From 2d8f1ef3d4d45f488b745d3c2c295a7750f71766 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 12:14:43 -0500 Subject: [PATCH 01/10] feat: replace os with Path, update handling for matching files with image types --- src/readii/io/loaders/features.py | 51 ++++++++++++++++++++----------- 1 file changed, 33 insertions(+), 18 deletions(-) diff --git a/src/readii/io/loaders/features.py b/src/readii/io/loaders/features.py index a499798..2252100 100644 --- a/src/readii/io/loaders/features.py +++ b/src/readii/io/loaders/features.py @@ -1,14 +1,11 @@ -import os import pandas as pd -from typing import Optional, Dict - +from pathlib import Path from readii.io.loaders.general import loadFileToDataFrame - from readii.utils import logger +from typing import Optional, Union, Dict - -def loadFeatureFilesFromImageTypes(extracted_feature_dir:str, +def loadFeatureFilesFromImageTypes(extracted_feature_dir:Union[Path|str], image_types:list, drop_labels:Optional[bool]=True, labels_to_drop:Optional[list]=None)->Dict[str,pd.DataFrame]: @@ -31,6 +28,10 @@ def loadFeatureFilesFromImageTypes(extracted_feature_dir:str, feature_sets : dict Dictionary of dataframes containing the extracted radiomics features. """ + # Convert directory to Path object if it is a string + if isinstance(extracted_feature_dir, str): + extracted_feature_dir = Path(extracted_feature_dir) + # Set default labels to drop if not specified if labels_to_drop is None: labels_to_drop = ["patient_ID","survival_time_in_years","survival_event_binary"] @@ -39,28 +40,42 @@ def loadFeatureFilesFromImageTypes(extracted_feature_dir:str, feature_sets = {} # Check if the passed in extracted feature directory exists - if not os.path.isdir(extracted_feature_dir): + if not extracted_feature_dir.exists() or not extracted_feature_dir.is_dir(): raise FileNotFoundError(f"Extracted feature directory {extracted_feature_dir} does not exist.") - feature_file_list = os.listdir(extracted_feature_dir) + feature_file_list = sorted(extracted_feature_dir.glob("*.csv")) # Loop through all the files in the directory for image_type in image_types: try: # Extract the image type feature csv file from the feature directory - matching_files = [file for file in feature_file_list if (image_type in file) and (file.endswith(".csv"))] - if matching_files: - image_type_feature_file = matching_files[0] - # Remove the image type file from the list of feature files - feature_file_list.remove(image_type_feature_file) - except IndexError as e: - logger.warning(f"No {image_type} feature csv files found in {extracted_feature_dir}") - # Skip to the next image type - continue + matching_files = [file for file in feature_file_list if (image_type in file)] + + match len(matching_files): + case 1: + # Only one file found, use it + pass + case 0: + # No files found for this image type + logger.warning(f"No {image_type} feature csv files found in {extracted_feature_dir}") + # Skip to the next image type + continue + case _: + # Multiple files found + msg = f"Multiple {image_type} feature csv files found in {extracted_feature_dir}. First one will be used." + logger.warning(msg) + + image_type_feature_file = matching_files[0] + # Remove the image type file from the list of feature files + feature_file_list.remove(image_type_feature_file) + + except Exception as e: + logger.warning(f"Error loading {image_type} feature csv files from {extracted_feature_dir}: {e}") + raise e # Get the full path to the feature file - feature_file_path = os.path.join(extracted_feature_dir, image_type_feature_file) + feature_file_path = extracted_feature_dir / image_type_feature_file # Load the feature data into a pandas dataframe raw_feature_data = loadFileToDataFrame(feature_file_path) From 614481e0353ea3af5df7e743cbc707ee22fb0a26 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 12:21:43 -0500 Subject: [PATCH 02/10] refactor: ruff fixes, adding logger --- src/readii/io/loaders/features.py | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/src/readii/io/loaders/features.py b/src/readii/io/loaders/features.py index 2252100..50e96a3 100644 --- a/src/readii/io/loaders/features.py +++ b/src/readii/io/loaders/features.py @@ -1,15 +1,17 @@ -import pandas as pd - from pathlib import Path +from typing import Dict, Optional, Union + +import pandas as pd + from readii.io.loaders.general import loadFileToDataFrame from readii.utils import logger -from typing import Optional, Union, Dict + def loadFeatureFilesFromImageTypes(extracted_feature_dir:Union[Path|str], image_types:list, drop_labels:Optional[bool]=True, labels_to_drop:Optional[list]=None)->Dict[str,pd.DataFrame]: - """Function to load in all the extracted imaging feature sets from a directory and return them as a dictionary of dataframes. + """Load in all the specified extracted imaging feature sets from a directory and return them as a dictionary of dataframes. Parameters ---------- @@ -41,7 +43,9 @@ def loadFeatureFilesFromImageTypes(extracted_feature_dir:Union[Path|str], # Check if the passed in