Le 04/07/2017 21:00:23, Florian Weimer a écrit :
> Can you attach the contents of this file? This is very odd.
Here it is.
It’s a symlink to /usr/share/pyshared/io.py.
> ll /usr/lib/python2.7/dist-packages/io.py
lrwxrwxrwx 1 root root 25 avril 26 2011 /usr/lib/python2.7/dist-
packages/io.py -> /usr/share/pyshared/io.py
> ll /usr/share/pyshared/io.py
-rw-r--r-- 1 root root 39506 nov. 27 2007 /usr/share/pyshared/io.py
nicolas patrois : pts noir asocial
--
RÉALISME
M : Qu'est-ce qu'il nous faudrait pour qu'on nous considère comme des
humains ? Un cerveau plus gros ?
P : Non... Une carte bleue suffirait...
# Copyright (c) 2000-2007 Gary Strangman. All rights reserved
#
# Disclaimer
#
# This software is provided "as-is". There are no expressed or implied
# warranties of any kind, including, but not limited to, the warranties
# of merchantability and fittness for a given application. In no event
# shall Gary Strangman be liable for any direct, indirect, incidental,
# special, exemplary or consequential damages (including, but not limited
# to, loss of use, data or profits, or business interruption) however
# caused and on any theory of liability, whether in contract, strict
# liability or tort (including negligence or otherwise) arising in any way
# out of the use of this software, even if advised of the possibility of
# such damage.
#
# Comments and/or additions are welcome (send e-mail to:
# str...@nmr.mgh.harvard.edu).
#
"""
Defines a number of functions for pseudo-command-line OS functionality.
cd(directory)
pwd <-- can be used WITHOUT parens
ls(d='.')
rename(from,to)
get(namepatterns,verbose=1)
getstrings(namepatterns,verbose=1)
put(outlist,filename,writetype='w')
aget(namepatterns,verbose=1)
aput(outarray,filename,writetype='w')
bget(filename,numslices=1,xsize=64,ysize=64)
braw(filename,btype)
bput(outarray,filename,writeheader=0,packstring='h',writetype='wb')
mrget(filename)
find_dirs(sourcedir)
"""
## CHANGES:
## =======
## 07-11-26 ... more numpy conversion work
## 06-08-07 ... converted to numpy, changed version to 0.6
## 06-02-03 ... added add2afnihistory() to load modify afni HISTORY_NOTEs,
## and added that option to array2afni output
## 04-06-14 ... added getafniparam() to load in afni values from HEAD files
## 03-04-09 ... fixed brikget to load based on datatype, changed array2afni
## so that the default sliceorder is altplus, not seqplus
## 02-11-20 ... added binget(), binput(), array2afni(), version 0.5
## 02-10-20 ... added find_dirs() function, changed version to 0.4
## 01-11-15 ... changed aput() and put() to accept a delimiter
## 01-04-19 ... added oneperline option to put() function
## 99-11-07 ... added DAs quick flat-text-file loaders, load() and fload()
## 99-11-01 ... added version number (0.1) for distribution
## 99-08-30 ... Put quickload in here
## 99-06-27 ... Changed bget thing back ... confused ...
## 99-06-24 ... exchanged xsize and ysize in bget for non-square images (NT??)
## modified bget to raise an IOError when file not found
## 99-06-12 ... added load() and save() aliases for aget() and aput() (resp.)
## 99-04-13 ... changed aget() to ignore (!!!!) lines beginning with # or %
## 99-01-17 ... changed get() so ints come in as ints (not floats)
##
try:
import mmapfile
except:
pass
import pstat
import glob, re, string, types, os, struct, copy, time, tempfile, sys
from types import *
import numpy as N
__version__ = 0.6
def wrap(f):
"""
Wraps a function so that if it's entered *by itself*
in the interpreter without ()'s, it gets called anyway
"""
class W:
def __init__(self, f):
self.f = f
def __repr__(self):
x =apply(self.f)
if x:
return repr(x)
else:
return ''
return W(f)
def cd (directory):
"""
Changes the working python directory for the interpreter.
Usage: cd(directory) where 'directory' is a string
"""
os.chdir(directory)
return
def pwd():
"""
Changes the working python directory for the interpreter.
Usage: pwd (no parens needed)
"""
return os.getcwd()
pwd = wrap(pwd)
def ls(d='.'):
"""
Produces a directory listing. Default is the current directory.
Usage: ls(d='.')
"""
os.system('ls '+d)
return None
def rename(source, dest):
"""
Renames files specified by UNIX inpattern to those specified by UNIX
outpattern. Can only handle a single '*' in the two patterns!!!
