######################################################################## # # License: BSD # Created: February 10, 2004 # Author: Francesc Alted - falted@pytables.org # # $Id: ptdump.py 3102 2007-07-05 11:09:16Z faltet $ # ######################################################################## """This utility lets you look into the data and metadata of your data files. Pass the flag -h to this for help on usage. """ import sys import os.path import getopt from tables.file import openFile from tables.group import Group from tables.leaf import Leaf from tables.table import Table from tables.unimplemented import UnImplemented # default options class Options(object): rng = slice(None) showattrs = 0 verbose = 0 dump = 0 colinfo = 0 idxinfo = 0 options = Options() def dumpLeaf(leaf): if options.verbose: print repr(leaf) else: print str(leaf) if options.showattrs: print " "+repr(leaf.attrs) if options.dump and not isinstance(leaf, UnImplemented): print " Data dump:" # print leaf.read(options.rng.start, options.rng.stop, options.rng.step) # This is better for large objects if options.rng.start is None: start = 0 else: start = options.rng.start if options.rng.stop is None: if leaf.shape != (): stop = leaf.shape[0] else: stop = options.rng.stop if options.rng.step is None: step = 1 else: step = options.rng.step # print "nrows-->", leaf.nrows # print "shape-->", leaf.shape # print "start, stop, step-->", start, stop, step if leaf.shape == (): print "[SCALAR] %s" % (leaf[()]) else: for i in range(start, stop, step): print "[%s] %s" % (i, leaf[i]) if isinstance(leaf, Table) and options.colinfo: # Show info of columns #print repr(leaf.cols) for colname in leaf.colnames: print repr(leaf.cols._f_col(colname)) if isinstance(leaf, Table) and options.idxinfo: # Show info of indexes for colname in leaf.colnames: if leaf.cols._f_col(colname).index is not None: idx = leaf.cols._f_col(colname).index print repr(idx) # The next piece of code does not work very well :-/ # if options.dump: # row = idx.nelements % (idx.nelemslice # j = start # for i in range(start, stop, step): # if i > idx.nelemslice: # row += 1 # j = 0 # print "[%s] %s" % (i, idx.sorted[row][j]) # j += step def dumpGroup(h5file): if not options.verbose and not options.dump: # Print the simplest object tree print h5file return # Print detailed info on nodes for group in h5file.walkGroups(): print str(group) if options.showattrs: print " "+repr(group._v_attrs) for leaf in h5file.listNodes(group, 'Leaf'): dumpLeaf(leaf) def main(): usage = \ """usage: %s [-d] [-v] [-a] [-c] [-i] [-R start,stop,step] [-h] file[:nodepath] -d -- Dump data information on leaves -v -- Dump more metainformation on nodes -a -- Show attributes in nodes (only useful when -v or -d are active) -c -- Show info of columns in tables (only useful when -v or -d are active) -i -- Show info of indexed columns (only useful when -v or -d are active) -R RANGE -- Select a RANGE of rows in the form "start,stop,step" -h -- Print help on usage \n""" \ % os.path.basename(sys.argv[0]) try: opts, pargs = getopt.getopt(sys.argv[1:], 'R:ahdvci') except: sys.stderr.write(usage) sys.exit(0) # if we pass too much parameters, abort if len(pargs) <> 1: sys.stderr.write(usage) sys.exit(0) # Get the options for option in opts: if option[0] == '-R': try: options.rng = eval("slice("+option[1]+")") except: print "Error when getting the range parameter." (type, value, traceback) = sys.exc_info() print " The error was:", value sys.stderr.write(usage) sys.exit(0) elif option[0] == '-a': options.showattrs = 1 elif option[0] == '-h': sys.stderr.write(usage) sys.exit(0) elif option[0] == '-v': options.verbose = 1 elif option[0] == '-d': options.dump = 1 elif option[0] == '-c': options.colinfo = 1 elif option[0] == '-i': options.idxinfo = 1 else: print option[0], ": Unrecognized option" sys.stderr.write(usage) sys.exit(0) # Catch the files passed as the last arguments src = pargs[0].split(':') if len(src) == 1: filename, nodename = src[0], "/" else: filename, nodename = src if nodename == "": # case where filename == "filename:" instead of "filename:/" nodename = "/" # Check whether the specified node is a group or a leaf h5file = openFile(filename, 'r') nodeobject = h5file.getNode(nodename) if isinstance(nodeobject, Group): # Close the file again and reopen using the rootUEP # h5file.close() # h5file = openFile(filename, 'r', rootUEP=nodename) dumpGroup(h5file) elif isinstance(nodeobject, Leaf): # If it is not a Group, it must be a Leaf dumpLeaf(nodeobject) else: # This should never happen print "Unrecognized object:", nodeobject # Close the file h5file.close()