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libh5.py
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import numpy as np
import re
import os, sys
verbose = 0
# ------------------------------------------------------------------------------
def get_child_group_names(parent_group_pointer):
return parent_group_pointer.keys()
# ------------------------------------------------------------------------------
def get_group_keys(group_pointer):
key_list = []
for k in group_pointer.keys():
if not re.search('#', k):
key_list.append(k)
return sorted(key_list)
# ------------------------------------------------------------------------------
def get_data_from_refs_dataset(orig_h5, dataset_pointer):
path = dataset_pointer.name
if dataset_pointer.dtype.kind == 'O':
ref = orig_h5[path][0][0]
obj = orig_h5[ref]
value = ''.join(i for i in obj[:])
else:
obj = orig_h5[path]
value = ''.join(i.encode(ascii) for i in obj[:])
return value
# ------------------------------------------------------------------------------
def get_key_list(hash_group_pointer):
try:
keyNames_dataset = hash_group_pointer['keyNames/keyNames']
key_list = np.array(keyNames_dataset).tolist()
except:
key_list = []
return key_list
# ------------------------------------------------------------------------------
def get_value_by_key(hash_group_pointer, key):
if verbose:
print "In get_value_by_key: group_pointer.name=", hash_group_pointer.name
print " key=", key
key_list = get_key_list(hash_group_pointer)
if verbose:
print "In get_value_by_key: partial_key=", key, " key_list=", key_list
key_name = ""
for k in key_list:
if re.search(key, k):
key_name = k
if verbose:
print "In get_value_by_key: key_name=", key_name, "\n"
ind = key_list.index(key_name)
if verbose:
print "ind=", ind, "\n"
value_group = hash_group_pointer['value']
if verbose:
print "\nIn get_value_by_key: value_group.name=", value_group.name
print "\n value_group.keys()=", value_group.keys()
print "\nlen(value_group.keys())=", len(value_group.keys()), " ind=", ind
if len(value_group.keys()) == 1 and "value" in value_group.keys():
value_pointer = value_group['value']
if item_type(value_pointer) == "dataset":
if verbose:
print "Case1: returning an element of a dataset"
value = value_pointer[ind]
else:
if verbose:
print "Case2: value/value type is ", item_type(value_pointer)
sys.exit("Unsapported case in get_value_by_key()")
else:
if verbose:
print "level2 key_list=", value_group.keys(), "; ind+1=", ind+1
if str(ind+1) in value_group.keys():
value_pointer = value_group[str(ind+1)]
if item_type(value_pointer) == "dataset":
if verbose:
print "Case3: value/" + str(ind+1) + " is a dataset"
value = np.array(value_pointer).tolist()
else:
if str(ind+1) in value_pointer.keys() and \
item_type(value_pointer[str(ind+1)]) == "dataset":
if verbose:
print "Case4: value/" + str(ind+1) + "/" + str(ind+1) + " is ", item_type(value_pointer)
value = np.array(value_pointer[str(ind+1)]).tolist()
else:
if verbose:
print "Case5: value/" + str(ind+1) + " is ", item_type(value_pointer)
value = value_pointer
else:
value = value_group
return value
# ------------------------------------------------------------------------------
def get_value2_by_key2(hash_group1_pointer, key1, hash_group2, key2):
if verbose:
print "\n\nEntering get_value2_by_key2 ..."