Usage: rename (source, dest) e.g., rename('*.txt', '*.c')
"""
infiles = glob.glob(source)
outfiles = []
incutindex = string.index(source,'*')
outcutindex = string.index(source,'*')
findpattern1 = source[0:incutindex]
findpattern2 = source[incutindex+1:]
replpattern1 = dest[0:incutindex]
replpattern2 = dest[incutindex+1:]
for fname in infiles:
if incutindex > 0:
newname = re.sub(findpattern1,replpattern1,fname,1)
if outcutindex < len(dest)-1:
if incutindex > 0:
lastone = string.rfind(newname,replpattern2)
newname = newname[0:lastone] + re.sub(findpattern2,replpattern2,fname[lastone:],1)
else:
lastone = string.rfind(fname,findpattern2)
if lastone <> -1:
newname = fname[0:lastone]
newname = newname + re.sub(findpattern2,replpattern2,fname[lastone:],1)
print fname, newname
os.rename(fname,newname)
return
def get (namepatterns,verbose=1):
"""
Loads a list of lists from text files (specified by a UNIX-style
wildcard filename pattern) and converts all numeric values to floats.
Uses the glob module for filename pattern conversion. Loaded filename
is printed if verbose=1.
Usage: get (namepatterns,verbose=1)
Returns: a 1D or 2D list of lists from whitespace delimited text files
specified by namepatterns; numbers that can be converted to floats
are so converted
"""
fnames = []
if type(namepatterns) in [ListType,TupleType]:
for item in namepatterns:
fnames = fnames + glob.glob(item)
else:
fnames = glob.glob(namepatterns)
if len(fnames) == 0:
if verbose:
print 'NO FILENAMES MATCH ('+namepatterns+') !!'
return None
if verbose:
print fnames # so user knows what has been loaded
elements = []
for i in range(len(fnames)):
file = open(fnames[i])
newelements = map(string.split,file.readlines())
for i in range(len(newelements)):
for j in range(len(newelements[i])):
try:
newelements[i][j] = string.atoi(newelements[i][j])
except ValueError:
try:
newelements[i][j] = string.atof(newelements[i][j])
except:
pass
elements = elements + newelements
if len(elements)==1: elements = elements[0]
return elements
def getstrings (namepattern,verbose=1):
"""
Loads a (set of) text file(s), with all elements left as string type.
Uses UNIX-style wildcards (i.e., function uses glob). Loaded filename
is printed if verbose=1.
Usage: getstrings (namepattern, verbose=1)
Returns: a list of strings, one per line in each text file specified by
namepattern
"""
fnames = glob.glob(namepattern)
if len(fnames) == 0:
if verbose:
print 'NO FILENAMES MATCH ('+namepattern+') !!'
return None
if verbose:
print fnames
elements = []
for filename in fnames:
file = open(filename)
newelements = map(string.split,file.readlines())
elements = elements + newelements
return elements
def put (outlist,fname,writetype='w',oneperline=0,delimit=' '):
"""
Writes a passed mixed-type list (str and/or numbers) to an output
file, and then closes the file. Default is overwrite the destination
file.
Usage: put (outlist,fname,writetype='w',oneperline=0,delimit=' ')
Returns: None
"""
if type(outlist) in [N.ndarray]:
aput(outlist,fname,writetype)
return
if type(outlist[0]) not in [ListType,TupleType]: # 1D list
outfile = open(fname,writetype)
if not oneperline:
outlist = pstat.list2string(outlist,delimit)
outfile.write(outlist)
outfile.write('\n')
else: # they want one element from the list on each file line
for item in outlist:
outfile.write(str(item)+'\n')
outfile.close()
else: # 2D list (list-of-lists)
outfile = open(fname,writetype)
for row in outlist:
outfile.write(pstat.list2string(row,delimit))
outfile.write('\n')
outfile.close()
return None
def isstring(x):
if type(x)==StringType:
return 1
else:
return 0
def aget (namepattern,verbose=1):
"""
Loads an array from 2D text files (specified by a UNIX-style wildcard
filename pattern). ONLY 'GET' FILES WITH EQUAL NUMBERS OF COLUMNS
ON EVERY ROW (otherwise returned array will be zero-dimensional).
Usage: aget (namepattern)
Returns: an array of integers, floats or objects (type='O'), depending on the
contents of the files specified by namepattern
"""
fnames = glob.glob(namepattern)
if len(fnames) == 0:
if verbose:
print 'NO FILENAMES MATCH ('+namepattern+') !!'
return None
if verbose:
print fnames
elements = []
for filename in fnames:
file = open(filename)
newelements = file.readlines()
del_list = []
for row in range(len(newelements)):
if (newelements[row][0]=='%' or newelements[row][0]=='#'
or len(newelements[row])==1 or newelements[row][0]=='\r'):
del_list.append(row)
del_list.reverse()
for i in del_list:
newelements.pop(i)
newelements = map(string.split,newelements)
for i in range(len(newelements)):
for j in range(len(newelements[i])):
try:
newelements[i][j] = string.atof(newelements[i][j])
except:
pass
elements = elements + newelements
for row in range(len(elements)):
if N.add.reduce(N.array(map(isstring,elements[row])))==len(elements[row]):
print "A row of strings was found. Returning a LIST."
return elements
try:
elements = N.array(elements)
except TypeError:
elements = N.array(elements,dtype='O')
return elements
def aput (outarray,fname,writetype='w',delimit=' '):
"""
Sends passed 1D or 2D array to an output file and closes the file.
