atlas-ftag-tools 0.2.9__py3-none-any.whl → 0.2.11__py3-none-any.whl

ftag/utils/metrics.py

@@ -0,0 +1,431 @@
+"""Tools for metrics module."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import numpy as np
+from scipy.ndimage import gaussian_filter1d
+
+from ftag.utils import logger
+
+if TYPE_CHECKING:  # pragma: no cover
+    from ftag.labels import Label, LabelContainer
+
+
+def save_divide(
+    numerator: np.ndarray | float,
+    denominator: np.ndarray | float,
+    default: float = 1.0,
+):
+    """Save divide for denominator equal to 0.
+
+    Division using numpy divide function returning default value in cases where
+    denominator is 0.
+
+    Parameters
+    ----------
+    numerator: np.ndarray | float,
+        Numerator in the ratio calculation.
+    denominator: np.ndarray | float,
+        Denominator in the ratio calculation.
+    default: float
+        Default value which is returned if denominator is 0.
+
+    Returns
+    -------
+    ratio: np.ndarray | float
+        Result of the division
+    """
+    logger.debug("Calculating save division.")
+    logger.debug("numerator: %s", numerator)
+    logger.debug("denominator: %s", denominator)
+    logger.debug("default: %s", default)
+
+    if isinstance(numerator, (int, float, np.number)) and isinstance(
+        denominator, (int, float, np.number)
+    ):
+        output_shape = 1
+    else:
+        try:
+            output_shape = denominator.shape
+        except AttributeError:
+            output_shape = numerator.shape
+
+    ratio = np.divide(
+        numerator,
+        denominator,
+        out=np.ones(
+            output_shape,
+            dtype=float,
+        )
+        * default,
+        where=(denominator != 0),
+    )
+    if output_shape == 1:
+        return float(ratio)
+    return ratio
+
+
+def weighted_percentile(
+    arr: np.ndarray,
+    percentile: np.ndarray,
+    weights: np.ndarray = None,
+):
+    """Calculate weighted percentile.
+
+    Implementation according to https://stackoverflow.com/a/29677616/11509698
+    (https://en.wikipedia.org/wiki/Percentile#The_weighted_percentile_method)
+
+    Parameters
+    ----------
+    arr : np.ndarray
+        Data array
+    percentile : np.ndarray
+        Percentile array
+    weights : np.ndarray
+        Weights array, by default None
+
+    Returns
+    -------
+    np.ndarray
+        Weighted percentile array
+    """
+    logger.debug("Calculating weighted percentile.")
+    logger.debug("arr: %s", arr)
+    logger.debug("percentile: %s", percentile)
+    logger.debug("weights: %s", weights)
+
+    # Set weights to one if no weights are given
+    if weights is None:
+        weights = np.ones_like(arr)
+
+    # Set dtype to float64 if the weights are too large
+    dtype = np.float64 if np.sum(weights) > 1000000 else np.float32
+
+    # Get an array sorting and sort the array and the weights
+    ix = np.argsort(arr)
+    arr = arr[ix]
+    weights = weights[ix]
+
+    # Return the cumulative sum
+    cdf = np.cumsum(weights, dtype=dtype) - 0.5 * weights
+    cdf -= cdf[0]
+    cdf /= cdf[-1]
+
+    # Return the linear interpolation
+    return np.interp(percentile, cdf, arr)
+
+
+def calculate_efficiency(
+    sig_disc: np.ndarray,
+    bkg_disc: np.ndarray,
+    target_eff: float | list | np.ndarray,
+    return_cuts: bool = False,
+    sig_weights: np.ndarray = None,
+    bkg_weights: np.ndarray = None,
+):
+    """Calculate efficiency.
+
+    Parameters
+    ----------
+    sig_disc : np.ndarray
+        Signal discriminant
+    bkg_disc : np.ndarray
+        Background discriminant
+    target_eff : float or list or np.ndarray
+        Working point which is used for discriminant calculation
+    return_cuts : bool
+        Specifies if the cut values corresponding to the provided WPs are returned.
+        If target_eff is a float, only one cut value will be returned. If target_eff
+        is an array, target_eff is an array as well.
+    sig_weights : np.ndarray
+        Weights for signal events
+    bkg_weights : np.ndarray
+        Weights for background events
+
+    Returns
+    -------
+    eff : float or np.ndarray
+        Efficiency.
+        Return float if target_eff is a float, else np.ndarray
+    cutvalue : float or np.ndarray
+        Cutvalue if return_cuts is True.
+        Return float if target_eff is a float, else np.ndarray