key_list = get_key_list(hash_group1_pointer)
key_name = ""
for k in key_list:
if re.search(key1, k):
key_name = k
if verbose:
print "In get_value_by_key: key_name=", key_name, "\n"
ind = key_list.index(key_name)
if verbose:
print "ind=", ind, "\n"
value_group = hash_group1_pointer['value']
if verbose:
print "\nIn get_value_by_key: value_group.name=", value_group.name
print "\n value_group.keys()=", value_group.keys()
print "\nlen(value_group.keys())=", len(value_group.keys()), " ind=", ind
print "In get_value2_by_key2: level2 key_list=", value_group.keys()
print "str(ind+1)=", str(ind+1), " value_group.keys()=", value_group.keys()
if str(ind+1) in value_group.keys():
value_pointer = value_group[str(ind+1)]
else:
value_pointer = value_group
if verbose:
print "value_pointer.keys()=", value_pointer.keys(), "; hash_group2=", hash_group2
if 'valueMatrix' in value_pointer.keys() and \
'idStr' in value_pointer.keys():
# NL data
print " NL data"
key_list2 = np.array(value_pointer['idStr/idStr']).tolist()
# try:
ind2 = key_list2.index(key2)
if verbose:
print "ind2=", ind2, "\n"
value2 = value_pointer['valueMatrix/valueMatrix'][:,ind2]
# except:
# sys.exit("\nCannot determine value2 in get_value2_by_key2")
else:
# SP data
try:
value_pointer2 = value_pointer[hash_group2]
value2 = get_value_by_key(value_pointer2, key2)
except:
sys.exit("\nCannot determine value2 in get_value2_by_key2")
return value2
# ------------------------------------------------------------------------------
def get_value_pointer_by_path_items(orig_h5, path_items):
path = orig_h5.name
if verbose:
print "Enter get_value_pointer_by_path_items: orig_h5.name=", orig_h5.name, " path_items=", path_items
if len(path_items) > 0 and not path_items == ['']:
iter_len = len(path_items)
i = 0
while i < iter_len:
if verbose:
print " item=", path_items[i]
if path_items[i] in orig_h5[path].keys():
path += '/' + str(path_items[i])
if verbose:
print "Case1, path=", path
value_pointer = orig_h5[path]
if verbose:
print "item_type(value_pointer)=", item_type(value_pointer)
if item_type(value_pointer) == "dataset":
if verbose:
print "dataset_shape=", value_pointer.shape
if value_pointer.shape[0] > 1:
value = np.transpose(np.array(value_pointer)).tolist()
else:
value = np.array(value_pointer).tolist()
if verbose:
print "data=", value
return value
else:
iter_len = len(path_items) + 1
value = []
if verbose:
print "Case2, i=", i, " iter_len=", iter_len
for k in orig_h5[path].keys():
path2 = path + '/' + str(k)
value_pointer = orig_h5[path2]
if verbose:
print "item_type(value_pointer)=", item_type(value_pointer)
if verbose and item_type(orig_h5[path2]) == "dataset":
print "dataset_shape=", orig_h5[path2].shape
elif item_type(orig_h5[path2]) == "group":
for k1 in orig_h5[path2].keys():
path2 += '/' + str(k1)
if verbose:
print " \npath2=", path2
value_pointer = orig_h5[path2]
if verbose:
print "item_type(value_pointer1)=", item_type(value_pointer)
if item_type(orig_h5[path2]) == "dataset":
if verbose:
print "dataset_shape=", orig_h5[path2].shape
if value_pointer.shape[0] > 1:
value1 = np.transpose(np.array(value_pointer)).tolist()
else:
value1 = np.array(value_pointer).tolist()
if verbose:
print "data=", value
value.append(value1)
if verbose:
print "Case2, path=", path, " value=", value
return value
i += 1
if verbose:
print "path=", path
# print "value_pointer.name=", value_pointer.name
else:
value_pointer = orig_h5
if verbose:
print " In get_value_pointer_by_path_items: path=", path
if item_type(value_pointer) == "group":
print " key_list=", value_pointer.keys()
return value_pointer
# ------------------------------------------------------------------------------
def get_key_index(key_list, partial_key):
key_name = ""
for k in key_list:
if re.search(partial_key, k):
key_name = k
ind = key_list.index(key_name)
return ind
# ------------------------------------------------------------------------------
# Returns a pointer to the value
def get_value_pointer_by_key(hash_group_pointer, partial_key, verbose):
key_list = get_key_list(hash_group_pointer)
if len(key_list) > 1:
ind = get_key_index(key_list, partial_key) + 1
else:
ind = 1
value_group_pointer = hash_group_pointer['value']
if str(ind) in hash_group_pointer['value/'].keys():
value_group_pointer = hash_group_pointer['value/' + str(ind)]
if verbose:
print " In get_value_pointer_by_key: value_group_items=", value_group_pointer.keys(), " ind=", ind
