def afni_3dinfo_ad3( fname ) :
'''Get voxelsize information.
output:
list of dims
total volume (float)
'''
fname.replace("[", "'[")
fname.replace("]", "]'")
cmd = '''3dinfo \
-ad3 \
{dset}
'''.format( dset=fname )
status, so, se = BASE.simple_shell_exec(cmd, capture=1)
print("++ Voxel dimensions of {} are (in mm):\n"
" {}".format(fname, ' '.join(so.split())))
dims = so.split()
voxvol = 1.0
dims_fl = []
for ad in dims:
adfl = float(ad)
voxvol*= adfl
dims_fl.append(adfl)
print(" ... so volume is (in mm**3): {}"
"".format(voxvol))
return dims_fl, voxvol
def afni_3dBrickStat_nz_count( fname ) :
'''Get mask size information.
Return int: number of nonzero voxels
Check for zero voxels in mask (exit with error).
'''
fname.replace("[", "'[")
fname.replace("]", "]'")
cmd = '''3dBrickStat \
-non-zero \
-count \
{dset}
'''.format( dset=fname )
status, so, se = BASE.simple_shell_exec(cmd, capture=1)
Nnzvox = int(so.strip())
print("++ Voxel count of mask '{}' is (in mm): {}"
"".format(fname, Nnzvox))
if not(Nnzvox) :
print("** ERROR: zero voxels in mask '{}'"
"".format(fname))
sys.exit(6)
return Nnzvox
def afni_3dinfo_is_single_vol( fname1, verb=0 ) :
'''Has one volume been specified (either a 3D vol, or a 4D, with
subbrick selectors)?
Returns True or False
'''
fname1.replace("[", "'[") ; fname1.replace("]", "]'")
cmd = '''3dinfo \
-nv \
{dset1} \
'''.format( dset1=fname1 )
status, so, se = BASE.simple_shell_exec(cmd, capture=1)
SINGLE_VOL = int(so.split()[0]) == 1
if verb > 0 :
print("++ Is this a single volume?\n"
" {}\n"
" --> {}"
"".format( fname1, SINGLE_VOL ))
return SINGLE_VOL
def afni_3dinfo_same_grid( fname1, fname2 ) :
'''Are 2 dsets on the same grid?
Returns True or False
'''
fname1.replace("[", "'[") ; fname1.replace("]", "]'")
fname2.replace("[", "'[") ; fname2.replace("]", "]'")
cmd = '''3dinfo \
-same_grid \
{dset1} \
{dset2}
'''.format( dset1=fname1, dset2=fname2 )
status, so, se = BASE.simple_shell_exec(cmd, capture=1)
SAME_GRID = bool(int(so.split()[0]))
print("++ Are these dsets on same grid?\n"
" {}\n {}\n"
" --> {}"
"".format(fname1, fname2, SAME_GRID ))
return SAME_GRID
def afni_3droistats( fname ) :
'''Get ROI size information.
Now using the 'AFNI_ATLAS_NAME_TYPE = name' env variable, so even
with both short and long labels present for ROIs, only the short
will be used (and numbers will match).
'''
fname.replace("[", "'[")
fname.replace("]", "]'")
cmd = '''3dROIstats \
-DAFNI_ATLAS_NAME_TYPE=name \
-nzvoxels \
-nobriklab \
-mask {dset} \
{dset}
'''.format( dset=fname )
status, so, se = BASE.simple_shell_exec(cmd, capture=1)
# split by line
so_lined = so.split("\n")
if len(so_lined) > 3 :
print("** ERROR: unexpected length in 3dROIstats output: \n"
"{}".format(so_lined))
sys.exit(4)
# ['File', 'Sub-brick', 'Mean_ROI', 'NZcount_ROI', ... ]
so_labs = so_lined[0].split() ; Nlabs = len(so_labs)
