def set_afni_version(self):
# version number and package type
cmd = '''afni -vnum -package'''
com = BASE.shell_com(cmd, capture=1, save_hist=0)
com.run()
check_for_shell_com_failure(com, cmd, disp_so=False, disp_se=False)
self.afni_ver = ", ".join(com.so)
def __init__(self):
self.full_cmd = '' # existential...
self.prog_ver = ddefs['DEF_ver']
self.afni_ver = ''
self.is_verbose = False
self.dset = ''
self.dset_info = ''
self.rep_vox_iso = False
self.rep_mat_even = False
self.rep_vox_1mm_max = False
self.rep_vox_05mm_min = False
self.vox_dim = []
self.mat_dim = []
self.vox_dim_str = ''
self.mat_dim_str = ''
self.eps_iso = ddefs['DEF_eps_iso']
self.eps_size = ddefs['DEF_eps_size']
self.check_all = -1 # def: do all
self.stat_mat_even = -1 # status
self.stat_vox_iso = -1 # status
self.stat_vox_1mm_max = -1 # status
self.stat_vox_05mm_min = -1 # status
self.stat_fs_safe = -1 # status
# This is here basically to just initialize the 'comm' obj
cmd = 'pwd'
self.comm = BASE.shell_com( cmd, capture=1 )
self.comm.run()
check_for_shell_com_failure( self.comm, cmd,
disp_so=False, disp_se=False )
def get_all_3dinfo_dset_basic(fname):
'''Input: a volume 'pon which to run 3dinfo.
Output: dictionary whose keys are 3dinfo opt names relevant for a
single volume (not helpy ones or comparison ones like -same*); the
'-' part is part of the key here, at the moment.
There is no filtering of empty fields here-- the bog standard
outputs are all returned; each value in the dictionary is a list
of string(s), which may be null. See
"get_all_3dinfo_dset_neatly()" for some filtering/proc'ing of
opts.
'''
# ------- Quick check on dset being valid
cmd = '''3dinfo -prefix {fff}'''.format(fff=fname)
com = BASE.shell_com(cmd, capture=1, save_hist=0)
com.run()
if com.so[0] == 'NO-DSET':
print('+* WARNING: No valid dset of that name: {fff}\n.'
' Bye.'.format(fff=fname))
return {}
# ------- Get list of all opts in 3dinfo
cmd = '''apsearch -list_popts 3dinfo'''
com = BASE.shell_com(cmd, capture=1, save_hist=0)
com.run()
# filter out some ones we don't want
list_3dinfo_opts = []
for x in com.so:
y = x.strip()
if not (list_3dinfo_ignore.__contains__(y)):
list_3dinfo_opts.append(y)
dict_info = {}
for opt in list_3dinfo_opts:
cmd = '''3dinfo {ooo} {fff}'''.format(ooo=opt, fff=fname)
com = BASE.shell_com(cmd, capture=1, save_hist=0)
com.run()
dict_info[opt] = com.so
return dict_info
def finish_defs(self):
# get some basic versions that matter
cmd = '''afni -ver'''
com = BASE.shell_com(cmd, capture=1, save_hist=0)
com.run()
check_for_shell_com_failure(com, cmd, disp_so=False, disp_se=False)
self.set_afni_ver(com.so[0])
def __init__(self):
self.full_cmd = '' # existential...
self.code_ver = ddefs['DEF_ver']
self.afni_ver = ''
self.overwrite = '' # pass along overwrite flag (or not)
# This is here basically to just initialize the 'comm' obj
cmd = 'pwd'
self.comm = BASE.shell_com(cmd, capture=1)
self.comm.run()
check_for_shell_com_failure(self.comm,
cmd,
disp_so=False,
disp_se=False)
def run_fix_all(self):
# all tests for resampling voxel size
if self.stat_vox_iso == False or \
self.stat_vox_1mm_max == False or \
self.stat_vox_05mm_min == False :