print " item_type(value_group_pointer)=", item_type(value_group_pointer)
if str(ind) in value_group_pointer.keys():
if verbose:
print " In get_value_pointer_by_key: case 1"
value_pointer1 = value_group_pointer[str(ind)]
if item_type(value_pointer1) == "group" and str(ind) in value_pointer1.keys():
if verbose:
print " In get_value_pointer_by_key: case 11"
value_pointer = value_pointer1[str(ind)]
else:
if verbose:
print " In get_value_pointer_by_key: case 12"
print " item_type(value_pointer1)=", item_type(value_pointer1)
print " value_pointer1.name=", value_pointer1.name
value_pointer = value_pointer1
else:
if verbose:
print " In get_value_pointer_by_key: case 2"
value_pointer = value_group_pointer
if item_type(value_pointer) == "dataset":
value_pointer = np.array(value_pointer).tolist()
return value_pointer
# ------------------------------------------------------------------------------
def get_value_by_path_items(orig_h5, path_items):
value_pointer = get_value_pointer_by_path_items(orig_h5, path_items)
if verbose:
print " In get_value_by_path_items: value_pointer.name=", value_pointer.name
if hasattr(value_pointer , '__dict__') and len(value_pointer.keys()) > 1:
print " Case 1"
data = []
for k in value_pointer.keys():
data1 = np.array(value_pointer[k + "/" + k]).tolist()
data.append(data1)
else:
print " Case 2"
data = np.array(value_pointer[path_items[len(path_items)-1]]).tolist()
return data
# ------------------------------------------------------------------------------
def get_all_keys(orig_h5, meta_h5):
all_keys = []
# Extract data keys
top_groups = get_child_group_names(orig_h5)
for group in top_groups:
if not re.search("Hash", group):
continue
group_keys = orig_h5[group].keys()
if len(group_keys) < 2:
continue
path_items = [group, "keyNames", "keyNames"]
print "path_items=", path_items
key_list = get_value_pointer_by_path_items(orig_h5, path_items)
for k in key_list:
if not k in all_keys:
all_keys.append(k)
# Extract metadata keys
if len(meta_h5) > 0:
top_groups = get_child_group_names(meta_h5)
for k in top_groups:
if not k in key_list:
all_keys.append(k)
return all_keys
# ------------------------------------------------------------------------------
def get_description_by_key(hash_group_pointer, partial_key):
key_list = get_key_list(hash_group_pointer)
ind = get_key_index(key_list, partial_key) + 1
descr_data = np.array(hash_group_pointer['descr/descr']).tolist()
if verbose:
print "\nIn get_description_by_key: len(descr_data)=", len(descr_data), \
"\n descr_data_items=", descr_data, " ind=", ind
print "\nFunction get_description_by_key returns: ", descr_data[ind-1]
return descr_data[ind-1]
# ------------------------------------------------------------------------------
def get_file_list(data, match_string):
# Compile a file list
file_list = []
if os.path.isfile(data) and (re.search(".h5", data) or re.search(".nwb", data) or re.search(".borg", data)):
file_list = [ data ]
elif os.path.isdir(data):
file_list = []
if verbose:
print "num_files=", len(os.listdir(data))
for file in os.listdir(data):
if len(match_string) > 0 and not re.search(match_string, file):
continue
if (re.search(".h5", file) or re.search(".nwb", data)) \
and os.path.isfile(os.path.join(data, file)):
file_path = os.path.join(data, file)
file_list.append(file_path)
else:
sys.exit("Cannot process " + data)
return file_list
# ------------------------------------------------------------------------------
def item_type(item_pointer):
item_type = ""
try:
keys = item_pointer.keys()
item_type = "group"
except:
try:
keys = np.array(item_pointer).tolist()
item_type = "dataset"
except:
item_type = "data_item"
return item_type
# ------------------------------------------------------------------------------
def get_data_by_key(nwb_root, item_path, verbose):
item_pointer = h5_root[item_path]
try:
# item is group
keys = item_pointer.keys()
if verbose:
# print "group: path=", item_path, " members=" + str(keys)
print "group: path=", item_path, " num_members=", len(keys)
for k in keys:
if len(item_path) == 1: # item_path == '/'
item_path1 = item_path + k
else:
item_path1 = item_path + '/' + k
parse_h5_item(h5_root, item_path1, verbose)
except:
# item is dataset
try:
data = np.array(item_pointer)
if verbose:
print "dataset: path=", item_path, " , shape=", data.shape, \
" , dtype=", data.dtype, " data=", data.tolist()
except:
sys.exit("Path " + path + " is not valid")