reboost 0.8.4__py3-none-any.whl → 0.8.5__py3-none-any.whl

reboost/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.8.4'
-__version_tuple__ = version_tuple = (0, 8, 4)
+__version__ = version = '0.8.5'
+__version_tuple__ = version_tuple = (0, 8, 5)
 
 __commit_id__ = commit_id = None

reboost/optmap/convolve.py

@@ -156,15 +156,70 @@ def iterate_stepwise_depositions_scintillate(
         raise ValueError(msg)
 
     rng = np.random.default_rng() if rng is None else rng
-    output_list = _iterate_stepwise_depositions_scintillate(edep_hits, rng, scint_mat_params, mode)
+    counts = ak.num(edep_hits.edep)
+    output_array = _iterate_stepwise_depositions_scintillate(
+        edep_hits, rng, scint_mat_params, mode, ak.sum(counts)
+    )
 
-    # convert the numba result back into an awkward array.
-    builder = ak.ArrayBuilder()
-    for r in output_list:
-        with builder.list():
-            builder.extend(r)
+    return ak.unflatten(output_array, counts)
 
-    return builder.snapshot()
+
+def iterate_stepwise_depositions_numdet(
+    edep_hits: ak.Array,
+    optmap: OptmapForConvolve,
+    det: str,
+    map_scaling: float = 1,
+    map_scaling_sigma: float = 0,
+    rng: np.random.Generator | None = None,
+):
+    if edep_hits.xloc.ndim == 1:
+        msg = "the pe processors only support already reshaped output"
+        raise ValueError(msg)
+
+    rng = np.random.default_rng() if rng is None else rng
+    counts = ak.num(edep_hits.num_scint_ph)
+    output_array, res = _iterate_stepwise_depositions_numdet(
+        edep_hits,
+        rng,
+        np.where(optmap.dets == det)[0][0],
+        map_scaling,
+        map_scaling_sigma,
+        optmap.edges,
+        optmap.weights,
+        ak.sum(counts),
+    )
+
+    if res["det_no_stats"] > 0:
+        log.warning(
+            "had edep out in voxels without stats: %d",
+            res["det_no_stats"],
+        )
+    if res["oob"] > 0:
+        log.warning(
+            "had edep out of map bounds: %d (%.2f%%)",
+            res["oob"],
+            (res["oob"] / (res["ib"] + res["oob"])) * 100,
+        )
+
+    return ak.unflatten(output_array, counts)
+
+
+def iterate_stepwise_depositions_times(
+    edep_hits: ak.Array,
+    scint_mat_params: sc.ComputedScintParams,
+    rng: np.random.Generator | None = None,
+):
+    if edep_hits.particle.ndim == 1:
+        msg = "the pe processors only support already reshaped output"
+        raise ValueError(msg)
+
+    rng = np.random.default_rng() if rng is None else rng
+    counts = ak.sum(edep_hits.num_det_ph, axis=1)
+    output_array = _iterate_stepwise_depositions_times(
+        edep_hits, rng, scint_mat_params, ak.sum(counts)
+    )
+
+    return ak.unflatten(output_array, counts)
 
 
 _pdg_func = numba_pdgid_funcs()
@@ -270,17 +325,15 @@ def _iterate_stepwise_depositions_pois(
 # - cache=True does not work with outer prange, i.e. loading the cached file fails (numba bug?)
 @njit(parallel=False, nogil=True, cache=True)
 def _iterate_stepwise_depositions_scintillate(
-    edep_hits, rng, scint_mat_params: sc.ComputedScintParams, mode: str
+    edep_hits, rng, scint_mat_params: sc.ComputedScintParams, mode: str, output_length: int
 ):
     pdgid_map = {}
-    output_list = []
+    output = np.empty(shape=output_length, dtype=np.int64)
 
+    output_index = 0
     for rowid in range(len(edep_hits)):  # iterate hits
         hit = edep_hits[rowid]
-        hit_output = []
-
-        # iterate steps inside the hit
-        for si in range(len(hit.particle)):
+        for si in range(len(hit.particle)):  # iterate steps inside the hit
             # get the particle information.
             particle = hit.particle[si]
             if particle not in pdgid_map:
@@ -295,12 +348,106 @@ def _iterate_stepwise_depositions_scintillate(
                 rng,
                 emission_term_model=("poisson" if mode == "no-fano" else "normal_fano"),
             )
-            hit_output.append(num_phot)
+            output[output_index] = num_phot
+            output_index += 1
 