extracted feature directory exists if not extracted_feature_dir.exists() or not extracted_feature_dir.is_dir(): - raise FileNotFoundError(f"Extracted feature directory {extracted_feature_dir} does not exist.") + msg = f"Extracted feature directory {extracted_feature_dir} does not exist." + logger.error(f"Extracted feature directory {extracted_feature_dir} does not exist.") + raise FileNotFoundError() feature_file_list = sorted(extracted_feature_dir.glob("*.csv")) @@ -85,16 +89,18 @@ def loadFeatureFilesFromImageTypes(extracted_feature_dir:Union[Path|str], if drop_labels: # Data is now only extracted features raw_feature_data.drop(labels_to_drop, axis=1, inplace=True) - except KeyError as e: + except KeyError: logger.warning(f"{feature_file_path} does not have the labels {labels_to_drop} to drop.") # Skip to the next image type continue # Save the dataframe to the feature_sets dictionary feature_sets[image_type] = raw_feature_data + # end image type loop # After processing all image types, check if any feature sets were loaded if not feature_sets: - raise ValueError(f"No valid feature sets were loaded from {extracted_feature_dir}") + logger.error(f"No valid feature sets were loaded from {extracted_feature_dir}") + raise ValueError() return feature_sets \ No newline at end of file From cfced34d823fd6e931b57bbca87592846347c8fb Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 12:23:35 -0500 Subject: [PATCH 03/10] style: skip qa on function name --- src/readii/io/loaders/features.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/readii/io/loaders/features.py b/src/readii/io/loaders/features.py index 50e96a3..b03f485 100644 --- a/src/readii/io/loaders/features.py +++ b/src/readii/io/loaders/features.py @@ -7,10 +7,10 @@ from readii.utils import logger -def loadFeatureFilesFromImageTypes(extracted_feature_dir:Union[Path|str], +def loadFeatureFilesFromImageTypes(extracted_feature_dir:Union[Path|str], # noqa image_types:list, drop_labels:Optional[bool]=True, - labels_to_drop:Optional[list]=None)->Dict[str,pd.DataFrame]: + labels_to_drop:Optional[list]=None)->Dict[str,pd.DataFrame]: """Load in all the specified extracted imaging feature sets from a directory and return them as a dictionary of dataframes. Parameters From c1133e901045710584b0ff0b26be881ead03e86f Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 12:30:07 -0500 Subject: [PATCH 04/10] feat: add readii logger --- src/readii/io/loaders/general.py | 36 ++++++++++++++++++++++++-------- 1 file changed, 27 insertions(+), 9 deletions(-) diff --git a/src/readii/io/loaders/general.py b/src/readii/io/loaders/general.py index 643b9a6..e389663 100644 --- a/src/readii/io/loaders/general.py +++ b/src/readii/io/loaders/general.py @@ -3,6 +3,8 @@ import pandas as pd import yaml +from readii.utils import logger + class ConfigError(Exception): """Base class for errors in the config module.""" @@ -40,16 +42,21 @@ def loadImageDatasetConfig(dataset_name: str, config_dir_path: str | Path) -> di if not config_file_path.exists(): msg = f"Config file {config_file_path} does not exist." - raise FileNotFoundError(msg) + logger.error(msg) + raise FileNotFoundError() try: with config_file_path.open("r") as f: config = yaml.safe_load(f) except yaml.YAMLError as ye: - raise ConfigError("Invalid YAML in config file") from ye + msg = f"Invalid YAML config file for {dataset_name}." + logger.exception(msg) + raise ConfigError() from ye if not config: - raise ConfigError("Config file is empty or invalid") + msg = f"{dataset_name} config file is empty or invalid." + logger.error(msg) + raise ConfigError() return config @@ -70,11 +77,14 @@ def loadFileToDataFrame(file_path: str | Path) -> pd.DataFrame: """ file_path = Path(file_path) if not file_path: - raise ValueError("File is empty") + msg = f"File {file_path} is empty" + logger.error(msg) + raise ValueError() if not file_path.exists(): msg = f"File {file_path} does not exist" - raise FileNotFoundError(msg) + logger.error(msg) + raise FileNotFoundError() # Get the file extension file_extension = file_path.suffix @@ -86,14 +96,22 @@ def loadFileToDataFrame(file_path: str | Path) -> pd.DataFrame: df = pd.read_csv(file_path) else: msg = f"Unsupported file format {file_extension}. Please provide a .csv or .xlsx file." - raise ValueError(msg) + logger.exception(msg) + raise ValueError() except pd.errors.EmptyDataError as e: - raise DataFrameLoadError("File is empty") from e + msg = f"File {file_path} is empty" + logger.exception(msg) + raise DataFrameLoadError() from e except (pd.errors.ParserError, ValueError) as e: - raise DataFrameLoadError("Error parsing file") from e + msg = "Error pargins {file_path}" + logger.exception(msg) + raise DataFrameLoadError() from e if df.empty: - raise DataFrameLoadError("Dataframe is empty") + msg = "Loaded Dataframe is empty" + logger.exception(msg) + raise DataFrameLoadError() + return df \ No newline at end of file From 6b3aaa31a5c317ee30f3880d5ea1b1a549c2f9e5 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 12:31:16 -0500 Subject: [PATCH 05/10] style: make docstring imperative --- src/readii/io/loaders/images.