def __run(prog, args, inp, out, verb, exe, postproc=None):
prog = prog.strip()
if args == None:
args = ''
else:
args = args.strip()
cmd = os.path.join(rsf.prog.RSFROOT, 'bin', prog)
if exe == 'g': # get output
assert out == None
out_str = ivlad.getout(prog, args, inp, verb)
if postproc == None:
return out_str
else:
return postproc(out_str)
elif exe == 'p': # call part of a pipe
if args != '':
cmd += ' ' + args
return cmd
else:
if inp != None:
cmd += ' <' + inp.strip()
if out != None:
cmd += ' >' + out.strip()
if args != '':
cmd += ' ' + args
if exe == 'l': # log
return cmd
else: # exe=='x', execute
ivlad.exe(cmd, verb)
def main(par):
f1 = sys.argv[1] + ' '
f2 = sys.argv[2]
f1_type = ivlad.getout('sfgettype', stdin=f1)
if f1_type != 'SF_FLOAT':
raise m8rex.TypeHandlingNotImplemented(f1_type)
dims_str = ivlad.getout('sffiledims', 'parform=n', f1)
ndims = int(dims_str.split(':')[0])
cmd = 'sfspike mag=0 '
fields = 'n o d unit label'.split()
for i in range(ndims):
for z in fields:
cmd += ivlad.getout('sfget', ['parform=y', z + str(i + 1)],
f1) + ' '
cmd += ' >' + f2
ivlad.exe(cmd)
return ivlad.unix_success
def __run(prog, args, inp, out, verb, exe, postproc=None):
prog = prog.strip()
if args == None:
args = ''
else:
args = args.strip()
cmd = os.path.join(rsf.prog.RSFROOT,'bin',prog)
if exe == 'g': # get output
assert out == None
out_str = ivlad.getout(prog, args, inp, verb)
if postproc == None:
return out_str
else:
return postproc(out_str)
elif exe == 'p': # call part of a pipe
if args != '':
cmd += ' ' + args
return cmd
else:
if inp != None:
cmd += ' <' + inp.strip()
if out != None:
cmd += ' >' + out.strip()
if args != '':
cmd += ' ' + args
if exe == 'l': # log
return cmd
else: # exe=='x', execute
ivlad.exe(cmd, verb)
def download_imgs(imgs_to_download, wikiroot, imgdir):
for imgfile in sorted(imgs_to_download.keys()):
ivlad.msg('Downloading: ' + imgfile)
img_url = wikiroot + img_dir_basename + '/' + \
imgs_to_download[imgfile] + '/' + imgfile
img_file = os.path.join(imgdir, imgfile)
ivlad.exe('curl ' + img_url + '>' + img_file)
def download_imgs(imgs_to_download, wikiroot, imgdir):
for imgfile in sorted(imgs_to_download.keys()):
ivlad.msg('Downloading: ' + imgfile)
img_url = wikiroot + img_dir_basename + '/' + \
imgs_to_download[imgfile] + '/' + imgfile
img_file = os.path.join(imgdir,imgfile)
ivlad.exe('curl ' + img_url + '>' + img_file)
def main(par):
verb = par.bool('verb', False)
dryrun = par.bool('dryrun', False)
# sfbyte arguments:
bytepars = {}
for key in ['gainpanel', 'pclip', 'clip']:
bytepars[key] = par.string(key, None)
# sfgrey3 arguments:
color = par.string('color', None)
lbl = int(100000000 * random.random())
suffix = '.' + str(lbl) + ivlad.ext
prefix = sys.argv[0].rstrip('.py') + '.'
tmp_filenm = prefix + 'inp' + suffix
bar_filenm = prefix + 'bar' + suffix
# Redirect the input
if not dryrun:
tmp_file = open(tmp_filenm, 'w')
tmp_file.write(sys.stdin.read())
tmp_file.close()
sf._set_xmode('l')
cmd_list = [
'# Redirect input to ' + tmp_filenm,
sf.bar(tmp_filenm, bar_filenm)
]
ivlad.exe(cmd_list, verb, dryrun)
if dryrun:
cmd = '<' + tmp_filenm + ' sfbyte | sfgrey3 scalebar=y bar='
cmd += bar_filenm + ' >stdout'
ivlad.msg(cmd, verb)
else:
p1 = subprocess.Popen(['sfbyte'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
tmp_file = open(tmp_filenm, 'r')
p1.stdin.write(tmp_file.read())
p2 = subprocess.Popen(['sfgrey3', 'scalebar=y', 'bar=' + bar_filenm],
stdin=p1.stdout,
stdout=subprocess.PIPE)
sys.stdout.write(p2.stdout.read())
p1.stdin.close()
tmp_file.close()
p2.stdout.close()
cmd = sf.rm([tmp_filenm, bar_filenm])
ivlad.exe(cmd, verb, dryrun)
return ivlad.unix_success
def main(par):
verb = par.bool('verb' , False)
dryrun = par.bool('dryrun', False)
# sfbyte arguments:
bytepars = {}
for key in ['gainpanel', 'pclip', 'clip']:
bytepars[key] = par.string(key, None)
# sfgrey3 arguments:
color = par.string('color', None)
lbl = int(100000000*random.random())
suffix = '.' + str(lbl) + ivlad.ext
prefix = sys.argv[0].rstrip('.py') + '.'
