def filter_h5(input_path, output_path, condition):
print "filtering for '%s'" % condition
input_file = tables.openFile(input_path, mode="r")
output_file = tables.openFile(output_path, mode="w")
# copy globals
input_file.root.globals._f_copy(output_file.root, recursive=True)
output_entities = output_file.createGroup("/", "entities", "Entities")
for table in input_file.iterNodes(input_file.root.entities):
print table._v_name, "..."
copyTable(table, output_entities, condition=condition)
input_file.close()
output_file.close()
def filter_h5(input_path, output_path, condition):
print "filtering for '%s'" % condition
input_file = tables.openFile(input_path, mode="r")
output_file = tables.openFile(output_path, mode="w")
output_globals = output_file.createGroup("/", "globals", "Globals")
copyTable(input_file.root.globals.periodic, output_file, output_globals)
output_entities = output_file.createGroup("/", "entities", "Entities")
for table in input_file.iterNodes(input_file.root.entities):
print table._v_name, "..."
copyTable(table, output_file, output_entities, condition=condition)
input_file.close()
output_file.close()
def dropfields(input_path, output_path, todrop):
input_file = tables.openFile(input_path, mode="r")
input_root = input_file.root
output_file = tables.openFile(output_path, mode="w")
output_globals = output_file.createGroup("/", "globals", "Globals")
print " * copying globals ...",
copyTable(input_root.globals.periodic, output_file, output_globals)
print "done."
output_entities = output_file.createGroup("/", "entities", "Entities")
for table in input_file.iterNodes(input_root.entities):
table_fields = get_fields(table)
table_fields = [(fname, ftype) for fname, ftype in table_fields
if fname not in todrop]
print " * copying table %s (%.2f Mb) ..." % (table._v_name,
table_size(table)),
copyTable(table, output_file, output_entities,
table_fields)
print "done."
input_file.close()
output_file.close()
def merge_h5(input1_path, input2_path, output_path):
input1_file = tables.openFile(input1_path, mode="r")
input2_file = tables.openFile(input2_path, mode="r")
output_file = tables.openFile(output_path, mode="w")
output_globals = output_file.createGroup("/", "globals", "Globals")
print "copying globals from", input1_path,
copyTable(input1_file.root.globals.periodic, output_file, output_globals)
print "done."
input1_entities = input1_file.root.entities
input2_entities = input2_file.root.entities
fields1 = get_h5_fields(input1_file)
fields2 = get_h5_fields(input2_file)
ent_names1 = set(fields1.keys())
ent_names2 = set(fields2.keys())
output_entities = output_file.createGroup("/", "entities", "Entities")
for ent_name in sorted(ent_names1 | ent_names2):
print
print ent_name
ent_fields1 = fields1.get(ent_name, [])
ent_fields2 = fields2.get(ent_name, [])
output_fields = merge_items(ent_fields1, ent_fields2)
output_table = output_file.createTable(output_entities, ent_name,
np.dtype(output_fields))
if ent_name in ent_names1:
table1 = getattr(input1_entities, ent_name)
print " * indexing table from %s ..." % input1_path,
input1_rows = index_table_light(table1)
print "done."
else:
table1 = None
input1_rows = {}
if ent_name in ent_names2:
table2 = getattr(input2_entities, ent_name)
print " * indexing table from %s ..." % input2_path,
input2_rows = index_table_light(table2)
print "done."
else:
table2 = None
input2_rows = {}
print " * merging: ",
input1_periods = input1_rows.keys()
input2_periods = input2_rows.keys()
output_periods = sorted(set(input1_periods) | set(input2_periods))
def merge_period(period_idx, period):
if ent_name in ent_names1:
start, stop = input1_rows.get(period, (0, 0))
input1_array = table1.read(start, stop)
else:
input1_array = None
if ent_name in ent_names2:
start, stop = input2_rows.get(period, (0, 0))
input2_array = table2.read(start, stop)
else:
input2_array = None
if ent_name in ent_names1 and ent_name in ent_names2:
output_array, _ = mergeArrays(input1_array, input2_array)
elif ent_name in ent_names1:
output_array = input1_array
elif ent_name in ent_names2:
output_array = input2_array
else:
raise Exception("this shouldn't have happened")
output_table.append(output_array)
output_table.flush()
loop_wh_progress(merge_period, output_periods)
print " done."
input1_file.close()
input2_file.close()
output_file.close()