Usage: aput (outarray,fname,writetype='w',delimit=' ')
Returns: None
"""
outfile = open(fname,writetype)
if len(outarray.shape) == 1:
outarray = outarray[N.newaxis,:]
if len(outarray.shape) > 2:
raise TypeError, "put() and aput() require 1D or 2D arrays. Otherwise use some kind of pickling."
else: # must be a 2D array
for row in outarray:
outfile.write(string.join(map(str,row),delimit))
outfile.write('\n')
outfile.close()
return None
def bget(imfile,shp=None,unpackstr=N.int16,bytesperpixel=2.0,sliceinit=0):
"""
Reads in a binary file, typically with a .bshort or .bfloat extension.
If so, the last 3 parameters are set appropriately. If not, the last 3
parameters default to reading .bshort files (2-byte integers in big-endian
binary format).
Usage: bget(imfile,shp=None,unpackstr=N.int16,bytesperpixel=2.0,sliceinit=0)
"""
if imfile[:3] == 'COR':
return CORget(imfile)
if imfile[-2:] == 'MR':
return mrget(imfile,unpackstr)
if imfile[-4:] == 'BRIK':
return brikget(imfile,unpackstr,shp)
if imfile[-3:] in ['mnc','MNC','inc','INC']:
return mincget(imfile,unpackstr,shp)
if imfile[-3:] == 'img':
return mghbget(imfile,unpackstr,shp)
if imfile[-6:] == 'bshort' or imfile[-6:] == 'bfloat':
if shp == None:
return mghbget(imfile,unpackstr=unpackstr,bytesperpixel=bytesperpixel,sliceinit=sliceinit)
else:
return mghbget(imfile,shp[0],shp[1],shp[2],unpackstr,bytesperpixel,sliceinit)
def CORget(infile):
"""
Reads a binary COR-nnn file (flattening file).
Usage: CORget(imfile)
Returns: 2D array of 16-bit ints
"""
d=braw(infile,N.int8)
d.shape = (256,256)
d = N.where(d>=0,d,256+d)
return d
def mincget(imfile,unpackstr=N.int16,shp=None):
"""
Loads in a .MNC file.
Usage: mincget(imfile,unpackstr=N.int16,shp=None) default shp = -1,20,64,64
"""
if shp == None:
shp = (-1,20,64,64)
os.system('mincextract -short -range 0 4095 -image_range 0 4095 ' +
imfile+' > minctemp.bshort')
try:
d = braw('minctemp.bshort',unpackstr)
except:
print "Couldn't find file: "+imfile
raise IOError, "Couldn't find file in mincget()"
print shp, d.shape
d.shape = shp
os.system('rm minctemp.bshort')
return d
def brikget(imfile,unpackstr=N.int16,shp=None):
"""
Gets an AFNI BRIK file.
Usage: brikget(imfile,unpackstr=N.int16,shp=None) default shp: (-1,48,61,51)
"""
if shp == None:
shp = (-1,48,61,51)
try:
file = open(imfile, "rb")
except:
print "Couldn't find file: "+imfile
raise IOError, "Couldn't find file in brikget()"
try:
header = imfile[0:-4]+'HEAD'
lines = open(header).readlines()
for i in range(len(lines)):
if string.find(lines[i],'DATASET_DIMENSIONS') <> -1:
dims = string.split(lines[i+2][0:string.find(lines[i+2],' 0')])
dims = map(string.atoi,dims)
if string.find(lines[i],'BRICK_FLOAT_FACS') <> -1:
count = string.atoi(string.split(lines[i+1])[2])
mults = []
for j in range(int(N.ceil(count/5.))):
mults += map(string.atof,string.split(lines[i+2+j]))
mults = N.array(mults)
if string.find(lines[i],'BRICK_TYPES') <> -1:
first5 = lines[i+2]
first5 = map(string.atoi,string.split(first5))
if first5[0] == 0:
unpackstr = N.uint8
elif first5[0] == 1:
unpackstr = N.int16
elif first5[0] == 3:
unpackstr = N.float32
elif first5[0] == 5:
unpackstr = N.complex32
dims.reverse()
shp = [-1]+dims
except IOError:
print "No header file. Continuing ..."
