def test_read_write_hdf(tmpdir, input_arr):
tmp_file = tmpdir / "example.h5"
# Write
with h5py.File(str(tmp_file), "w") as hf:
a = awkward.JaggedArray.fromiter(input_arr)
ah5 = awkward.hdf5(hf)
ah5["example"] = a
# Read
with h5py.File(str(tmp_file)) as hf:
ah5 = awkward.hdf5(hf)
b = ah5["example"]
assert a.tolist() == b.tolist()
def save(filename, item):
typename = type(item).__name__
if typename in vetoed_typenames:
return False
if typename == "DataFrame":
item.to_hdf(filename, key="data")
return True
if typename in ["ndarray", "JaggedArray"]:
with h5py.File(filename, "w") as hf:
ah5 = awkward.hdf5(hf)
if typename == "JaggedArray":
ah5["data"] = awkward_utils.ascontiguousarray(item)
else:
ah5["data"] = np.ascontiguousarray(item)
return True
try:
with open(filename, "wb") as f:
pickle.dump(item, f)
return True
except:
return False
return False
def _get_from_cache(filename):
basename = os.path.basename(filename)
if "__StreamList" in basename:
filenames = glob.glob(filename + "/*")
stream_list = StreamList(
[_get_from_cache(f) for f in sorted(filenames)])
return stream_list
if "__DataFrame" in basename:
return pd.read_hdf(filename, key="data")
# For TLorentsVectorArray from ptetaphimass
if "JaggedArrayMethods_PtEtaPhiMassLorentzVectorArray_Table" in basename:
content = OrderedDict()
with h5py.File(filename, "r") as hf:
ah5 = awkward.hdf5(hf)
for k in ah5:
content[k] = ah5[k]
particles = uproot_methods.TLorentzVectorArray.from_ptetaphim(
content["fPt"], content["fEta"], content["fPhi"], content["fMass"])
for k in content:
if k not in ["fPt", "fEta", "fPhi", "fMass"]:
particles[k] = content[k]
return particles
if "__ndarray" in basename or "__JaggedArray" in basename:
with h5py.File(filename, "r") as hf:
ah5 = awkward.hdf5(hf)
array = ah5["data"]
return array
# for pytorch nn models
if filename.endswith(".pt"):
model = torch.load(filename)
model.eval()
return model
if filename.endswith(".pkl"):
with open(filename, "rb") as pf:
product = pickle.load(pf)
return product
def load_h5(file):
"""
read an hdf5 file created by awkward
"""
h5arrs = {}
file = os.path.expanduser(file)
with h5py.File(file) as hf:
ah5 = awkward.hdf5(hf)
for ds in ah5:
h5arrs[ds] = ah5[ds]
return h5arrs
def write_h5(file, uarrs, mode="w"):
"""
write an hdf5 file created by awkward, from awkward.JaggedArrays.
- awkward/awkward/persist.py
- awkward/tests/test_hdf5.py
"""
file = os.path.expanduser(file)
with h5py.File(file, mode) as hf:
ah5 = awkward.hdf5(hf)
for ds in uarrs:
awk = awkward.JaggedArray.fromiter(uarrs[ds])
ah5[ds] = awk
def __getitem__(self, key):
print("Getting from cache {0}...".format(key))
file_name = self._get_file_name(key)
if not key in self:
raise KeyError(key + "not found in scratch cache.")
with h5py.File(file_name, "r") as hf:
ah5 = awkward.hdf5(hf)
array = ah5[key]
if isinstance(array, np.ndarray):
print("got ndarray of length " + str(len(array)))
else:
print("got jagged array of length " + str(len(array)) +
" (flattened " + str(len(array.flatten())) + ")")
return array
def load(filename, typename):
if typename == "DataFrame":
return pd.read_hdf(filename, key="data")
if typename in ["ndarray", "JaggedArray"]:
with h5py.File(filename, "r") as hf:
ah5 = awkward.hdf5(hf)
array = ah5["data"]
return array
try:
with open(filename, "rb") as pf:
product = pickle.load(pf)
return product
except:
return None
return None
def __setitem__(self, key, item):
file_name = self._get_file_name(key)
with h5py.File(file_name, "w") as hf:
ah5 = awkward.hdf5(hf)
ah5[key] = item
def write_HDF5(run=None, infile=None, mode="pandas", nevt=None):
"""
primary writer function. contains several Majorana-specific choices.
works on gatified or skim data. (TODO: simulation data?)
