halib 0.2.1__py3-none-any.whl → 0.2.2__py3-none-any.whl

halib/research/perf/perfcalc.py

@@ -0,0 +1,363 @@
+import os
+import glob
+from typing import Optional, Tuple
+import pandas as pd
+
+from abc import ABC, abstractmethod
+from collections import OrderedDict
+
+
+from ...common.common import now_str
+from ...system import filesys as fs
+
+from .perftb import PerfTB
+from .perfmetrics import *
+
+
+REQUIRED_COLS = ["experiment", "dataset"]
+CSV_FILE_POSTFIX = "__perf"
+METRIC_PREFIX = "metric_"
+
+
+class PerfCalc(ABC):  # Abstract base class for performance calculation
+    @abstractmethod
+    def get_experiment_name(self) -> str:
+        """
+        Return the name of the experiment.
+        This function should be overridden by the subclass if needed.
+        """
+        pass
+
+    @abstractmethod
+    def get_dataset_name(self) -> str:
+        """
+        Return the name of the dataset.
+        This function should be overridden by the subclass if needed.
+        """
+        pass
+
+    @abstractmethod
+    def get_metric_backend(self) -> MetricsBackend:
+        """
+        Return a list of metric names to be used for performance calculation OR a dictionaray with keys as metric names and values as metric instances of torchmetrics.Metric. For example: {"accuracy": Accuracy(), "precision": Precision()}
+
+        """
+        pass
+
+    def valid_proc_extra_data(self, proc_extra_data):
+        # make sure that all items in proc_extra_data are dictionaries, with same keys
+        if proc_extra_data is None or len(proc_extra_data) == 0:
+            return
+        if not all(isinstance(item, dict) for item in proc_extra_data):
+            raise TypeError("All items in proc_extra_data must be dictionaries")
+
+        if not all(
+            item.keys() == proc_extra_data[0].keys() for item in proc_extra_data
+        ):
+            raise ValueError(
+                "All dictionaries in proc_extra_data must have the same keys"
+            )
+
+    def valid_proc_metric_raw_data(self, metric_names, proc_metric_raw_data):
+        # make sure that all items in proc_metric_raw_data are dictionaries, with same keys as metric_names
+        assert (
+            isinstance(proc_metric_raw_data, list) and len(proc_metric_raw_data) > 0
+        ), "raw_data_for_metrics must be a non-empty list of dictionaries"
+
+        # make sure that all items in proc_metric_raw_data are dictionaries with keys as metric_names
+        if not all(isinstance(item, dict) for item in proc_metric_raw_data):
+            raise TypeError("All items in raw_data_for_metrics must be dictionaries")
+        if not all(
+            set(item.keys()) == set(metric_names) for item in proc_metric_raw_data
+        ):
+            raise ValueError(
+                "All dictionaries in raw_data_for_metrics must have the same keys as metric_names"
+            )
+
+    # ! only need to override this method if torchmetrics are not used
+    def calc_exp_perf_metrics(
+        self, metric_names, raw_metrics_data, extra_data=None, *args, **kwargs
+    ):
+        assert isinstance(raw_metrics_data, dict) or isinstance(
+            raw_metrics_data, list
+        ), "raw_data_for_metrics must be a dictionary or a list"
+
+        if extra_data is not None:
+            assert isinstance(
+                extra_data, type(raw_metrics_data)
+            ), "extra_data must be of the same type as raw_data_for_metrics (dict or list)"
+        # prepare raw_metric data for processing
+        proc_metric_raw_data_ls = (
+            raw_metrics_data
+            if isinstance(raw_metrics_data, list)
+            else [raw_metrics_data.copy()]
+        )
+        self.valid_proc_metric_raw_data(metric_names, proc_metric_raw_data_ls)
+        # prepare extra data for processing
+        proc_extra_data_ls = []
+        if extra_data is not None:
+            proc_extra_data_ls = (
+                extra_data if isinstance(extra_data, list) else [extra_data.copy()]
+            )
+            assert len(proc_extra_data_ls) == len(
+                proc_metric_raw_data_ls
+            ), "extra_data must have the same length as raw_data_for_metrics if it is a list"
