reboost 0.6.2__py3-none-any.whl → 0.8.0__py3-none-any.whl

reboost/spms/pe.py

@@ -0,0 +1,178 @@
+from __future__ import annotations
+
+import logging
+
+import awkward as ak
+import numpy as np
+from lgdo import VectorOfVectors
+
+from ..optmap import convolve
+from ..units import units_conv_ak
+
+log = logging.getLogger(__name__)
+
+
+def load_optmap_all(map_file: str) -> convolve.OptmapForConvolve:
+    """Load an optical map file for later use with :py:func:`detected_photoelectrons`."""
+    return convolve.open_optmap(map_file)
+
+
+def load_optmap(map_file: str, spm_det_uid: int) -> convolve.OptmapForConvolve:
+    """Load an optical map file for later use with :py:func:`detected_photoelectrons`."""
+    return convolve.open_optmap_single(map_file, spm_det_uid)
+
+
+def _nested_unflatten(data: ak.Array, lengths: ak.Array):
+    return ak.unflatten(ak.unflatten(ak.flatten(data), ak.flatten(lengths)), ak.num(lengths))
+
+
+def corrected_photoelectrons(
+    simulated_pe: ak.Array,
+    simulated_uids: ak.Array,
+    data_pe: ak.Array,
+    data_uids: ak.Array,
+    *,
+    seed: int | None = None,
+) -> tuple[ak.Array, ak.Array]:
+    r"""Add a correction to the observed number of photoelectrons (p.e.) using forced trigger data.
+
+    For every simulated event a corresponding forced trigger event in data is chosen
+    and the resulting number of p.e. for each channel (i) is:
+
+     .. math::
+
+        n_i = n_{\text{sim},i} + n_{\text{data},i}
+
+    .. warning::
+       The number of supplied forced trigger events in data should ideally be
+       more than that in the simulations. If this is not the case and "allow_data_reuse"
+       is True then some data events will be used multiple times. This introduces
+       a small amount of correlation between the simulated events, but is probably acceptable
+       in most circumstances.
+
+    Parameters
+    ----------
+    simulated_pe
+        The number of number of detected pe per sipm channel.
+    simulated_uids
+        The unique identifier (uid) for each sipm hit.
+    data_pe
+        The collection of forced trigger pe.
+    data_uids
+        The uids for each forced trigger event.
+    seed
+        Seed for random number generator
+
+    Returns
+    -------
+    a tuple of the corrected pe and sipm uids.
+    """
+    rand = np.random.default_rng(seed=seed)
+    rand_ints = rand.integers(0, len(data_pe), size=len(simulated_pe))
+
+    selected_data_pe = data_pe[rand_ints]
+    selected_data_uids = data_uids[rand_ints]
+
+    # combine sims with data
+    pe_tot = ak.concatenate([simulated_pe, selected_data_pe], axis=1)
+    uid_tot = ak.concatenate([simulated_uids, selected_data_uids], axis=1)
+
+    # sort by uid
+    order = ak.argsort(uid_tot)
+    pe_tot = pe_tot[order]
+    uid_tot = uid_tot[order]
+
+    # add an extra axis
+    n = ak.run_lengths(uid_tot)
+
+    # add another dimension
+    pe_tot = _nested_unflatten(pe_tot, n)
+    uid_tot = _nested_unflatten(uid_tot, n)
+
+    # sum pe and take the first uid (should all be the same)
+    corrected_pe = ak.sum(pe_tot, axis=-1)
+    uid_tot = ak.fill_none(ak.firsts(uid_tot, axis=-1), np.nan)
+
+    return corrected_pe, uid_tot
+
+
+def detected_photoelectrons(
+    num_scint_ph: ak.Array,
+    particle: ak.Array,
+    time: ak.Array,
+    xloc: ak.Array,
+    yloc: ak.Array,
+    zloc: ak.Array,
+    optmap: convolve.OptmapForConvolve,
+    material: str,
+    spm_detector_uid: int,
+    map_scaling: float = 1,
+    map_scaling_sigma: float = 0,
+) -> VectorOfVectors:
+    """Derive the number of detected photoelectrons (p.e.) from scintillator hits using an optical map.
+
+    Parameters
+    ----------
+    num_scint_ph
+        array of emitted scintillation photons, as generated by
+        :func:`emitted_scintillation_photons`.
+    particle
+        array of particle PDG IDs of scintillation events.
+    time
+        array of timestamps of scintillation events.
+    xloc
+        array of x coordinate position of scintillation events.
+    yloc
+        array of y coordinate position of scintillation events.
+    zloc
+        array of z coordinate position of scintillation events.
+    optmap
+        the optical map loaded via py:func:`load_optmap`.
+    material
+        scintillating material name.
+    spm_detector_uid
+        SiPM detector uid as used in the optical map.
+    map_scaling
+        scale the detection probability in the map for this detector by this factor.
+    map_scaling_sigma
+        if larger than zero, sample the used scaling factor for each (reshaped) event
+        from a normal distribution with this standard deviation.
+    """
+    hits = ak.Array(
+        {
+            "num_scint_ph": num_scint_ph,
+            "particle": particle,
+            "time": units_conv_ak(time, "ns"),
+            "xloc": units_conv_ak(xloc, "m"),
+            "yloc": units_conv_ak(yloc, "m"),
+            "zloc": units_conv_ak(zloc, "m"),
+        }
+    )
+
+    scint_mat_params = convolve._get_scint_params(material)
+    pe = convolve.iterate_stepwise_depositions_pois(
+        hits, optmap, scint_mat_params, spm_detector_uid, map_scaling, map_scaling_sigma
+    )
+
+    return VectorOfVectors(pe, attrs={"units": "ns"})
+
+
+def emitted_scintillation_photons(
+    edep: ak.Array, particle: ak.Array, material: str
+) -> VectorOfVectors:
+    """Derive the number of emitted scintillation photons from scintillator hits.
+
+    Parameters
+    ----------
+    edep
+        array of deposited energy in scintillation events.
+    particle
+        array of particle PDG IDs of scintillation events.
+    material
+        scintillating material name.
+    """
+    hits = ak.Array({"edep": units_conv_ak(edep, "keV"), "particle": particle})
+
+    scint_mat_params = convolve._get_scint_params(material)
+    ph = convolve.iterate_stepwise_depositions_scintillate(hits, scint_mat_params)
+    return VectorOfVectors(ph)