tmp_filenm = prefix + 'inp' + suffix
bar_filenm = prefix + 'bar' + suffix
# Redirect the input
if not dryrun:
tmp_file = open(tmp_filenm, 'w')
tmp_file.write(sys.stdin.read())
tmp_file.close()
sf._set_xmode('l')
cmd_list = ['# Redirect input to ' + tmp_filenm,
sf.bar(tmp_filenm, bar_filenm)]
ivlad.exe(cmd_list, verb, dryrun)
if dryrun:
cmd = '<' + tmp_filenm + ' sfbyte | sfgrey3 scalebar=y bar='
cmd+= bar_filenm + ' >stdout'
ivlad.msg(cmd, verb)
else:
p1 = subprocess.Popen(['sfbyte'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
tmp_file = open(tmp_filenm, 'r')
p1.stdin.write(tmp_file.read())
p2 = subprocess.Popen(['sfgrey3', 'scalebar=y', 'bar='+bar_filenm],
stdin=p1.stdout,
stdout=subprocess.PIPE)
sys.stdout.write(p2.stdout.read())
p1.stdin.close()
tmp_file.close()
p2.stdout.close()
cmd = sf.rm([tmp_filenm, bar_filenm])
ivlad.exe(cmd, verb, dryrun)
return ivlad.unix_success
def main(par):
verb = par.bool('verb', False)
inp = par.string('inp') # ifile.rsf
out_basenm = os.path.basename(inp).rstrip(ivlad.ext) + '_split'
outdir = par.string('outdir',
(out_basenm + ivlad.ext)) # Default is ifile_split.rsf
nthick = par.int('nthick', 1) # slice thickness
ivlad.chk_param_limit(nthick, 'nthick', 1, '>')
lastdim = str(ivlad.ndims(inp))
n = int(ivlad.getout('sfget', ['parform=n', 'n' + lastdim], inp))
ivlad.chk_param_limit(nthick, 'nthick', n, '<')
if not os.path.isdir(outdir):
os.mkdir(outdir)
# Slices will be called 01.rsf, etc. Avoid datapath aliasing:
dpath = 'datapath=$DATAPATH/' + out_basenm + '_'
nslices_whole = int(math.floor(n / nthick))
f = 0
for i in range(nslices_whole):
i_str = ivlad.add_zeros(i, nslices_whole)
i_slc = os.path.join(outdir, i_str + '_stdout' + ivlad.ext)
cmd = '<%s sfwindow f%s=%d ' % (inp, lastdim, f)
cmd += 'n%s=%d %s > %s' % (lastdim, nthick, dpath, i_slc)
ivlad.exe(cmd, verb)
f += nthick
ist = n - nslices_whole * nthick # Incomplete Slice Thickness
if ist > 0:
i_str = ivlad.add_zeros(i + 1, nslices_whole)
i_slc = os.path.join(outdir, i_str + '_stdout' + ivlad.ext)
cmd = '<%s sfwindow f%s=%d ' % (inp, lastdim, f)
cmd += 'n%s=%d > %s' % (lastdim, ist, i_slc)
ivlad.exe(cmd, verb)
return ivlad.unix_success
def main(par):
verb = par.bool('verb', False)
inp = par.string('inp') # ifile.rsf
out_basenm = os.path.basename(inp).rstrip(ivlad.ext) + '_split'
outdir = par.string('outdir',(out_basenm+ivlad.ext)) # Default is ifile_split.rsf
nthick = par.int('nthick', 1) # slice thickness
ivlad.chk_param_limit(nthick, 'nthick', 1, '>')
lastdim = str(ivlad.ndims(inp))
n = int(ivlad.getout('sfget',['parform=n','n'+lastdim], inp))
ivlad.chk_param_limit(nthick, 'nthick', n, '<')
if not os.path.isdir(outdir):
os.mkdir(outdir)
# Slices will be called 01.rsf, etc. Avoid datapath aliasing:
dpath = 'datapath=$DATAPATH/' + out_basenm + '_'
nslices_whole = int(math.floor(n/nthick))
f = 0
for i in range(nslices_whole):
i_str = ivlad.add_zeros(i,nslices_whole)
i_slc = os.path.join(outdir, i_str + '_stdout' + ivlad.ext)
cmd = '<%s sfwindow f%s=%d ' % (inp, lastdim,f)
cmd += 'n%s=%d %s > %s' % (lastdim, nthick, dpath, i_slc)
ivlad.exe(cmd, verb)
f += nthick
ist = n - nslices_whole * nthick # Incomplete Slice Thickness
if ist > 0:
i_str = ivlad.add_zeros(i+1,nslices_whole)
i_slc = os.path.join(outdir, i_str + '_stdout' + ivlad.ext)