lines = None
print shp
print 'Using unpackstr:',unpackstr #,', bytesperpixel=',bytesperpixel
file = open(imfile, "rb")
bdata = file.read()
# the > forces big-endian (for or from Sun/SGI)
bdata = N.fromstring(bdata,unpackstr)
# littleEndian = ( struct.pack('i',1)==struct.pack('<i',1) )
if (max(bdata)>1e30):
bdata = bdata.byteswap()
try:
bdata.shape = shp
except:
print 'Incorrect shape ...',shp,len(bdata)
raise ValueError, 'Incorrect shape for file size'
if len(bdata) == 1:
bdata = bdata[0]
if N.sum(mults) == 0:
return bdata
try:
multshape = [1]*len(bdata.shape)
for i in range(len(bdata.shape)):
if len(mults) == bdata.shape[i]:
multshape[i] = len(mults)
break
mults.shape = multshape
return bdata*mults
except:
return bdata
def mghbget(imfile,numslices=-1,xsize=64,ysize=64,
unpackstr=N.int16,bytesperpixel=2.0,sliceinit=0):
"""
Reads in a binary file, typically with a .bshort or .bfloat extension.
If so, the last 3 parameters are set appropriately. If not, the last 3
parameters default to reading .bshort files (2-byte integers in big-endian
binary format).
Usage: mghbget(imfile, numslices=-1, xsize=64, ysize=64,
unpackstr=N.int16, bytesperpixel=2.0, sliceinit=0)
"""
try:
file = open(imfile, "rb")
except:
print "Couldn't find file: "+imfile
raise IOError, "Couldn't find file in bget()"
try:
header = imfile[0:-6]+'hdr'
vals = get(header,0) # '0' means no missing-file warning msg
if type(vals[0]) == ListType: # it's an extended header
xsize = int(vals[0][0])
ysize = int(vals[0][1])
numslices = int(vals[0][2])
else:
xsize = int(vals[0])
ysize = int(vals[1])
numslices = int(vals[2])
except:
print "No header file. Continuing ..."
suffix = imfile[-6:]
if suffix == 'bshort':
pass
elif suffix[-3:] == 'img':
pass
elif suffix == 'bfloat':
unpackstr = N.float32
bytesperpixel = 4.0
sliceinit = 0.0
else:
print 'Not a bshort, bfloat or img file.'
print 'Using unpackstr:',unpackstr,', bytesperpixel=',bytesperpixel
imsize = xsize*ysize
file = open(imfile, "rb")
bdata = file.read()
numpixels = len(bdata) / bytesperpixel
if numpixels%1 != 0:
raise ValueError, "Incorrect file size in fmri.bget()"
else: # the > forces big-endian (for or from Sun/SGI)
bdata = N.fromstring(bdata,unpackstr)
# littleEndian = ( struct.pack('i',1)==struct.pack('<i',1) )
# if littleEndian:
# bdata = bdata.byteswap()
if (max(bdata)>1e30):
bdata = bdata.byteswap()
if suffix[-3:] == 'img':
if numslices == -1:
numslices = len(bdata)/8200 # 8200=(64*64*2)+8 bytes per image
xsize = 64
ysize = 128
slices = N.zeros((numslices,xsize,ysize),N.int32)
for i in range(numslices):
istart = i*8 + i*xsize*ysize
iend = i*8 + (i+1)*xsize*ysize
print i, istart,iend
slices[i] = N.reshape(N.array(bdata[istart:iend]),(xsize,ysize))
else:
if numslices == 1:
slices = N.reshape(N.array(bdata),[xsize,ysize])
else:
slices = N.reshape(N.array(bdata),[numslices,xsize,ysize])
if len(slices) == 1:
slices = slices[0]
return slices
def braw(fname,btype,shp=None):
"""
Opens a binary file, unpacks it, and returns a flat array of the
type specified. Use Numeric types ... N.float32, N.int64, etc.
Usage: braw(fname,btype,shp=None)
Returns: flat array of floats, or ints (if btype=N.int16)
"""
file = open(fname,'rb')
bdata = file.read()
bdata = N.fromstring(bdata,btype)
# littleEndian = ( struct.pack('i',1)==struct.pack('<i',1) )
# if littleEndian:
# bdata = bdata.byteswap() # didn't used to need this with '>' above
if (max(bdata)>1e30):
bdata = bdata.byteswap()
if shp:
try:
bdata.shape = shp
return bdata
except:
pass
return N.array(bdata)
def glget(fname,btype):
"""
Load in a file containing pixels from glReadPixels dump.