# ['FILE_NAME', 'SUBBRICK_IDX', 'ROI_IDX', 'ROI_COUNT', ...]
so_vals = so_lined[1].split() ; Nvals = len(so_vals)
#print("HEY")
#print(so_lined[0])
#print(so_lined[1])
if Nlabs != Nvals :
print("** ERROR: length of labels {} does not match that of vals {}"
"".format(Nlabs, Nvals))
sys.exit(2)
elif Nlabs % 2 :
print("** ERROR: expected even number of values per row, not {}"
"".format(Nlabs))
sys.exit(2)
so_null = so_lined[2].strip()
if so_null :
print("** ERROR: non-null 3rd line: \n"
"{}".format(so_null))
sys.exit(3)
return so_labs, so_vals
def parse_args_this_prog(full_argv):
argv = full_argv[1:]
Narg = len(argv)
if not (Narg):
print(help_string_this_prog)
sys.exit(0)
i = 0
while i < Narg:
if argv[i] == "{ver}".format(**all_opts):
print(ver)
sys.exit(0)
elif argv[i] == "{date}".format(**all_opts):
print(date)
sys.exit(0)
elif argv[i] == "{help}".format(**all_opts) or \
argv[i] == "{h}".format(**all_opts) :
print(help_string_this_prog)
sys.exit(0)
elif argv[i] == "{hview}".format(**all_opts):
prog = os.path.basename(full_argv[0])
cmd = 'apsearch -view_prog_help {}'.format(prog)
BASE.simple_shell_exec(cmd)
sys.exit(0)
# --------- finish -------------
else:
print("** ERROR: unknown opt: '{}'".format(argv[i]))
sys.exit(2)
i += 1
# --------------------------------------------------------------------
return 0
def copy_images_to_subdir(iopts):
count_fail = 0
list_fail = []
for ii in range(iopts.nmedia):
iname = iopts.list_media[ii]
oname = iopts.subdir + '/' + os.path.basename(iopts.list_media[ii])
a, b, c = ab.simple_shell_exec("\cp {} {}".format(iname, oname))
if a:
count_fail += 1
list_fail.append(iname)
return count_fail, list_fail
def exec_or_error(cmd, error_msg="See above!!!", showerr=1, showcmd=1):
"""return text output from the given command
if showcmd, print the cmd
if showerr and there is a command error, show it
This will exit on status other than 0 so BE CAREFULL!!!
"""
status, cmd_output, error_out = afni_base.simple_shell_exec(cmd,capture=1)
if showcmd:
print(cmd)
if showerr:
print(error_out)
if status != 0:
if error_msg != "See above!!!":
error_msg = error_msg+"!!!"
printNcolor("** ERROR:"," "+error_msg,"Red","White","Bold")
sys.exit(1)
return status,cmd_output
def check_for_progs(self, plist, repos=0, show_missing=0):
"""see whether the programs seem to be found, and show version
repos: if set, append any found to self.repo_prog list
show_missing: if set, show empty prog line to indicate failed test
"""
# check for programs
nfound = 0
for prog in plist:
# the version file is treated specially here
if prog == 'AFNI_version.txt':
vinfo = UTIL.read_AFNI_version_file()
if vinfo != '':
nfound += 1
else:
self.comments.append('missing %s, maybe package is old'%prog)
print('%-20s : %s' % (prog, vinfo))
continue
# as is afni
elif prog == 'afni label':
nfound += 1 # do not call this an error yet
s, v = self.get_prog_version('afni')
print('%-20s : %s' % ('', self.afni_label))
continue
# XQuartz/X11?
elif prog in ['XQuartz', 'X11']:
s, v = self.get_prog_version(prog)
print('%-20s : %s' % ('%s version'%prog, v))
continue
# and python - add a comment if they are using version 3 (no continue)
# - do not 'continue'
elif prog == 'python':
s, vstr = self.get_prog_version(prog)
vf = self.get_python_ver_float()
mesg = ''
if vf >= 3.0:
mesg = 'have python version %s, some programs need 2.7.x' % vstr
elif vf < 2.7:
mesg = 'have python version %s, consider using 2.7.x' % vstr
if mesg != '':
self.comments.append(mesg)
# now run the normal test
cmd = 'which %s' % prog
s, so, se = BASE.simple_shell_exec(cmd, capture=1)
if not s: # found one
# if we do not yet know of a repo program, mark as this one
if repos and self.repo_prog == '': self.repo_prog = prog
progpath = so.strip()
print('%-20s : %s' % (cmd, progpath))
s, v = self.get_prog_version(prog)
if s: print('%-20s : %s' % ('%s version'%prog, v))
# save some results
if prog == 'afni': self.afni_ver = v
if prog == 'python': self.python_prog = progpath
nfound += 1
elif show_missing:
print('%-20s : %s' % (cmd, se))
print('')
return nfound
def get_afni_dir(self):
s, so, se = BASE.simple_shell_exec('which afni', capture=1)
if s: return ''
adir = so.strip()
if adir[-5:] == '/afni': return adir[0:-5]
else: return ''
def parse_args(full_argv):
"""Go through user-entered options and fill an object with the values.
These will be used to setup plotting.
