reboost 0.8.0__tar.gz → 0.8.1__tar.gz

{reboost-0.8.0 → reboost-0.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: reboost
-Version: 0.8.0
+Version: 0.8.1
 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
@@ -704,6 +704,7 @@ 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: legend-pygeom-hpges
 Requires-Dist: hist
 Requires-Dist: dbetto
 Requires-Dist: particle

{reboost-0.8.0 → reboost-0.8.1}/pyproject.toml

@@ -40,6 +40,7 @@ dependencies = [
     "legend-pydataobj >=1.15.1",
     "legend-pygeom-optics >=0.12.0",
     "legend-pygeom-tools >=0.0.11",
+    "legend-pygeom-hpges",
     "hist",
     "dbetto",
     "particle",

{reboost-0.8.0 → reboost-0.8.1}/src/reboost/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.8.0'
-__version_tuple__ = version_tuple = (0, 8, 0)
+__version__ = version = '0.8.1'
+__version_tuple__ = version_tuple = (0, 8, 1)
 
-__commit_id__ = commit_id = 'g1c98fe8fc'
+__commit_id__ = commit_id = 'g3148f45bd'

{reboost-0.8.0 → reboost-0.8.1}/src/reboost/hpge/psd.py

@@ -262,11 +262,13 @@ def _current_pulse_model(
 
     Consists of a Gaussian, a high side exponential tail and a low side tail:
 
-     .. math::
+    .. math::
 
-       A(t) = A_{max}\times (1-p-p_h)\times \text{Gauss}(t,\mu,\sigma)+ A \times p (1-\text{Erf}((t-\mu)/sigma_i))\times
-        \frac{e^{( t/\tau)}}{2e^{\mu/\tau}} + A \times p_h (1-\text{Erf}(-(t-\mu)/sigma_i))\times
-        \frac{e^{-( t/\tau)}}{2}
+      \begin{align}
+      A(t) = \; &A_\text{max} \times (1-p-p_h) \times \text{Gauss}(t;\mu,\sigma) \\
+        &+ A \times p \; \left(1 - \text{erf}\left(\frac{t-\mu}{\sigma_i}\right)\right) \times \frac{e^{t/\tau}}{2e^{\mu/\tau}} \\
+        &+ A \times p_h \; \left(1 - \text{erf}\left(-\frac{t-\mu}{\sigma_i}\right)\right) \times \frac{1}{2}e^{-t/\tau}
+      \end{align}
 
     Parameters
     ----------
@@ -397,13 +399,13 @@ def get_current_waveform(
     the template.
 
     .. math::
-        A(t) = \sum_i E_i \times N f(t,dt_i,\vector{\theta})
+        A(t) = \sum_i E_i \times N f(t, dt_i, \vec{\theta})
 
     Where:
-        - $f(t)$ is the template
-        - $\vector{\theta}$ are the parameters (sigma, p, tau)
-        - $E_i$ and $dt_i$ are the deposited energy and drift time.
-        - N is a normalisation term
+        - :math:`f(t)` is the template
+        - :math`\vec{\theta}` are the parameters :math:`(\sigma, p, \tau)`
+        - :math:`E_i` and :math:`dt_i` are the deposited energy and drift time.
+        - :math:`N` is a normalisation term
 
     Parameters
     ----------

{reboost-0.8.0 → reboost-0.8.1}/src/reboost/optmap/convolve.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import logging
-import re
 from typing import NamedTuple
 
 import awkward as ak
@@ -10,7 +9,7 @@ import numba
 import numpy as np
 from legendoptics import fibers, lar, pen
 from lgdo import lh5
-from lgdo.types import Array, Histogram, Table
+from lgdo.types import Histogram
 from numba import njit
 from numpy.typing import NDArray
 
@@ -20,24 +19,20 @@ log = logging.getLogger(__name__)
 
 
 OPTMAP_ANY_CH = -1
-OPTMAP_SUM_CH = -2
 
 
 class OptmapForConvolve(NamedTuple):
     """A loaded optmap for convolving."""
 