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/readii/io/loaders/images.py b/src/readii/io/loaders/images.py index abf631e..70c2e72 100644 --- a/src/readii/io/loaders/images.py +++ b/src/readii/io/loaders/images.py @@ -4,7 +4,7 @@ def getImageTypesFromDirectory(raw_data_dir:Union[Path|str], feature_file_prefix:str = "", feature_file_suffix:str = ".csv"): - """ Function to get a list of image types from a directory containing image feature files. + """Get a list of image types from a directory containing image feature files. Parameters ---------- From 132b9f1efab8af572714af38afb99c0618f9e43b Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 12:32:06 -0500 Subject: [PATCH 06/10] feat: add return type annotation --- src/readii/io/loaders/images.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/readii/io/loaders/images.py b/src/readii/io/loaders/images.py index 70c2e72..5217f67 100644 --- a/src/readii/io/loaders/images.py +++ b/src/readii/io/loaders/images.py @@ -3,7 +3,7 @@ def getImageTypesFromDirectory(raw_data_dir:Union[Path|str], feature_file_prefix:str = "", - feature_file_suffix:str = ".csv"): + feature_file_suffix:str = ".csv") -> list: """Get a list of image types from a directory containing image feature files. Parameters From 45606c0a3889210428b28e535d7a71fdabd43afc Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 12:33:17 -0500 Subject: [PATCH 07/10] feat: add readii logger --- src/readii/io/loaders/images.py | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/src/readii/io/loaders/images.py b/src/readii/io/loaders/images.py index 5217f67..47f2f6d 100644 --- a/src/readii/io/loaders/images.py +++ b/src/readii/io/loaders/images.py @@ -1,6 +1,9 @@ from pathlib import Path from typing import Union +from readii.utils import logger + + def getImageTypesFromDirectory(raw_data_dir:Union[Path|str], feature_file_prefix:str = "", feature_file_suffix:str = ".csv") -> list: @@ -26,15 +29,21 @@ def getImageTypesFromDirectory(raw_data_dir:Union[Path|str], # Check if the directory exists if not raw_data_dir.exists(): - raise FileNotFoundError(f"Directory {raw_data_dir} does not exist.") + msg = f"Directory {raw_data_dir} does not exist." + logger.error(msg) + raise FileNotFoundError() # Check if the directory is a directory if not raw_data_dir.is_dir(): - raise NotADirectoryError(f"Path {raw_data_dir} is not a directory.") + msg = f"Path {raw_data_dir} is not a directory." + logger.error(msg) + raise NotADirectoryError() # Check that directory contains files with the specified prefix and suffix if not any(raw_data_dir.glob(f"{feature_file_prefix}*{feature_file_suffix}")): - raise FileNotFoundError(f"No files with prefix {feature_file_prefix} and suffix {feature_file_suffix} found in directory {raw_data_dir}.") + msg = f"No files with prefix {feature_file_prefix} and suffix {feature_file_suffix} found in directory {raw_data_dir}." + logger.error(msg) + raise FileNotFoundError() # Initialize an empty list to store the image types image_types = [] From 7dda5ed65121658d991f61d1c2329854481880d6 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 12:33:44 -0500 Subject: [PATCH 08/10] feat: add io/loaders to ruff config --- config/ruff.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/ruff.toml b/config/ruff.toml index 935bf10..e2cedf9 100644 --- a/config/ruff.toml +++ b/config/ruff.toml @@ -6,7 +6,7 @@ include = [ "src/readii/feature_extraction.py", "src/readii/cli/**/*.py", "src/readii/negative_controls_refactor/**.py", - "src/readii/io/writers/**.py", + "src/readii/io/**/**.py", ] # extend-exclude is used to exclude directories from the flake8 checks From 87e562eaf2103721a343036086c72e17b1d9d476 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 12:38:33 -0500 Subject: [PATCH 09/10] fix: remove duplicate except line --- src/readii/io/loaders/features.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/readii/io/loaders/features.py b/src/readii/io/loaders/features.py index d227e6d..d51247d 100644 --- a/src/readii/io/loaders/features.py +++ b/src/readii/io/loaders/features.py @@ -89,7 +89,7 @@ def loadFeatureFilesFromImageTypes(extracted_feature_dir:Union[Path|str], # noqa if drop_labels: # Data is now only extracted features raw_feature_data.drop(labels_to_drop, axis=1, inplace=True) - except KeyError: + except KeyError: logger.warning(f"{feature_file_path} does not have the labels {labels_to_drop} to drop.") # Skip to the next image type From 99e8924fe1bce151021259c6788a133534aba0b3 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 12:50:54 -0500 Subject: [PATCH 10/10] build: updated lock file --- pixi.lock | 3665 ++++++++--------------------------------------------- 1 file changed, 503 insertions(+), 3162 deletions(-) diff --git a/pixi.lock b/pixi.lock index e29e659..6dc0b9c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3572,57 +3572,6 @@ packages: - 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