+    """
+    logger.debug("Calculating efficiency.")
+    logger.debug("sig_disc: %s", sig_disc)
+    logger.debug("bkg_disc: %s", bkg_disc)
+    logger.debug("target_eff: %s", target_eff)
+    logger.debug("return_cuts: %s", return_cuts)
+    logger.debug("sig_weights: %s", sig_weights)
+    logger.debug("bkg_weights: %s", bkg_weights)
+
+    # float | np.ndarray for both target_eff and the returned values
+    return_float = False
+    if isinstance(target_eff, float):
+        return_float = True
+
+    # Flatten the target efficiencies
+    target_eff = np.asarray([target_eff]).flatten()
+
+    # Get the cutvalue for the given target efficiency
+    cutvalue = weighted_percentile(arr=sig_disc, percentile=1.0 - target_eff, weights=sig_weights)
+
+    # Sort the cutvalues to get the correct order
+    sorted_args = np.argsort(1 - target_eff)
+
+    # Get the histogram for the backgrounds
+    hist, _ = np.histogram(bkg_disc, (-np.inf, *cutvalue[sorted_args], np.inf), weights=bkg_weights)
+
+    # Calculate the efficiencies for the calculated cut values
+    eff = hist[::-1].cumsum()[-2::-1] / hist.sum()
+    eff = eff[sorted_args]
+
+    # Ensure that a float is returned if float was given
+    if return_float:
+        eff = eff[0]
+        cutvalue = cutvalue[0]
+
+    # Also return the cuts if wanted
+    if return_cuts:
+        return eff, cutvalue
+
+    return eff
+
+
+def calculate_rejection(
+    sig_disc: np.ndarray,
+    bkg_disc: np.ndarray,
+    target_eff,
+    return_cuts: bool = False,
+    sig_weights: np.ndarray = None,
+    bkg_weights: np.ndarray = None,
+    smooth: bool = False,
+):
+    """Calculate rejection.
+
+    Parameters
+    ----------
+    sig_disc : np.ndarray
+        Signal discriminant
+    bkg_disc : np.ndarray
+        Background discriminant
+    target_eff : float or list
+        Working point which is used for discriminant calculation
+    return_cuts : bool
+        Specifies if the cut values corresponding to the provided WPs are returned.
+        If target_eff is a float, only one cut value will be returned. If target_eff
+        is an array, target_eff is an array as well.
+    sig_weights : np.ndarray
+        Weights for signal events, by default None
+    bkg_weights : np.ndarray
+        Weights for background events, by default None
+
+    Returns
+    -------
+    rej : float or np.ndarray
+        Rejection.
+        If target_eff is a float, a float is returned if it's a list a np.ndarray
+    cut_value : float or np.ndarray
+        Cutvalue if return_cuts is True.
+        If target_eff is a float, a float is returned if it's a list a np.ndarray
+    """
+    logger.debug("Calculating rejection.")
+    logger.debug("sig_disc: %s", sig_disc)
+    logger.debug("bkg_disc: %s", bkg_disc)
+    logger.debug("target_eff: %s", target_eff)
+    logger.debug("return_cuts: %s", return_cuts)
+    logger.debug("sig_weights: %s", sig_weights)
+    logger.debug("bkg_weights: %s", bkg_weights)
+    logger.debug("smooth: %s", smooth)
+
+    # Calculate the efficiency
+    eff = calculate_efficiency(
+        sig_disc=sig_disc,
+        bkg_disc=bkg_disc,
+        target_eff=target_eff,
+        return_cuts=return_cuts,
+        sig_weights=sig_weights,
+        bkg_weights=bkg_weights,
+    )
+
+    # Invert the efficiency to get a rejection
+    rej = save_divide(1, eff[0] if return_cuts else eff, np.inf)
+
+    # Smooth out the rejection if wanted
+    if smooth:
+        rej = gaussian_filter1d(rej, sigma=1, radius=2, mode="nearest")
+
+    # Return also the cut values if wanted
+    if return_cuts:
+        return rej, eff[1]
+
+    return rej
+
+
+def calculate_efficiency_error(
+    arr: np.ndarray,
+    n_counts: int,
+    suppress_zero_divison_error: bool = False,
+    norm: bool = False,
+) -> np.ndarray:
+    """Calculate statistical efficiency uncertainty.
+
+    Parameters
+    ----------
+    arr : numpy.array
+        Efficiency values
+    n_counts : int
+        Number of used statistics to calculate efficiency
+    suppress_zero_divison_error : bool
+        Not raising Error for zero division
+    norm : bool, optional
+        If True, normed (relative) error is being calculated, by default False
+
+    Returns
+    -------
+    numpy.array
+        Efficiency uncertainties
+
+    Raises
+    ------
+    ValueError
+        If n_counts <=0
+
