Recent changes to bugs

Segmentation fault when reading vdata from HDF4 file

Vincent Noel — Wed, 07 May 2014 10:10:14 -0000

I am attempting to read a vdata field from an HDF file (version 4) using the pyhdf module.

The field is called "Lidar_Data_Altitudes" and is stored in the vdata called "metadata". So I do:

from pyhdf import VS
from pyhdf.HDF import *

hdffile = HDF(filename, HC.READ)
vs = hdffile.vstart()
vd = vs.attach('metadata', write=0)
alt = vd.field('Lidar_Data_Altitude')
the code segfaults at the last line, but any attempt to access the contents of vd (e.g. vd.read()) will segfault.

I have found a similar issue reported and resolved here: http://proj.badc.rl.ac.uk/cedaservices/ticket/37
apparently it involves a small patch to the file hdfext_wrap.c part of pyhdf.

The file I'm trying to read Lidar_Data_Altitudes from is too big to link here, but here is another HDF file from which attempting to read vdata segfaults: http://www.lmd.polytechnique.fr/~noel/Files/CAL_LID_L2_05kmCLay-Prov-V3-30.2013-08-26T14-52-35ZN.hdf

replace the last line of the sample code above with data = vd.read(), and it segfaults.

Pyhdf 0.8.3 read deprecation

Anonymous — Mon, 10 Nov 2008 20:03:34 -0000

Reading from an HDF file produces the following deprecation messages:

/usr/lib64/python2.5/site-packages/pyhdf-0.8.3-py2.5-linux-x86_64.egg/pyhdf/SD.py:1876: DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
return _C._SDreaddata_0(self._id, data_type, start, count, stride)
/usr/lib64/python2.5/site-packages/pyhdf-0.8.3-py2.5-linux-x86_64.egg/pyhdf/SD.py:1876: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
return _C._SDreaddata_0(self._id, data_type, start, count, stride)

Example Code:
-------------
file = HDF(filename)
field = file.SD.select(fieldname)
data[:] = field[:] # or data[:] = field.get

Seg fault when char attribute lenght > 296

Jack — Fri, 09 Nov 2007 23:47:15 -0000

I am using pycdf-0.6-3b with netcdf-3.6.2. When reading a NC.CHAR type attribute I get a segmentation fault whenever the length of the character string exceeds 296. Is this a known issue.

- Jack

80 variable limitation

Anonymous — Thu, 03 Nov 2005 12:07:28 -0000

Hello,

It seems that one cannot store more than 80 vars in one
HDF file (SDwritedata failed). I guess that this
limitation come from the '80' magic value in
hdfext_wrap.c code. So, I began to change it to a
larger one (on lines 975 and 1097 wee below for snippet).

But it's not sufficient, SDwritedata still failed
wirth more than 80 vars to write. Is there some others
magic values based upon 80 ?

Thanks for your help.

Please answer to denis (dot) pithon (at)
boost-technologies (dot) com

PS: yes, I need more than 80 vars. Some satellites
products could contain more than 120 vars and I must
store them all in one HDF file.

#define NR_VARIABLES 118

int startArr[NR_VARIABLES], strideArr[NR_VARIABLES],
edgesArr[NR_VARIABLES], dims[NR_VARIABLES];

...