Add h5utils

tomoscan/esrf/scan/h5utils.py

+import numpy as np
+from ...io import HDF5File
+
+
+def get_first_hdf5_entry(fname):
+    with HDF5File(fname, "r") as fid:
+        entry = list(fid.keys())[0]
+    return entry
+
+
+def get_h5_value(fname, h5_path, default_ret=None):
+    with HDF5File(fname, "r") as fid:
+        try:
+            val_ptr = fid[h5_path][()]
+        except KeyError:
+            val_ptr = default_ret
+    return val_ptr
+
+
+def get_h5obj_value(h5_obj, name, default=None):
+    if name in h5_obj:
+        return h5_obj[name][()]
+    return default
+
+
+def _get_3D_subregion(sub_region):
+    if sub_region is None:
+        xmin, xmax, ymin, ymax, zmin, zmax = None, None, None, None, None, None
+    elif len(sub_region) == 3:
+        first_part, second_part, third_part = sub_region
+        xmin, xmax = first_part
+        ymin, ymax = second_part
+        zmin, zmax = third_part
+    elif len(sub_region) == 6:
+        xmin, xmax, ymin, ymax, zmin, zmax = sub_region
+    else:
+        raise ValueError(
+            "Expected parameter in the form (xmin, xmax, ymin, ymax, zmin, zmax) or ((xmin, xmax), (ymin, ymax), (zmin, zmax))"
+        )
+    return xmin, xmax, ymin, ymax, zmin, zmax
+
+
+def get_hdf5_dataset_shape(fname, h5_data_path, sub_region=None):
+    zmin, zmax, ymin, ymax, xmin, xmax = _get_3D_subregion(sub_region)
+    with HDF5File(fname, "r") as f:
+        d_ptr = f[h5_data_path]
+        shape = d_ptr.shape
+    n_z, n_y, n_x = shape
+    # perhaps there is more elegant
+    res_shape = []
+    for n, bounds in zip([n_z, n_y, n_x], ((zmin, zmax), (ymin, ymax), (xmin, xmax))):
+        res_shape.append(np.arange(n)[bounds[0] : bounds[1]].size)
+    return tuple(res_shape)