add histogram LGDO

pyproject.toml

@@ -36,6 +36,7 @@ dependencies = [
     "colorlog",
     "h5py>=3.2",
     "hdf5plugin",
+    "hist",
     "numba!=0.53.*,!=0.54.*",
     "numexpr",
     "numpy>=1.21",

src/lgdo/__init__.py

@@ -50,6 +50,8 @@
     ArrayOfEncodedEqualSizedArrays,
     ArrayOfEqualSizedArrays,
     FixedSizeArray,
+    Histogram,
+    HistogramAxis,
     Scalar,
     Struct,
     Table,
@@ -63,6 +65,8 @@
     "ArrayOfEqualSizedArrays",
     "ArrayOfEncodedEqualSizedArrays",
     "FixedSizeArray",
+    "Histogram",
+    "HistogramAxis",
     "LGDO",
     "Scalar",
     "Struct",

src/lgdo/lh5/_serializers/__init__.py

@@ -7,6 +7,7 @@
     _h5_read_ndarray,
 )
 from .read.composite import (
+    _h5_read_histogram,
     _h5_read_lgdo,
     _h5_read_struct,
     _h5_read_table,
@@ -32,6 +33,7 @@
     "_h5_read_array_of_equalsized_arrays",
     "_h5_read_struct",
     "_h5_read_table",
+    "_h5_read_histogram",
     "_h5_read_scalar",
     "_h5_read_array_of_encoded_equalsized_arrays",
     "_h5_read_vector_of_encoded_vectors",

src/lgdo/lh5/_serializers/read/composite.py

@@ -13,6 +13,7 @@
     ArrayOfEncodedEqualSizedArrays,
     ArrayOfEqualSizedArrays,
     FixedSizeArray,
+    Histogram,
     Scalar,
     Struct,
     Table,
@@ -168,6 +169,17 @@ def _h5_read_lgdo(
             decompress=decompress,
         )
 
+    if lgdotype is Histogram:
+        return _h5_read_histogram(
+            h5o,
+            start_row=start_row,
+            n_rows=n_rows,
+            idx=idx,
+            use_h5idx=use_h5idx,
+            field_mask=field_mask,
+            decompress=decompress,
+        )
+
     if lgdotype is ArrayOfEncodedEqualSizedArrays:
         return _h5_read_array_of_encoded_equalsized_arrays(
             h5o,
@@ -385,3 +397,33 @@ def _h5_read_table(
     utils.check_obj_buf_attrs(obj_buf.attrs, attrs, h5g)
 
     return obj_buf, n_rows_read
+
+
+def _h5_read_histogram(
+    h5g,
+    start_row=0,
+    n_rows=sys.maxsize,
+    idx=None,
+    use_h5idx=False,
+    field_mask=None,
+    decompress=True,
+):
+    struct, n_rows_read = _h5_read_struct(
+        h5g,
+        start_row,
+        n_rows,
+        idx,
+        use_h5idx,
+        field_mask,
+        decompress,
+    )
+    isdensity = struct.isdensity.value
+    binning = [
+        (a.binedges.first, a.binedges.last, a.binedges.step, a.closedleft)
+        for _, a in struct.binning.items()
+    ]
+    binning = [tuple(v.value for v in b) for b in binning]
+    weights = struct.weights.view_as("np")
+    histogram = Histogram(weights, binning, isdensity)
+
+    return histogram, n_rows_read

src/lgdo/lh5/_serializers/write/composite.py

@@ -63,8 +63,12 @@ def _h5_write_lgdo(
         msg = f"can't overwrite '{name}' in wo_mode 'write_safe'"
         raise LH5EncodeError(msg, lh5_file, group, name)
 
-    # struct or table or waveform table
+    # struct, table, waveform table or histogram.
     if isinstance(obj, types.Struct):
+        if isinstance(obj, types.Histogram) and wo_mode not in ["w", "of"]:
+            msg = f"can't append-write histogram in wo_mode '{wo_mode}'"
+            raise LH5EncodeError(msg, lh5_file, group, name)
+
         return _h5_write_struct(
             obj,
             name,

src/lgdo/lh5/datatype.py

@@ -14,6 +14,7 @@
             lgdo.ArrayOfEncodedEqualSizedArrays,
             r"^array_of_encoded_equalsized_arrays<1,1>\{.+\}$",
         ),
+        (lgdo.Histogram, r"^struct\{binning,weights,isdensity\}$"),
         (lgdo.Struct, r"^struct\{.*\}$"),
         (lgdo.Table, r"^table\{.*\}$"),
         (lgdo.FixedSizeArray, r"^fixedsize_array<\d+>\{.+\}$"),

src/lgdo/lh5_store.py

@@ -20,6 +20,7 @@
     ArrayOfEncodedEqualSizedArrays,  # noqa: F401
     ArrayOfEqualSizedArrays,  # noqa: F401
     FixedSizeArray,  # noqa: F401
+    Histogram,  # noqa: F401
     Scalar,
     Struct,
     Table,  # noqa: F401

src/lgdo/types/__init__.py

@@ -6,6 +6,7 @@
 from .arrayofequalsizedarrays import ArrayOfEqualSizedArrays
 from .encoded import ArrayOfEncodedEqualSizedArrays, VectorOfEncodedVectors
 from .fixedsizearray import FixedSizeArray
+from .histogram import Histogram, HistogramAxis
 from .lgdo import LGDO
 from .scalar import Scalar
 from .struct import Struct
@@ -18,6 +19,8 @@
     "ArrayOfEqualSizedArrays",
     "ArrayOfEncodedEqualSizedArrays",
     "FixedSizeArray",
+    "Histogram",
+    "HistogramAxis",
     "LGDO",
     "Scalar",
     "Struct",