As we are at it, Andre Gosselin (the guy who wrote pycdf) also wrote an interface to HDF4 (not 5) named pyhdf. I'm using that with numpy as well (patch attached), but I haven't tested it much - little more than just running the examples, really (which appear to be ok). Maybe it's useful...
In pyhdf, the author didn't support different array interfaces; so the attached patch just modifes the existing source code and moves it over to numpy. I've also attached a "install script" which makes use of the particular lacotion of the HDF4 libraries (in $PREFIX/lib) and header files (in $PREFIX/include/hdf), so it it almost certainly needs to be adapted to the location of the actual HDF libraries and headers. Regards, Christian. On Fri, February 9, 2007 22:00, Christian Marquardt wrote: > Dear list, > > attached is a patch for the original pycdf-0.6.2-rc1 distribution as > available through sourceforge - and a little shell script illustrating > how to install it. After applyng the patch, it should be configured for > numpy. Note that the "installation" script uses an environment variable > PREFIX to define where the pacjkage is installed; it also assumes that > the netcdf libraries are installed in $PREFIX/lib. > > The orginal author already supported both numeric and numarray, so I just > added a new subdirectory for numpy - which is simply the numeric version > slightly changed. The patch is only that large because it replicates much > of already existing code... > > I have been using this "port" for many weeks now without any problems or > difficulties. I hope it's useful for others as well;-) > > Christian. > > > > On Fri, February 9, 2007 15:31, Daran L. Rife wrote: >> Hi Travis, >> >> If you're still offering NumPy "patches" to third party >> packages that rely upon Numeric, I would really like for >> pycdf to be ported to NumPy. This would allow me to >> completely transition to NumPy. >> >> Thanks very much for considering my request. >> >> >> Daran Rife >> >> _______________________________________________ >> Numpy-discussion mailing list >> Numpy-discussion@scipy.org >> http://projects.scipy.org/mailman/listinfo/numpy-discussion >> > _______________________________________________ > Numpy-discussion mailing list > Numpy-discussion@scipy.org > http://projects.scipy.org/mailman/listinfo/numpy-discussion >
diff -r -N -C 3 pyhdf-0.7-3/examples/hdfstruct/hdfstruct.py pyhdf-0.7-3-numpy/examples/hdfstruct/hdfstruct.py
*** pyhdf-0.7-3/examples/hdfstruct/hdfstruct.py 2004-11-03 15:41:12.000000000 +0100
--- pyhdf-0.7-3-numpy/examples/hdfstruct/hdfstruct.py 2007-01-20 21:08:53.000000000 +0100
***************
*** 2,8 ****
import sys
from pyhdf.SD import *
! from Numeric import *
# Dictionnary used to convert from a numeric data type to its symbolic
# representation
--- 2,8 ----
import sys
from pyhdf.SD import *
! from numpy import *