reboost/units.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 import logging
 from typing import Any
 
+import awkward as ak
 import pint
 import pyg4ometry as pg4
 from lgdo import LGDO
@@ -16,7 +17,7 @@ ureg = pint.get_application_registry()
 ureg.formatter.default_format = "~P"
 
 
-def pg4_to_pint(obj) -> pint.Quantity:
+def pg4_to_pint(obj: pint.Quantity | pg4.gdml.Defines.VectorBase) -> pint.Quantity:
     """Convert pyg4ometry object to pint Quantity."""
     if isinstance(obj, pint.Quantity):
         return obj
@@ -26,32 +27,54 @@ def pg4_to_pint(obj) -> pint.Quantity:
     raise ValueError(msg)
 
 
-def units_convfact(data: Any, target_units: pint.Units) -> float:
+def units_convfact(data: Any | LGDO | ak.Array, target_units: pint.Unit | str) -> float:
     """Calculate numeric conversion factor to reach `target_units`.
 
     Parameters
     ----------
     data
-        starting data structure. If an LGDO, try to determine units by peeking
-        into its attributes. Otherwise, just return 1.
+        starting data structure. If an :class:`LGDO` or :class:`ak.Array`, try to
+        determine units by peeking into its attributes. Otherwise, just return 1.
     target_units
         units you wish to convert data to.
     """
     if isinstance(data, LGDO) and "units" in data.attrs:
         return ureg(data.attrs["units"]).to(target_units).magnitude
+    if isinstance(data, ak.Array) and "units" in ak.parameters(data):
+        return ureg(ak.parameters(data)["units"]).to(target_units).magnitude
     return 1
 
 
-def unwrap_lgdo(data: Any, library: str = "ak") -> tuple(Any, pint.Unit | None):
+def units_conv_ak(data: Any | LGDO | ak.Array, target_units: pint.Unit | str) -> ak.Array:
+    """Calculate numeric conversion factor to reach `target_units`, and apply to data converted to ak.
+
+    Parameters
+    ----------
+    data
+        starting data structure. If an :class:`LGDO` or :class:`ak.Array`, try to
+        determine units by peeking into its attributes. Otherwise, return the data
+        unchanged.
+    target_units
+        units you wish to convert data to.
+    """
+    fact = units_convfact(data, target_units)
+    if isinstance(data, LGDO) and fact != 1:
+        return ak.without_parameters(data.view_as("ak") * fact)
+    if isinstance(data, ak.Array) and fact != 1:
+        return ak.without_parameters(data * fact)
+    return data.view_as("ak") if isinstance(data, LGDO) else data
+
+
+def unwrap_lgdo(data: Any | LGDO | ak.Array, library: str = "ak") -> tuple[Any, pint.Unit | None]:
     """Return a view of the data held by the LGDO and its physical units.
 