"""
if run is None and infile is None:
print("You must specify either a run number or input filename.")
exit()
# declare inputs and outputs
if run is not None:
from ROOT import GATDataSet
gds = GATDataSet()
gfile = gds.GetPathToRun(run, GATDataSet.kGatified)
infile, tname = gfile, "mjdTree"
ufile = uproot.open(infile)
if infile is not None:
ufile = uproot.open(infile)
# auto-detect and use the name of the first TTree we find
for uc in ufile.allclasses():
cname, ctype = uc[0], str(uc[1])
if "TTree" in ctype:
tname = cname.decode("utf-8").split(";")[0]
print("Found TTree:", tname)
break
# strip the path and extension off the filename to create the hfile
if run is None:
label = infile.split("/")[-1].split(".root")[0]
hfile = "{}/hdf5/{}.h5".format(os.environ["MJDDATADIR"], label)
else:
hfile = "{}/hdf5/mjd_run{}.h5".format(os.environ["MJDDATADIR"], run)
# these MGDO object members don't have the same number of entries
# as the rest of the vector-valued branches, so skip them for now
skip_names = ["i", "iH", "iL", "j", "jH", "jL", "rawRun", "c0Channels"]
# get all relevant TTree branches & sort by data type
event_names, hit_names = [], []
utree = ufile[tname]
uarrs = utree.arrays(entrystop=1)
for k in sorted(uarrs.keys()):
name = k.decode('utf-8')
vals = uarrs[k]
if isinstance(vals, np.ndarray):
event_names.append(k)
elif isinstance(vals, awkward.JaggedArray):
if name in skip_names:
continue
hit_names.append(k)
elif isinstance(vals, awkward.ObjectArray):
# print("Skipping branch:", name)
continue
# write to pandas HDF5 (pytables)
if mode == "pandas":
print("writing pandas hdf5.\n input:{}\n output:{}".format(
infile, hfile))
df_events = ufile[tname].pandas.df(event_names, entrystop=nevt)
df_hits = ufile[tname].pandas.df(hit_names, entrystop=nevt)
if os.path.isfile(hfile):
os.remove(hfile)
opts = {
"mode": "a", # 'r', 'r+', 'a' and 'w'
"format": "table", # "fixed" can't be indexed w/ data_columns
"complib": "blosc:snappy",
"complevel": 2,
# "data_columns":["ievt"] # used for pytables' fast HDF5 dataset indexing
}
df_events.to_hdf(hfile, key="events", **opts)
df_hits.to_hdf(hfile, key="hits", **opts)
# -- write to awkward.hdf5 --
elif mode == "awkward":
print("Writing awkward hdf5.\n input:{}\n output:{}".format(
infile, hfile))
print("Warning: this mode is not well-developed and needs work")
# FIXME: separate values, as above
uarrs = utree.arrays(entrystop=nevt)
# set awkward hdf5 options
opts = {
# "compression":2 # hmm, doesn't work?
}
with h5py.File(os.path.expanduser(hfile), "w") as hf:
awk_h5 = awkward.hdf5(hf, **opts)
for ds in uarrs:
if isinstance(uarrs[ds], awkward.ObjectArray):
print("skipping dataset:", ds.decode('utf-8'))
continue
awk_h5[ds.decode('utf-8')] = uarrs[ds]
# ehhh, it's a work in progress. probably won't need this until LEGEND
# check the groups saved into the file
with pd.HDFStore(hfile, 'r') as f:
print("Keys:", f.keys())
def _save_to_cache(filename, item):
classname = type(item).__name__
if classname in vetoed_classnames:
return
if classname == "StreamList":
if type(item[0]).__name__ in vetoed_classnames:
return
mkdir(filename)
for i, subitem in enumerate(item):
subclassname = type(subitem).__name__
if subclassname == "StreamList":
raise TypeError(
"StreamList in a StreamList found, which should not happen."
)
subfilename = os.path.join(
filename,
os.path.basename(filename.replace(classname, subclassname)) +
"__{0:04d}".format(i))
_save_to_cache(subfilename, subitem)
return
if classname == "DataFrame":
item.to_hdf(filename + ".h5", key="data")
return
if classname in ["ndarray", "JaggedArray"]:
with h5py.File(filename + ".h5", "w") as hf:
ah5 = awkward.hdf5(hf)
if classname == "JaggedArray":
ah5["data"] = awkward_utils.ascontiguousarray(item)
else:
ah5["data"] = np.ascontiguousarray(item)
return
# For TLorentsVectorArray from ptetaphimass
if (classname == "JaggedArrayMethods" and type(
item._content).__name__ == "PtEtaPhiMassLorentzVectorArray"
and type(item._content._content).__name__ == "Table"):
starts = item._starts
stops = item._stops
contents = item._content._content._contents
filename = filename.replace(
"JaggedArrayMethods",
"JaggedArrayMethods_PtEtaPhiMassLorentzVectorArray_Table")
with h5py.File(filename + ".h5", "w") as hf:
ah5 = awkward.hdf5(hf)
for k, v in contents.items():
a = awkward.JaggedArray(starts, stops, v)
ah5[k] = awkward_utils.ascontiguousarray(a)
return
# for pytorch nn models
if issubclass(type(item), torch.nn.Module):
torch.save(item, filename + ".pt")
return
with open(filename + ".pkl", "wb") as f:
pickle.dump(item, f)
return