+        # validate the extra_data
+        self.valid_proc_extra_data(proc_extra_data_ls)
+
+        # calculate the metrics output results
+        metrics_backend = self.get_metric_backend()
+        proc_outdict_list = []
+        for idx, raw_metrics_data in enumerate(proc_metric_raw_data_ls):
+            out_dict = {
+                "dataset": self.get_dataset_name(),
+                "experiment": self.get_experiment_name(),
+            }
+            custom_fields = []
+            if len(proc_extra_data_ls) > 0:
+                # add extra data to the output dictionary
+                extra_data_item = proc_extra_data_ls[idx]
+                out_dict.update(extra_data_item)
+                custom_fields = list(extra_data_item.keys())
+            metric_results = metrics_backend.calc_metrics(
+                metrics_data_dict=raw_metrics_data, *args, **kwargs
+            )
+            metric_results_prefix = {
+                f"metric_{k}": v for k, v in metric_results.items()
+            }
+            out_dict.update(metric_results_prefix)
+            ordered_cols = (
+                REQUIRED_COLS + custom_fields + list(metric_results_prefix.keys())
+            )
+            out_dict = OrderedDict(
+                (col, out_dict[col]) for col in ordered_cols if col in out_dict
+            )
+            proc_outdict_list.append(out_dict)
+
+        return proc_outdict_list
+
+    #! custom kwargs:
+    #! outfile - if provided, will save the output to a CSV file with the given path
+    #! outdir - if provided, will save the output to a CSV file in the given directory with a generated filename
+    #! return_df - if True, will return a DataFrame instead of a dictionary
+    def calc_perfs(
+        self,
+        raw_metrics_data: Union[List[dict], dict],
+        extra_data: Optional[Union[List[dict], dict]] = None,
+        *args,
+        **kwargs,
+    ) -> Tuple[Union[List[OrderedDict], pd.DataFrame], Optional[str]]:
+        """
+        Calculate the metrics.
+        This function should be overridden by the subclass if needed.
+        Must return a dictionary with keys as metric names and values as the calculated metrics.
+        """
+        metric_names = self.get_metric_backend().metric_names
+        out_dict_list = self.calc_exp_perf_metrics(
+            metric_names=metric_names,
+            raw_metrics_data=raw_metrics_data,
+            extra_data=extra_data,
+            *args,
+            **kwargs,
+        )
+        csv_outfile = kwargs.get("outfile", None)
+        if csv_outfile is not None:
+            filePathNoExt, _ = os.path.splitext(csv_outfile)
+            # pprint(f"CSV Outfile Path (No Ext): {filePathNoExt}")
+            csv_outfile = f"{filePathNoExt}{CSV_FILE_POSTFIX}.csv"
+        elif "outdir" in kwargs:
+            csvoutdir = kwargs["outdir"]
+            csvfilename = f"{now_str()}_{self.get_dataset_name()}_{self.get_experiment_name()}_{CSV_FILE_POSTFIX}.csv"
+            csv_outfile = os.path.join(csvoutdir, csvfilename)
+
+        # convert out_dict to a DataFrame
+        df = pd.DataFrame(out_dict_list)
+        # get the orders of the columns as the orders or the keys in out_dict
+        ordered_cols = list(out_dict_list[0].keys())
+        df = df[ordered_cols]  # reorder columns
+        if csv_outfile:
+            df.to_csv(csv_outfile, index=False, sep=";", encoding="utf-8")
+        return_df = kwargs.get("return_df", False)
+        if return_df:  # return DataFrame instead of dict if requested
+            return df, csv_outfile
+        else:
+            return out_dict_list, csv_outfile
+
+    @staticmethod
+    def default_exp_csv_filter_fn(exp_file_name: str) -> bool:
+        """
+        Default filter function for experiments.
+        Returns True if the experiment name does not start with "test_" or "debug_".
+        """
+        return "__perf.csv" in exp_file_name
+
+    @classmethod
+    def get_perftb_for_multi_exps(
+        cls,
+        indir: str,
+        exp_csv_filter_fn=default_exp_csv_filter_fn,
+        include_file_name=False,
+        csv_sep=";",
+    ) -> PerfTB:
+        """
+        Generate a performance report by scanning experiment subdirectories.