-    detids: NDArray
+    dets: NDArray
     detidx: NDArray
     edges: NDArray
     weights: NDArray
 
 
 def open_optmap(optmap_fn: str) -> OptmapForConvolve:
-    maps = lh5.ls(optmap_fn)
-    # only accept _<number> (/all is read separately)
-    det_ntuples = [m for m in maps if re.match(r"_\d+$", m)]
-    detids = np.array([int(m.lstrip("_")) for m in det_ntuples])
-    detidx = np.arange(0, detids.shape[0])
+    dets = lh5.ls(optmap_fn, "/channels/")
+    detidx = np.arange(0, dets.shape[0])
 
     optmap_all = lh5.read("/all/prob", optmap_fn)
     assert isinstance(optmap_all, Histogram)
@@ -46,7 +41,7 @@ def open_optmap(optmap_fn: str) -> OptmapForConvolve:
     ow = np.empty((detidx.shape[0] + 2, *optmap_all.weights.nda.shape), dtype=np.float64)
     # 0, ..., len(detidx)-1 AND OPTMAP_ANY_CH might be negative.
     ow[OPTMAP_ANY_CH] = optmap_all.weights.nda
-    for i, nt in zip(detidx, det_ntuples, strict=True):
+    for i, nt in zip(detidx, dets, strict=True):
         optmap = lh5.read(f"/{nt}/prob", optmap_fn)
         assert isinstance(optmap, Histogram)
         ow[i] = optmap.weights.nda
@@ -54,61 +49,51 @@ def open_optmap(optmap_fn: str) -> OptmapForConvolve:
     # if we have any individual channels registered, the sum is potentially larger than the
     # probability to find _any_ hit.
     if len(detidx) != 0:
-        ow[OPTMAP_SUM_CH] = np.sum(ow[0:-2], axis=0, where=(ow[0:-2] >= 0))
-        assert not np.any(ow[OPTMAP_SUM_CH] < 0)
+        map_sum = np.sum(ow[0:-2], axis=0, where=(ow[0:-2] >= 0))
+        assert not np.any(map_sum < 0)
+
+        # give this check some numerical slack.
+        if np.any(
+            np.abs(map_sum[ow[OPTMAP_ANY_CH] >= 0] - ow[OPTMAP_ANY_CH][ow[OPTMAP_ANY_CH] >= 0])
+            < -1e-15
+        ):
+            msg = "optical map does not fulfill relation sum(p_i) >= p_any"
+            raise ValueError(msg)
     else:
         detidx = np.array([OPTMAP_ANY_CH])
-        detids = np.array([0])
-        ow[OPTMAP_SUM_CH] = ow[OPTMAP_ANY_CH]
+        dets = np.array(["all"])
 
-    # give this check some numerical slack.
-    if np.any(
-        np.abs(
-            ow[OPTMAP_SUM_CH][ow[OPTMAP_ANY_CH] >= 0] - ow[OPTMAP_ANY_CH][ow[OPTMAP_ANY_CH] >= 0]
-        )
-        < -1e-15
-    ):
-        msg = "optical map does not fulfill relation sum(p_i) >= p_any"
-        raise ValueError(msg)
+    # check the exponent from the optical map file
+    if "_hitcounts_exp" in lh5.ls(optmap_fn):
+        msg = "found _hitcounts_exp which is not supported any more"
+        raise RuntimeError(msg)
+
+    dets = [d.replace("/channels/", "") for d in dets]
+
+    return OptmapForConvolve(dets, detidx, optmap_edges, ow)
 