# Dictionnary used to convert from a numeric data type to its symbolic
# representation
diff -r -N -C 3 pyhdf-0.7-3/examples/szip/szip16.py pyhdf-0.7-3-numpy/examples/szip/szip16.py
*** pyhdf-0.7-3/examples/szip/szip16.py 2005-07-13 05:19:19.000000000 +0200
--- pyhdf-0.7-3-numpy/examples/szip/szip16.py 2007-01-20 21:04:14.000000000 +0100
***************
*** 1,7 ****
#!/usr/bin/env python
from pyhdf.SD import *
! import Numeric
SZIP = True
--- 1,7 ----
#!/usr/bin/env python
from pyhdf.SD import *
! import numpy
SZIP = True
***************
*** 12,18 ****
WIDTH = 100
fill_value = 0
! #data = Numeric.array(((100,100,200,200,300,400),
# (100,100,200,200,300,400),
# (100,100,200,200,300,400),
# (300,300, 0,400,300,400),
--- 12,18 ----
WIDTH = 100
fill_value = 0
! #data = numpy.array(((100,100,200,200,300,400),
# (100,100,200,200,300,400),
# (100,100,200,200,300,400),
# (300,300, 0,400,300,400),
***************
*** 20,28 ****
# (300,300, 0,400,300,400),
# (0, 0,600,600,300,400),
# (500,500,600,600,300,400),
! # (0, 0,600,600,300,400)), Numeric.Int16)
! data = Numeric.zeros((LENGTH, WIDTH), Numeric.Int16)
for i in range(LENGTH):
for j in range(WIDTH):
data[i,j] = i+j
--- 20,28 ----
# (300,300, 0,400,300,400),
# (0, 0,600,600,300,400),
# (500,500,600,600,300,400),
! # (0, 0,600,600,300,400)), numpy.int16)
! data = numpy.zeros((LENGTH, WIDTH), numpy.int16)
for i in range(LENGTH):
for j in range(WIDTH):
data[i,j] = i+j
diff -r -N -C 3 pyhdf-0.7-3/examples/szip/szip32.py pyhdf-0.7-3-numpy/examples/szip/szip32.py
*** pyhdf-0.7-3/examples/szip/szip32.py 2005-07-13 22:51:18.000000000 +0200
--- pyhdf-0.7-3-numpy/examples/szip/szip32.py 2007-01-20 21:06:15.000000000 +0100
***************
*** 26,32 ****
#
from pyhdf.SD import *
! import Numeric
# Set SZIP to True to compress data using SZIP. Set to False to bypass compression.
SZIP = True
--- 26,32 ----
#
from pyhdf.SD import *
! import numpy
# Set SZIP to True to compress data using SZIP. Set to False to bypass compression.
SZIP = True
***************
*** 39,45 ****
#LENGTH = 9
#WIDTH = 6
#
! #data = Numeric.array(((100,100,200,200,300,400),
# (100,100,200,200,300,400),
# (100,100,200,200,300,400),
# (300,300, 0,400,300,400),
--- 39,45 ----
#LENGTH = 9
#WIDTH = 6
#
! #data = numpy.array(((100,100,200,200,300,400),
# (100,100,200,200,300,400),
# (100,100,200,200,300,400),
# (300,300, 0,400,300,400),
***************
*** 47,59 ****
# (300,300, 0,400,300,400),
# (0, 0,600,600,300,400),
# (500,500,600,600,300,400),
! # (0, 0,600,600,300,400)), Numeric.Int32)
# The above dataset is too small to show a significant size reduction after
# compression. Try the following for a more realistic example.
LENGTH = 250
WIDTH = 100
! data = Numeric.zeros((LENGTH, WIDTH), Numeric.Int32)
for i in range(LENGTH):
for j in range(WIDTH):
data[i,j] = (i+j)*(i-j)
--- 47,59 ----
# (300,300, 0,400,300,400),
# (0, 0,600,600,300,400),
# (500,500,600,600,300,400),
! # (0, 0,600,600,300,400)), numpy.int32)