Usage: glget(fname,btype)
Returns: array of 'btype elements with shape 'shape', suitable for im.ashow()
"""
d = braw(fname,btype)
d = d[8:]
f = open(fname,'rb')
shp = f.read(8)
f.close()
shp = N.fromstring(shp,N.int32)
shp[0],shp[1] = shp[1],shp[0]
try:
carray = N.reshape(d,shp)
return
except:
pass
try:
r = d[0::3]+0
g = d[1::3]+0
b = d[2::3]+0
r.shape = shp
g.shape = shp
b.shape = shp
carray = N.array([r,g,b])
except:
outstr = "glget: shape not correct for data of length "+str(len(d))
raise ValueError, outstr
return carray
def mget(fname,btype):
"""
Load in a file that was saved from matlab
Usage: mget(fname,btype)
"""
d = braw(fname,btype)
try:
header = fname[0:-6]+'hdr'
vals = get(header,0) # '0' means no missing-file warning msg
if type(vals[0]) == ListType: # it's an extended header
xsize = int(vals[0][0])
ysize = int(vals[0][1])
numslices = int(vals[0][2])
else:
xsize = int(vals[0])
ysize = int(vals[1])
numslices = int(vals[2])
print xsize,ysize,numslices, d.shape
except:
print "No header file. Continuing ..."
if numslices == 1:
d.shape = [ysize,xsize]
return N.transpose(d)*1
else:
d.shape = [numslices,ysize,xsize]
return N.transpose(d)*1
def mput(outarray,fname,writeheader=0,btype=N.int16):
"""
Save a file for use in matlab.
"""
outarray = N.transpose(outarray)
outdata = N.ravel(outarray).astype(btype)
outdata = outdata.tostring()
outfile = open(fname,'wb')
outfile.write(outdata)
outfile.close()
if writeheader == 1:
try:
suffixindex = string.rfind(fname,'.')
hdrname = fname[0:suffixindex]
except ValueError:
hdrname = fname
if len(outarray.shape) == 2:
hdr = [outarray.shape[1],outarray.shape[0], 1, 0]
else:
hdr = [outarray.shape[2],outarray.shape[1],outarray.shape[0], 0,'\n']
print hdrname+'.hdr'
outfile = open(hdrname+'.hdr','w')
outfile.write(pstat.list2string(hdr))
outfile.close()
return None
def bput(outarray,fname,writeheader=0,packtype=N.int16,writetype='wb'):
"""
Writes the passed array to a binary output file, and then closes
the file. Default is overwrite the destination file.
Usage: bput (outarray,filename,writeheader=0,packtype=N.int16,writetype='wb')
"""
suffix = fname[-6:]
if suffix == 'bshort':
packtype = N.int16
elif suffix == 'bfloat':
packtype = N.float32
else:
print 'Not a bshort or bfloat file. Using packtype=',packtype
outdata = N.ravel(outarray).astype(packtype)
# littleEndian = ( struct.pack('i',1)==struct.pack('<i',1) )
# if littleEndian:
# outdata = outdata.byteswap()
outdata = outdata.tostring()
outfile = open(fname,writetype)
outfile.write(outdata)
outfile.close()
if writeheader == 1:
try:
suffixindex = string.rfind(fname,'.')
hdrname = fname[0:suffixindex]
except ValueError:
hdrname = fname
if len(outarray.shape) == 2:
hdr = [outarray.shape[0],outarray.shape[1], 1, 0]
else:
hdr = [outarray.shape[1],outarray.shape[2],outarray.shape[0], 0,'\n']
print hdrname+'.hdr'
outfile = open(hdrname+'.hdr','w')
outfile.write(pstat.list2string(hdr))
outfile.close()
return None
def mrget(fname,datatype=N.int16):
"""
Opens a binary .MR file and clips off the tail data portion of it, returning
the result as an array.
Usage: mrget(fname,datatype=N.int16)
"""
d = braw(fname,datatype)
if len(d) > 512*512:
return N.reshape(d[-512*512:],(512,512))
elif len(d) > 320*320:
return N.reshape(d[-320*320:],(320,320))
elif len(d) > 256*256:
return N.reshape(d[-256*256:],(256,256))
elif len(d) > 128*128:
return N.reshape(d[-128*128:],(128,128))
elif len(d) > 64*64:
return N.reshape(d[-64*64:],(64,64))
else:
return N.reshape(d[-32*32:],(32,32))
def quickload(fname,linestocut=4):
"""
Quickly loads in a long text file, chopping off first n 'linestocut'.
Usage: quickload(fname,linestocut=4)
Returns: array filled with data in fname
"""
f = open(fname,'r')
d = f.readlines()
f.close()
print fname,'read in.'
d = d[linestocut:]
d = map(string.split,d)
print 'Done with string.split on lines.'
for i in range(len(d)):
d[i] = map(string.atoi,d[i])
print 'Conversion to ints done.'
return N.array(d)
def writedelimited (listoflists, delimiter, file, writetype='w'):
"""
Writes a list of lists in columns, separated by character(s) delimiter
to specified file. File-overwrite is the default.