-    try:
-        # check the exponent from the optical map file
-        optmap_multi_det_exp = lh5.read("/_hitcounts_exp", optmap_fn).value
-        assert isinstance(optmap_multi_det_exp, float)
-        if np.isfinite(optmap_multi_det_exp):
-            msg = f"found finite _hitcounts_exp {optmap_multi_det_exp} which is not supported any more"
-            raise RuntimeError(msg)
-    except lh5.exceptions.LH5DecodeError:  # the _hitcounts_exp might not be always present.
-        pass
-
-    return OptmapForConvolve(detids, detidx, optmap_edges, ow)
-
-
-def open_optmap_single(optmap_fn: str, spm_det_uid: int) -> OptmapForConvolve:
-    try:
-        # check the exponent from the optical map file
-        optmap_multi_det_exp = lh5.read("/_hitcounts_exp", optmap_fn).value
-        assert isinstance(optmap_multi_det_exp, float)
-        if np.isfinite(optmap_multi_det_exp):
-            msg = f"found finite _hitcounts_exp {optmap_multi_det_exp} which is not supported any more"
-            raise RuntimeError(msg)
-    except lh5.exceptions.LH5DecodeError:  # the _hitcounts_exp might not be always present.
-        pass
-
-    optmap = lh5.read(f"/_{spm_det_uid}/prob", optmap_fn)
+
+def open_optmap_single(optmap_fn: str, spm_det: str) -> OptmapForConvolve:
+    # check the exponent from the optical map file
+    if "_hitcounts_exp" in lh5.ls(optmap_fn):
+        msg = "found _hitcounts_exp which is not supported any more"
+        raise RuntimeError(msg)
+
+    h5_path = f"channels/{spm_det}" if spm_det != "all" else spm_det
+    optmap = lh5.read(f"/{h5_path}/prob", optmap_fn)
     assert isinstance(optmap, Histogram)
     ow = np.empty((1, *optmap.weights.nda.shape), dtype=np.float64)
     ow[0] = optmap.weights.nda
     optmap_edges = tuple([b.edges for b in optmap.binning])
 
-    return OptmapForConvolve(np.array([spm_det_uid]), np.array([0]), optmap_edges, ow)
+    return OptmapForConvolve(np.array([spm_det]), np.array([0]), optmap_edges, ow)
 
 
 def iterate_stepwise_depositions_pois(
     edep_hits: ak.Array,
     optmap: OptmapForConvolve,
     scint_mat_params: sc.ComputedScintParams,
-    det_uid: int,
+    det: str,
     map_scaling: float = 1,
     map_scaling_sigma: float = 0,
     rng: np.random.Generator | None = None,
@@ -117,11 +102,15 @@ def iterate_stepwise_depositions_pois(
         msg = "the pe processors only support already reshaped output"
         raise ValueError(msg)
 
+    if det not in optmap.dets:
+        msg = f"channel {det} not available in optical map (contains {optmap.dets})"
+        raise ValueError(msg)
+
     rng = np.random.default_rng() if rng is None else rng
     res, output_list = _iterate_stepwise_depositions_pois(
         edep_hits,
         rng,
-        np.where(optmap.detids == det_uid)[0][0],
+        np.where(optmap.dets == det)[0][0],
         map_scaling,
         map_scaling_sigma,
         optmap.edges,
@@ -314,38 +303,6 @@ def _iterate_stepwise_depositions_scintillate(
     return output_list
 
 
-def get_output_table(output_map):
-    ph_count_o = 0
-    for _rawid, (_evtid, det, _times) in output_map.items():
-        ph_count_o += det.shape[0]
-
-    out_idx = 0
-    out_evtid = np.empty(ph_count_o, dtype=np.int64)
-    out_det = np.empty(ph_count_o, dtype=np.int64)
-    out_times = np.empty(ph_count_o, dtype=np.float64)
-    for _rawid, (evtid, det, times) in output_map.items():
-        o_len = det.shape[0]
-        out_evtid[out_idx : out_idx + o_len] = evtid
-        out_det[out_idx : out_idx + o_len] = det
-        out_times[out_idx : out_idx + o_len] = times
-        out_idx += o_len
-
-    tbl = Table({"evtid": Array(out_evtid), "det_uid": Array(out_det), "time": Array(out_times)})
-    return ph_count_o, tbl
-
-
-def _reflatten_scint_vov(arr: ak.Array) -> ak.Array:
-    if all(arr[f].ndim == 1 for f in ak.fields(arr)):
-        return arr
-
-    group_num = ak.num(arr["edep"]).to_numpy()
-    flattened = {
-        f: ak.flatten(arr[f]) if arr[f].ndim > 1 else np.repeat(arr[f].to_numpy(), group_num)
-        for f in ak.fields(arr)
-    }
-    return ak.Array(flattened)
-
-
 def _get_scint_params(material: str):
     if material == "lar":
         return sc.precompute_scintillation_params(

{reboost-0.8.0 → reboost-0.8.1}/src/reboost/optmap/create.py

@@ -369,11 +369,8 @@ def check_optical_map(map_l5_file: str):
 