"""
argv = full_argv[1:]
Narg = len(argv)
if not (Narg):
print(help_string)
sys.exit(0)
# initialize objs
iopts = iopts_obj()
iopts.full_cmd = full_argv
i = 0
while i < Narg:
if argv[i] == "{ver}".format(**opts_dict):
print(ver)
sys.exit(0)
elif argv[i] == "{date}".format(**opts_dict):
print(date)
sys.exit(0)
elif argv[i] == "{help}".format(**opts_dict) or \
argv[i] == "{h}".format(**opts_dict) :
print(help_string)
sys.exit(0)
elif argv[i] == "{hview}".format(**opts_dict):
prog = os.path.basename(full_argv[0])
cmd = 'apsearch -view_prog_help {}'.format(prog)
ab.simple_shell_exec(cmd)
sys.exit(0)
# ---------- req ---------------
# can be a list of many
elif argv[i] == "{in_mat}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
while i < Narg:
if opts_list.__contains__(argv[i]):
i -= 1
break
else:
iopts.in_mat.append(argv[i])
i += 1
elif argv[i] == "{prefix}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.prefix = argv[i]
# ---------- opt ---------------
# can be a list of many
elif argv[i] == "{pars}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
while i < Narg:
if opts_list.__contains__(argv[i]):
i -= 1
break
else:
iopts.pars_list.append(argv[i])
i += 1
elif argv[i] == "{in_csv}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.in_csv = argv[i]
elif argv[i] == "{in_listfile}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.in_listfile = argv[i]
# --------- finish -------------
else:
print("** ERROR: unknown opt: '{}'".format(argv[i]))
sys.exit(2)
i += 1
if iopts.check_req():
print(" -------------------------------")
ab.EP("Problem with input arguments. See detailed whining above.")
iopts.finish_defs()
return iopts
# might have several scripts to parse
for ii in range(iopts.ninfile):
ainfo.add_text(lmsar.read_text_to_list(iopts.infile_list[ii]))
# only include TOC for the first file
oscript_txt, orst_txt = \
lmsar.interpret_MSAR_list( ainfo.text_list[ii], iopts, ii,
DO_TOC=not(ii) )
ainfo.add_oscript_txt(oscript_txt)
ainfo.add_orst_txt(orst_txt)
# ------------------ write output files ------------------
# Make dir to hold script/any images
a, b, c = ab.simple_shell_exec("\mkdir -p {}".format(iopts.subdir))
if not (a):
print("++ Wrote directory to hold scripts")
else:
print("** Badness writing dir to hold scripts {}".format(iopts.subdir))
sys.exit(12)
# write script to local dir
for ii in range(iopts.nscript):
fff = open(iopts.oname_script_list[ii], 'w')
fff.write(ainfo.oscript_txt_list[ii])
fff.close()
if iopts.tarball_name:
all_script = ' '.join(iopts.oname_script_list)
# \\ needed before the t, because \t is a TAB!
def parse_args_mat_plot(full_argv):
"""Go through user-entered options and fill an object with the values.
These will be used to setup plotting.
"""
argv = full_argv[1:]
Narg = len(argv)
if not (Narg):
print(help_string_mat_plot)
sys.exit(0)
# initialize objs
iopts = iopts_to_plot_mat2d()
iopts.full_cmd = full_argv
i = 0
while i < Narg:
if argv[i] == "{ver}".format(**opts_dict):
print(ver)
sys.exit(0)
elif argv[i] == "{date}".format(**opts_dict):
print(date)
sys.exit(0)
elif argv[i] == "{help}".format(**opts_dict) or \
argv[i] == "{h}".format(**opts_dict) :
print(help_string_mat_plot)
sys.exit(0)
elif argv[i] == "{hview}".format(**opts_dict):
prog = os.path.basename(full_argv[0])
cmd = 'apsearch -view_prog_help {}'.format(prog)
ab.simple_shell_exec(cmd)
sys.exit(0)
# ---------- req ---------------
elif argv[i] == "{input}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.input = argv[i]
# ---------- opt ---------------
elif argv[i] == "{prefix}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.prefix = argv[i]
# can be a list of many
elif argv[i] == "{pars}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
while i < Narg:
if opts_list.__contains__(argv[i]):
i -= 1
break
else:
iopts.pars_list.append(argv[i])
i += 1
elif argv[i] == "{ftype}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.ftype = argv[i]
elif argv[i] == "{dpi}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.dpi = float(argv[i])
elif argv[i] == "{vmin}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.vmin = float(argv[i])
elif argv[i] == "{vmax}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.vmax = float(argv[i])
elif argv[i] == "{fs_xticks}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.fs_xticks = float(argv[i])
elif argv[i] == "{fs_yticks}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.fs_yticks = float(argv[i])
elif argv[i] == "{fs_title}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.fs_title = float(argv[i])
elif argv[i] == "{fs_cbar}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.fs_cbar = float(argv[i])
elif argv[i] == "{cbar_n_intervals}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.cbar_n_intervals = int(argv[i])
elif argv[i] == "{cbar}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.cbar = argv[i]
elif argv[i] == "{cbar_width_perc}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.cbar_width_perc = float(argv[i])
elif argv[i] == "{figsize_x}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.figsize_x = float(argv[i])
elif argv[i] == "{figsize_y}".format(**opts_dict):
if i >= Narg:
ab.ARG_missing_arg(argv[i])
i += 1
iopts.figsize_y = float(argv[i])
elif argv[i] == "{hold_image}".format(**opts_dict):
iopts.hold_image = True
elif argv[i] == "{tight_layout}".format(**opts_dict):
iopts.tight_layout = True
elif argv[i] == "{cbar_off}".format(**opts_dict):
iopts.cbar_off = True
elif argv[i] == "{xticks_off}".format(**opts_dict):
iopts.xticks_off = True
elif argv[i] == "{yticks_off}".format(**opts_dict):
iopts.yticks_off = True
# --------- finish -------------
else:
print("** ERROR: unknown opt: '{}'".format(argv[i]))
sys.exit(2)
i += 1
if iopts.check_req():
print(" -------------------------------")
ab.EP("Problem with input arguments. See detailed whining above.")