# The above dataset is too small to show a significant size reduction after
# compression. Try the following for a more realistic example.
LENGTH = 250
WIDTH = 100
! data = numpy.zeros((LENGTH, WIDTH), numpy.int32)
for i in range(LENGTH):
for j in range(WIDTH):
data[i,j] = (i+j)*(i-j)
diff -r -N -C 3 pyhdf-0.7-3/examples/txttohdf/txttohdf.py pyhdf-0.7-3-numpy/examples/txttohdf/txttohdf.py
*** pyhdf-0.7-3/examples/txttohdf/txttohdf.py 2004-11-03 15:42:11.000000000 +0100
--- pyhdf-0.7-3-numpy/examples/txttohdf/txttohdf.py 2007-01-20 14:43:34.000000000 +0100
***************
*** 1,6 ****
#!/usr/bin/env python
! from Numeric import *
from pyhdf.SD import *
import os
--- 1,6 ----
#!/usr/bin/env python
! from numpy import *
from pyhdf.SD import *
import os
diff -r -N -C 3 pyhdf-0.7-3/pyhdf/hdfext_wrap.c pyhdf-0.7-3-numpy/pyhdf/hdfext_wrap.c
*** pyhdf-0.7-3/pyhdf/hdfext_wrap.c 2005-07-14 00:04:21.000000000 +0200
--- pyhdf-0.7-3-numpy/pyhdf/hdfext_wrap.c 2007-01-20 13:07:23.000000000 +0100
***************
*** 904,910 ****
#include "hdfi.h" /* declares int32, float32, etc */
! #include "Numeric/arrayobject.h"
#define DFNT_FLOAT32 5
#define DFNT_FLOAT 5 /* For backward compat; don't use */
--- 904,910 ----
#include "hdfi.h" /* declares int32, float32, etc */
! #include "numpy/oldnumeric.h"
#define DFNT_FLOAT32 5
#define DFNT_FLOAT 5 /* For backward compat; don't use */
diff -r -N -C 3 pyhdf-0.7-3/pyhdf/SD.py pyhdf-0.7-3-numpy/pyhdf/SD.py
*** pyhdf-0.7-3/pyhdf/SD.py 2005-07-14 03:36:41.000000000 +0200
--- pyhdf-0.7-3-numpy/pyhdf/SD.py 2007-01-20 13:07:09.000000000 +0100
***************
*** 1,3 ****
--- 1,5 ----
+ ## Automatically adapted for numpy.oldnumeric Jan 20, 2007 by
+
# $Id: SD.py,v 1.7 2005/07/14 01:36:41 gosselin_a Exp $
# $Log: SD.py,v $
# Revision 1.7 2005/07/14 01:36:41 gosselin_a
***************
*** 997,1003 ****
__all__ = ['SD', 'SDAttr', 'SDC', 'SDS', 'SDim', 'HDF4Error']
try:
! import Numeric as _toto
del _toto
except ImportError:
raise HDF4Error, "Numeric package required but not installed"
--- 999,1005 ----
__all__ = ['SD', 'SDAttr', 'SDC', 'SDS', 'SDim', 'HDF4Error']
try:
! import numpy.oldnumeric as _toto
del _toto
except ImportError:
raise HDF4Error, "Numeric package required but not installed"
***************
*** 1093,1101 ****
INT32,
CHAR8, UCHAR8]
try:
! from Numeric import UInt16 as _bozo
equivNumericTypes.append(UINT16)
! from Numeric import UInt32 as _bozo
equivNumericTypes.append(UINT32)
del _bozo
except ImportError:
--- 1095,1103 ----
INT32,
CHAR8, UCHAR8]
try:
! from numpy.oldnumeric import UInt16 as _bozo
equivNumericTypes.append(UINT16)
! from numpy.oldnumeric import UInt32 as _bozo
equivNumericTypes.append(UINT32)
del _bozo
except ImportError:
***************
*** 1973,1979 ****
"number of dimensions")
else: # Convert single index to sequence
elem = [elem]
! if type(shape) == types.IntType:
shape = [shape]
start = []
--- 1975,1981 ----
"number of dimensions")
else: # Convert single index to sequence
elem = [elem]
! if isinstance(shape, types.IntType):
shape = [shape]
start = []
***************
*** 1986,1992 ****
# See if the dimension is unlimited (always at index 0)
unlim = n == 0 and unlimited
# Simple index
! if type(e) == types.IntType:
slice = 0
if e < 0 :
e += shape[n]
--- 1988,1994 ----
# See if the dimension is unlimited (always at index 0)
unlim = n == 0 and unlimited
# Simple index
! if isinstance(e, types.IntType):
slice = 0
if e < 0 :
e += shape[n]
***************
*** 2727,2733 ****
# Get the number of dimensions and their lengths.
nDims, dimLen = self.info()[1:3]
! if type(dimLen) == types.IntType: # need a sequence
dimLen = [dimLen]
# Check if the dataset is appendable.
unlim = self.isrecord()
