yarikoptic

$> nifti_tool -diff_hdr -infiles phantom_haxby2001_3_1.nii ../../phantom_haxby2001_03_1-FEEPI.nii.gz
  name                offset  nvals  values
  ------------------- ------  -----  ------
  pixdim                76      8    1.0 3.75 3.75 3.5 2.5 0.0 0.0 0.0
  pixdim                76      8    1.0 3.75 3.75 3.5 2500.0 1.0 1.0 1.0
  vox_offset           108      1    352.0
  vox_offset           108      1    1423952.0
  scl_slope            112      1    1.242735
  scl_slope            112      1    3356.35791
  slice_end            120      1    39

yarikoptic

We couldn’t find that file to show.

yarikoptic

(gdb) up
#3  0x00000000005a0583 in PyCFunction_Call (func=0xacaaa38, arg=0x191b0420, kw=0x0)
    at ../Objects/methodobject.c:81
81	../Objects/methodobject.c: No such file or directory.
	in ../Objects/methodobject.c
(gdb) 
#4  0x0000000000425fe5 in PyObject_Call (func=0xacaaa38, arg=0x191b0420, kw=0x0)
    at ../Objects/abstract.c:2492
2492	../Objects/abstract.c: No such file or directory.
	in ../Objects/abstract.c

yarikoptic

$> PYTHONPATH=build/lib.linux-x86_64-2.6 sphinx-build docs/src/ build/html/     
Running Sphinx v1.0.7
loading pickled environment... done
No builder selected, using default: html
building [html]: targets for 0 source files that are out of date
updating environment: 0 added, 18 changed, 0 removed
Traceback (most recent call last):roller/ec2                                                                                                                                                                                                                                                                 
  File "/usr/lib/pymodules/python2.6/sphinx/ext/autodoc.py", line 329, in import_object
    __import__(self.modname)
  File "/tmp/pebl-1.0.2/build/lib.linux-x86_64-2.6/pebl/taskcontroller/ec2.py", line 11, in <module>

yarikoptic

$> quilt diff
--- a/src/pebl/taskcontroller/ec2ipy1.py
+++ b/src/pebl/taskcontroller/ec2ipy1.py
@@ -2,7 +2,11 @@ import sys, os, time
 import ConfigParser
 from itertools import groupby
 
-import ipython1.kernel.api as kernel
+try:
+    import ipython1.kernel.api as kernel

yarikoptic

$> PATH=/usr/lib/ccache:$PATH make
make  all-am
make[1]: Entering directory `/home/yoh/deb/gits/pkg-exppsy/freesurfer/freeview'
g++ -DHAVE_CONFIG_H -I. -I..  -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4 -I. -I/usr/X11R6/include -I.  -g -O3 -msse2 -mfpmath=sse -Wall  -DUSE_SSE_MATHFUN -m64 -DLinux -DANSI   -pipe -O2 -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -fno-strict-aliasing -Wno-deprecated -Wno-unused -Wno-uninitialized -Wno-return-type -Wno-reorder -Wno-sign-compare -I../include -I/usr/X11R6/include -pthread -I/usr/include/GL -I/usr/include/vtk-5.6 -I../vtkfsio -I../vtkutils -I/usr/include/InsightToolkit -I/usr/include/InsightToolkit/Algorithms -I/usr/include/InsightToolkit/BasicFilters -I/usr/include/InsightToolkit/Common -I/usr/include/InsightToolkit/IO -I/usr/include/InsightToolkit/Numerics -I/us

yarikoptic

while running 

CCACHE_CPP2=1 CCACHE_LOGFILE=/tmp/1.log PATH=/usr/lib/ccache:$PATH make

got

[2011-05-06T14:12:24.132205 2214 ] === CCACHE STARTED =========================================
[2011-05-06T14:12:24.132538 2214 ] Hostname: novo
[2011-05-06T14:12:24.132554 2214 ] Working directory: /home/yoh/deb/gits/pkg-exppsy/freesurfer/freeview
[2011-05-06T14:12:24.132771 2214 ] Source file: moc_LayerPropertyPointSet.cpp

yarikoptic

Features

• compatible with all recent Linux kernels
• no need for kernel rebuilding/patching
• verified (to what degree?) compatibility with Python (what versions?)
• ...

Scientific Python

yarikoptic

#!/usr/bin/python
#emacs: -*- mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*- 
#ex: set sts=4 ts=4 sw=4 noet:

"""The target is to compare Fisher transformation to simply taking std values from rdist
"""

import numpy as np
from scipy.stats import rdist, norm, t

yarikoptic

CPUSERIAL 000069        # CPU serial number
#CPUMODEL  9672          # CPU model number
CPUMODEL  2097          # CPU model number
MAINSIZE  256           # Main storage size in megabytes
XPNDSIZE  0             # Expanded storage size in megabytes
CNSLPORT  3270          # TCP port number to which consoles connect
NUMCPU    2             # Number of CPUs
LOADPARM  0120....      # IPL parameter
OSTAILOR  LINUX         # OS tailoring
PANRATE   SLOW          # Panel refresh rate (SLOW, FAST)