+    Notes
+    -----
+    This method uses binomial errors as described in section 2.2 of
+    https://inspirehep.net/files/57287ac8e45a976ab423f3dd456af694
+    """
+    logger.debug("Calculating efficiency error.")
+    logger.debug("arr: %s", arr)
+    logger.debug("n_counts: %i", n_counts)
+    logger.debug("suppress_zero_divison_error: %s", suppress_zero_divison_error)
+    logger.debug("norm: %s", norm)
+    if np.any(n_counts <= 0) and not suppress_zero_divison_error:
+        raise ValueError(f"You passed as argument `N` {n_counts} but it has to be larger 0.")
+    if norm:
+        return np.sqrt(arr * (1 - arr) / n_counts) / arr
+    return np.sqrt(arr * (1 - arr) / n_counts)
+
+
+def calculate_rejection_error(
+    arr: np.ndarray,
+    n_counts: int,
+    norm: bool = False,
+) -> np.ndarray:
+    """Calculate the rejection uncertainties.
+
+    Parameters
+    ----------
+    arr : numpy.array
+        Rejection values
+    n_counts : int
+        Number of used statistics to calculate rejection
+    norm : bool, optional
+        If True, normed (relative) error is being calculated, by default False
+
+    Returns
+    -------
+    numpy.array
+        Rejection uncertainties
+
+    Raises
+    ------
+    ValueError
+        If n_counts <=0
+    ValueError
+        If any rejection value is 0
+
+    Notes
+    -----
+    Special case of `eff_err()`
+    """
+    logger.debug("Calculating rejection error.")
+    logger.debug("arr: %s", arr)
+    logger.debug("n_counts: %i", n_counts)
+    logger.debug("norm: %s", norm)
+    if np.any(n_counts <= 0):
+        raise ValueError(f"You passed as argument `n_counts` {n_counts} but it has to be larger 0.")
+    if np.any(arr == 0):
+        raise ValueError("One rejection value is 0, cannot calculate error.")
+    if norm:
+        return np.power(arr, 2) * calculate_efficiency_error(1 / arr, n_counts) / arr
+    return np.power(arr, 2) * calculate_efficiency_error(1 / arr, n_counts)
+
+
+def get_discriminant(
+    jets: np.ndarray,
+    tagger: str,
+    signal: Label,
+    flavours: LabelContainer,
+    fraction_values: dict[str, float],
+    epsilon: float = 1e-10,
+) -> np.ndarray:
+    """Calculate the tagging discriminant for a given tagger.
+
+    Calculated as the logarithm of the ratio of a specified signal probability
+    to a weighted sum ofbackground probabilities.
+
+    Parameters
+    ----------
+    jets : np.ndarray
+        Structured array of jets containing tagger outputs
+    tagger : str
+        Name of the tagger
+    signal : Label
+        Signal flavour (bjets/cjets or hbb/hcc)
+    fraction_values : dict
+        Dict with the fraction values for the background classes for the given tagger
+    epsilon : float, optional
+        Small number to avoid division by zero, by default 1e-10
+
+    Returns
+    -------
+    np.ndarray
+        Array of discriminant values.
+
+    Raises
+    ------
+    ValueError
+        If the signal flavour is not recognised.
+    """
+    # Init the denominator
+    denominator = 0.0
+
+    # Loop over background flavours
+    for flav in flavours:
+        # Skip signal flavour for denominator
+        if flav == signal:
+            continue
+
+        # Get the probability name of the tagger/flavour combo + fraction value
+        prob_name = f"{tagger}_{flav.px}"
+        fraction_value = fraction_values[flav.frac_str]
+
+        # If fraction_value for the given flavour is zero, skip it
+        if fraction_value == 0:
+            continue
+
+        # Check that the probability value for the flavour is available
+        if fraction_value > 0 and prob_name not in jets.dtype.names:
+            raise ValueError(
+                f"Nonzero fraction value for {flav.name}, but '{prob_name}' "
+                "not found in input array."
+            )
+
+        # Update denominator
+        denominator += jets[prob_name] * fraction_value if prob_name in jets.dtype.names else 0
+
+    # Calculate numerator
+    signal_field = f"{tagger}_{signal.px}"
+
+    # Check that the probability of the signal is available
+    if signal_field not in jets.dtype.names:
+        raise ValueError(
+            f"No signal probability value(s) found for tagger {tagger}. "
+            f"Missing variable: {signal_field}"
+        )
+
+    return np.log((jets[signal_field] + epsilon) / (denominator + epsilon))