Usage: writedelimited (listoflists,delimiter,filename,writetype='w')
Returns: None
"""
if type(listoflists[0]) not in [ListType,TupleType]:
listoflists = [listoflists]
outfile = open(file,writetype)
rowstokill = []
list2print = copy.deepcopy(listoflists)
for i in range(len(listoflists)):
if listoflists[i] == ['\n'] or listoflists[i]=='\n' or listoflists[i]=='dashes':
rowstokill = rowstokill + [i]
rowstokill.reverse()
for row in rowstokill:
del list2print[row]
maxsize = [0]*len(list2print[0])
for row in listoflists:
if row == ['\n'] or row == '\n':
outfile.write('\n')
elif row == ['dashes'] or row == 'dashes':
dashes = [0]*len(maxsize)
for j in range(len(maxsize)):
dashes[j] = '------'
outfile.write(pstat.linedelimited(dashes,delimiter))
else:
outfile.write(pstat.linedelimited(row,delimiter))
outfile.write('\n')
outfile.close()
return None
def writecc (listoflists,file,writetype='w',extra=2):
"""
Writes a list of lists to a file in columns, customized by the max
size of items within the columns (max size of items in col, +2 characters)
to specified file. File-overwrite is the default.
Usage: writecc (listoflists,file,writetype='w',extra=2)
Returns: None
"""
if type(listoflists[0]) not in [ListType,TupleType]:
listoflists = [listoflists]
outfile = open(file,writetype)
rowstokill = []
list2print = copy.deepcopy(listoflists)
for i in range(len(listoflists)):
if listoflists[i] == ['\n'] or listoflists[i]=='\n' or listoflists[i]=='dashes':
rowstokill = rowstokill + [i]
rowstokill.reverse()
for row in rowstokill:
del list2print[row]
maxsize = [0]*len(list2print[0])
for col in range(len(list2print[0])):
items = pstat.colex(list2print,col)
items = map(pstat.makestr,items)
maxsize[col] = max(map(len,items)) + extra
for row in listoflists:
if row == ['\n'] or row == '\n':
outfile.write('\n')
elif row == ['dashes'] or row == 'dashes':
dashes = [0]*len(maxsize)
for j in range(len(maxsize)):
dashes[j] = '-'*(maxsize[j]-2)
outfile.write(pstat.lineincustcols(dashes,maxsize))
else:
outfile.write(pstat.lineincustcols(row,maxsize))
outfile.write('\n')
outfile.close()
return None
def writefc (listoflists,colsize,file,writetype='w'):
"""
Writes a list of lists to a file in columns of fixed size. File-overwrite
is the default.
Usage: writefc (listoflists,colsize,file,writetype='w')
Returns: None
"""
if type(listoflists) == N.ndarray:
listoflists = listoflists.tolist()
if type(listoflists[0]) not in [ListType,TupleType]:
listoflists = [listoflists]
outfile = open(file,writetype)
rowstokill = []
list2print = copy.deepcopy(listoflists)
for i in range(len(listoflists)):
if listoflists[i] == ['\n'] or listoflists[i]=='\n' or listoflists[i]=='dashes':
rowstokill = rowstokill + [i]
rowstokill.reverse()
for row in rowstokill:
del list2print[row]
n = [0]*len(list2print[0])
for row in listoflists:
if row == ['\n'] or row == '\n':
outfile.write('\n')
elif row == ['dashes'] or row == 'dashes':
dashes = [0]*colsize
for j in range(len(n)):
dashes[j] = '-'*(colsize)
outfile.write(pstat.lineincols(dashes,colsize))
else:
outfile.write(pstat.lineincols(row,colsize))
outfile.write('\n')
outfile.close()
return None
def load(fname,lines_to_ignore=4,type='i'):
"""
Load in huge, flat, 2D text files. Can handle differing line-lengths AND
can strip #/% on UNIX (or with a better NT grep). Requires wc, grep, and
mmapfile.lib/.pyd. Type can be 'i', 'f' or 'd', for ints, floats or doubles,
respectively. Lines_to_ignore determines how many lines at the start of the
file to ignore (required for non-working grep).