+        Must return a dictionary with keys as metric names and values as performance tables.
+        """
+
+        def get_df_for_all_exp_perf(csv_perf_files, csv_sep=";"):
+            """
+            Create a single DataFrame from all CSV files.
+            Assumes all CSV files MAY have different metrics
+            """
+            cols = []
+            FILE_NAME_COL = "file_name" if include_file_name else None
+
+            for csv_file in csv_perf_files:
+                temp_df = pd.read_csv(csv_file, sep=csv_sep)
+                if FILE_NAME_COL:
+                    temp_df[FILE_NAME_COL] = fs.get_file_name(
+                        csv_file, split_file_ext=False
+                    )
+                    # csvfile.fn_display_df(temp_df)
+                temp_df_cols = temp_df.columns.tolist()
+                for col in temp_df_cols:
+                    if col not in cols:
+                        cols.append(col)
+
+            df = pd.DataFrame(columns=cols)
+            for csv_file in csv_perf_files:
+                temp_df = pd.read_csv(csv_file, sep=csv_sep)
+                if FILE_NAME_COL:
+                    temp_df[FILE_NAME_COL] = fs.get_file_name(
+                        csv_file, split_file_ext=False
+                    )
+                # Drop all-NA columns to avoid dtype inconsistency
+                temp_df = temp_df.dropna(axis=1, how="all")
+                # ensure all columns are present in the final DataFrame
+                for col in cols:
+                    if col not in temp_df.columns:
+                        temp_df[col] = None  # fill missing columns with None
+                df = pd.concat([df, temp_df], ignore_index=True)
+            # assert that REQUIRED_COLS are present in the DataFrame
+            # pprint(df.columns.tolist())
+            sticky_cols = REQUIRED_COLS + (
+                [FILE_NAME_COL] if include_file_name else []
+            )  # columns that must always be present
+            for col in sticky_cols:
+                if col not in df.columns:
+                    raise ValueError(
+                        f"Required column '{col}' is missing from the DataFrame. REQUIRED_COLS = {sticky_cols}"
+                    )
+            metric_cols = [col for col in df.columns if col.startswith(METRIC_PREFIX)]
+            assert (
+                len(metric_cols) > 0
+            ), "No metric columns found in the DataFrame. Ensure that the CSV files contain metric columns starting with 'metric_'."
+            final_cols = sticky_cols + metric_cols
+            df = df[final_cols]
+            # # !hahv debug
+            # pprint("------ Final DataFrame Columns ------")
+            # csvfile.fn_display_df(df)
+            # ! validate all rows in df before returning
+            # make sure all rows will have at least values for REQUIRED_COLS and at least one metric column
+            for index, row in df.iterrows():
+                if not all(col in row and pd.notna(row[col]) for col in sticky_cols):
+                    raise ValueError(
+                        f"Row {index} is missing required columns or has NaN values in required columns: {row}"
+                    )
+                if not any(pd.notna(row[col]) for col in metric_cols):
+                    raise ValueError(f"Row {index} has no metric values: {row}")
+            # make sure these is no (experiment, dataset) pair that is duplicated
+            duplicates = df.duplicated(subset=sticky_cols, keep=False)
+            if duplicates.any():
+                raise ValueError(
+                    "Duplicate (experiment, dataset) pairs found in the DataFrame. Please ensure that each experiment-dataset combination is unique."
+                )
+            return df
+
+        def mk_perftb_report(df):
+            """
+            Create a performance report table from the DataFrame.
+            This function should be customized based on the specific requirements of the report.
+            """
+            perftb = PerfTB()
+            # find all "dataset" values (unique)
+            dataset_names = list(df["dataset"].unique())
+            # find all columns that start with METRIC_PREFIX
+            metric_cols = [col for col in df.columns if col.startswith(METRIC_PREFIX)]
+
+            # Determine which metrics are associated with each dataset.
+            # Since a dataset may appear in multiple rows and may not include all metrics in each, identify the row with the same dataset that contains the most non-NaN metric values. The set of metrics for that dataset is defined by the non-NaN metrics in that row.