ftag/vds.py

@@ -2,6 +2,9 @@ from __future__ import annotations
 
 import argparse
 import glob
+import os
+import re
+import sys
 from pathlib import Path
 
 import h5py
@@ -13,6 +16,8 @@ def parse_args(args):
     )
     parser.add_argument("pattern", type=Path, help="quotes-enclosed glob pattern of files to merge")
     parser.add_argument("output", type=Path, help="path to output virtual file")
+    parser.add_argument("--use_regex", help="if provided pattern is a regex", action="store_true")
+    parser.add_argument("--regex_path", type=str, required="--regex" in sys.argv, default=None)
     return parser.parse_args(args)
 
 
@@ -43,13 +48,36 @@ def get_virtual_layout(fnames: list[str], group: str):
     return layout
 
 
+def glob_re(pattern, regex_path):
+    return list(filter(re.compile(pattern).match, os.listdir(regex_path)))
+
+
+def regex_files_from_dir(reg_matched_fnames, regex_path):
+    parent_dir = regex_path or str(Path.cwd())
+    full_paths = [parent_dir + "/" + fname for fname in reg_matched_fnames]
+    paths_to_glob = [fname + "/*.h5" if Path(fname).is_dir() else fname for fname in full_paths]
+    nested_fnames = [glob.glob(fname) for fname in paths_to_glob]
+    return sum(nested_fnames, [])
+
+
 def create_virtual_file(
-    pattern: Path | str, out_fname: Path | None = None, overwrite: bool = False
+    pattern: Path | str,
+    out_fname: Path | None = None,
+    use_regex: bool = False,
+    regex_path: str | None = None,
+    overwrite: bool = False,
 ):
     # get list of filenames
-    fnames = glob.glob(str(pattern))
+    pattern_str = str(pattern)
+    if use_regex:
+        reg_matched_fnames = glob_re(pattern_str, regex_path)
+        print("reg matched fnames: ", reg_matched_fnames)
+        fnames = regex_files_from_dir(reg_matched_fnames, regex_path)
+    else:
+        fnames = glob.glob(pattern_str)
     if not fnames:
         raise FileNotFoundError(f"No files matched pattern {pattern}")
+    print("Files to merge to vds: ", fnames)
 
