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 __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):
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):
verb = par.bool('verb',
False) # Display headers and binaries being deleted
mydir = par.string('dir') # Directory with files
recursive = par.bool('rec', False) # Whether to go down recursively
# Clean up headers with existing binaries
valid_files_list = []
if recursive:
for root, dirs, files in 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=False)
for f in valid_files_list:
ivlad.msg(f + ': ' + ivlad.getout('sfin', ['info=n', f]), verb)
sf.rm(f, verb)
# Clean up headers with no binaries
if recursive:
hdr_str = ivlad.getout('find',
[mydir, '-type', 'f', '-name', '"*.rsf"'])
hdr_list = hdr_str.split('\n')
else:
hdr_list = [
x for x in glob.glob(os.path.join(mydir, '*.rsf'))
if os.path.isfile(x)
]
for f in hdr_list:
ivlad.msg(f)
os.remove(f)
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):
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):
verb = par.bool('verb', False) # Display headers and binaries being deleted
mydir = par.string('dir') # Directory with files
recursive = par.bool('rec', False) # Whether to go down recursively
# Clean up headers with existing binaries
valid_files_list = []
if recursive:
for root, dirs, files in 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=False)
for f in valid_files_list:
ivlad.msg(f + ': ' + ivlad.getout('sfin',['info=n',f]), verb)
sf.rm(f, verb)
# Clean up headers with no binaries
if recursive:
hdr_str = ivlad.getout('find',[mydir, '-type', 'f', '-name', '"*.rsf"'])
hdr_list = hdr_str.split('\n')
else:
hdr_list = filter(lambda x:os.path.isfile(x),
glob.glob(os.path.join(mydir,'*.rsf')))
for f in hdr_list:
ivlad.msg(f)
os.remove(f)
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):
inp = par.string('inp') # input file
out = par.string('out') # output file
verb = par.bool('verb', False) # if y, print system commands, outputs
pclip = par.float('pclip', 99) # percentile clip
if pclip < 0 or pclip > 100:
raise m8rex.ParamOutOfRange('pclip', 0, 100)
prog_nm_root = os.path.join(RSFROOT, 'bin', 'sf')
sfquantile = prog_nm_root + 'quantile'
sfclip = prog_nm_root + 'clip'
clip = ivlad.getout('sfquantile', 'pclip=' + str(pclip), inp, verb, True)
sf.clip(inp, out, clip, verb)
return ivlad.unix_success
def main(par):
inp = par.string('inp') # input file
out = par.string('out') # output file
verb = par.bool('verb', False) # if y, print system commands, outputs
pclip = par.float('pclip',99) # percentile clip
if pclip < 0 or pclip > 100:
raise m8rex.ParamOutOfRange('pclip',0,100)
prog_nm_root = os.path.join(RSFROOT,'bin','sf')
sfquantile = prog_nm_root + 'quantile'
sfclip = prog_nm_root + 'clip'
clip = ivlad.getout('sfquantile', 'pclip='+str(pclip), inp, verb, True)
sf.clip(inp, out, clip, verb)
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
def main(par):
inp = par.string('inp') # input file
out = par.string('out') # output file
verb = par.bool('verb', False) # if y, print system commands, outputs
ivlad.chk_file_dims(inp, 2)
n1 = ivlad.getout('sfget',['parform=n','n1'], inp, verb)
n2 = ivlad.getout('sfget',['parform=n','n2'], inp, verb)
n1 = int(n1)
n2 = int(n2)
h = par.int('h', 768) # output height
w = par.int('w', 1024) # output width
has_h = par.string('h')
has_w = par.string('w')
if has_h and has_w: # both w and h were read. Check for sanity:
ivlad.chk_param_limit(w, 'w')
ivlad.chk_param_limit(h, 'h')
if (h,w) == (n1,n2):
ivlad.msg('Change h or w if you want out != inp')
sf.cp(inp, out, verb)
return ivlad.unix_success
# Transform h and w to pixels, if they are not
# No default value for par.string -- Quirk of rsf, replicated in rsfbak
unit = par.string('unit', 'px') # unit of h and w. Can be: px, mm, cm, in
ivlad.chk_par_in_list(unit,['mm','cm','in','px'])
if unit != 'px':
ppi = par.int('ppi') # outp. resolution (px/in). Necessary when unit!=px
ivlad.chk_param_limit(ppi, 'ppi')
# Transform w and h to px
if unit == 'in':
scale = 1
elif unit == 'mm':
scale = 254
elif unit == 'cm':
scale = 25.4
w *= ppi / float(scale)
h *= ppi / float(scale)