+
+            dataset_metrics = {}
+            for dataset_name in dataset_names:
+                dataset_rows = df[df["dataset"] == dataset_name]
+                # Find the row with the most non-NaN metric values
+                max_non_nan_row = dataset_rows[metric_cols].count(axis=1).idxmax()
+                metrics_for_dataset = (
+                    dataset_rows.loc[max_non_nan_row, metric_cols]
+                    .dropna()
+                    .index.tolist()
+                )
+                dataset_metrics[dataset_name] = metrics_for_dataset
+
+            for dataset_name, metrics in dataset_metrics.items():
+                # Create a new row for the performance table
+                perftb.add_dataset(dataset_name, metrics)
+
+            for _, row in df.iterrows():
+                dataset_name = row["dataset"]
+                ds_metrics = dataset_metrics.get(dataset_name)
+                if dataset_name in dataset_metrics:
+                    # Add the metrics for this row to the performance table
+                    exp_name = row.get("experiment")
+                    exp_metric_values = {}
+                    for metric in ds_metrics:
+                        if metric in row and pd.notna(row[metric]):
+                            exp_metric_values[metric] = row[metric]
+                    perftb.add_experiment(
+                        experiment_name=exp_name,
+                        dataset_name=dataset_name,
+                        metrics=exp_metric_values,
+                    )
+
+            return perftb
+
+        assert os.path.exists(indir), f"Input directory {indir} does not exist."
+
+        csv_perf_files = []
+        # Find experiment subdirectories
+        exp_dirs = [
+            os.path.join(indir, d)
+            for d in os.listdir(indir)
+            if os.path.isdir(os.path.join(indir, d))
+        ]
+        if len(exp_dirs) == 0:
+            csv_perf_files = glob.glob(os.path.join(indir, f"*.csv"))
+            csv_perf_files = [
+                file_item
+                for file_item in csv_perf_files
+                if exp_csv_filter_fn(file_item)
+            ]
+        else:
+            # multiple experiment directories found
+            # Collect all matching CSV files in those subdirs
+            for exp_dir in exp_dirs:
+                # pprint(f"Searching in experiment directory: {exp_dir}")
+                matched = glob.glob(os.path.join(exp_dir, f"*.csv"))
+                matched = [
+                    file_item for file_item in matched if exp_csv_filter_fn(file_item)
+                ]
+                csv_perf_files.extend(matched)
+
+        assert (
+            len(csv_perf_files) > 0
+        ), f"No CSV files matching pattern '{exp_csv_filter_fn}' found in the experiment directories."
+
+        assert (
+            len(csv_perf_files) > 0
+        ), f"No CSV files matching pattern '{exp_csv_filter_fn}' found in the experiment directories."
+
+        all_exp_perf_df = get_df_for_all_exp_perf(csv_perf_files, csv_sep=csv_sep)
+        # csvfile.fn_display_df(all_exp_perf_df)
+        perf_tb = mk_perftb_report(all_exp_perf_df)
+        return perf_tb

halib/research/perf/perfmetrics.py

@@ -0,0 +1,137 @@
+# -------------------------------
+# Metrics Backend Interface
+# -------------------------------
+import inspect
+from typing import Dict, Union, List, Any
+from abc import ABC, abstractmethod
+
+class MetricsBackend(ABC):
+    """Interface for pluggable metrics computation backends."""
+
+    def __init__(self, metrics_info: Union[List[str], Dict[str, Any]]):
+        """
+        Initialize the backend with optional metrics_info.
+        `metrics_info` can be either:
+        - A list of metric names (strings). e.g., ["accuracy", "precision"]
+        - A dict mapping metric names with object that defines how to compute them. e.g: {"accuracy": torchmetrics.Accuracy(), "precision": torchmetrics.Precision()}
+
+        """
+        self.metric_info = metrics_info
+        self.validate_metrics_info(self.metric_info)
+
+    @property
+    def metric_names(self) -> List[str]:
+        """
+        Return a list of metric names.
+        If metric_info is a dict, return its keys; if it's a list, return it directly.
