[AstroPy] pywcs problem on Linux
OKUMURA, Akira
oxon at ceres.phys.s.u-tokyo.ac.jp
Wed May 6 10:49:58 EDT 2009
Hello Mike,
The build log is here.
http://www-utheal.phys.s.u-tokyo.ac.jp/~oxon/build.log
Would you investigate it, please?
0)
$ gcc --version
gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-10)
$ uname -a
Linux yashi 2.6.9-78.0.1.ELsmp #1 SMP Tue Aug 5 13:53:03 CDT 2008
x86_64 x86_64 x86_64 GNU/Linux
$ python
Python 2.5.4 (r254:67916, May 6 2009, 07:09:17)
[GCC 3.4.6 20060404 (Red Hat 3.4.6-10)] on linux2
1)
$ sudo rm -rf /usr/local/lib/python2.5/site-packages/pywcs*
2)
$ cd sw/pywcs-1.4-4.3
$ rm -rf build
$ python setup.py build > build.log 2>&1
# => see the above link
$ sudo python setup.py install
$ python
>>> import pywcs
>>> pywcs.__path__
['/usr/local/lib/python2.5/site-packages/pywcs']
3)
$ gdb python
GNU gdb Red Hat Linux (6.3.0.0-1.159.el4rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and
you are
welcome to change it and/or distribute copies of it under certain
conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for
details.
This GDB was configured as "x86_64-redhat-linux-gnu"...Using host
libthread_db library "/lib64/tls/libthread_db.so.1".
(gdb) run test.py tmp
Starting program: /usr/local/bin/python test.py tmp
[Thread debugging using libthread_db enabled]
[New Thread 182896753024 (LWP 22366)]
=
=
=
========================================================================
tmp/model_total_ICHII_bin00.fits
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 182896753024 (LWP 22366)]
PyType_IsSubtype (a=0xfff688d8fff688d8, b=0x2a9579a500)
at Objects/typeobject.c:827
827 if (!(a->tp_flags & Py_TPFLAGS_HAVE_CLASS))
(gdb) bt
#0 PyType_IsSubtype (a=0xfff688d8fff688d8, b=0x2a9579a500)
at Objects/typeobject.c:827
#1 0x0000002a9562ba08 in PyArg_ParseTupleAndKeywords
(args=0x2a9aaeb4d0,
keywords=0x2a95661058, format=0x2a9a1f0006 "Oi:p2s",
kwlist=0x7fbfffd650)
at Python/getargs.c:1242
#2 0x0000002a9a1a7773 in PyWcsprm_p2s (self=0x7e44d0,
args=0xfff688d8fff688d8, kwds=0x2a9579a500) at src/wcslib_wrap.c:
746
#3 0x0000002a95615fa4 in PyEval_EvalFrameEx (f=0x7e9020,
throwflag=Variable "throwflag" is not available.
)
at Python/ceval.c:3612
#4 0x0000002a95617335 in PyEval_EvalCodeEx (co=0x2a9a126c60,
globals=Variable "globals" is not available.
)
at Python/ceval.c:2875
#5 0x0000002a95616026 in PyEval_EvalFrameEx (f=0x7e8bd0,
throwflag=Variable "throwflag" is not available.
)
at Python/ceval.c:3707
#6 0x0000002a95617335 in PyEval_EvalCodeEx (co=0x2a9a126b70,
globals=Variable "globals" is not available.
)
at Python/ceval.c:2875
#7 0x0000002a955b7444 in function_call (func=0x2a9a13f1b8,
arg=0x2a958498e8,
kw=0x7c8e40) at Objects/funcobject.c:517
#8 0x0000002a95597a33 in PyObject_Call (func=0xfff688d8fff688d8,
arg=0x2a9579a500, kw=0x2a9562b9cf) at Objects/abstract.c:1861
#9 0x0000002a9561425b in PyEval_EvalFrameEx (f=0x7e89e0,
throwflag=Variable "throwflag" is not available.
)
at Python/ceval.c:3892
#10 0x0000002a95617335 in PyEval_EvalCodeEx (co=0x2a9a126cd8,
globals=Variable "globals" is not available.
