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#!/usr/bin/env python
import pickle
from time import perf_counter as clock
import tables as tb
def is_scalar(item):
try:
iter(item)
# could be a string
try:
item[:0] + "" # check for string
return "str"
except Exception:
return 0
except Exception:
return "notstr"
def is_dict(item):
try:
item.items()
return 1
except Exception:
return 0
def make_col(row_type, row_name, row_item, str_len):
"""for strings it will always make at least 80 char or twice mac char size"""
set_len = 80
if str_len:
if 2 * str_len > set_len:
set_len = 2 * str_len
row_type[row_name] = tb.StringCol(set_len)
else:
type_matrix = {
int: tb.Int32Col(),
float: tb.Float32Col(),
}
row_type[row_name] = type_matrix[type(row_item)]
def make_row(data):
row_type = {}
scalar_type = is_scalar(data)
if scalar_type:
if scalar_type == "str":
make_col(row_type, "scalar", data, len(data))
else:
make_col(row_type, "scalar", data, 0)
else: # it is a list-like
the_type = is_scalar(data[0])
if the_type == "str":
# get max length
the_max = 0
for i in data:
if len(i) > the_max:
the_max = len(i)
make_col(row_type, "col", data[0], the_max)
elif the_type:
make_col(row_type, "col", data[0], 0)
else: # list within the list, make many columns
make_col(row_type, "col_depth", 0, 0)
count = 0
for col in data:
the_type = is_scalar(col[0])
if the_type == "str":
# get max length
the_max = 0
for i in data:
if len(i) > the_max:
the_max = len(i)
make_col(row_type, "col_" + str(count), col[0], the_max)
elif the_type:
make_col(row_type, "col_" + str(count), col[0], 0)
else:
raise ValueError("too many nested levels of lists")
count += 1
return row_type
def add_table(fileh, group_obj, data, table_name):
# figure out if it is a list of lists or a single list
# get types of columns
row_type = make_row(data)
table1 = fileh.create_table(group_obj, table_name, row_type, "H")
row = table1.row
if is_scalar(data):
row["scalar"] = data
row.append()
else:
if is_scalar(data[0]):
for i in data:
row["col"] = i
row.append()
else:
count = 0
for col in data:
row["col_depth"] = len(col)
for the_row in col:
if is_scalar(the_row):
row["col_" + str(count)] = the_row
row.append()
else:
raise ValueError("too many levels of lists")
count += 1
table1.flush()
def add_cache(fileh, cache):
group_name = "pytables_cache_v0"
table_name = "cache0"
root = fileh.root
group_obj = fileh.create_group(root, group_name)
cache_str = pickle.dumps(cache, 0).decode()
cache_str = cache_str.replace("\n", chr(1))
cache_pieces = []
while cache_str:
cache_part = cache_str[:8000]
cache_str = cache_str[8000:]
if cache_part:
cache_pieces.append(cache_part)
row_type = {}
row_type["col_0"] = tb.StringCol(8000)
#
table_cache = fileh.create_table(group_obj, table_name, row_type, "H")
for piece in cache_pieces:
print(len(piece))
table_cache.row["col_0"] = piece
table_cache.row.append()
table_cache.flush()
def save2(hdf_file, data):
fileh = tb.open_file(hdf_file, mode="w", title="logon history")
root = fileh.root
cache_root = cache = {}
root_path = root._v_pathname
root = 0
stack = [(root_path, data, cache)]
table_num = 0
count = 0
while stack:
(group_obj_path, data, cache) = stack.pop()
for grp_name in data:
count += 1
cache[grp_name] = {}
new_group_obj = fileh.create_group(group_obj_path, grp_name)
new_path = new_group_obj._v_pathname
# if dict, you have a bunch of groups
if is_dict(data[grp_name]): # {'mother':[22,23,24]}
stack.append((new_path, data[grp_name], cache[grp_name]))
# you have a table
else:
# data[grp_name]=[110,130,140],[1,2,3]
add_table(fileh, new_path, data[grp_name], f"tbl_{table_num}")
table_num += 1
add_cache(fileh, cache_root)
fileh.close()
class HdfDict(dict):