-        assert len(hit_output) == len(hit.particle)
-        output_list.append(hit_output)
+    assert output_index == output_length
+    return output
+
+
+# - run with NUMBA_FULL_TRACEBACKS=1 NUMBA_BOUNDSCHECK=1 for testing/checking
+# - cache=True does not work with outer prange, i.e. loading the cached file fails (numba bug?)
+@njit(parallel=False, nogil=True, cache=True)
+def _iterate_stepwise_depositions_numdet(
+    edep_hits,
+    rng,
+    detidx: int,
+    map_scaling: float,
+    map_scaling_sigma: float,
+    optmap_edges,
+    optmap_weights,
+    output_length: int,
+):
+    oob = ib = det_no_stats = 0
+    output = np.empty(shape=output_length, dtype=np.int64)
+
+    output_index = 0
+    for rowid in range(len(edep_hits)):  # iterate hits
+        hit = edep_hits[rowid]
+
+        map_scaling_evt = map_scaling
+        if map_scaling_sigma > 0:
+            map_scaling_evt = rng.normal(loc=map_scaling, scale=map_scaling_sigma)
+
+        # iterate steps inside the hit
+        for si in range(len(hit.xloc)):
+            loc = np.array([hit.xloc[si], hit.yloc[si], hit.zloc[si]], dtype=np.float64)
+            # coordinates -> bins of the optical map.
+            bins = np.empty(3, dtype=np.int64)
+            for j in range(3):
+                edges = optmap_edges[j].astype(np.float64)
+                start = edges[0]
+                width = edges[1] - edges[0]
+                nbins = edges.shape[0] - 1
+                bins[j] = int((loc[j] - start) / width)
+
+                if bins[j] < 0 or bins[j] >= nbins:
+                    bins[j] = -1  # normalize all out-of-bounds bins just to one end.
+
+            if bins[0] == -1 or bins[1] == -1 or bins[2] == -1:
+                detp = 0.0  # out-of-bounds of optmap
+                oob += 1
+            else:
+                # get probabilities from map.
+                detp = optmap_weights[detidx, bins[0], bins[1], bins[2]] * map_scaling_evt
+                if detp < 0:
+                    det_no_stats += 1
+                ib += 1
+
+            pois_cnt = 0 if detp <= 0.0 else rng.poisson(lam=hit.num_scint_ph[si] * detp)
+            output[output_index] = pois_cnt
+            output_index += 1
+
+    assert output_index == output_length
+    return output, {"oob": oob, "ib": ib, "det_no_stats": det_no_stats}
+
+
+# - run with NUMBA_FULL_TRACEBACKS=1 NUMBA_BOUNDSCHECK=1 for testing/checking
+# - cache=True does not work with outer prange, i.e. loading the cached file fails (numba bug?)
+# - the output dictionary is not threadsafe, so parallel=True is not working with it.
+@njit(parallel=False, nogil=True, cache=True)
+def _iterate_stepwise_depositions_times(
+    edep_hits, rng, scint_mat_params: sc.ComputedScintParams, output_length: int
+):
+    pdgid_map = {}
+    output = np.empty(shape=output_length, dtype=np.float64)
+
+    output_index = 0
+    for rowid in range(len(edep_hits)):  # iterate hits
+        hit = edep_hits[rowid]
+
+        assert len(hit.particle) == len(hit.num_det_ph)
+        # iterate steps inside the hit
+        for si in range(len(hit.particle)):
+            pois_cnt = hit.num_det_ph[si]
+            if pois_cnt <= 0:
+                continue
+
+            # get the particle information.
+            particle = hit.particle[si]
+            if particle not in pdgid_map:
+                pdgid_map[particle] = (_pdgid_to_particle(particle), _pdg_func.charge(particle))
+            part, _charge = pdgid_map[particle]
+
+            # get time spectrum.
+            # note: we assume "immediate" propagation after scintillation.
+            scint_times = sc.scintillate_times(scint_mat_params, part, pois_cnt, rng) + hit.time[si]
+            assert len(scint_times) == pois_cnt
+            output[output_index : output_index + len(scint_times)] = scint_times
+            output_index += len(scint_times)
 
-    return output_list
+    assert output_index == output_length
+    return output
 
 
 def _get_scint_params(material: str):

reboost/spms/__init__.py

@@ -1,10 +1,19 @@
 from __future__ import annotations
 
-from .pe import detected_photoelectrons, emitted_scintillation_photons, load_optmap, load_optmap_all
+from .pe import (
+    detected_photoelectrons,
+    emitted_scintillation_photons,
+    load_optmap,
+    load_optmap_all,
+    number_of_detected_photoelectrons,
+    photoelectron_times,
+)
 