Usage: load(fname,lines_to_ignore=4,type='i')
Returns: numpy array of specified type
"""
start = time.time() ## START TIMER
if type == 'i':
intype = int
elif type in ['f','d']:
intype = float
else:
raise ValueError, "type can be 'i', 'f' or 'd' in load()"
## STRIP OUT % AND # LINES
tmpname = tempfile.mktemp()
if sys.platform == 'win32':
# NT VERSION OF GREP DOESN'T DO THE STRIPPING ... SIGH
cmd = "grep.exe -v \'%\' "+fname+" > "+tmpname
print cmd
os.system(cmd)
else:
# UNIX SIDE SHOULD WORK
cmd = "cat "+fname+" | grep -v \'%\' |grep -v \'#\' > "+tmpname
print cmd
os.system(cmd)
## GET NUMBER OF ROWS, COLUMNS AND LINE-LENGTH, USING WC
wc = string.split(os.popen("wc "+tmpname).read())
numlines = int(wc[0]) - lines_to_ignore
tfp = open(tmpname)
if lines_to_ignore <> 0:
for i in range(lines_to_ignore):
junk = tfp.readline()
numcols = len(string.split(tfp.readline())) #int(float(wc[1])/numlines)
tfp.close()
## PREPARE INPUT SPACE
a = N.zeros((numlines*numcols), type)
block = 65536 # chunk to read, in bytes
data = mmapfile.mmapfile(tmpname, '', 0)
if lines_to_ignore <> 0 and sys.platform == 'win32':
for i in range(lines_to_ignore):
junk = data.readline()
i = 0
d = ' '
carryover = ''
while len(d) <> 0:
d = carryover + data.read(block)
cutindex = string.rfind(d,'\n')
carryover = d[cutindex+1:]
d = d[:cutindex+1]
d = map(intype,string.split(d))
a[i:i+len(d)] = d
i = i + len(d)
end = time.time()
print "%d sec" % round(end-start,2)
data.close()
os.remove(tmpname)
return N.reshape(a,[numlines,numcols])
def find_dirs(sourcedir):
"""Finds and returns all directories in sourcedir
Usage: find_dirs(sourcedir)
Returns: list of directory names (potentially empty)
"""
files = os.listdir(sourcedir)
dirs = []
for fname in files:
if os.path.isdir(os.path.join(sourcedir,fname)):
dirs.append(fname)
return dirs
# ALIASES ...
save = aput
def binget(fname,btype=None):
"""
Loads a binary file from disk. Assumes associated hdr file is in same
location. You can force an unpacking type, or else it tries to figure
it out from the filename (4th-to-last character). Hence, readable file
formats are ...
1bin=int8, sbin=int16, ibin=int32, fbin=float32, dbin=float64, etc.
Usage: binget(fname,btype=None)
Returns: data in file fname of type btype
"""
file = open(fname,'rb')
bdata = file.read()
file.close()
# if none given, assume character preceeding 'bin' is the unpacktype
if not btype:
btype = fname[-4]
try:
bdata = N.fromstring(bdata,btype)
except:
raise ValueError, "Bad unpacking type."
# force the data on disk to be LittleEndian (for more efficient PC/Linux use)
if not N.little_endian:
bdata = bdata.byteswap()
try:
header = fname[:-3]+'hdr'
vals = get(header,0) # '0' means no missing-file warning msg
print vals
if type(vals[0]) == ListType: # it's an extended header
xsize = int(vals[0][0])
ysize = int(vals[0][1])
numslices = int(vals[0][2])
else:
bdata.shape = vals
except:
print "No (or bad) header file. Returning unshaped array."
return N.array(bdata)
def binput(outarray,fname,packtype=None,writetype='wb'):
"""
Unravels outarray and writes the data to a file, always in LittleEndian
format, along with a header file containing the original data shape. Default
is overwrite the destination file. Tries to figure out packtype from
4th-to-last character in filename. Thus, the routine understands these
file formats ...
1bin=int8, sbin=int16, ibin=int32, fbin=float32, dbin=float64, etc.
Usage: binput(outarray,filename,packtype=None,writetype='wb')
"""
if not packtype:
packtype = fname[-4]
# a speck of error checking
if packtype == N.int16 and outarray.dtype.char == 'f':
# check to see if there's data loss
if max(N.ravel(outarray)) > 32767 or min(N.ravel(outarray))<-32768:
print "*** WARNING: CONVERTING FLOAT DATA TO OUT-OF RANGE INT16 DATA"
outdata = N.ravel(outarray).astype(packtype)
# force the data on disk to be little_endian (for more efficient PC/Linux use)
if not N.little_endian:
outdata = outdata.byteswap()
outdata = outdata.tostring()
outfile = open(fname,writetype)
outfile.write(outdata)
outfile.close()
# Now, write the header file
try:
suffixindex = string.rfind(fname,'.')
hdrname = fname[0:suffixindex+2]+'hdr' # include .s or .f or .1 or whatever
except ValueError:
hdrname = fname
hdr = outarray.shape
print hdrname
outfile = open(hdrname,'w')
outfile.write(pstat.list2string(hdr))
outfile.close()
return None
def getafniparam(headfilename,paramname):
"""
Loads in an AFNI header file, and returns the values of 'paramname'.