     Parameters
     ----------
     data
-        the data container. If not an LGDO, it will be returned as is with
-        ``None`` units.
+        the data container. If not an :class:`LGDO` or :class:`ak.Array`, it will be
+        returned as is with ``None`` units.
     library
-        forwarded to :func:`lgdo.view_as`.
+        forwarded to :meth:`LGDO.view_as`.
 
     Returns
     -------
@@ -64,6 +87,15 @@ def unwrap_lgdo(data: Any, library: str = "ak") -> tuple(Any, pint.Unit | None):
         if "units" in data.attrs:
             ret_units = ureg(data.attrs["units"]).u
 
+    if isinstance(data, ak.Array):
+        if library != "ak":
+            msg = "cannot unwrap an awkward array as a non-awkward type"
+            raise ValueError(msg)
+
+        if "units" in ak.parameters(data):
+            ret_units = ureg(ak.parameters(data)["units"]).u
+            ret_data = ak.without_parameters(data)
+
     return ret_data, ret_units
 
 

reboost/utils.py

@@ -9,6 +9,7 @@ from collections.abc import Iterable, Mapping
 from contextlib import contextmanager
 from pathlib import Path
 
+import h5py
 from dbetto import AttrsDict
 from lgdo import lh5
 from lgdo.types import Struct, Table, VectorOfVectors
@@ -164,7 +165,7 @@ def get_file_dict(
     files = {}
 
     for file_type, file_list in zip(
-        ["stp", "glm", "hit"], [stp_files, glm_files_list, hit_files_list]
+        ["stp", "glm", "hit"], [stp_files, glm_files_list, hit_files_list], strict=True
     ):
         if isinstance(file_list, str):
             files[file_type] = [file_list]
@@ -283,7 +284,7 @@ def get_function_string(expr: str, aliases: dict | None = None) -> tuple[str, di
         if "." not in func_call:
             continue
 
-        subpackage, func = func_call.rsplit(".", 1)
+        subpackage, _func = func_call.rsplit(".", 1)
         package = subpackage.split(".")[0]
 
         # import the subpackage
@@ -303,7 +304,10 @@ def get_function_string(expr: str, aliases: dict | None = None) -> tuple[str, di
             globs = globs | {
                 package: importlib.import_module(package_import),
             }
-        except Exception:
+        except Exception as e:
+            # for imports of our own package, raise the error back to the user
+            if package_import == "reboost":
+                raise e
             msg = f"Function {package_import} cannot be imported"
             log.debug(msg)
             continue
@@ -439,3 +443,61 @@ def write_lh5(
         )
     if time_dict is not None:
         time_dict.update_field("write", start_time)
+
+
+def get_remage_detector_uids(h5file: str | Path) -> dict:
+    """Get mapping of detector names to UIDs from a remage output file.
+
+    The remage LH5 output files contain a link structure that lets the user
+    access detector tables by UID. For example:
+
+    .. code-block:: text
+
+        ├── stp · struct{det1,det2,optdet1,optdet2,scint1,scint2}
+        └── __by_uid__ · struct{det001,det002,det011,det012,det101,det102}
+            ├── det001 -> /stp/scint1
+            ├── det002 -> /stp/scint2
+            ├── det011 -> /stp/det1
+            ├── det012 -> /stp/det2
+            ├── det101 -> /stp/optdet1
+            └── det102 -> /stp/optdet2
+
+    This function analyzes this structure and returns:
+
+    .. code-block:: text
+
+        {1: 'scint1',
+         2: 'scint2',
+         11: 'det1',
+         12: 'det2',
+         101: 'optdet1',
+         102: 'optdet2'g
+
+    Parameters
+    ----------
+    h5file
+        path to remage output file.
+    """
+    if isinstance(h5file, Path):
+        h5file = h5file.as_posix()
+
+    out = {}
+    with h5py.File(h5file, "r") as f:
+        g = f["/stp/__by_uid__"]
+        # loop over links
+        for key in g:
+            # is this a link?
+            link = g.get(key, getlink=True)
+            if isinstance(link, h5py.SoftLink):
+                m = re.fullmatch(r"det(\d+)", key)
+                if m is None:
+                    msg = rf"'{key}' is not formatted as expected, i.e. 'det(\d+)', skipping"
+                    log.warning(msg)
+                    continue
+
+                # get the name of the link target without trailing groups (to
+                # i.e. remove /stp)
+                name = link.path.split("/")[-1]
+
+                out[int(m.group(1))] = name
+    return out

