make tem problem
Closed this issue · 4 comments
make tem
mkdir -p atlases/tem/src
mkdir -p atlases/tem/caf
python bin/parsers/tem/preprocess_data.py
--2011-09-12 14:37:20-- http://www.ini.uzh.ch/~acardona/data/membranes-neurites-glia.tif.tar.bz2
Auflösen des Hostnamen www.ini.uzh.ch... 130.60.230.182
Verbindungsaufbau zu www.ini.uzh.ch|130.60.230.182|:80... verbunden.
HTTP-Anforderung gesendet, warte auf Antwort... 200 OK
Länge: 348495 (340K) [application/x-tar]
In »atlases/tem/src/membranes-neurites-glia.tif.tar.bz2« speichern.
100%[================================================================================================================================================>] 348'495 2.02M/s in 0.2s
2011-09-12 14:37:20 (2.02 MB/s) - »atlases/tem/src/membranes-neurites-glia.tif.tar.bz2« gespeichert [348495/348495]
bunzip2: Output file atlases/tem/src/membranes-neurites-glia.tif.tar already exists.
-rw-r--r-- albert/albert 15734092 2010-02-26 14:18 membranes-neurites-glia.tif
* buffer overflow detected _: python terminated
======= Backtrace: =========
/lib/i386-linux-gnu/libc.so.6(__fortify_fail+0x50)[0x40319df0]
/lib/i386-linux-gnu/libc.so.6(+0xe4cca)[0x40318cca]
/lib/i386-linux-gnu/libc.so.6(__strcpy_chk+0x3f)[0x4031805f]
/usr/lib/python2.7/dist-packages/PIL/_imaging.so(ImagingNewPrologueSubtype+0xa6)[0x413c4a36]
/usr/lib/python2.7/dist-packages/PIL/_imaging.so(ImagingNewPrologue+0x33)[0x413c4f13]
/usr/lib/python2.7/dist-packages/PIL/_imaging.so(ImagingNewBlock+0x2d)[0x413c50dd]
/usr/lib/python2.7/dist-packages/PIL/_imaging.so(ImagingNew+0x51)[0x413c51a1]
/usr/lib/python2.7/dist-packages/PIL/_imaging.so(+0xa869)[0x413a5869]
python(PyEval_EvalFrameEx+0x2e5)[0x80da7d5]
python(PyEval_EvalCodeEx+0x127)[0x80e11e7]
python(PyEval_EvalFrameEx+0x73a)[0x80dac2a]
python(PyEval_EvalCodeEx+0x127)[0x80e11e7]
python(PyEval_EvalFrameEx+0x73a)[0x80dac2a]
python(PyEval_EvalCodeEx+0x127)[0x80e11e7]
python(PyEval_EvalCode+0x57)[0x812c477]
python[0x813c010]
python(PyRun_FileExFlags+0x84)[0x80700b3]
python(PyRun_SimpleFileExFlags+0x2cb)[0x8070af9]
python(Py_Main+0xbc6)[0x805c069]
python(main+0x1b)[0x805b25b]
/lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x4024ae37]
python[0x81074ad]
======= Memory map: ========
08048000-08238000 r-xp 00000000 08:01 27249 /usr/bin/python2.7
08238000-08239000 r--p 001ef000 08:01 27249 /usr/bin/python2.7
08239000-0828d000 rw-p 001f0000 08:01 27249 /usr/bin/python2.7
0828d000-08299000 rw-p 00000000 00:00 0
09413000-09948000 rw-p 00000000 00:00 0 [heap]
40000000-4001c000 r-xp 00000000 08:01 64907 /lib/i386-linux-gnu/ld-2.13.so
4001c000-4001d000 r--p 0001b000 08:01 64907 /lib/i386-linux-gnu/ld-2.13.so
4001d000-4001e000 rw-p 0001c000 08:01 64907 /lib/i386-linux-gnu/ld-2.13.so
4001e000-4001f000 r-xp 00000000 00:00 0 [vdso]
4001f000-40021000 rw-p 00000000 00:00 0
40021000-40037000 r-xp 00000000 08:01 918318 /usr/lib/pyshared/python2.7/numpy/core/_sort.so
40037000-40038000 r--p 00016000 08:01 918318 /usr/lib/pyshared/python2.7/numpy/core/_sort.so