     This checks for consistency, and outputs details on map statistics.
     """
-    if (
-        "_hitcounts_exp" in lh5.ls(map_l5_file)
-        and lh5.read("_hitcounts_exp", lh5_file=map_l5_file).value != np.inf
-    ):
-        log.error("unexpected _hitcounts_exp not equal to positive infinity")
+    if "_hitcounts_exp" in lh5.ls(map_l5_file):
+        log.error("found _hitcounts_exp which is not supported any more")
         return
 
     all_binning = None

{reboost-0.8.0 → reboost-0.8.1}/src/reboost/spms/pe.py

@@ -105,7 +105,7 @@ def detected_photoelectrons(
     zloc: ak.Array,
     optmap: convolve.OptmapForConvolve,
     material: str,
-    spm_detector_uid: int,
+    spm_detector: str,
     map_scaling: float = 1,
     map_scaling_sigma: float = 0,
 ) -> VectorOfVectors:
@@ -130,8 +130,8 @@ def detected_photoelectrons(
         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.
+    spm_detector
+        SiPM detector name as used in the optical map.
     map_scaling
         scale the detection probability in the map for this detector by this factor.
     map_scaling_sigma
@@ -151,7 +151,7 @@ def detected_photoelectrons(
 
     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
+        hits, optmap, scint_mat_params, spm_detector, map_scaling, map_scaling_sigma
     )
 
     return VectorOfVectors(pe, attrs={"units": "ns"})

{reboost-0.8.0 → reboost-0.8.1}/src/reboost.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: reboost
-Version: 0.8.0
+Version: 0.8.1
 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
@@ -704,6 +704,7 @@ 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: legend-pygeom-hpges
 Requires-Dist: hist
 Requires-Dist: dbetto
 Requires-Dist: particle

{reboost-0.8.0 → reboost-0.8.1}/src/reboost.egg-info/requires.txt

@@ -6,6 +6,7 @@ numba>=0.60
 legend-pydataobj>=1.15.1
 legend-pygeom-optics>=0.12.0
 legend-pygeom-tools>=0.0.11
+legend-pygeom-hpges
 hist
 dbetto
 particle

{reboost-0.8.0 → reboost-0.8.1}/tests/hit/configs/spms.yaml

@@ -1,11 +1,11 @@
 objects:
-  spms: "{'S001': 11, 'S002': 12}"
+  spms: "['S001', 'S002']"
 
 processing_groups:
   - name: spms
 
     detector_mapping:
-      - output: OBJECTS.spms.keys()
+      - output: OBJECTS.spms
         input: det001
 
     outputs:
@@ -21,10 +21,10 @@ processing_groups:
         "lar")
 
     detector_objects:
-      optmap_lar: reboost.spms.load_optmap(ARGS.optmap_path, OBJECTS.spms[DETECTOR])
+      optmap_lar: reboost.spms.load_optmap(ARGS.optmap_path, DETECTOR)
 
     operations:
       pe_times_lar:
         reboost.spms.detected_photoelectrons( HITS.num_scint_ph, HITS.particle,
         HITS.time, HITS.xloc, HITS.yloc, HITS.zloc, DETECTOR_OBJECTS.optmap_lar,
-        "lar", OBJECTS.spms[DETECTOR] )
+        "lar", DETECTOR )

{reboost-0.8.0 → reboost-0.8.1}/tests/hit/test_build_hit.py

@@ -327,14 +327,12 @@ def test_spms(test_gen_lh5_scint, tmptestdir):
 
     # create a simple test map
     map_file = f"{tmptestdir}/spms_hit_map.lh5"
-    m = OpticalMap.create_empty(
-        "_11", {"range_in_m": [[-1, 1], [-1, 1], [-1, 1]], "bins": [1, 1, 1]}
-    )
+    m = OpticalMap.create_empty("_", {"range_in_m": [[-1, 1], [-1, 1], [-1, 1]], "bins": [1, 1, 1]})
     m._nda(m.h_vertex)[0, 0, 0] = 100
     m._nda(m.h_hits)[0, 0, 0] = 10
     m.create_probability()
-    m.write_lh5(map_file, "_11", "overwrite_file")
-    m.write_lh5(map_file, "_12", "write_safe")
+    m.write_lh5(map_file, "channels/S001", "overwrite_file")
+    m.write_lh5(map_file, "channels/S002", "write_safe")
 
     outfile = f"{tmptestdir}/spms_hit.lh5"
     reboost.build_hit(