)
at Python/ceval.c:2875
---Type <return> to continue, or q <return> to quit---
#11 0x0000002a95616026 in PyEval_EvalFrameEx (f=0x7dddc0,
throwflag=Variable "throwflag" is not available.
)
at Python/ceval.c:3707
#12 0x0000002a95616834 in PyEval_EvalFrameEx (f=0x74a0b0,
throwflag=Variable "throwflag" is not available.
)
at Python/ceval.c:3698
#13 0x0000002a95616834 in PyEval_EvalFrameEx (f=0x56ff50,
throwflag=Variable "throwflag" is not available.
)
at Python/ceval.c:3698
#14 0x0000002a95617335 in PyEval_EvalCodeEx (co=0x2a95860030,
globals=Variable "globals" is not available.
)
at Python/ceval.c:2875
#15 0x0000002a956174b2 in PyEval_EvalCode (co=0xfff688d8fff688d8,
globals=0x2a9579a500, locals=0x2a9562b9cf) at Python/ceval.c:514
#16 0x0000002a9563934c in PyRun_FileExFlags (fp=0x501010,
filename=0x7fbffff113 "test.py", start=Variable "start" is not
available.
) at Python/pythonrun.c:1273
#17 0x0000002a95639fd3 in PyRun_SimpleFileExFlags (fp=0x501010,
filename=0x7fbffff113 "test.py", closeit=1, flags=0x7fbfffec2c)
at Python/pythonrun.c:879
#18 0x0000002a95645288 in Py_Main (argc=Variable "argc" is not
available.
) at Modules/main.c:532
#19 0x00000032b951c40b in __libc_start_main () from /lib64/tls/libc.so.6
#20 0x00000000004006ba in _start ()
#21 0x0000007fbfffedb8 in ?? ()
#22 0x000000000000001c in ?? ()
#23 0x0000000000000003 in ?? ()
#24 0x0000007fbffff0fd in ?? ()
#25 0x0000007fbffff113 in ?? ()
---Type <return> to continue, or q <return> to quit---
#26 0x0000007fbffff11b in ?? ()
#27 0x0000000000000000 in ?? ()
Regards,
OKUMURA, Akira oxon at ceres.phys.s.u-tokyo.ac.jp
Department of Physics, The University of Tokyo
7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
TEL/FAX +81 3-5841-4173/4059
Skype : okumura.akira
On 2009/05/06, at 23:29, Michael Droettboom wrote:
> Hmmm... I'm not seeing this problem here with your linked fits file
> and test.py.
>
> Occasionally the distutils build script that pywcs uses doesn't
> rebuild enough. Try deleting the build directory and then
> rebuilding and installing.
>
> If that still doesn't work, can you send the following:
>
> - Your version of gcc
> - The output of the build
> - A gdb backtrace
>
> This last can be obtained by running "gdb python" and the command
> prompt. Then "run test.py ." (assuming test.py and the fits file
> are in the current directory). When it crashes, type "bt" to get a
> backtrace.
>
> Cheers,
> Mike
>
> OKUMURA, Akira wrote:
>> Hello again,
>>
>> ver 1.4-4.3 runs properly with the sample FITS and the modified
>> script on my Mac (10.5). So the problem seems to happen only with
>> Linux.
>>
>>
>> On 2009/05/06, at 23:07, OKUMURA, Akira wrote:
>>
>>
>>> Hello Mike and Thomas,
>>>
>>> I modified test.py to use the second or third argument, but still I
>>> get a seg fault after calling wcs_pix2sky. And wcs.wcs.fix() always
>>> cause a seg fault. I have uploaded my sample FITS and modified
>>> test.py.
>>>
>>> http://www-utheal.phys.s.u-tokyo.ac.jp/~oxon/model_total_ICHII_bin00.fits
>>> http://www-utheal.phys.s.u-tokyo.ac.jp/~oxon/test.py
>>>
>>> Could you investigate it?