+        """
+        if isinstance(self.metric_info, dict):
+            return list(self.metric_info.keys())
+        elif isinstance(self.metric_info, list):
+            return self.metric_info
+        else:
+            raise TypeError("metric_info must be a list or a dict")
+
+    def validate_metrics_info(self, metrics_info):
+        if isinstance(metrics_info, list):
+            return metrics_info
+        elif isinstance(metrics_info, dict):
+            return {k: v for k, v in metrics_info.items() if isinstance(k, str)}
+        else:
+            raise TypeError(
+                "metrics_info must be a list of strings or a dict with string keys"
+            )
+
+    @abstractmethod
+    def compute_metrics(
+        self, metrics_info: Union[List[str], Dict[str, Any]],  metrics_data_dict: Dict[str, Any], *args, **kwargs
+    ) -> Dict[str, Any]:
+        pass
+
+    def prepare_metrics_backend_data(
+        self, raw_metric_data, *args, **kwargs
+    ):
+        """
+        Prepare the data for the metrics backend.
+        This method can be overridden by subclasses to customize data preparation.
+        """
+        return raw_metric_data
+
+    def calc_metrics(
+        self,  metrics_data_dict: Dict[str, Any], *args, **kwargs
+    ) -> Dict[str, Any]:
+        """
+        Calculate metrics based on the provided metrics_info and data.
+        This method should be overridden by subclasses to implement specific metric calculations.
+        """
+        # prevalidate the metrics_data_dict
+        for metric in self.metric_names:
+            if metric not in metrics_data_dict:
+                raise ValueError(f"Metric '{metric}' not found in provided data.")
+        # Prepare the data for the backend
+        metrics_data_dict = self.prepare_metrics_backend_data(
+            metrics_data_dict, *args, **kwargs
+        )
+        # Call the abstract method to compute metrics
+        return self.compute_metrics(self.metric_info, metrics_data_dict, *args, **kwargs)
+
+class TorchMetricsBackend(MetricsBackend):
+    """TorchMetrics-based backend implementation."""
+
+    def __init__(self, metrics_info: Union[List[str], Dict[str, Any]]):
+        try:
+            import torch
+            from torchmetrics import Metric
+        except ImportError:
+            raise ImportError(
+                "TorchMetricsBackend requires torch and torchmetrics to be installed."
+            )
+        self.metric_info = metrics_info
+        self.torch = torch
+        self.Metric = Metric
+        self.validate_metrics_info(metrics_info)
+
+    def validate_metrics_info(self, metrics_info):
+        if not isinstance(metrics_info, dict):
+            raise TypeError(
+                "TorchMetricsBackend requires metrics_info as a dict {name: MetricInstance}"
+            )
+        for k, v in metrics_info.items():
+            if not isinstance(k, str):
+                raise TypeError(f"Key '{k}' is not a string")
+            if not isinstance(v, self.Metric):
+                raise TypeError(f"Value for key '{k}' must be a torchmetrics.Metric")
+        return metrics_info
+
+    def compute_metrics(self, metrics_info, metrics_data_dict, *args, **kwargs):
+        out_dict = {}
+        for metric, metric_instance in metrics_info.items():
+            if metric not in metrics_data_dict:
+                raise ValueError(f"Metric '{metric}' not found in provided data.")
+
+            metric_data = metrics_data_dict[metric]
+            sig = inspect.signature(metric_instance.update)
+            expected_args = list(sig.parameters.values())
+
+            if isinstance(metric_data, dict):
+                args = [metric_data[param.name] for param in expected_args]
+            elif isinstance(metric_data, (list, tuple)):
+                args = metric_data
+            else:
+                args = metric_data
+            if len(expected_args) == 1:
+                metric_instance.update(args)
+            else:
+                metric_instance.update(*args)
+
+            computed_value = metric_instance.compute()
+            if isinstance(computed_value, self.torch.Tensor):
+                computed_value = (
+                    computed_value.item()
+                    if computed_value.numel() == 1
+                    else computed_value.tolist()
+                )
+
+
+            out_dict[metric] = computed_value
+        return out_dict