.csv"
... )
>>> importer.run()
"""
def __init__(self,
config_path: Union[str, os.PathLike],
rectangles_path: Optional[Union[str, os.PathLike]] = None,
circles_path: Optional[Union[str, os.PathLike]] = None,
polygon_path: Optional[Union[str, os.PathLike]] = None,
append: bool = False):
if rectangles_path is None and circles_path is None and polygon_path is None:
raise InvalidInputError(msg='Please pass at path to rectangles, circles, and/or polygon CSVs. They are all None', source=self.__class__.__name__)
ConfigReader.__init__(self, config_path=config_path, read_video_info=False, create_logger=False)
if rectangles_path is not None: check_file_exist_and_readable(file_path=rectangles_path, raise_error=True)
if circles_path is not None: check_file_exist_and_readable(file_path=circles_path, raise_error=True)
if polygon_path is not None: check_file_exist_and_readable(file_path=polygon_path, raise_error=True)
check_valid_boolean(value=append, source=f'{self.__class__.__name__} append', raise_error=True)
if append and not os.path.isfile(self.roi_coordinates_path):
NoFileFoundWarning(msg='Cannot APPEND ROI CSV data, the expected file {} does not exist to append data to. A new file will be created', source=self.__class__.__name__)
append = False
self.video_dict = find_all_videos_in_directory(directory=self.video_dir, as_dict=True, raise_error=False, sort_alphabetically=True)
self.project_video_names = list(self.video_dict.keys())
self.write_mode = 'w' if not append else 'a'
self.circles_df, self.rectangles_df, self.polygon_df, self.append = None, None, None, append
self.new_rect_cnt, self.new_circ_cnt, self.new_poly_cnt, self.new_video_names = 0, 0, 0, set()
if rectangles_path is not None:
self.rectangles_df = pd.read_csv(filepath_or_buffer=rectangles_path, index_col=0)
self.new_rect_cnt += len(self.rectangles_df)
self.new_video_names.update(list(self.rectangles_df[VIDEO]))
missing_cols = [x for x in list(self.rectangles_df.columns) if x not in EXPECTED_RECT_COLS]
if len(missing_cols) > 0:
raise InvalidInputError(msg=f'The RECTANGLE ROI CSV file {rectangles_path} is missing the expected columns {missing_cols}', source=self.__class__.__name__)
else:
self.rectangles_df = pd.DataFrame(columns=get_rectangle_df_headers())
if circles_path is not None:
self.circles_df = pd.read_csv(filepath_or_buffer=circles_path, index_col=0)
self.new_circ_cnt += len(self.circles_df)
self.new_video_names.update(list(self.circles_df[VIDEO]))
missing_cols = [x for x in list(self.circles_df.columns) if x not in EXPECTED_CIRC_COLS]
if len(missing_cols) > 0:
raise InvalidInputError(msg=f'The CIRCLE ROI CSV file {circles_path} is missing the expected columns {missing_cols}', source=self.__class__.__name__)
else:
self.circles_df = pd.DataFrame(columns=get_circle_df_headers())
if polygon_path is not None:
self.polygon_df = pd.read_csv(filepath_or_buffer=polygon_path, index_col=0)
self.new_poly_cnt += len(self.polygon_df)
self.new_video_names.update(list(self.polygon_df[VIDEO]))
missing_cols = [x for x in list(self.polygon_df.columns) if x not in EXPECTED_POLY_COLS]
if len(missing_cols) > 0:
raise InvalidInputError(msg=f'The POLYGON ROI CSV file {polygon_path} is missing the expected columns {missing_cols}', source=self.__class__.__name__)
else:
self.polygon_df = pd.DataFrame(columns=get_polygon_df_headers())
def run(self):
store = pd.HDFStore(self.roi_coordinates_path, mode=self.write_mode)
store[Keys.ROI_RECTANGLES.value] = self.rectangles_df
store[Keys.ROI_CIRCLES.value] = self.circles_df
store[Keys.ROI_POLYGONS.value] = self.polygon_df
store[Keys.ROI_RECTANGLES.value] = store[Keys.ROI_RECTANGLES.value].drop_duplicates()
store[Keys.ROI_CIRCLES.value] = store[Keys.ROI_CIRCLES.value].drop_duplicates()
store[Keys.ROI_POLYGONS.value] = store[Keys.ROI_POLYGONS.value].drop_duplicates()
store.close()
new_roi_cnt = self.new_poly_cnt + self.new_rect_cnt + self.new_circ_cnt
new_video_names = list(self.new_video_names)
missing_videos = [x for x in new_video_names if x not in self.project_video_names]
if len(missing_videos) > 0:
MissingFileWarning(msg=f'Imported ROIs for {len(missing_videos)} videos which do not exist in the {self.video_dir} directory: {missing_videos}.', source=self.__class__.__name__)
self.timer.stop_timer()
stdout_success(msg=f'{new_roi_cnt} new ROIs for {len(new_video_names)} videos imported to SimBA project.', source=self.__class__.__name__, elapsed_time=self.timer.elapsed_time_str)
# u = ROIDefinitionsCSVImporter(config_path=r"C:\troubleshooting\mouse_open_field\project_folder\project_config.ini", circles_path=r"C:\troubleshooting\mouse_open_field\project_folder\logs\measures\circles_20251122110043.csv", rectangles_path=r"C:\troubleshooting\mouse_open_field\project_folder\logs\measures\rectangles_20251122110043.csv", polygon_path=r"C:\troubleshooting\mouse_open_field\project_folder\logs\measures\polygons_20251122110043.csv")
# u.run()