 __all__ = [
     "detected_photoelectrons",
     "emitted_scintillation_photons",
     "load_optmap",
     "load_optmap_all",
+    "number_of_detected_photoelectrons",
+    "photoelectron_times",
 ]

reboost/spms/pe.py

@@ -109,7 +109,12 @@ def detected_photoelectrons(
     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.
+    """Derive the number and arrival times of detected photoelectrons (p.e.) from scintillator hits using an optical map.
+
+    .. deprecated :: 0.8.5
+        Use the other, more fine-granular and split processors
+        :func:`number_of_detected_photoelectrons` and :func:`photoelectron_times` to
+        replace this legacy processor.
 
     Parameters
     ----------
@@ -181,3 +186,77 @@ def emitted_scintillation_photons(
     scint_mat_params = convolve._get_scint_params(material)
     ph = convolve.iterate_stepwise_depositions_scintillate(hits, scint_mat_params)
     return VectorOfVectors(ph)
+
+
+def number_of_detected_photoelectrons(
+    xloc: ak.Array,
+    yloc: ak.Array,
+    zloc: ak.Array,
+    num_scint_ph: ak.Array,
+    optmap: convolve.OptmapForConvolve,
+    spm_detector: str,
+    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
+    ----------
+    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.
+    num_scint_ph
+        array of emitted scintillation photons, as generated by
+        :func:`emitted_scintillation_photons`.
+    detp
+    """
+    hits = ak.Array(
+        {
+            "xloc": units_conv_ak(xloc, "m"),
+            "yloc": units_conv_ak(yloc, "m"),
+            "zloc": units_conv_ak(zloc, "m"),
+            "num_scint_ph": units_conv_ak(num_scint_ph, "dimensionless"),
+        }
+    )
+
+    ph = convolve.iterate_stepwise_depositions_numdet(
+        hits, optmap, spm_detector, map_scaling, map_scaling_sigma
+    )
+    return VectorOfVectors(ph)
+
+
+def photoelectron_times(
+    num_det_ph: ak.Array,
+    particle: ak.Array,
+    time: ak.Array,
+    material: str,
+) -> VectorOfVectors:
+    """Derive the arrival times of scintillation photons.
+
+    Parameters
+    ----------
+    num_det_ph
+        array of detected 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.
+    material
+        scintillating material name.
+    """
+    hits = ak.Array(
+        {
+            "num_det_ph": units_conv_ak(num_det_ph, "dimensionless"),
+            "particle": units_conv_ak(particle, "dimensionless"),
+            "time": units_conv_ak(time, "ns"),
+        }
+    )
+
+    scint_mat_params = convolve._get_scint_params(material)
+    pe = convolve.iterate_stepwise_depositions_times(hits, scint_mat_params)
+
+    return VectorOfVectors(pe, attrs={"units": "ns"})

reboost/utils.py

@@ -445,7 +445,7 @@ def write_lh5(
         time_dict.update_field("write", start_time)
 
 
-def get_remage_detector_uids(h5file: str | Path) -> dict:
+def get_remage_detector_uids(h5file: str | Path, *, lh5_table: str = "stp") -> 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
@@ -483,7 +483,7 @@ def get_remage_detector_uids(h5file: str | Path) -> dict:
 
     out = {}
     with h5py.File(h5file, "r") as f:
-        g = f["/stp/__by_uid__"]
+        g = f[f"/{lh5_table}/__by_uid__"]
         # loop over links
         for key in g:
             # is this a link?

{reboost-0.8.4.dist-info → reboost-0.8.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: reboost
-Version: 0.8.4
+Version: 0.8.5
 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