     # infer output path if not given
     if out_fname is None:
@@ -94,8 +122,15 @@ def create_virtual_file(
 
 def main(args=None) -> None:
     args = parse_args(args)
-    print(f"Globbing {args.pattern}...")
-    create_virtual_file(args.pattern, args.output, overwrite=True)
+    matching_mode = "Applying regex to" if args.use_regex else "Globbing"
+    print(f"{matching_mode} {args.pattern}...")
+    create_virtual_file(
+        args.pattern,
+        args.output,
+        use_regex=args.use_regex,
+        regex_path=args.regex_path,
+        overwrite=True,
+    )
     with h5py.File(args.output) as f:
         key = next(iter(f.keys()))
         num = len(f[key])

ftag/{wps/working_points.py → working_points.py}

@@ -14,7 +14,7 @@ from ftag import Flavours
 from ftag.cli_utils import HelpFormatter
 from ftag.cuts import Cuts
 from ftag.hdf5 import H5Reader
-from ftag.wps.discriminant import get_discriminant
+from ftag.utils import get_discriminant
 
 if TYPE_CHECKING:  # pragma: no cover
     from collections.abc import Sequence

atlas_ftag_tools-0.2.9.dist-info/METADATA

@@ -1,150 +0,0 @@
-Metadata-Version: 2.2
-Name: atlas-ftag-tools
-Version: 0.2.9
-Summary: ATLAS Flavour Tagging Tools
-Author: Sam Van Stroud, Philipp Gadow
-License: MIT
-Project-URL: Homepage, https://github.com/umami-hep/atlas-ftag-tools/
-Requires-Python: <3.12,>=3.8
-Description-Content-Type: text/markdown
-Requires-Dist: h5py>=3.0
-Requires-Dist: numpy
-Requires-Dist: PyYAML>=5.1
-Provides-Extra: dev
-Requires-Dist: ruff==0.6.2; extra == "dev"
-Requires-Dist: mypy==1.11.2; extra == "dev"
-Requires-Dist: pre-commit==3.1.1; extra == "dev"
-Requires-Dist: pytest==7.2.2; extra == "dev"
-Requires-Dist: pytest-cov==4.0.0; extra == "dev"
-Requires-Dist: pytest_notebook==0.10.0; extra == "dev"
-Requires-Dist: ipykernel==6.21.3; extra == "dev"
-
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-[![PyPI version](https://badge.fury.io/py/atlas-ftag-tools.svg)](https://badge.fury.io/py/atlas-ftag-tools)
-[![codecov](https://codecov.io/gh/umami-hep/atlas-ftag-tools/branch/main/graph/badge.svg?token=MBHLIYYQ7I)](https://codecov.io/gh/umami-hep/atlas-ftag-tools)
-
-# ATLAS FTAG Python Tools
-
-This is a collection of Python tools for working with files produced with the FTAG [ntuple dumper](https://gitlab.cern.ch/atlas-flavor-tagging-tools/training-dataset-dumper/).
-The code is intended to be used a [library](https://iscinumpy.dev/post/app-vs-library/) for other projects.
-Please see the [example notebook](ftag/example.ipynb) for usage.
-
-# Quickstart 
-
-## Installation
-
-If you want to use this package without modification, you can install from [pypi](https://pypi.org/project/atlas-ftag-tools/) using `pip`.
-
-```bash
-pip install atlas-ftag-tools
-```
-
-To additionally install the development dependencies (for formatting and linting) use
-```bash
-pip install atlas-ftag-tools[dev]
-```
-
-## Development
-
-If you plan on making changes to teh code, instead clone the repository and install the package from source in editable mode with
-
-```bash
-python -m pip install -e .
-```
-
-Include development dependencies with
-
-```bash
-python -m pip install -e ".[dev]"
-```
-
-You can set up and run pre-commit hooks with
-
-```bash
-pre-commit install
-pre-commmit run --all-files
-```
-
-To run the tests you can use the `pytest` or `coverage` command, for example
-
-```bash