40038000-40039000 rw-p 00017000 08:01 918318 /usr/lib/pyshared/python2.7/numpy/core/_sort.so
40039000-4003e000 r-xp 00000000 08:01 918320 /usr/lib/pyshared/python2.7/numpy/core/_dotblas.so
4003e000-4003f000 r--p 00004000 08:01 918320 /usr/lib/pyshared/python2.7/numpy/core/_dotblas.so
4003f000-40040000 rw-p 00005000 08:01 918320 /usr/lib/pyshared/python2.7/numpy/core/_dotblas.so
40040000-40041000 r-xs 00000000 08:01 6415 /tmp/ffiavZqHj (deleted)
40041000-40042000 rw-s 00000000 08:01 6415 /tmp/ffiavZqHj (deleted)
40042000-40057000 r-xp 00000000 08:01 64895 /lib/i386-linux-gnu/libpthread-2.13.so
40057000-40058000 r--p 00015000 08:01 64895 /lib/i386-linux-gnu/libpthread-2.13.so
40058000-40059000 rw-p 00016000 08:01 64895 /lib/i386-linux-gnu/libpthread-2.13.so
40059000-4005b000 rw-p 00000000 00:00 0
4005b000-4005d000 r-xp 00000000 08:01 64899 /lib/i386-linux-gnu/libdl-2.13.so
4005d000-4005e000 r--p 00001000 08:01 64899 /lib/i386-linux-gnu/libdl-2.13.so
4005e000-4005f000 rw-p 00002000 08:01 64899 /lib/i386-linux-gnu/libdl-2.13.so
4005f000-40060000 rw-p 00000000 00:00 0
40060000-40062000 r-xp 00000000 08:01 64848 /lib/i386-linux-gnu/libutil-2.13.so
40062000-40063000 r--p 00001000 08:01 64848 /lib/i386-linux-gnu/libutil-2.13.so
40063000-40064000 rw-p 00002000 08:01 64848 /lib/i386-linux-gnu/libutil-2.13.so
40064000-400a8000 r-xp 00000000 08:01 38557 /lib/libssl.so.0.9.8
400a8000-400a9000 r--p 00044000 08:01 38557 /lib/libssl.so.0.9.8
400a9000-400ac000 rw-p 00045000 08:01 38557 /lib/libssl.so.0.9.8
400ac000-401de000 r-xp 00000000 08:01 38559 /lib/libcrypto.so.0.9.8
401de000-401e6000 r--p 00131000 08:01 38559 /lib/libcrypto.so.0.9.8
401e6000-401f5000 rw-p 00139000 08:01 38559 /lib/libcrypto.so.0.9.8
401f5000-401f8000 rw-p 00000000 00:00 0
401f8000-4020b000 r-xp 00000000 08:01 21949 /lib/i386-linux-gnu/libz.so.1.2.3.4
4020b000-4020c000 r--p 00012000 08:01 21949 /lib/i386-linux-gnu/libz.so.1.2.3.4
4020c000-4020d000 rw-p 00013000 08:01 21949 /lib/i386-linux-gnu/libz.so.1.2.3.4
4020d000-40231000 r-xp 00000000 08:01 64906 /lib/i386-linux-gnu/libm-2.13.so
40231000-40232000 r--p 00023000 08:01 64906 /lib/i386-linux-gnu/libm-2.13.so
40232000-40233000 rw-p 00024000 08:01 64906 /lib/i386-linux-gnu/libm-2.13.so
40233000-40234000 rw-p 00000000 00:00 0
40234000-4038e000 r-xp 00000000 08:01 64834 /lib/i386-linux-gnu/libc-2.13.so
4038e000-4038f000 ---p 0015a000 08:01 64834 /lib/i386-linux-gnu/libc-2.13.so
4038f000-40391000 r--p 0015a000 08:01 64834 /lib/i386-linux-gnu/libc-2.13.so
40391000-40392000 rw-p 0015c000 08:01 64834 /lib/i386-linux-gnu/libc-2.13.so
40392000-40418000 rw-p 00000000 00:00 0
40418000-40618000 r--p 00000000 08:01 786476 /usr/lib/locale/locale-archive
40618000-40687000 r-xp 00000000 08:01 918321 /usr/lib/pyshared/python2.7/numpy/core/multiarray.so
40687000-40688000 r--p 0006e000 08:01 918321 /usr/lib/pyshared/python2.7/numpy/core/multiarray.so
40688000-4068e000 rw-p 0006f000 08:01 918321 /usr/lib/pyshared/python2.7/numpy/core/multiarray.so
4068e000-4068f000 rw-p 00000000 00:00 0
4068f000-406d1000 r-xp 00000000 08:01 918317 /usr/lib/pyshared/python2.7/numpy/core/umath.so