self.fix_vox = True
# all tests for changing matrix dims-- note that if we
# resample the vox sizes, then we will also do the
# pad_to_evens, just to be sure the grid hasn't changed (and
# to have consistent output naming); so, leave this check
# after the 'fix_vox' one.
if self.stat_mat_even == False or \
self.fix_vox == True :
self.fix_mat = True
# have this be a bool, for verbose output
if self.fix_mat or self.fix_vox:
self.fix_make_changes = True
else:
self.fix_make_changes = False
# determine output voxel size; user might have entered a value
# (and that will have already been checked for validity at input)
if self.fix_vox:
if self.fix_out_vox_dim == None: # then it hasn't been set by user
if self.vox_dim_min < 0.5:
self.fix_out_vox_dim = 0.5
elif 1.0 < self.vox_dim_min:
self.fix_out_vox_dim = 1.0
else:
self.fix_out_vox_dim = self.vox_dim_min
# do resampling and/or matrix padding, in that order:
if self.fix_vox:
# generate name with random string for fix_vox
# use this function here, because this file won't exist yet!
pp = os.path.dirname(self.fix_out_prefix)
if not (pp):
pp = '.' # the above returns '' for local dir-- not cool
cmd = '''3dnewid -fun11'''
com = BASE.shell_com(cmd, capture=1, save_hist=0)
com.run()
check_for_shell_com_failure(com, cmd, disp_so=False, disp_se=False)
self.fix_tmp_fname = pp + '/' + ddefs['DEF_dset_tmp_base']
self.fix_tmp_fname += com.so[0] + '.nii'
# resampling to iso vox
cmd = '''3dAllineate {ow} \
-1Dmatrix_apply IDENTITY \
-mast_dxyz {dxyz} \
-final wsinc5 \
-source {src} \
-prefix {pref}
'''.format(ow=self.fix_overwrite,
dxyz=self.fix_out_vox_dim,
src=self.dset,
pref=self.fix_tmp_fname)
com = BASE.shell_com(cmd, capture=1, save_hist=0)
com.run()
check_for_shell_com_failure(com, cmd, disp_so=False, disp_se=False)
# any fixing will lead to having this performed
if self.fix_mat:
# decide if we already did one correction step or not
if self.fix_tmp_fname:
input_dset = self.fix_tmp_fname
else:
input_dset = self.dset
# resampling to iso vox
cmd = '''3dZeropad {ow} \
-pad2evens \
-prefix {pref} \
{src}
'''.format(ow=self.fix_overwrite,
src=input_dset,
pref=self.fix_out_prefix)
com = BASE.shell_com(cmd, capture=1, save_hist=0)
com.run()
check_for_shell_com_failure(com, cmd, disp_so=False, disp_se=False)
# clean up, if intermed dset exists
if self.fix_vox:
cmd = '''\\rm {pref}
'''.format(pref=self.fix_tmp_fname)
com = BASE.shell_com(cmd, capture=1, save_hist=0)
com.run()
check_for_shell_com_failure(com, cmd, disp_so=False, disp_se=False)
if not (self.fix_make_changes):
# no changes, but output a dset with the correct file name
cmd = '''3dcalc {ow} \
-a {src} \
-expr 'a' \
-prefix {pref}
'''.format(ow=self.fix_overwrite,
src=self.dset,
pref=self.fix_out_prefix)
com = BASE.shell_com(cmd, capture=1, save_hist=0)
com.run()
check_for_shell_com_failure(com, cmd, disp_so=False, disp_se=False)
# get info about output set
self.set_fix_out_info()
# --------------------------------------------------------------------
# QC block: "warns"
# item : censor fraction, per stimulus
# use if: there are stim files present, and censoring
ldep = ['stats_dset', 'censor_dset', 'ss_review_dset', 'xmat_stim']
if lat.check_dep(ap_ssdict, ldep):
# get the ss_review_basic info as a dict
rev_dict = lat.read_in_txt_to_dict(ap_ssdict['ss_review_dset'],
tmp_name='__tmp_ss_rev.json')
cmd = '''1d_tool.py -verb 0 -infile {xmat_stim} -show_labels
'''.format(**ap_ssdict)
com = BASE.shell_com(cmd, capture=1, save_hist=0)
com.run()
all_labels = com.so[0].split() # list of all labels
ban = lat.bannerize('Censor fraction (per stim)')
obase = 'qc_{:02d}'.format(idx)
cmd = lat.apqc_warns_cen_stim(obase,
"warns",
"cen_stim",
rev_dict=rev_dict,
label_list=all_labels)
str_FULL += ban
str_FULL += cmd
idx += 1
