From 5dcbf0d61f247a22496efcdf4ece0d2ebc918c9c Mon Sep 17 00:00:00 2001 From: sfmig <33267254+sfmig@users.noreply.github.com> Date: Mon, 16 Dec 2024 18:42:41 +0000 Subject: [PATCH] Remove dataloader (now in separate PR) --- ethology/annotations/io.py | 195 ------------------------------------- 1 file changed, 195 deletions(-) delete mode 100644 ethology/annotations/io.py diff --git a/ethology/annotations/io.py b/ethology/annotations/io.py deleted file mode 100644 index 1cf137e..0000000 --- a/ethology/annotations/io.py +++ /dev/null @@ -1,195 +0,0 @@ -"""Module for reading and writing manually labelled annotations.""" - -import json -from pathlib import Path - -import pandas as pd -from movement.validators.files import ValidFile - -from ethology.annotations.json_schemas import COCO_SCHEMA, VIA_SCHEMA -from ethology.annotations.validators import ( - ValidCOCOJSON, - ValidJSON, - ValidVIAJSON, -) - -STANDARD_DF_COLUMNS = [ - "annotation_id", - "image_filename", - "image_id", - "x_min", - "y_min", - "width", - "height", - "supercategory", - "category", -] - - -def df_from_via_json_file(file_path: Path) -> pd.DataFrame: - """Validate and read untracked VIA JSON file. - - The data is formatted as an untracked annotations DataFrame. - - Parameters - ---------- - file_path : Path - Path to the untracked VIA JSON file. - - Returns - ------- - pd.DataFrame - Untracked annotations DataFrame. - - """ - # Run validators - file = ValidFile( - file_path, expected_permission="r", expected_suffix=[".json"] - ) - json_file = ValidJSON(path=file.path, schema=VIA_SCHEMA) - via_untracked_file = ValidVIAJSON(json_file.path) - - # Read as standard dataframe - return _df_from_validated_via_json_file(via_untracked_file.path) - - -def df_from_coco_json_file(file_path: Path) -> pd.DataFrame: - """Validate and read untracked COCO JSON file. - - The data is formatted as an untracked annotations DataFrame. - - Parameters - ---------- - file_path : Path - Path to the untracked COCO JSON file. - - Returns - ------- - pd.DataFrame - Untracked annotations DataFrame. - - """ - # Run validators - file = ValidFile( - file_path, expected_permission="r", expected_suffix=[".json"] - ) - json_file = ValidJSON(path=file.path, schema=COCO_SCHEMA) - coco_untracked_file = ValidCOCOJSON(json_file.path) - - # Read as standard dataframe - return _df_from_validated_coco_json_file(coco_untracked_file.path) - - -def _df_from_validated_via_json_file(file_path): - """Read VIA JSON file as standard untracked annotations DataFrame.""" - # Read validated json as dict - with open(file_path) as file: - data_dict = json.load(file) - - # Prepare data - image_metadata_dict = data_dict["_via_img_metadata"] - via_image_id_list = data_dict[ - "_via_image_id_list" - ] # ordered list of the keys in image_metadata_dict - - # map filename to keys in image_metadata_dict - map_filename_to_via_img_id = { - img_dict["filename"]: ky - for ky, img_dict in image_metadata_dict.items() - } - - # Build standard dataframe - list_rows = [] - # loop thru images - for _, img_dict in image_metadata_dict.items(): - # loop thru annotations in the image - for region in img_dict["regions"]: - region_shape = region["shape_attributes"] - region_attributes = region["region_attributes"] - - row = { - "image_filename": img_dict["filename"], - "x_min": region_shape["x"], - "y_min": region_shape["y"], - "width": region_shape["width"], - "height": region_shape["height"], - "supercategory": list(region_attributes.keys())[ - 0 - ], # takes first key as supercategory - "category": region_attributes[ - list(region_attributes.keys())[0] - ], - } - - # append annotations to df - list_rows.append(row) - - df = pd.DataFrame( - list_rows, - # columns=list(row.keys()), # do I need this? - ) - - # add image_id column - df["image_id"] = df["image_filename"].apply( - lambda x: via_image_id_list.index(map_filename_to_via_img_id[x]) - ) - - # add annotation_id column based on index - df["annotation_id"] = df.index - - # reorder columns to match standard - df = df.reindex(columns=STANDARD_DF_COLUMNS) - - return df - - -def _df_from_validated_coco_json_file(file_path: Path) -> pd.DataFrame: - """Read COCO JSON file as standard untracked annotations DataFrame.""" - # Read validated json as dict - with open(file_path) as file: - data_dict = json.load(file) - - # Prepare data - map_image_id_to_filename = { - img_dict["id"]: img_dict["file_name"] - for img_dict in data_dict["images"] - } - - map_category_id_to_category_data = { - cat_dict["id"]: (cat_dict["name"], cat_dict["supercategory"]) - for cat_dict in data_dict["categories"] - } - - # Build standard dataframe - list_rows = [] - for annot_dict in data_dict["annotations"]: - annotation_id = annot_dict["id"] - # image data - image_id = annot_dict["image_id"] - image_filename = map_image_id_to_filename[image_id] - - # bbox data - x_min, y_min, width, height = annot_dict["bbox"] - - # class data - category_id = annot_dict["category_id"] - category, supercategory = map_category_id_to_category_data[category_id] - - row = { - "annotation_id": annotation_id, - "image_filename": image_filename, - "image_id": image_id, - "x_min": x_min, - "y_min": y_min, - "width": width, - "height": height, - "supercategory": supercategory, - "category": category, - } - - list_rows.append(row) - - df = pd.DataFrame(list_rows) - df.reindex(columns=STANDARD_DF_COLUMNS) - - return df