# -*- coding: utf-8 -*-
from __future__ import absolute_import
import calendar
import datetime as dt
import locale
import os
import shutil
import re
from six.moves import range
def moveSpmOutFiles(inDir, outPath, spmPrefixes=['w'], outDir=None, ext='.nii'):
if not isinstance(spmPrefixes, list):
raise TypeError('a list is required for spmPrefixes')
else:
for i in range(0, len(spmPrefixes)):
if(spmPrefixes[i].startswith("""'""")):
spmPrefixes[i] = spmPrefixes[i][1:-1]
for root, _dirs, filenames in os.walk(inDir):
for f in filenames:
goodPrefix = False
for spmPrefix in spmPrefixes:
if(f.startswith(spmPrefix)):
goodPrefix = True
break
goodExtension = f.endswith(ext) or f.endswith('.txt')
if (goodPrefix and goodExtension):
if(outPath is not None):
movePath(root + '/' + f, outPath)
else:
movePath(root + '/' + f, outDir + '/' + f)
def movePathToDiskItem(srcPath, dstDI):
if(dstDI is not None):
return movePath(srcPath, dstDI.fullPath())
def movePath(srcPath, dstPath):
if (os.path.exists(srcPath)):
if(os.path.exists(dstPath)):
os.remove(dstPath)
# do not use directly os.rename (but remove before)
# because : on windows, rename with dstPath already
# exists causes exception
shutil.move(srcPath, dstPath)
# shutil.move is better than os.rename, because os.rename
# failed if src and dst are not on the same filesystem
if (os.path.exists(srcPath)):
os.remove(srcPath)
[docs]def merge_mat_files(mergedMatFile, *matFiles):
"""
Create a .m file from a set of .m files
:param string mergedMatFile
The .m file containing the merge result
:param set *matFiles
The .m files to merge
:returns:
True if the merge succeeds and False otherwise
"""
mergedMatFileFo = open(mergedMatFile, 'w')
moduleNum = 1
for f in matFiles:
currentNum = None
previousNum = None
for l in open(f, 'r'):
if not l.strip():
continue
try:
currentNum = re.match(
r"matlabbatch\{([0-9]*)\}(.*)", l).group(1)
except Exception:
pass
if previousNum and currentNum != previousNum:
moduleNum += 1
previousNum = currentNum
try:
mergedMatFileFo.write(
re.sub(r"matlabbatch{([0-9]*)}", "matlabbatch{" + str(moduleNum) + "}", l))
except Exception:
return False
moduleNum += 1
mergedMatFileFo.close()
return True
def spm_today():
now = dt.datetime.now()
currentLocale = locale.getlocale(locale.LC_TIME)
# locale.setlocale(locale.LC_TIME, ("en","us"))# mika : doesn't works for
# me
locale.setlocale(locale.LC_TIME, ('en_US', 'UTF8'))
month_name = calendar.month_name[now.month]
locale.setlocale(locale.LC_TIME, currentLocale)
month = month_name[:3]
mth = month[0].upper() + month[1:]
mth = mth.replace('é', 'e')
mth = mth.replace('û', 'u')
spm_today = str(now.day)
if (now.day < 10):
spm_today = '0' + str(now.day)
d = str(now.year) + mth + spm_today
return d
def removeNan(filePath):
fileMinfPath = filePath + '.minf'
if(os.path.exists(fileMinfPath)):
os.remove(fileMinfPath)
AimsRemoveNaNCmd = 'AimsRemoveNaN' + ' -i "' + \
str(filePath) + '" -o "' + str(filePath) + '.noNan.nii"'
os.system(AimsRemoveNaNCmd)
os.remove(filePath)
os.rename(filePath + '.noNan.nii', filePath)
os.rename(filePath + '.noNan.nii.minf', filePath + '.minf')
#------------------------------------------------------------------------------
#
# Write smooth batch for one image to smooth
#
def writeSmoothMatFile(context, data, matfileDI, mat_file,
fwhm="""[8 8 8]""",
dtype="""0""",
im="""0""",
prefix="""spmSmooth_"""
):
mat_file.write("""
matlabbatch{1}.spm.spatial.smooth.data = {'%s,1'};
matlabbatch{1}.spm.spatial.smooth.fwhm = %s;
matlabbatch{1}.spm.spatial.smooth.dtype = %s;
matlabbatch{1}.spm.spatial.smooth.im = %s;
matlabbatch{1}.spm.spatial.smooth.prefix = '%s';
""" % (data
, fwhm, dtype, im, prefix)
)
mat_file.close()
return mat_file.name
# def initializeSmooth_withSPM8DefaultValues(process):
# process.fwhm = """[12 12 12]"""
# process.dtype = """0"""
# process.im = """0"""
# process.prefix = """spmSmooth_12"""
#
# Write smooth batch for a list of images to smooth
#
# def writeSmoothListMatFile(context, images, matfileDI, mat_file
# , fwhm="""[8 8 8]"""
# , dtype="""0"""
# , im="""0"""
# , prefix="""'spmSmooth8_'"""
# ):
#
# images_to_smooth = ""
# for img in images:
# images_to_smooth = images_to_smooth + " '" + img.fullPath() + ",1'"
#
# mat_file.write("""
# matlabbatch{1}.spm.spatial.smooth.data = { %s };
# matlabbatch{1}.spm.spatial.smooth.fwhm = %s;
# matlabbatch{1}.spm.spatial.smooth.dtype = %s;
# matlabbatch{1}.spm.spatial.smooth.im = %s;
# matlabbatch{1}.spm.spatial.smooth.prefix = '%s';
# """ % (images_to_smooth, fwhm, dtype, im, prefix)
# )
# mat_file.close()
# return mat_file.name
#
#------------------------------------------------------------------------------
#
# SPM 8 imcalc batch creation
#
# def writeImageCalculatorMatFile(context, subjectsPathList, matfileDI, mat_file
# , output_filename
# , output_dir
# , expression
# , dmtx="""0"""
# , mask="""0"""
# , interp="""1"""
# , dtype="""4"""
# ):
# scans = convertPathList(subjectsPathList)
# mat_file.write("""matlabbatch{1}.spm.util.imcalc.input = {%s
# };
#
# matlabbatch{1}.spm.util.imcalc.output = %s
# matlabbatch{1}.spm.util.imcalc.outdir = %s;
# matlabbatch{1}.spm.util.imcalc.expression = %s;
# matlabbatch{1}.spm.util.imcalc.options.dmtx = %s;
# matlabbatch{1}.spm.util.imcalc.options.mask = %s;
# matlabbatch{1}.spm.util.imcalc.options.interp = %s;
# matlabbatch{1}.spm.util.imcalc.options.dtype = %s;
#""" % (scans
#, output_filename, output_dir, expression, dmtx, mask, interp, dtype)
# )
# mat_file.close()
# return mat_file.name
