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',
'-all_opts', '-h_find', '-h_view' ]
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)
if '-all_opts' in argv:
oname = '-all_opts'
ind = argv.index(oname)
prog = os.path.basename(argv[0])
self.show(verb=1)
sys.exit(0)
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 self.verb > 1:
print '-- argv: orig len %d, new len %d' % (alen,len(argv))
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
# 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
print('%-20s : %s' % (cmd, so.strip()))
s, v = self.get_prog_version(prog)
if s: print('%-20s : %s' % ('%s version' % prog, v))
if prog == 'afni': self.afni_ver = v # save result
nfound += 1
elif show_missing:
print('%-20s : %s' % (cmd, se))
print('')
return nfound
def show_general_afni_info(self, header=1):
print UTIL.section_divider('AFNI and related program tests', hchar='-')
for prog in ['afni', 'python', 'R', 'tcsh']:
cmd = 'which %s' % prog
s, so, se = BASE.simple_shell_exec(cmd, capture=1)
if s: print '%-20s : %s' % (cmd, se)
else:
print '%-20s : %s' % (cmd, so.strip())
s, v = self.get_prog_version(prog)
if s:
print '%-20s : %s' % ('%s version'%prog, v)
if prog == 'afni': self.afni_ver = v # save result
def show_general_afni_info(self, header=1):
print UTIL.section_divider('AFNI and related program tests', hchar='-')
for prog in ['afni', 'python', 'R', 'tcsh']:
cmd = 'which %s' % prog
s, so, se = BASE.simple_shell_exec(cmd, capture=1)
if s: print '%-20s : %s' % (cmd, se)
else:
print '%-20s : %s' % (cmd, so.strip())
s, v = self.get_prog_version(prog)
if s:
print '%-20s : %s' % ('%s version' % prog, v)
if prog == 'afni': self.afni_ver = v # save result
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 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
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
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
print '%-20s : %s' % (cmd, so.strip())
s, v = self.get_prog_version(prog)
if s: print '%-20s : %s' % ('%s version' % prog, v)
if prog == 'afni': self.afni_ver = v # save result
nfound += 1
elif show_missing:
print '%-20s : %s' % (cmd, se)
print
return nfound
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
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
print '%-20s : %s' % (cmd, so.strip())
s, v = self.get_prog_version(prog)
if s: print '%-20s : %s' % ('%s version'%prog, v)
if prog == 'afni': self.afni_ver = v # save result
nfound += 1
elif show_missing:
print '%-20s : %s' % (cmd, se)
print
return nfound
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 self.verb > 1:
print('-- argv: orig len %d, new len %d' % (alen, len(argv)))
return data
# --------------------------------------------------------------------------
if __name__ == "__main__":
for n in ncolors:
print("Ncolors = {}".format(n))
nn = n + 1
sn = str(n)
snn = str(nn)
ncolor = snn + ' '
ofile = "ROI_glasbey_" + snn
oname = "ROI_glasbey_" + sn
cmd = "python glasbey.py "
cmd += "--no-black "
cmd += "--format=byte " # so we can convert to hex
cmd += ncolor
cmd += ofile
ab.simple_shell_exec(cmd)
ddd = ReadIn_CodeOut(ofile, oname)
print("DONE!")
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)
# initialize objs
iopts = iopts_this_prog()
iopts.set_full_cmd(full_argv)
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)
# ---------- req ---------------
elif argv[i] == "{input}".format(**all_opts):
if i >= Narg:
ARG_missing_arg(argv[i])
i += 1
iopts.set_input(argv[i])
elif argv[i] == "{eps_iso}".format(**all_opts):
if i >= Narg:
ARG_missing_arg(argv[i])
i += 1
iopts.set_eps_iso(argv[i])
elif argv[i] == "{eps_size}".format(**all_opts):
if i >= Narg:
ARG_missing_arg(argv[i])
i += 1
iopts.set_eps_size(argv[i])
# can be outweighed by "-check_all"
elif argv[i] == "{is_vox_iso}".format(**all_opts):
if iopts.check_all != 1:
iopts.set_rep_vox_iso(True)
iopts.set_check_all_val(0)
# can be outweighed by "-check_all"
elif argv[i] == "{is_mat_even}".format(**all_opts):
if iopts.check_all != 1:
iopts.set_rep_mat_even(True)
iopts.set_check_all_val(0)
# can be outweighed by "-check_all"
elif argv[i] == "{is_vox_1mm_max}".format(**all_opts):
if iopts.check_all != 1:
iopts.set_rep_vox_1mm_max(True)
iopts.set_check_all_val(0)
# can be outweighed by "-check_all"
elif argv[i] == "{is_vox_05mm_min}".format(**all_opts):
if iopts.check_all != 1:
iopts.set_rep_vox_05mm_min(True)
iopts.set_check_all_val(0)
# default behavior; and/or will supercede indiv opts
elif argv[i] == "{check_all}".format(**all_opts):
iopts.set_check_all_val(1)
elif argv[i] == "{fix_all}".format(**all_opts):
iopts.set_fix_all_val(True)
# if not entered, will use min vox dim, floored at min allowed val
elif argv[i] == "{fix_out_vox_dim}".format(**all_opts):
if i >= Narg:
ARG_missing_arg(argv[i])
i += 1
fovd = float(argv[i])
if fovd < 0.5 or 1.0 < fovd:
print("** ERROR: value for output voxel size ({}) is"
" outside the allowed range [0.5, 1.0]"
"".format(fovd))
sys.exit(3)
else:
iopts.set_fix_out_vox_dim(fovd)
elif argv[i] == "{fix_out_prefix}".format(**all_opts):
if i >= Narg:
ARG_missing_arg(argv[i])
i += 1
iopts.set_fix_out_prefix(argv[i])
elif argv[i] == "{overwrite}".format(**all_opts):
iopts.set_fix_overwrite('-overwrite')
elif argv[i] == "{verbose}".format(**all_opts) or \
argv[i] == "{verb}".format(**all_opts) :
iopts.set_verbose(True)
# --------- finish -------------
else:
print("** ERROR: unknown opt: '{}'".format(argv[i]))
sys.exit(2)
i += 1
# --------------------------------------------------------------------
if iopts.check_req():
print(" -------------------------------")
print("** ERROR with input arguments (see detailed whining above).")