-coverage run --source ftag -m pytest --show-capture=stdout
-```
-
-Running `coverage report` will display the test coverage.
-
-
-# Usage
-
-Please see the [example notebook](ftag/example.ipynb) for full usage.
-Additional functionality is also documented below.
-
-## Calculate WPs
-
-This package contains a script to calculate tagger working points (WPs).
-The script is `working_points.py` and can be run after installing this package with
-
-```
-wps \
-    --ttbar "path/to/ttbar/*.h5" \
-    --tagger GN2v01 \
-    --fc 0.1
-```
-
-Both the `--tagger` and `--fc` options accept a list if you want to get the WPs for multiple taggers.
-If you are doing c-tagging or xbb-tagging, dedicated fx arguments are available ()you can find them all with `-h`.
-
-If you want to use the `ttbar` WPs get the efficiencies and rejections for the `zprime` sample, you can add `--zprime "path/to/zprime/*.h5"` to the command.
-Note that a default selection of $p_T > 250 ~GeV$ to jets in the `zprime` sample.
-
-If instead of defining the working points for a series of signal efficiencies, you wish to calculate a WP corresponding to a specific background rejection, the `--rejection` option can be given along with the desired background.
-
-By default the working points are printed to the terminal, but you can save the results to a YAML file with the `--outfile` option.
-
-See `wps --help` for more options and information.
-
-## Calculate efficiency at discriminant cut 
-
-The same script can be used to calculate the efficiency and rejection values at a given discriminant cut value.
-The script `working_points.py` can be run after intalling this package as follows
-
-```
-wps \
-    --ttbar "path/to/ttbar/*.h5" \
-    --tagger GN2v01 \
-    --fx 0.1
-    --disc_cuts 1.0 1.5
-```
-The `--tagger`, `--fx`, and `--outfile` follow the same procedure as in the 'Calculate WPs' script as described above.
-
-## H5 Utils
-
-### Create virtual file
-
-This package contains a script to easily merge a set of H5 files.
-A virtual file is a fast and lightweight way to wrap a set of files.
-See the [h5py documentation](https://docs.h5py.org/en/stable/vds.html) for more information on virtual datasets.
-
-The script is `vds.py` and can be run after installing this package with
-
-```
-vds <pattern> <output path>
-```
-
-The `<pattern>` argument should be a quotes enclosed [glob pattern](https://en.wikipedia.org/wiki/Glob_(programming)), for example `"dsid/path/*.h5"`
-
-See `vds --help` for more options and information.
-
-
-### [h5move](ftag/hdf5/h5move.py)
-
-A script to move/rename datasets inside an h5file.
-Useful for correcting discrepancies between group names.
-See [h5move.py](ftag/hdf5/h5move.py) for more info.
-
-
-### [h5split](ftag/hdf5/h5split.py)
-
-A script to split a large h5 file into several smaller files.
-Useful if output files are too large for EOS/grid storage.
-See [h5split.py](ftag/hdf5/h5split.py) for more info.

atlas_ftag_tools-0.2.9.dist-info/RECORD

@@ -1,28 +0,0 @@
-ftag/__init__.py,sha256=YRug5UslRbNoQACbEhdenDS6wXmsmeLjlz4JaKP6eHs,737
-ftag/cli_utils.py,sha256=w3TtQmUHSyAKChS3ewvOtcSDAUJAZGIIomaNi8f446U,298
-ftag/cuts.py,sha256=9_ooLZHaO3SnIQBNxwbaPZn-qptGdKnB27FdKQGTiTY,2933
-ftag/flavours.py,sha256=ShH4M2UjQZpZ_NlCctTm2q1tJbzYxjmGteioQ2GcqEU,114
-ftag/flavours.yaml,sha256=87xBvLkMDkicuRMaXtxcao8gjEAgvlTbgjAzpvx4YFM,9021
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