def dir_to_h5(directory, h5_obj, h5_path="/"):
# Use the openDIR object to deal with the ugliness
dir_listing = openDIR( directory )
# You know what they say about assertions
assert (len(dir_listing.exp_paths) == 1), "This function only does 1 run at a time:" + str(dir_listing.exp_paths)
print dir_listing.total_trial_count, "blockfiles detected, compressing . . ."
# Create a leaf in the h5 for HTB and LOG file related data
htb_leaf = h5_obj.createGroup(h5_path, "htb")
log_leaf = h5_obj.createGroup(h5_path, "log")
# Create filenodes
htb_fn = filenode.newNode(h5_obj, where=htb_leaf, name='htbfile')
log_fn = filenode.newNode(h5_obj, where=log_leaf, name='logfile')
# Get file paths
log_file = dir_listing.get_LOG(dir_listing.exp_paths[0])
htb_file = dir_listing.get_HTB(dir_listing.exp_paths[0])
# Store the raw files (they are pretty small, so why not)
htb_fn.write(open(htb_file).read())
log_fn.write(open(log_file).read())
# Close to force flush
htb_fn.close()
log_fn.close()
# Open the HTB file, and break out and write each array
htb_file = openHTB(htb_file)
for a_name, htb_arr in zip( htb_file.db_names, htb_file.db_array ):
# Figure out the type in terms of tables symantics
atm = tables.Atom.from_dtype(htb_arr.dtype)
# Takes spaces out of the name, so we can use natural naming
nat_name = a_name.replace(" ","")
# Create the array and throw the data in it
leaf_arr = h5_obj.createCArray(htb_leaf, nat_name,
atm, htb_arr.shape,
a_name)
leaf_arr[:] = htb_arr
# Block file bits
# Conv. lists
condition = []
trial_num = []
# Pack in the block files
array_created = False
for n, (cn, bn, tn, f) in enumerate(dir_listing.BLK_iter(dir_listing.exp_paths[0])):
print "Starting", n, "of", dir_listing.total_trial_count
print "\tLoading .BLK (%s) cn:%i tn:%i" % (f, cn, tn)
# Open the block file
bf = openBLK(f)
bf.load_data()
# Create a c-array
if not array_created:
new_shape = bf.data_array.shape + tuple([0])
ear = h5_obj.createEArray("/", "block", tables.Int32Atom(), new_shape, "Data from '%s'" % directory)
array_created = True
print "\tWriting to h5."
# Make the stings for the name and description of each data bloc
ear.append( bf.data_array[:,:,:,newaxis] )
# Mem clear necessary? TODO
ear.flush()
h5_obj.flush()
del bf
# For later conv.
condition.append(cn)
trial_num.append(tn)
print "\tDone."
# Create the condition and trial number arrays.
# (i.e avoid redoing that ugly file name munging each time)
h5_obj.createArray(h5_path, "condition", array(condition))
h5_obj.createArray(h5_path, "trial_num", array(trial_num))
# Yay done!
print "Done!"
from DIR_reader import openDIR
from DataBlocker import dir_to_h5
import os, tables, shutil
dr = openDIR("/media/jupiter/data/archive/working/frodo/")
temp_file = "/tmp/tmp-data2.h5"
b0rked = []
for path in dr.exp_paths:
if "run" not in path:
print "skipping", path
continue
print "Doing:", path
# Include the folder name it came from and the run number in the filename
output_stuff = path.split("/")[-2:]
out_fn = "-".join(output_stuff) + ".h5"
# Assemble the full path to the aws virtual directory
out_full = os.path.join("/home/mrg/aws-esdata/frodo", out_fn)
# if it is already present remotley, skip it.
if os.path.isfile(out_full):
try:
print "Testing: (%s)" % out_full
test = tables.openFile(out_full, "r+")
test.close()
print "Looks good, so skipping", out_fn
continue