iopts.finish_defs()
return iopts
def check_special_opts(self, argv):
"""process known '-optlist_* options' and other global_opts,
nuking them from argv
some options are terminal
"""
# global options (some take a parameter)
global_opts = [
'-optlist_verbose', '-optlist_no_show_count',
'-optlist_show_global_opts', '-optlist_show_valid_opts',
'-optlist_show_argv_array', '-h_find', '-h_view', '-hview'
]
alen = len(argv)
if '-optlist_verbose' in argv:
ind = argv.index('-optlist_verbose')
self.verb = 4
argv[ind:ind + 1] = []
print('++ optlist: setting verb to %d' % self.verb)
if '-optlist_no_show_count' in argv:
ind = argv.index('-optlist_no_show_count')
self.show_count = 0
argv[ind:ind + 1] = []
if self.verb > 1: print('++ optlist: clearing show_count')
# terminal options (all end in exit)
# terminal opts specific to this library
if '-optlist_show_global_opts' in argv:
global_opts.sort()
print("-- global OptionList options (%d):" % len(global_opts))
print(" %s\n" % '\n '.join(global_opts))
sys.exit(0)
if '-optlist_show_valid_opts' in argv:
oname = '-optlist_show_valid_opts'
ind = argv.index(oname)
prog = os.path.basename(argv[0])
self.show(verb=1)
sys.exit(0)
if '-optlist_show_argv_array' in argv:
oname = '-optlist_show_argv_array'
ind = argv.index(oname)
# this takes one parameter, which must be in list
atype = ''
if alen >= ind + 2:
atype = argv[ind + 1]
if atype not in self.argv_array_types:
print("** %s: requires a parameter in %s" \
% (oname, self.argv_array_types))
sys.exit(1)
argv[ind:ind + 2] = []
self.show_argv_array = atype
# terminal general options
if '-h_find' in argv:
oname = '-h_find'
ind = argv.index(oname)
prog = os.path.basename(argv[0])
if ind == alen - 1:
print('** global opt %s needs %s option as parameter' \
% (oname, prog))
sys.exit(1)
cmd = 'apsearch -phelp %s -word %s' % (prog, argv[ind + 1])
if self.verb > 1:
print('++ optlist: applying %s via: %s' % (oname, cmd))
BASE.simple_shell_exec(cmd)
sys.exit(0)
if '-h_view' in argv:
oname = '-h_view'
ind = argv.index(oname)
prog = os.path.basename(argv[0])
cmd = 'apsearch -view_prog_help %s' % prog
if self.verb > 1:
print('++ optlist: applying %s via: %s' % (oname, cmd))
BASE.simple_shell_exec(cmd)
sys.exit(0)
if '-hview' in argv:
oname = '-hview'
ind = argv.index(oname)
prog = os.path.basename(argv[0])
cmd = 'apsearch -view_prog_help %s' % prog
if self.verb > 1:
print('++ optlist: applying %s via: %s' % (oname, cmd))
BASE.simple_shell_exec(cmd)
sys.exit(0)
if '-hweb' in argv: oname = '-hweb'
elif '-h_web' in argv: oname = '-h_web'
else: oname = ''
if oname != '':
ind = argv.index(oname)
prog = os.path.basename(argv[0])
cmd = 'apsearch -web_prog_help %s' % prog
if self.verb > 1:
print('++ optlist: applying %s via: %s' % (oname, cmd))
BASE.simple_shell_exec(cmd)
sys.exit(0)
if self.verb > 1:
print('-- argv: orig len %d, new len %d' % (alen, len(argv)))