sys.exit(1)
iopts.finish_defs() # make some paths we need later
return iopts
def get_afni_dir(self):
s, so, se = BASE.simple_shell_exec('which afni', capture=1)
if s: return ''
return so.strip()
# 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_this_prog(full_argv):
argv = full_argv[1:]
Narg = len(argv)
if not (Narg):
print(help_string_this_prog)
sys.exit(0)
# initialize objs
iopts = iopts_this_prog()
iopts.set_full_cmd(full_argv)
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_b0_corr)
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)
# ---------- req ---------------
elif argv[i] == "{prefix}".format(**all_opts):
if i >= Narg:
ARG_missing_arg(argv[i])
i += 1
iopts.set_prefix(argv[i])
elif argv[i] == "{overwrite}".format(**all_opts):
iopts.set_overwrite(True)
# --------- finish -------------
else:
print("** ERROR: unknown opt: '{}'".format(argv[i]))
sys.exit(2)
i += 1
if iopts.check_req():
print(" -------------------------------")
print("** ERROR with input arguments (see detailed whining above).")
sys.exit(1)
iopts.finish_defs() # make some paths we need later
return iopts
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 get_afni_dir(self):
s, so, se = BASE.simple_shell_exec('which afni', capture=1)
if s: return ''
return so.strip()
# =============================================================================
if __name__ == "__main__" :
iopts = lmsar.parse_MSAR_args(sys.argv[1:])
text_list = lmsar.read_text_to_list( iopts.infile )
oscript_txt, orst_txt = \
lmsar.interpret_MSAR_list( text_list, iopts )
# --------- 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))
# write script to local dir
fff = open(iopts.oname_script, 'w')
fff.write(oscript_txt)
fff.close()
# execute script, if desired
if iopts.do_execute :
a, b, c = ab.simple_shell_exec("tcsh -ef {}".format(iopts.oname_script))
if not(a) :
print("++ Success running script {}".format(iopts.oname_script))
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)
# initialize objs
iopts = iopts_this_prog()
iopts.set_full_cmd(full_argv)
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)
# ---------- req ---------------
elif argv[i] == "{input}".format(**all_opts) :
if i >= Narg:
ARG_missing_arg(argv[i])
i+= 1
iopts.set_input(argv[i])
elif argv[i] == "{eps_iso}".format(**all_opts) :
if i >= Narg:
ARG_missing_arg(argv[i])
i+= 1
iopts.set_eps_iso(argv[i])
elif argv[i] == "{eps_size}".format(**all_opts) :
if i >= Narg:
ARG_missing_arg(argv[i])
i+= 1
iopts.set_eps_size(argv[i])
# can be outweighed by "-check_all"
elif argv[i] == "{is_vox_iso}".format(**all_opts) :
if iopts.check_all != 1:
iopts.set_rep_vox_iso(True)
iopts.set_check_all_val( 0 )
# can be outweighed by "-check_all"
elif argv[i] == "{is_mat_even}".format(**all_opts) :
if iopts.check_all != 1:
iopts.set_rep_mat_even(True)
iopts.set_check_all_val( 0 )
# can be outweighed by "-check_all"
elif argv[i] == "{is_vox_1mm_max}".format(**all_opts) :
if iopts.check_all != 1:
iopts.set_rep_vox_1mm_max(True)
iopts.set_check_all_val( 0 )
# can be outweighed by "-check_all"
elif argv[i] == "{is_vox_05mm_min}".format(**all_opts) :
if iopts.check_all != 1:
iopts.set_rep_vox_05mm_min(True)
iopts.set_check_all_val( 0 )
# default behavior; and/or will supercede indiv opts
elif argv[i] == "{check_all}".format(**all_opts) :
iopts.set_check_all_val( 1 )
elif argv[i] == "{verbose}".format(**all_opts) or \
argv[i] == "{verb}".format(**all_opts) :
iopts.set_verbose(True)
# --------- finish -------------
else:
print("** ERROR: unknown opt: '{}'".format(argv[i]))
sys.exit(2)
i+=1
# --------------------------------------------------------------------
if iopts.check_req():
print(" -------------------------------")
print("** ERROR with input arguments (see detailed whining above).")
sys.exit(1)
iopts.finish_defs() # make some paths we need later
return iopts
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 ''