--- 2729,2735 ----
# Get the number of dimensions and their lengths.
nDims, dimLen = self.info()[1:3]
! if isinstance(dimLen, types.IntType): # need a sequence
dimLen = [dimLen]
# Check if the dataset is appendable.
unlim = self.isrecord()
diff -r -N -C 3 pyhdf-0.7-3/pyhdf/VS.py pyhdf-0.7-3-numpy/pyhdf/VS.py
*** pyhdf-0.7-3/pyhdf/VS.py 2005-07-14 03:36:41.000000000 +0200
--- pyhdf-0.7-3-numpy/pyhdf/VS.py 2007-01-20 13:07:10.000000000 +0100
***************
*** 1,3 ****
--- 1,5 ----
+ ## Automatically adapted for numpy.oldnumeric Jan 20, 2007 by
+
# $Id: VS.py,v 1.4 2005/07/14 01:36:41 gosselin_a Exp $
# $Log: VS.py,v $
# Revision 1.4 2005/07/14 01:36:41 gosselin_a
***************
*** 2016,2022 ****
for e in elem:
n += 1
# Simple index
! if type(e) == types.IntType:
slice = 0
if e < 0:
e += shape[n]
--- 2018,2024 ----
for e in elem:
n += 1
# Simple index
! if isinstance(e, types.IntType):
slice = 0
if e < 0:
e += shape[n]
diff -r -N -C 3 pyhdf-0.7-3/setup.py pyhdf-0.7-3-numpy/setup.py
*** pyhdf-0.7-3/setup.py 2005-07-14 03:36:41.000000000 +0200
--- pyhdf-0.7-3-numpy/setup.py 2007-01-20 21:28:55.000000000 +0100
***************
*** 28,39 ****
# Date: July 13 2005
from distutils.core import setup, Extension
! HDF_include = "/usr/local/hdf-4.2r1/include"
! HDF_lib = "/usr/local/hdf-4.2r1/lib"
_hdfext = Extension('pyhdf._hdfext',
! sources = ["pyhdf/hdfext_wrap.c"],
! include_dirs=[HDF_include],
# Define NOUINT if your version of Numeric does not support
# unsigned shorts or unsigned ints. Only versions 22 and above
--- 28,40 ----
# Date: July 13 2005
from distutils.core import setup, Extension
! from numpy.distutils.misc_util import get_numpy_include_dirs
!
! include_dirs = get_numpy_include_dirs()
_hdfext = Extension('pyhdf._hdfext',
! sources = ["pyhdf/hdfext_wrap.c"],
! include_dirs = include_dirs,
# Define NOUINT if your version of Numeric does not support
# unsigned shorts or unsigned ints. Only versions 22 and above
***************
*** 42,49 ****
# support.
#extra_compile_args=["-DNOUINT"],
#extra_compile_args=["-DNOSZIP"],
!
! library_dirs=[HDF_lib],
#extra_link_args=["extra stuff passed to the linker"],
# 'libraries' is set to the list of libraries to link
--- 43,50 ----
# support.
#extra_compile_args=["-DNOUINT"],
#extra_compile_args=["-DNOSZIP"],
!
! #library_dirs=["extra libraries required"],
#extra_link_args=["extra stuff passed to the linker"],
# 'libraries' is set to the list of libraries to link
***************
*** 66,72 ****
author = 'Andre Gosselin',
author_email = '[EMAIL PROTECTED]',
description = 'Python interface to the NCSA HDF4 library',
! keywords = ['hdf', 'netcdf', 'Numeric', 'python'],
license = 'public',
long_description = 'The pyhdf package wraps the functionality\n '
'of the NCSA HDF version 4 library inside a Python OOP\n '
--- 67,73 ----
author = 'Andre Gosselin',
author_email = '[EMAIL PROTECTED]',
description = 'Python interface to the NCSA HDF4 library',
! keywords = ['hdf', 'netcdf', 'numpy', 'python'],
license = 'public',
long_description = 'The pyhdf package wraps the functionality\n '
'of the NCSA HDF version 4 library inside a Python OOP\n '
build_pyhdf-0.7-3-numpy-linux.sh
Description: application/shellscript
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