Usage: getafniparam(headfile,paramname)
Returns: appropriate "type" for params, or None if fails
"""
if headfilename[-4:] == 'BRIK': # if asked for BRIK, change it to HEAD
headfilename = headfilename[:-4]+'HEAD'
d = get(headfilename)
lines = open(headfilename,'r').readlines()
for i in range(len(lines)):
if string.find(lines[i],paramname) <> -1:
count = d[i+1][-1]
gotten = 0
result = []
for j in range(i+2,len(lines)):
for k in range(len(d[j])):
if type(d[j][k]) == StringType:
result = d[j][k][1:count]
return result
else:
result.append(d[j][k])
gotten += 1
if gotten == count:
break
return result
return None
def add2afnihistory(headfilename,newtext):
"""
Adds 'newtext' to HISTORY_NOTE in afni file specified in headfilename.
Usage: add2afnihistory(headfile,newtext)
Returns: None
"""
if headfilename[-4:] == 'BRIK': # if asked for BRIK, change it to HEAD
headfilename = headfilename[:-4]+'HEAD'
d = get(headfilename)
lines = open(headfilename,'r').readlines()
for i in range(len(lines)):
if string.find(lines[i],'HISTORY_NOTE') <> -1:
bytecount = d[i+1][-1]
oldstr = lines[i+2][:-2]
date = '[python:*** %s] ' %time.asctime()
lines[i+2] = oldstr +'\\n' +date +newtext +'~\n'
lines[i+1] = ' count = %s\n' %str(len(lines[i+2]))
f = open(headfilename,'w')
f.writelines(lines)
f.close()
return
def array2afni(d,brikprefix,voltype=None,TR=2000,sliceorder='seqplus',geomparent=None,view=None,corrlength=1,briklabels=None,historytext=None):
"""
Converts an array 'd' to an AFNI BRIK/HEAD combo via putbin and to3d. Tries to
guess the AFNI volume type
voltype = {'-anat','-epan','-fim'}
geomparent = filename of the afni BRIK file with the same geometry
view = {'tlrc', 'acpc' or 'orig'}
corrlength = # of images used in the (single-timeseries) correlation (for fico)
briklabels = list of names (strings) to use for brick labels
historytext = string to be appended to the history file, if any
Usage: array2afni(d,brikprefix,voltype=None,TR=2000,
sliceorder='seqplus',geomparent=None,view=None,
corrlength=1,briklabels=None,historytext=None)
Returns: None
"""
# converts numpy typecode()s into appropriate strings for to3d command line
typecodemapping = {'c':'b', # character
'B':'b', # UnsignedInt8
'f':'f', # float0, float8, float16, float32
'd':'f', # float64
'b':'b', # int0, int8
'h':'', # int16
'i':'i', # int32
'l':'i'} # int
# Verify that the data is proper size (3- or 4-D)
if len(d.shape) not in [3,4]:
raise ValueError, "A 3D or 4D array is required for array2afni() ... %s" %d.shape
# Save out the array to a binary file, homebrew style
if d.dtype.char == N.float64:
outcode = 'f'
else:
outcode = d.dtype.char
tmpoutname = 'afnitmp.%sbin' % outcode
binput(d.astype(outcode),tmpoutname)
if not voltype:
if len(d.shape) == 3: # either anatomy or functional
if d.dtype.char in ['s','i','l']: # if floats, assume functional
voltype = '-anat'
else:
voltype = '-fim'
else: # 4D dataset, must be anatomical timeseries (epan)
voltype = '-anat'
if voltype[0] != '-':
voltype = '-'+voltype
if len(d.shape) == 3: # either anatomy or functional
timepts = 1
slices = d.shape[0]
timestr = ''
elif len(d.shape) == 4:
if voltype=='-fico':
timepts = 1
d = N.reshape(d,[d.shape[0]*d.shape[1],d.shape[2],d.shape[3]])
slices = d.shape[0]
timestr = '-statpar %s 1 1 ' % corrlength
else:
timepts = d.shape[0]
slices = d.shape[1]
timestr = '-time:zt %d %d %0.3f %s ' % (slices,timepts,TR,sliceorder)
cmd = 'to3d %s -prefix %s -session . ' % (voltype, brikprefix)
if not view:
view = 'orig'
cmd += '-view %s ' % view
if geomparent:
cmd += '-geomparent %s ' % geomparent
cmd += timestr
cmd += '3D%s:0:0:%d:%d:%d:%s' % (typecodemapping[d.dtype.char],d.shape[-1],d.shape[-2],slices*timepts,tmpoutname)
print cmd
os.system(cmd)
os.remove(tmpoutname)
os.remove(tmpoutname[:-3]+'hdr')
if len(d.shape)==4 and briklabels:
names = ''
for label in briklabels:
names += str(label)+'~'
count = len(names)
appendstr = """\n\ntype = string-attribute
name = BRICK_LABS
count = %s
'%s""" % (count, names)
f = open('%s+%s.HEAD' %(brikprefix,view), 'a')
f.write(appendstr)
f.close()
if historytext:
add2afnihistory('%s+%s.HEAD'%(brikprefix,view),historytext)