# Don't worry, we'll convert to int after prar block
del scale
# Now h and w are in pixels
# If prar=y, then h and/or w define a bounding box.
# Find the dimensions of the image inside this box
prar = par.bool('prar', True) # if y, PReserve Aspect Ratio of input
if prar: # preserve aspect ratio
if has_h and not has_w:
w = n2 * float(h) / n1
elif has_w and not has_h:
h = n1 * float(w) / n2
else: # Full bounding box specified
hscale = float(h) / n1
wscale = float(w) / n2
if hscale < wscale:
w = n2 * hscale
else:
h = n1 * wscale
h = int(h)
w = int(w)
assert h > 1
assert w > 1
h = ivlad.valswitch(h, n1, None)
w = ivlad.valswitch(w, n2, None)
tmp = tempfile.mktemp(dir=rsf.path.datapath())
# Interpolation and, if needed, bandpass
if h != None:
d1 = ivlad.getout('sfget', ['parform=n','d1'], inp, verb)
d1 = float(d1) * (n1-1)/float(h-1)
if h < n1:
ready_for_remap_1 = tmp + '1'
sf.bandpass(inp, ready_for_remap_1, fhi=0.5/d1, verb=verb)
rem2del_junk1 = True
else:
ready_for_remap_1 = inp
rem2del_junk1 = False
if w:
out_remap1 = tmp + '2'
rem2del_junk2 = True
else:
out_remap1 = out
rem2del_junk2 = False
sf.remap1(ready_for_remap_1, out_remap1, n1=h, d1=d1, verb=verb)
if rem2del_junk1:
sf.rm(ready_for_remap_1, verb)
else: # no action on axis 1
out_remap1 = inp
rem2del_junk2 = False
if w != None:
d2 = ivlad.getout('sfget', ['parform=n','d2'], inp, verb)
d2 = float(d2) * (n2-1)/float(w-1)
out_transp1 = tmp + '3'
sf.transp(out_remap1, out_transp1, verb=verb)
if rem2del_junk2:
sf.rm(out_remap1, verb)
if w < n2:
ready_for_remap_2 = tmp + '4'
sf.bandpass(out_transp1, ready_for_remap_2, fhi=0.5/d2, verb=verb)
rem2del_junk4 = True
else:
ready_for_remap_2 = out_transp1
rem2del_junk4 = False
ready_for_transp2 = tmp + '5'
sf.remap1(ready_for_remap_2,ready_for_transp2,n1=w,d1=d2,verb=verb)
sf.rm(out_transp1, verb)
if rem2del_junk4:
sf.rm(ready_for_remap_2, verb)
sf.transp(ready_for_transp2, out, verb=verb)
sf.rm(ready_for_transp2, verb)
return ivlad.unix_success
def main(par):
inp = par.string('inp') # input file
out = par.string('out') # output file
verb = par.bool('verb', False) # if y, print system commands, outputs
ivlad.chk_file_dims(inp, 2)
n1 = ivlad.getout('sfget', ['parform=n', 'n1'], inp, verb)
n2 = ivlad.getout('sfget', ['parform=n', 'n2'], inp, verb)
n1 = int(n1)
n2 = int(n2)
h = par.int('h', 768) # output height
w = par.int('w', 1024) # output width
has_h = par.string('h')
has_w = par.string('w')
if has_h and has_w: # both w and h were read. Check for sanity:
ivlad.chk_param_limit(w, 'w')
ivlad.chk_param_limit(h, 'h')
if (h, w) == (n1, n2):
ivlad.msg('Change h or w if you want out != inp')