{reboost-0.6.2.dist-info → reboost-0.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: reboost
-Version: 0.6.2
+Version: 0.8.0
 Summary: New LEGEND Monte-Carlo simulation post-processing
 Author-email: Manuel Huber <info@manuelhu.de>, Toby Dixon <toby.dixon.23@ucl.ac.uk>, Luigi Pertoldi <gipert@pm.me>
 Maintainer: The LEGEND Collaboration
@@ -693,16 +693,16 @@ Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: hdf5plugin
 Requires-Dist: colorlog
 Requires-Dist: numpy
 Requires-Dist: scipy
-Requires-Dist: numba
-Requires-Dist: legend-pydataobj>=1.14
-Requires-Dist: legend-pygeom-optics>=0.9.2
+Requires-Dist: numba>=0.60
+Requires-Dist: legend-pydataobj>=1.15.1
+Requires-Dist: legend-pygeom-optics>=0.12.0
 Requires-Dist: legend-pygeom-tools>=0.0.11
 Requires-Dist: hist
 Requires-Dist: dbetto
@@ -728,6 +728,8 @@ Dynamic: license-file
 
 # reboost
 
+[![PyPI](https://img.shields.io/pypi/v/reboost?logo=pypi)](https://pypi.org/project/reboost/)
+[![conda-forge](https://img.shields.io/conda/vn/conda-forge/reboost.svg)](https://anaconda.org/conda-forge/reboost)
 ![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/legend-exp/reboost?logo=git)
 [![GitHub Workflow Status](https://img.shields.io/github/checks-status/legend-exp/reboost/main?label=main%20branch&logo=github)](https://github.com/legend-exp/reboost/actions)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)

