bugfix: filename

python/ucf/tools/ucftar_mpiio_pack

@@ -8,7 +8,7 @@ import numpy as np
 import ucf
 import configparser
 
-parser = argparse.ArgumentParser(description='Reads an ucf.tar archive, downsamples it and saves it to a new ucf.tar archive. Can be used as a pipe.')
+parser = argparse.ArgumentParser(description='Packs UCF MPIIO data into a tar archive. The single output file is split into multiple files due to file size restrictions.')
 parser.add_argument('indir', metavar='dirin', help='input directory')
 parser.add_argument('iseq',  metavar='iseq', help='sequence number')
 parser.add_argument('base',  metavar='base', help='filebase to be archived: "uvwp" or "scal"')
@@ -52,7 +52,7 @@ if verbose:
 ftar = tarfile.open(name=file_out,mode='w',pax_headers=tarfile.USTAR_FORMAT)
 
 def transform_filename(filename,iseq):
-  return os.path.basename(file_in).replace('_{:04d}'.format(iseq),'')
+  return os.path.basename(filename).replace('_{:04d}'.format(iseq),'')
 
 # Parse parameters to construct file headers, then add it to tar
 file_in = '{}/parameters_{:04d}.asc'.format(dir_in,iseq)

python/ucf/tools/ucftar_mpiio_unpack

@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+import sys
+import io
+import os
+import tarfile
+import argparse
+import numpy as np
+import ucf
+import configparser
+
+parser = argparse.ArgumentParser(description='Unpacks an UCF tar file as MPIIO input file.')
+parser.add_argument('infile', metavar='filein', help='input file')
+parser.add_argument('iseq',  metavar='iseq', help='sequence number')
+#parser.add_argument('base',  metavar='base', help='filebase to be archived: "uvwp" or "scal"')
+parser.add_argument("-o", "--outdir", metavar='directory',nargs='?', default=None, help="name of the output directory", action="store")
+parser.add_argument("-v", "--verbose", help="activate verbose output", action="store_true")
+args = parser.parse_args()
+
+file_in = args.infile
+iseq    = int(args.iseq)
+#base    = args.base
+verbose = args.verbose
+
+if args.outdir is None:
+  dir_out = './'
+else:
+  dir_out = args.outdir
+
+# Open tar file for input
+ftar = tarfile.open(name=file_in,mode='r')
+
+# Extract files
+def transform_filename(filename,iseq):
+  return filename.replace('.','_{:04d}.'.format(iseq))
+
+files_all = ftar.getnames()
+#files_aux = ('parameters.asc','proc.bin','grid.bin','particles.bin')
+files_aux = [s for s in files_all if not s.startswith('uvwp') or s.startswith('scal')]
+for files in files_aux:
+  print(files)
+  ucf_bytes = ftar.extractfile(files).read()
+  file_out = dir_out+transform_filename(files,iseq)
+  fidw = open(file_out,'wb')
+  fidw.write(ucf_bytes)
+  fidw.close()
+
+files_data = [s for s in files_all if s.startswith('uvwp') or s.startswith('scal')]
+base = files_data[0].split('.')[0]
+iproc = 0
+file_out = dir_out+'/'+base+'_{:04d}.bin'.format(iseq)
+fidw = open(file_out,'wb')
+for files in files_data:
+  print(files)
+  sproc = files.split('.')[1]
+  if iproc!=int(sproc):
+    raise ValueError('Invalid file order in tar: {}, {}'.format(iproc,files))
+  ucf_bytes = ftar.extractfile(files).read()
+  if iproc==0:
+    fidw.write(ucf_bytes)
+  else:
+    fidw.write(ucf_bytes[64:])
+  iproc += 1
+fidw.close()
+
+# Close tar file
+ftar.close()