>>>
>>> Regards,
>>>
>>> OKUMURA, Akira oxon at ceres.phys.s.u-tokyo.ac.jp
>>> Department of Physics, The University of Tokyo
>>> 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
>>> TEL/FAX +81 3-5841-4173/4059
>>> Skype : okumura.akira
>>>
>>> On 2009/05/06, at 22:30, Michael Droettboom wrote:
>>>
>>>
>>>> It looks as if your new traceback is related to an API change --
>>>> all
>>>> of the transformation functions now require an "offset" argument,
>>>> which should be 0 for C/Numpy indexing or 1 for Fortran/FITS
>>>> indexing.
>>>>
>>>> If that change doesn't work for you, can you send me a FITS file
>>>> and
>>>> script to reproduce this off list? I'll see if I can reproduce
>>>> what
>>>> you're seeing here.
>>>>
>>>> Mike
>>>>
>>>>
>>>>
>>>> OKUMURA, Akira wrote:
>>>>
>>>>> Hello Nadia,
>>>>>
>>>>> Thank you for your reply. I didn't know that new version has been
>>>>> released recently. I installed pywcs-1.4-4.3.tar.gz and tried
>>>>> test.py in the package. But I got errors again.
>>>>>
>>>>> 1)
>>>>> $ ./test.py .
>>>>> = = =
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> ==================================================================
>>>>> ./cmap.fits
>>>>> zsh: segmentation fault ./test.py .
>>>>>
>>>>> the line wcs.wcs.fix() causes the seg fault.
>>>>>
>>>>> 2) comment out wcs.wcs.fix()
>>>>> $ ./test.py .
>>>>> = = =
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> ==================================================================
>>>>> ./cmap.fits
>>>>> Traceback (most recent call last):
>>>>> File "./test.py", line 82, in <module>
>>>>> run_directory(directory)
>>>>> File "./test.py", line 74, in run_directory
>>>>> test_file(filepath)
>>>>> File "./test.py", line 38, in test_file
>>>>> world = wcs.wcs_pix2sky(data3)
>>>>> File "/usr/local/lib/python2.5/site-packages/pywcs/pywcs.py",
>>>>> line 419, in wcs_pix2sky
>>>>> *args, **kwargs)
>>>>> File "/usr/local/lib/python2.5/site-packages/pywcs/pywcs.py",
>>>>> line 378, in _array_converter
>>>>> raise TypeError("Expected 2 or 3 arguments, %d given" %
>>>>> len(args))
>>>>> TypeError: Expected 2 or 3 arguments, 1 given
>>>>>
>>>>> I tried several FITS files but I got the same errors. Do you have
>>>>> any idea?
>>>>>
>>>>> Regards,
>>>>>
>>>>> OKUMURA, Akira oxon at ceres.phys.s.u-tokyo.ac.jp
>>>>> Department of Physics, The University of Tokyo
>>>>> 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
>>>>> TEL/FAX +81 3-5841-4173/4059
>>>>> Skype : okumura.akira
>>>>>
>>>>> On 2009/05/06, at 20:47, Nadezhda Dencheva wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> You are running an older version of pywcs.
>>>>>> I believe an upgrade to the latest release will fix this.
>>>>>>
>>>>>>
>>>>>> Nadia Dencheva
>>>>>>
>>>>>> ---- Original message ----
>>>>>>
>>>>>>
>>>>>>> Date: Wed, 6 May 2009 15:30:23 +0900
>>>>>>> From: astropy-bounces at scipy.org (on behalf of "OKUMURA, Akira"
>>>>>>> <oxon at ceres.phys.s.u-tokyo.ac.jp
>>>>>>>
>>>>>>>> )
>>>>>>>>
>>>>>>>>
>>>>>>> Subject: [AstroPy] pywcs problem on Linux
>>>>>>> To: astropy at scipy.org
>>>>>>>
>>>>>>> Hello all,
>>>>>>>
>>>>>>> I have installed pywcs in two environments.
>>>>>>> (1) Scientific Linux 4.7 (64 bit)
>>>>>>> + Python 2.5.4 (r254:67916, May 6 2009, 07:09:17)
>>>>>>> + GCC 3.4.6 20060404 (Red Hat 3.4.6-10)] on linux2
>>>>>>> + pyfits-1.3
>>>>>>> + pywcs-1.3a1-4.3
>>>>>>> (2) Red Hat Enterprise Linux 4 (32 bit).