reboost-0.8.0.dist-info/RECORD

@@ -0,0 +1,42 @@
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+reboost/_version.py,sha256=Rttl-BDadtcW1QzGnNffCWA_Wc9mUKDMOBPZp--Mnsc,704
+reboost/build_evt.py,sha256=VXIfK_pfe_Cgym6gI8dESwONZi-v_4fll0Pn09vePQY,3767
+reboost/build_glm.py,sha256=IerSLQfe51ZO7CQP2kmfPnOIVaDtcfw3byOM02Vaz6o,9472
+reboost/build_hit.py,sha256=pjEaiPW63Q3MfpjI29uJXx9gtwfiOIgOcADRDrDpRrA,17409
+reboost/cli.py,sha256=68EzKiWTHJ2u1RILUv7IX9HaVq6nTTM80_W_MUnWRe4,6382
+reboost/core.py,sha256=TPxvZgUaHZdxfQSDdX2zIerQXt3Gq-zQaA6AeXZKNvA,15232
+reboost/iterator.py,sha256=qlEqRv5qOh8eIs-dyVOLYTvH-ZpQDx9fLckpcAdtWjs,6975
+reboost/log_utils.py,sha256=VqS_9OC5NeNU3jcowVOBB0NJ6ssYvNWnirEY-JVduEA,766
+reboost/profile.py,sha256=EOTmjmS8Rm_nYgBWNh6Rntl2XDsxdyed7yEdWtsZEeg,2598
+reboost/units.py,sha256=LUwl6swLQoG09Rt9wcDdu6DTrwDsy-C751BNGzX4sz8,3651
+reboost/utils.py,sha256=-4315U6m1M-rwoaI_inI1wIo_l20kvoGmC84D_QOhkE,14563
+reboost/daq/__init__.py,sha256=rNPhxx1Yawt3tENYhmOYSum9_TdV57ZU5kjxlWFAGuo,107
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+reboost/hpge/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+reboost/hpge/psd.py,sha256=P9lxji4njwFwPBR0vfh6gkvt7GQx2BRajvCsUUmtEqU,24407
+reboost/hpge/surface.py,sha256=ROewOsSoq8zRAaiamWdMDl-UR7ZfsimgH2Lv9k0flKg,8494
+reboost/hpge/utils.py,sha256=AcMS86v8s0SbeC4YA3CfH73GBZcC7Sb_RR3pRPjWAwU,2857
+reboost/math/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+reboost/math/functions.py,sha256=OymiYTcA0NXxxm-MBDw5kqyNwHoLCmuv4J48AwnSrbU,5633
+reboost/math/stats.py,sha256=Rq4Wdzv-3aoSK7EsPZCuOEHfnOz3w0moIzCEHbC07xw,3173
+reboost/optmap/__init__.py,sha256=imvuyld-GLw8qdwqW-lXCg2feptcTyQo3wIzPvDHwmY,93
+reboost/optmap/cli.py,sha256=KJFyO4Sd2oYlRC65Kvrdq0BN_Qygp6o7LgO36D5O6_s,8887
+reboost/optmap/convolve.py,sha256=UVc-KjiYvi8LoAlykL__5qDd5T8teT89aDjiE7WYjE4,12464
+reboost/optmap/create.py,sha256=R9W8Wyl8cgXIYESenVpCRuN_MoHhLfaEv4a44cf3AxU,14479
+reboost/optmap/evt.py,sha256=p5ngsCuvOxIZDDQNL9efcLn8Q4CfGL7G726BRrCpE6Y,5637
+reboost/optmap/mapview.py,sha256=_zGiONqCWc4kCp1yHvNFRkh7svvud4ZLqaSHkNieo_M,6878
+reboost/optmap/numba_pdg.py,sha256=y8cXR5PWE2Liprp4ou7vl9do76dl84vXU52ZJD9_I7A,731
+reboost/optmap/optmap.py,sha256=3clc1RA8jA4YJte83w085MY8zLpG-G7DBkpZ2UeKPpM,12825
+reboost/shape/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+reboost/shape/cluster.py,sha256=nwR1Dnf00SDICGPqpXeM1Q7_DwTtO9uP3wmuML45c3g,8195
+reboost/shape/group.py,sha256=gOCYgir2gZqmW1JXtbNRPlQqP0gmUcbe7RVb9CbY1pU,5540
+reboost/shape/reduction.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+reboost/spms/__init__.py,sha256=ffi0rH-ZFGmpURbFt-HY1ZAHCdady0mLXNsblRNh-JY,207
+reboost/spms/pe.py,sha256=Q_GzN5HEp2BmgB4fni5mfc5ZOXh4mlJepDwZd1EzFdc,5696
+reboost-0.8.0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+reboost-0.8.0.dist-info/METADATA,sha256=t8uYwYlKBZPoO5Rbrv4RVr5AQj4D_rglFCQ-HFrYe1I,44442
+reboost-0.8.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+reboost-0.8.0.dist-info/entry_points.txt,sha256=DxhD6BidSWNot9BrejHJjQ7RRLmrMaBIl52T75oWTwM,93
+reboost-0.8.0.dist-info/top_level.txt,sha256=q-IBsDepaY_AbzbRmQoW8EZrITXRVawVnNrB-_zyXZs,8
+reboost-0.8.0.dist-info/RECORD,,

reboost-0.6.2.dist-info/RECORD

@@ -1,37 +0,0 @@
-reboost/__init__.py,sha256=VZz9uo7i2jgAx8Zi15SptLZnE_qcnGuNWwqkD3rYHFA,278
-reboost/_version.py,sha256=DhO-RAVJdQTjYPaMf0M6q_WAXdD6jcx2tWl_B9FtuhM,511
-reboost/build_evt.py,sha256=VXIfK_pfe_Cgym6gI8dESwONZi-v_4fll0Pn09vePQY,3767
-reboost/build_glm.py,sha256=IerSLQfe51ZO7CQP2kmfPnOIVaDtcfw3byOM02Vaz6o,9472
-reboost/build_hit.py,sha256=BwcAzr7hkhLqQpyULYPqM70VEvENaw-j90fvBYKh-68,15649
-reboost/cli.py,sha256=HZgqUZK0tSmnlGqoXjrbmLitW_i001TzibxvDrRxLLg,6324
-reboost/core.py,sha256=WGbWe2rcfMDEaehVyw7peqAHoTFWoCu5J6CdWHC5aWA,14974
-reboost/iterator.py,sha256=fATFDxu2PUc0e48OdJJujZo2kwykfRLH1oBtcB-s5pM,6905
-reboost/log_utils.py,sha256=VqS_9OC5NeNU3jcowVOBB0NJ6ssYvNWnirEY-JVduEA,766
-reboost/profile.py,sha256=EOTmjmS8Rm_nYgBWNh6Rntl2XDsxdyed7yEdWtsZEeg,2598
-reboost/units.py,sha256=3EH8XlpbsObdu5vLgxhm1600L6UNYD5jng4SjJT_1QE,2202
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