import h5py
[docs]
def print_h5_structure(node, indent=0):
""" Recursively print groups and datasets with metadata of an h5 file.
Example
-------
>>> import gamdpy as gp
>>> sim = gp.get_default_sim(num_timeblocks=2)
>>> for _ in sim.run_timeblocks(): pass
>>> gp.tools.print_h5_structure(sim.output)
initial_configuration/ (Group)
ptype (Dataset, shape=(2048,), dtype=int32)
r_im (Dataset, shape=(2048, 3), dtype=int32)
scalars (Dataset, shape=(2048, 4), dtype=float32)
topology/ (Group)
angles (Dataset, shape=(0,), dtype=int32)
bonds (Dataset, shape=(0,), dtype=int32)
dihedrals (Dataset, shape=(0,), dtype=int32)
molecules/ (Group)
vectors (Dataset, shape=(3, 2048, 3), dtype=float32)
restarts/ (Group)
restart0000/ (Group)
integrator_state (Dataset, shape=(1,), dtype=float32)
ptype (Dataset, shape=(2048,), dtype=int32)
r_im (Dataset, shape=(2048, 3), dtype=int32)
scalars (Dataset, shape=(2048, 4), dtype=float32)
topology/ (Group)
angles (Dataset, shape=(0,), dtype=int32)
bonds (Dataset, shape=(0,), dtype=int32)
dihedrals (Dataset, shape=(0,), dtype=int32)
molecules/ (Group)
vectors (Dataset, shape=(3, 2048, 3), dtype=float32)
restart0001/ (Group)
integrator_state (Dataset, shape=(1,), dtype=float32)
ptype (Dataset, shape=(2048,), dtype=int32)
r_im (Dataset, shape=(2048, 3), dtype=int32)
scalars (Dataset, shape=(2048, 4), dtype=float32)
topology/ (Group)
angles (Dataset, shape=(0,), dtype=int32)
bonds (Dataset, shape=(0,), dtype=int32)
dihedrals (Dataset, shape=(0,), dtype=int32)
molecules/ (Group)
vectors (Dataset, shape=(3, 2048, 3), dtype=float32)
scalars/ (Group)
scalars (Dataset, shape=(2, 64, 3), dtype=float32)
steps (Dataset, shape=(65,), dtype=int32)
trajectory/ (Group)
images (Dataset, shape=(2, 12, 2048, 3), dtype=int32)
positions (Dataset, shape=(2, 12, 2048, 3), dtype=float32)
ptypes (Dataset, shape=(2, 12, 2048), dtype=int32)
steps (Dataset, shape=(12,), dtype=int32)
topologies/ (Group)
block0000/ (Group)
angles (Dataset, shape=(0,), dtype=int32)
bonds (Dataset, shape=(0,), dtype=int32)
dihedrals (Dataset, shape=(0,), dtype=int32)
molecules/ (Group)
block0001/ (Group)
angles (Dataset, shape=(0,), dtype=int32)
bonds (Dataset, shape=(0,), dtype=int32)
dihedrals (Dataset, shape=(0,), dtype=int32)
molecules/ (Group)
"""
for key, item in node.items():
pad = " " * indent
if isinstance(item, h5py.Dataset):
print(f"{pad}{key} (Dataset, shape={item.shape}, dtype={item.dtype})")
elif isinstance(item, h5py.Group):
print(f"{pad}{key}/ (Group)")
print_h5_structure(item, indent+1)
else: # This should not be relevant
print(f"{pad}{key} (Unknown type: {type(item)})")
[docs]
def print_h5_attributes(obj, path="/"):
""" Recursively print attrs of every group/dataset of an h5 file.
Example
-------
>>> import gamdpy as gp
>>> sim = gp.get_default_sim(num_timeblocks=2)
>>> for _ in sim.run_timeblocks(): pass
>>> gp.tools.print_h5_attributes(sim.output)
Attributes at /:
- dt: 0.005
- script_content: ...
- script_name: ...
Attributes at /initial_configuration/:
- simbox_data: [12.815602 12.815602 12.815602]
- simbox_name: Orthorhombic
Attributes at /initial_configuration/scalars:
- scalar_columns: ['U' 'W' 'K' 'm']
Attributes at /initial_configuration/topology/molecules/:
- names: []
Attributes at /initial_configuration/vectors:
- vector_columns: ['r' 'v' 'f']
Attributes at /restarts/:
- timeblocks_between_restarts: 1
Attributes at /restarts/restart0000/:
- simbox_data: [12.815602 12.815602 12.815602]
- simbox_name: Orthorhombic
Attributes at /restarts/restart0000/scalars:
- scalar_columns: ['U' 'W' 'K' 'm']
Attributes at /restarts/restart0000/topology/molecules/:
- names: []
Attributes at /restarts/restart0000/vectors:
- vector_columns: ['r' 'v' 'f']
Attributes at /restarts/restart0001/:
- simbox_data: [12.815602 12.815602 12.815602]
- simbox_name: Orthorhombic
Attributes at /restarts/restart0001/scalars:
- scalar_columns: ['U' 'W' 'K' 'm']
Attributes at /restarts/restart0001/topology/molecules/:
- names: []
Attributes at /restarts/restart0001/vectors:
- vector_columns: ['r' 'v' 'f']
Attributes at /scalars/:
- compression_info: gzip with opts 4
- scalar_columns: ['U' 'W' 'K']
- scheduler: Lin
- scheduler_info: {"steps_between": 16, "npoints": null}
- steps_between_output: 16
Attributes at /trajectory/:
- compression_info: gzip with opts 4
- num_timeblocks: 2
- scheduler: Log2
- scheduler_info: {}
- steps_per_timeblock: 1024
- trajectory_columns: ['r' 'img']
- update_ptype: False
- update_topology: False
Attributes at /trajectory/topologies/block0000/molecules/:
- names: []
Attributes at /trajectory/topologies/block0001/molecules/:
- names: []
"""
# obj could be the File or a Group
if obj.attrs:
print(f"Attributes at {path}:")
for name, val in obj.attrs.items():
if name == 'script_content' or name == 'script_name': # Exclude since output is unpredictable (and untestable)
print(f' - {name}: ...')
else:
print(f" - {name}: {val}")
# Recurse into sub‐groups/datasets
if isinstance(obj, h5py.Group):
for key, sub in obj.items():
print_h5_attributes(sub, path + key + ("/" if isinstance(sub, h5py.Group) else ""))