>>>>>>> + Python 2.5.1 (r251:54863, Aug 24 2007, 16:22:50)
>>>>>>> + GCC 3.4.3 (TWW)] on linux2
>>>>>>> + pywcs-1.3a1-4.3
>>>>>>> + pyfits-2.1.1
>>>>>>>
>>>>>>> But I got following errors even though it runs properly on
>>>>>>> Mac OS X
>>>>>>> 10.5.
>>>>>>> === Error on (1) ===
>>>>>>>
>>>>>>>
>>>>>>>>>> hdulist = pyfits.open("cmap.fits")
>>>>>>>>>> wcs = pywcs.WCS(hdulist[0].header)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>> zsh: segmentation fault python
>>>>>>>
>>>>>>> === Error on (2) ===
>>>>>>>
>>>>>>>
>>>>>>>>>> hdulist = pyfits.open("cmap.fits")
>>>>>>>>>> wcs = pywcs.WCS(hdulist[0].header)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>> Traceback (most recent call last):
>>>>>>> File "<stdin>", line 1, in <module>
>>>>>>> File "/u/gl/oxon/tmp/lib/python2.5/site-packages/pywcs/
>>>>>>> pywcs.py",
>>>>>>> line 155, in __init__
>>>>>>> self.footprint = self._calcFootprint(header)
>>>>>>> File "/u/gl/oxon/tmp/lib/python2.5/site-packages/pywcs/
>>>>>>> pywcs.py",
>>>>>>> line 181, in _calcFootprint
>>>>>>> return self.all_pix2sky(corners)
>>>>>>> File "/u/gl/oxon/tmp/lib/python2.5/site-packages/pywcs/
>>>>>>> pywcs.py",
>>>>>>> line 307, in all_pix2sky
>>>>>>> return self._array_converter(self._all_pix2sky, *args, **kwargs)
>>>>>>> File "/u/gl/oxon/tmp/lib/python2.5/site-packages/pywcs/
>>>>>>> pywcs.py",
>>>>>>> line 294, in _array_converter
>>>>>>> return func(args[0], **kwargs)
>>>>>>> SystemError: Python/getargs.c:1246: bad argument to internal
>>>>>>> function
>>>>>>>
>>>>>>> Is there any tips on running pywcs with Linux ?
>>>>>>>
>>>>>>> The FITS is as follows.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>>> print hdulist[0].header
>>>>>>>>>>
>>>>>>>>>>
>>>>>>> SIMPLE = T / File conforms to NOST standard
>>>>>>> BITPIX = 32 / Bits per pixel
>>>>>>> NAXIS = 2 / No data is associated with this
>>>>>>> header
>>>>>>> NAXIS1 = 160 / Length of data axis 1
>>>>>>> NAXIS2 = 160 / Length of data axis 2
>>>>>>> EXTEND = T / Extensions may be present
>>>>>>> COMMENT FITS (Flexible Image Transport System) format is
>>>>>>> defined in
>>>>>>> 'Astronomy
>>>>>>> COMMENT and Astrophysics', volume 376, page 359; bibcode:
>>>>>>> 2001A&A...