def __init__(self, hdf_file, hdf_dict=None, stack=None):
if hdf_dict is None:
hdf_dict = {}
if stack is None:
stack = []
self.hdf_file = hdf_file
self.stack = stack
if stack:
self.hdf_dict = hdf_dict
else:
self.hdf_dict = self.get_cache()
self.cur_dict = self.hdf_dict
def get_cache(self):
fileh = tb.open_file(self.hdf_file, root_uep="/pytables_cache_v0")
table = fileh.root.cache0
total = []
print("reading")
begin = clock()
for i in table.iterrows():
total.append(i["col_0"].decode())
total = "".join(total)
total = total.replace(chr(1), "\n")
print("loaded cache len=", len(total), clock() - begin)
begin = clock()
a = pickle.loads(total.encode())
print("cache", clock() - begin)
return a
def has_key(self, k):
return k in self.cur_dict
def keys(self):
return self.cur_dict.keys()
def get(self, key, default=None):
try:
return self.__getitem__(key)
except Exception:
return default
def items(self):
return list(self.cur_dict.items())
def values(self):
return list(self.cur_dict.values())
def __len__(self):
return len(self.cur_dict)
def __getitem__(self, k):
if k in self.cur_dict:
# now check if k has any data
if self.cur_dict[k]:
new_stack = self.stack[:]
new_stack.append(k)
return HdfDict(
self.hdf_file, hdf_dict=self.cur_dict[k], stack=new_stack
)
else:
new_stack = self.stack[:]
new_stack.append(k)
fileh = tb.open_file(
self.hdf_file, root_uep="/".join(new_stack)
)
for table in fileh.root:
try:
for item in table["scalar"]:
return item
except Exception:
# otherwise they stored a list of data
try:
return list(table["col"])
except Exception:
cur_column = []
total_columns = []
col_num = 0
cur_row = 0
num_rows = 0
for row in table:
if not num_rows:
num_rows = row["col_depth"]
if cur_row == num_rows:
cur_row = num_rows = 0
col_num += 1
total_columns.append(cur_column)
cur_column = []
cur_column.append(row["col_" + str(col_num)])
cur_row += 1
total_columns.append(cur_column)
return total_columns
else:
raise KeyError(k)
def iterkeys(self):
yield from self.keys()
def __iter__(self):
return self.iterkeys()
def itervalues(self):
for k in self.iterkeys():
v = self.__getitem__(k)
yield v
def iteritems(self):
# yield children
for k in self.iterkeys():
v = self.__getitem__(k)
yield (k, v)
def __repr__(self):
return "{Hdf dict}"
def __str__(self):
return self.__repr__()
#####
def setdefault(self, key, default=None):
try:
return self.__getitem__(key)
except Exception:
self.__setitem__(key)
return default
def update(self, d):
for k, v in d.items():
self.__setitem__(k, v)
def popitem(self):
try:
k, v = next(self.items())
del self[k]
return k, v
except StopIteration:
raise KeyError("Hdf Dict is empty")
def __setitem__(self, key, value):
raise NotImplementedError
def __delitem__(self, key):
raise NotImplementedError
def __hash__(self):
raise TypeError("Hdf dict bjects are unhashable")
if __name__ == "__main__":
def write_small(file=""):
data1 = {
"fred": ["a", "b", "c"],
"barney": [[9110, 9130, 9140], [91, 92, 93]],
"wilma": {
"mother": {"pebbles": [22, 23, 24], "bambam": [67, 68, 69]}
},
}
print("saving")
save2(file, data1)
print("saved")
def read_small(file=""):
a = HdfDict(file)
print(a["wilma"])
b = a["wilma"]
for i in b:
print(i)
print(a.keys())
print("has fred", bool("fred" in a))
print("length a", len(a))
print("get", a.get("fred"), a.get("not here"))
print("wilma keys", a["wilma"].keys())
print("barney", a["barney"])
print("get items")
print(a.items())
for i in a.items():
print("item", i)
for i in a.values():
print(i)
a = input("enter y to write out test file to test.hdf ")
if a.strip() == "y":
print("writing")
write_small("test.hdf")
print("reading")
read_small("test.hdf")
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