{reboost-0.8.4.dist-info → reboost-0.8.5.dist-info}/RECORD

@@ -1,6 +1,6 @@
 reboost/__init__.py,sha256=VZz9uo7i2jgAx8Zi15SptLZnE_qcnGuNWwqkD3rYHFA,278
 reboost/__main__.py,sha256=42koSxY2st4mMIRSAnKz06nP5HppMPxBVFf2jaHljGs,95
-reboost/_version.py,sha256=6jY56wQpNbuVX1aDDCpFgsBq74u7lloIJcrJSefeVec,704
+reboost/_version.py,sha256=ulkPqAGMUJNjTNjZ56AYF9MmX06386otNWNjTA8opI8,704
 reboost/build_evt.py,sha256=VXIfK_pfe_Cgym6gI8dESwONZi-v_4fll0Pn09vePQY,3767
 reboost/build_glm.py,sha256=IerSLQfe51ZO7CQP2kmfPnOIVaDtcfw3byOM02Vaz6o,9472
 reboost/build_hit.py,sha256=N_nxvH69SvILVNmyvVfhQwQdD_PDW8tlsqj2ciO5nKE,17409
@@ -10,7 +10,7 @@ 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/utils.py,sha256=vl-_BUOeXcazNs4zN-9k-OVEptdf3FtCeej2QZhClKc,14599
 reboost/daq/__init__.py,sha256=rNPhxx1Yawt3tENYhmOYSum9_TdV57ZU5kjxlWFAGuo,107
 reboost/daq/core.py,sha256=Rs6Q-17fzEod2iX_2WqEmnqKnNRFoWTYURl3wYhFihU,9915
 reboost/daq/utils.py,sha256=KcH6zvlInmD2YiF6V--DSYBTYudJw3G-hp2JGOcES2o,1042
@@ -24,7 +24,7 @@ reboost/math/stats.py,sha256=Rq4Wdzv-3aoSK7EsPZCuOEHfnOz3w0moIzCEHbC07xw,3173
 reboost/optmap/__init__.py,sha256=imvuyld-GLw8qdwqW-lXCg2feptcTyQo3wIzPvDHwmY,93
 reboost/optmap/__main__.py,sha256=DfzkXQ7labOe53hd7jH5pAbTW491jjQYSMLyl72L4Rk,111
 reboost/optmap/cli.py,sha256=_7WBlx55eRyW_wWB-ELbFaWXin2d3xsh6Q5bFoNJaHE,8694
-reboost/optmap/convolve.py,sha256=0UCOVy6BIu5OYoSWeAb6fuROqvGu9rVswly6XvnxYoE,10763
+reboost/optmap/convolve.py,sha256=e3vTBurYSM4UmicIdDif6_cI04pV8khHEG5n7M_DWNg,16079
 reboost/optmap/create.py,sha256=GmGd0-F0eWmw7ywH8pT1lKiMb60QXCq9al8Ka_ySD1Q,14382
 reboost/optmap/evt.py,sha256=nZcB3aOPtMhySu00J23KlOTijeI5Oazde-vfM5A71e8,5664
 reboost/optmap/mapview.py,sha256=fswwXolA6au8u8gljBKy8PSXC2W7Cy_GwOV86-duYG8,6880
@@ -34,11 +34,11 @@ 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=24b9GelP4ngXc7JibpWqLOtUuIaQQa0DzDQYP8lVKUc,262
-reboost/spms/pe.py,sha256=cFj-D1-pj5djRHmrfYMjNscNnQfveACMZMJq4u4th3w,5830
-reboost-0.8.4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-reboost-0.8.4.dist-info/METADATA,sha256=YdOpd1dR4rVjYwz6dkjtxvQ6qoJQmAMR6DXgvAvH1zM,3877
-reboost-0.8.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-reboost-0.8.4.dist-info/entry_points.txt,sha256=DxhD6BidSWNot9BrejHJjQ7RRLmrMaBIl52T75oWTwM,93
-reboost-0.8.4.dist-info/top_level.txt,sha256=q-IBsDepaY_AbzbRmQoW8EZrITXRVawVnNrB-_zyXZs,8
-reboost-0.8.4.dist-info/RECORD,,
+reboost/spms/__init__.py,sha256=8I6WT8i_kUPqEDnSD0aCf6A26cjKjQQZSNrvwZ3o-Ac,415
+reboost/spms/pe.py,sha256=LwqrK1HOZWzGcNZnntaqI6r4rnDww4KW9Mao4xLFbDE,8226
+reboost-0.8.5.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+reboost-0.8.5.dist-info/METADATA,sha256=4MY_lm3rUT_DfLU3hc-_U2LJIHuV_j-EPgi0SLRJYiU,3877
+reboost-0.8.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+reboost-0.8.5.dist-info/entry_points.txt,sha256=DxhD6BidSWNot9BrejHJjQ7RRLmrMaBIl52T75oWTwM,93
+reboost-0.8.5.dist-info/top_level.txt,sha256=q-IBsDepaY_AbzbRmQoW8EZrITXRVawVnNrB-_zyXZs,8
+reboost-0.8.5.dist-info/RECORD,,