406d1000-406d2000 r--p 00041000 08:01 918317 /usr/lib/pyshared/python2.7/numpy/core/umath.so
406d2000-406d5000 rw-p 00042000 08:01 918317 /usr/lib/pyshared/python2.7/numpy/core/umath.so
406d5000-406d6000 rw-p 00000000 00:00 0
406d6000-406d8000 r-xp 00000000 08:01 91768 /usr/lib/python2.7/lib-dynload/_heapq.so
406d8000-406d9000 r--p 00001000 08:01 91768 /usr/lib/python2.7/lib-dynload/_heapq.so
406d9000-406db000 rw-p 00002000 08:01 91768 /usr/lib/python2.7/lib-dynload/_heapq.so
406db000-406df000 r-xp 00000000 08:01 918323 /usr/lib/pyshared/python2.7/numpy/lib/_compiled_base.so
406df000-406e0000 r--p 00003000 08:01 918323 /usr/lib/pyshared/python2.7/numpy/lib/_compiled_base.so
406e0000-406e1000 rw-p 00004000 08:01 918323 /usr/lib/pyshared/python2.7/numpy/lib/compiled_base.so
406e1000-406e5000 r-xp 00000000 08:01 918324 /usr/lib/pyshared/python2.7/numpy/linalg/lapack_lite.so
406e5000-406e6000 r--p 00004000 08:01 918324 /usr/lib/pyshared/python2.7/numpy/linalg/lapack_lite.so
406e6000-406e7000 rw-p 00005000 08:01 918324 /usr/lib/pyshared/python2.7/numpy/linalg/lapack_lite.so
406e7000-406ef000 r-xp 00000000 08:01 918325 /usr/lib/pyshared/python2.7/numpy/fft/fftpack_lite.so
406ef000-406f0000 r--p 00007000 08:01 918325 /usr/lib/pyshared/python2.7/numpy/fft/fftpack_lite.so
406f0000-406f1000 rw-p 00008000 08:01 918325 /usr/lib/pyshared/python2.7/numpy/fft/fftpack_lite.so
406f1000-406f2000 rw-p 00000000 00:00 0
406f7000-409f3000 r-xp 00000000 08:01 2361006 /usr/lib/atlas-base/atlas/libblas.so.3gf.0
409f3000-409f7000 rw-p 002fc000 08:01 2361006 /usr/lib/atlas-base/atlas/libblas.so.3gf.0
409f7000-40aaf000 r-xp 00000000 08:01 27716 /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0
40aaf000-40ab0000 r--p 000b7000 08:01 27716 /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0
40ab0000-40ab1000 rw-p 000b8000 08:01 27716 /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0
40ab1000-40ab2000 rw-p 00000000 00:00 0
40ab2000-40acc000 r-xp 00000000 08:01 10056 /lib/i386-linux-gnu/libgcc_s.so.1
40acc000-40acd000 r--p 00019000 08:01 10056 /lib/i386-linux-gnu/libgcc_s.so.1make: ** [tem] Abgebrochen
I have the same problem on my 32bit machine, (Python 2.7). Also, it seems not to download the right file, because it is very small (a few kilobytes)
The size of the file is ok as tiffs are very efficient when it comes to compressing. I've set up VM with Ubuntu 11 and reproduced this issue. The problem is that the source data is 16bpp tiff thus hardly any usual Ubuntu software can handle it (apparently including PIL included with Python2.7, try 2.6). Fortunately, this issue is related to preprocessing set not to parser itself. I'll try to find other way to extract single images from stacked tiff. Current walkaround is to disable preprocessing step (by commenting line python ${PARSERS_DIR}tem/preprocess_data.py in Makefile) prepare single image tiffs, put them in atlases/tem/src then run the parser again.
Ok, thanks for the help!
Ha! Managed to correct by replacing PIL with ImageMagic.