sf.cp(inp, out, verb)
return ivlad.unix_success
# Transform h and w to pixels, if they are not
# No default value for par.string -- Quirk of rsf, replicated in rsfbak
unit = par.string('unit', 'px') # unit of h and w. Can be: px, mm, cm, in
ivlad.chk_par_in_list(unit, ['mm', 'cm', 'in', 'px'])
if unit != 'px':
ppi = par.int(
'ppi') # outp. resolution (px/in). Necessary when unit!=px
ivlad.chk_param_limit(ppi, 'ppi')
# Transform w and h to px
if unit == 'in':
scale = 1
elif unit == 'mm':
scale = 254
elif unit == 'cm':
scale = 25.4
w *= ppi / float(scale)
h *= ppi / float(scale)
# Don't worry, we'll convert to int after prar block
del scale
# Now h and w are in pixels
# If prar=y, then h and/or w define a bounding box.
# Find the dimensions of the image inside this box
prar = par.bool('prar', True) # if y, PReserve Aspect Ratio of input
if prar: # preserve aspect ratio
if has_h and not has_w:
w = n2 * float(h) / n1
elif has_w and not has_h:
h = n1 * float(w) / n2
else: # Full bounding box specified
hscale = float(h) / n1
wscale = float(w) / n2
if hscale < wscale:
w = n2 * hscale
else:
h = n1 * wscale
h = int(h)
w = int(w)
assert h > 1
assert w > 1
h = ivlad.valswitch(h, n1, None)
w = ivlad.valswitch(w, n2, None)
tmp = tempfile.mktemp(dir=rsf.path.datapath())
# Interpolation and, if needed, bandpass
if h != None:
d1 = ivlad.getout('sfget', ['parform=n', 'd1'], inp, verb)
d1 = float(d1) * (n1 - 1) / float(h - 1)
if h < n1:
ready_for_remap_1 = tmp + '1'
sf.bandpass(inp, ready_for_remap_1, fhi=0.5 / d1, verb=verb)
rem2del_junk1 = True
else:
ready_for_remap_1 = inp
rem2del_junk1 = False
if w:
out_remap1 = tmp + '2'
rem2del_junk2 = True
else:
out_remap1 = out
rem2del_junk2 = False
sf.remap1(ready_for_remap_1, out_remap1, n1=h, d1=d1, verb=verb)
if rem2del_junk1:
sf.rm(ready_for_remap_1, verb)
else: # no action on axis 1
out_remap1 = inp
rem2del_junk2 = False
if w != None:
d2 = ivlad.getout('sfget', ['parform=n', 'd2'], inp, verb)
d2 = float(d2) * (n2 - 1) / float(w - 1)
out_transp1 = tmp + '3'
sf.transp(out_remap1, out_transp1, verb=verb)
if rem2del_junk2:
sf.rm(out_remap1, verb)
if w < n2:
ready_for_remap_2 = tmp + '4'
sf.bandpass(out_transp1,
ready_for_remap_2,
fhi=0.5 / d2,
verb=verb)
rem2del_junk4 = True
else:
ready_for_remap_2 = out_transp1
rem2del_junk4 = False
ready_for_transp2 = tmp + '5'
sf.remap1(ready_for_remap_2, ready_for_transp2, n1=w, d1=d2, verb=verb)
sf.rm(out_transp1, verb)
if rem2del_junk4:
sf.rm(ready_for_remap_2, verb)
sf.transp(ready_for_transp2, out, verb=verb)
sf.rm(ready_for_transp2, verb)
return ivlad.unix_success