>>>>>>> 376..359H
>>>>>>> CTYPE1 = 'GLON-AIT' / RA---%%%, %%% represents the
>>>>>>> projection method
>>>>>>> CRPIX1 = 80.5 / Reference pixel
>>>>>>> CRVAL1 = 211. / RA at the reference pixel
>>>>>>> CDELT1 = -0.25 / X-axis incr per pixel of
>>>>>>> physical
>>>>>>> coord at posi
>>>>>>> CUNIT1 = 'deg ' / Physical unit of X-axis
>>>>>>> CTYPE2 = 'GLAT-AIT' / DEC---%%%, %%% represents the
>>>>>>> projection method
>>>>>>> CRPIX2 = 80.5 / Reference pixel
>>>>>>> CRVAL2 = -17. / DEC at the reference pixel
>>>>>>> CDELT2 = 0.25 / Y-axis incr per pixel of
>>>>>>> physical
>>>>>>> coord at posi
>>>>>>> CUNIT2 = 'deg ' / Physical unit of Y-axis
>>>>>>> CROTA2 = 0. / Image rotation (deg)
>>>>>>> DATE = '2009-04-01T15:34:22' / file creation date (YYYY-MM-
>>>>>>> DDThh:mm:ss U
>>>>>>> FILENAME= 'cmap.fits' /
>>>>>>> TELESCOP= 'GLAST ' / name of telescope
>>>>>>> generating data
>>>>>>> INSTRUME= 'LAT ' / name of instrument generating
>>>>>>> data
>>>>>>> DATE-OBS= '2009-03-11T21:33:18.000' / start date and time of the
>>>>>>> observation (U
>>>>>>> DATE-END= '2009-03-17T16:26:38.000' / end date and time of the
>>>>>>> observation (UTC
>>>>>>> NDSKEYS = 5
>>>>>>> EQUINOX = 2000. / Equinox of RA & DEC
>>>>>>> specifications
>>>>>>> OBSERVER= 'Peter Michelson' / GLAST/LAT PI
>>>>>>> CREATOR = 'gtbin ' / Software and version
>>>>>>> creating file
>>>>>>> HISTORY LatCountMapTemplate,v 1.3 2005/04/05
>>>>>>> 21:06:39 peachey
>>>>>>> HISTORY Exp
>>>>>>> CHECKSUM= 'c8JZf8JXc8JXc8JX' / HDU checksum updated
>>>>>>> 2009-04-01T06:34:22
>>>>>>> DATASUM = '182648 ' / data unit checksum updated
>>>>>>> 2009-04-01T06:34:22
>>>>>>> DSTYP1 = 'TIME '
>>>>>>> DSUNI1 = 's '
>>>>>>> DSVAL1 = 'TABLE '
>>>>>>> DSREF1 = ':GTI '
>>>>>>> DSTYP2 = 'POS(RA,DEC)'
>>>>>>> DSUNI2 = 'deg '
>>>>>>> DSVAL2 = 'CIRCLE(86.81257852,-6.005536809,20)'
>>>>>>> DSTYP3 = 'CTBCLASSLEVEL'
>>>>>>> DSUNI3 = 'dimensionless'
>>>>>>> DSVAL3 = '3: '
>>>>>>> DSTYP4 = 'ENERGY '
>>>>>>> DSUNI4 = 'MeV '
>>>>>>> DSVAL4 = '200:20000'
>>>>>>> DSTYP5 = 'ZENITH_ANGLE'
>>>>>>> DSUNI5 = 'deg '
>>>>>>> DSVAL5 = '0:100 '
>>>>>>>
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> OKUMURA, Akira oxon at ceres.phys.s.u-tokyo.ac.jp
>>>>>>> Department of Physics, The University of Tokyo
>>>>>>> 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
>>>>>>> TEL/FAX +81 3-5841-4173/4059
>>>>>>> Skype : okumura.akira
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AstroPy mailing list
>>>>>>> AstroPy at scipy.org
>>>>>>> http://mail.scipy.org/mailman/listinfo/astropy
>>>>>>>
>>>>>>>
>>>>> _______________________________________________
>>>>> AstroPy mailing list
>>>>> AstroPy at scipy.org
>>>>> http://mail.scipy.org/mailman/listinfo/astropy
>>>>>
>>>>>
>>>> --
>>>> Michael Droettboom
>>>> Science Software Branch
>>>> Operations and Engineering Division
>>>> Space Telescope Science Institute
>>>> Operated by AURA for NASA
>>>>
>>>>
>>> _______________________________________________
>>> AstroPy mailing list
>>> AstroPy at scipy.org
>>> http://mail.scipy.org/mailman/listinfo/astropy
>>>
>>
>>
>>
>>
>> Regards,
>>
>> OKUMURA, Akira oxon at ceres.phys.s.u-tokyo.ac.jp
>> Department of Physics, The University of Tokyo
>> 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
>> TEL/FAX +81 3-5841-4173/4059
>> Skype : okumura.akira
>>
>> _______________________________________________
>> AstroPy mailing list
>> AstroPy at scipy.org
>> http://mail.scipy.org/mailman/listinfo/astropy
>>
>
> --
> Michael Droettboom
> Science Software Branch
> Operations and Engineering Division
> Space Telescope Science Institute
> Operated by AURA for NASA
>
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