cmd = '<%s sfwindow f%s=%d ' % (inp, lastdim, f)
cmd += 'n%s=%d > %s' % (lastdim, ist, i_slc)
ivlad.exe(cmd, verb)
return ivlad.unix_success
def main(par):
prog = par.string('prog') # Non-madagascar utility
inp = par.string('inp') # Input file
tpar_str = par.string('tpar') # Translated params, i.e.: "ni1=n1 ni2=n2"
ipar_str = par.string('ipar') # Independent params, i.e. "perc=100 cmap=rgb"
verb = par.bool('verb',False)
tpar_out = ''
if tpar_str != None:
for tpar in tpar_str.split():
thispar = tpar.split('=')
tpar_out += thispar[0] + '=' + \
ivlad.getout('sfget', ['parform=n', thispar[1]], inp, verb) +' '
data = ivlad.getout('sfin',['info=n',inp])
ivlad.exe(prog + ' <' + data + ' ' + tpar_out + ' ' + ipar_str, verb)
return ivlad.unix_success
def main(par):
prog = par.string('prog') # Non-madagascar utility
inp = par.string('inp') # Input file
tpar_str = par.string('tpar') # Translated params, i.e.: "ni1=n1 ni2=n2"
ipar_str = par.string(
'ipar') # Independent params, i.e. "perc=100 cmap=rgb"
verb = par.bool('verb', False)
tpar_out = ''
if tpar_str != None:
for tpar in tpar_str.split():
thispar = tpar.split('=')
tpar_out += thispar[0] + '=' + \
ivlad.getout('sfget', ['parform=n', thispar[1]], inp, verb) +' '
data = ivlad.getout('sfin', ['info=n', inp])
ivlad.exe(prog + ' <' + data + ' ' + tpar_out + ' ' + ipar_str, verb)
return ivlad.unix_success
def main(par):
f1 = sys.argv[1] + ' '
f2 = sys.argv[2]
f1_type = ivlad.getout('sfgettype', stdin=f1)
if f1_type != 'SF_FLOAT':
raise m8rex.TypeHandlingNotImplemented(f1_type)
dims_str = ivlad.getout('sffiledims','parform=n',f1)
ndims = int(dims_str.split(':')[0])
cmd = 'sfspike mag=0 '
fields = 'n o d unit label'.split()
for i in range(ndims):
for z in fields:
cmd += ivlad.getout('sfget',['parform=y',z+str(i+1)],f1) + ' '
cmd += ' >' + f2
ivlad.exe(cmd)
return ivlad.unix_success
def main(par):
verb = par.bool('verb', False) # Display what is wrong with the dataset
mydir = par.string('dir','.') # Directory with files
recursive = par.bool('rec', False) # Whether to go down recursively
chk4nan = par.bool('chk4nan',False) # Check for NaN values. Expensive!!
valid_files_list = []
if recursive:
for root, dirs, files in os.walk(mydir):
valid_files_list += \
ivlad.list_valid_rsf_files(root, files, chk4nan)
else:
files = [x for x in os.listdir(mydir) if os.path.isfile(x)]
valid_files_list += \
ivlad.list_valid_rsf_files(mydir, files, chk4nan)
for f in valid_files_list:
bfile = ivlad.getout('sfin',['info=n',f])
ivlad.msg(f + ': ' + bfile, verb)
ivlad.exe('touch -c ' + bfile)
return ivlad.unix_success
def main(par):
verb = par.bool('verb', False) # Display what is wrong with the dataset
mydir = par.string('dir','.') # Directory with files
recursive = par.bool('rec', False) # Whether to go down recursively
chk4nan = par.bool('chk4nan',False) # Check for NaN values. Expensive!!
valid_files_list = []
if recursive:
for root, dirs, files in os.walk(mydir):
valid_files_list += \
ivlad.list_valid_rsf_files(root, files, chk4nan)
else:
files = filter(lambda x:os.path.isfile(x),os.listdir(mydir))
valid_files_list += \
ivlad.list_valid_rsf_files(mydir, files, chk4nan)
for f in valid_files_list:
bfile = ivlad.getout('sfin',['info=n',f])
ivlad.msg(f + ': ' + bfile, verb)
ivlad.exe('touch -c ' + bfile)
return ivlad.unix_success
