def __init__(self,name):
if type(name) is not str:
print("\nError: "+str(name)+ " must be of type 'str'!!\n")
sys.exit(1)
## namey things
self.name = name
self.rel_path = os.path.dirname(name)
self.full_path_name = os.path.abspath(name)
self.full_path = os.path.dirname(self.full_path_name)
self.full_path_prefix = os.path.splitext(self.full_path_name)[0]
self.file_name = os.path.basename(name)
self.prefix = os.path.splitext(self.file_name)[0]
self.ext = os.path.splitext(self.file_name)[1]
## read in and get list of fields
self.dict = json_import(name)
self.fields = self.dict.keys()
## some useful fields
if "EchoTime" in self.fields:
self.te_sec = self.dict["EchoTime"]
self.te = self.te_sec * 1000
else:
self.te_sec = None ; self.te = None
if "RepetitionTime" in self.fields:
self.tr = self.dict["RepetitionTime"]
else:
self.tr = ""
if "SliceTiming" in self.fields:
self.slice_list = self.dict["SliceTiming"]
self.slice_str = ' '.join(map(str,self.slice_list))
else:
self.slice_list = None ; self.slice_str = None
## find matching nifti and return afni_name object
if os.path.isfile(self.full_path_prefix+".nii.gz"):
self.nii = afni_base.afni_name(self.full_path_prefix+".nii.gz")
elif os.path.isfile(self.full_path_prefix+".nii"):
self.nii = afni_base.afni_name(self.full_path_prefix+".nii")
else:
self.nii = afni_base.afni_name("None")
return
' mask: mask volume dataset\n' \
' out.script: name for output script to write\n' \
'\n' \
'R Reynolds July, 2010\n' % (prog, prog)
narg = 0
if len(sys.argv) != 5:
if len(sys.argv) == 1 or '-help' in sys.argv:
print(helpstr)
sys.exit(0)
else:
print('\n usage: %s dataset brick_index mask out.script\n' % prog)
sys.exit(1)
narg += 1
dset = B.afni_name(sys.argv[narg])
if not dset.exist():
print('** dataset %s not found' % dset.rpv())
sys.exit(1)
narg += 1
try:
sub = int(sys.argv[narg])
except:
print('** invalid sub-brick index %s' % sys.argv[narg])
sys.exit(1)
narg += 1
mask = B.afni_name(sys.argv[narg])
if not mask.exist():
print('** dataset %s not found' % mask.rpv())
def script_set_vars(self):
"""use variables for inputs (anat, epi, epi_base) and for
options (cost_main, cost_list, align_opts)
"""
U = self.uvars # for convenience
# init with a section comment
cmd = SUBJ.comment_section_string('set processing variables') + '\n'
# maybe init with top_dir
if not self.LV.is_trivial_dir('top_dir'):
cmd += '# top data directory\n' \
'set top_dir = %s\n\n' % self.LV.top_dir
# surf_vol and vol_mask might use top_dir
if self.LV.is_trivial_dir('top_dir'):
# if self.cvars.val('on_surface') != 'yes': self.LV.svol = U.surf_vol
#
# rcr - fix this, surf_vol should not be needed if only on surface
# (for getting the node count, avoid SurfMeasures or any other
# program that uses -sv)
self.LV.svol = U.surf_vol
self.LV.svset = BASE.afni_name(self.LV.svol)
self.LV.vmask = U.vol_mask
self.LV.vmset = BASE.afni_name(U.vol_mask)
self.LV.spec = U.spec_file
if self.uvars.surf_mask != '':
self.LV.smset = BASE.afni_name(self.uvars.surf_mask)
self.LV.smask = self.LV.smset.real_input()
else:
self.LV.svol = '$top_dir/%s' % self.LV.short_names[0][0]
self.LV.svset = BASE.afni_name(self.LV.svol)
self.LV.spec = '$top_dir/%s' % self.LV.short_names[0][1]
if self.cvars.val('on_surface') == 'yes':
if self.uvars.surf_mask != '':
self.LV.smask = '$top_dir/%s' % self.LV.short_names[0][2]
self.LV.smset = BASE.afni_name(self.LV.smask)
else:
self.LV.vmask = '$top_dir/%s' % self.LV.short_names[0][2]
self.LV.vmset = BASE.afni_name(self.LV.vmask)
cmd += '# input datasets and surface specification file\n' \
'# (absolute paths are used since inputs are not copied)\n' \
'set surf_vol = %s\n' \
'set spec_file = %s\n' % (self.LV.svol, self.LV.spec)
if self.cvars.val('on_surface') != 'yes':
cmd += 'set vol_mask = %s\n' % self.LV.vmask
if self.LV.val('smask'):
cmd += 'set surf_mask = %s\n' % self.LV.smask
# as a list, these might come is as strings or floats, be generic
plist = [ '%s'%p for p in U.pthr_list ]
cmd += '\n' \
'# iterations and blur/clust parameters\n' \
'set niter = %d\n' \
'set itersize = %d\n' \
'set pthr_list = ( %s )\n\n' \
'set blur = %g\n' \
'set rmm = %g\n\n' \
% (U.niter, U.itersize, ' '.join(plist), U.blur, U.rmm)
cmd += '# surface mapping parameters\n' \
'set surfA = %s\n' \
'set surfB = %s\n' \
'set map_func = %s\n' \
'set nsteps = %d\n\n' \
% (U.surfA, U.surfB, U.map_func, self.cvars.nsteps)
if self.cvars.keepblocks > 0:
cmd += '# note how many blocks to keep output datasets for\n' \
'set keepblocks = %d\n\n' % self.cvars.keepblocks
if self.cvars.time_process:
cmd += "# prepare to possibly time programs (/usr/bin/time or '')\n" \
"set time_str = /usr/bin/time \n\n"
self.LV.time_str = '$time_str \\\n'
else: self.LV.time_str = ''
return cmd
if ted_bin is None:
ted_bin = afni_dir + "/meica.libs/tedana.py"
if not os.path.exists(ted_bin):
print("\nERROR: tedana.py version: " + ted_bin + " not found!!\n")
sys.exit(1)
else:
print("\nUsing: " + ted_bin + " for tedana.py.\n")
########################################################################
## proc loop
## place holder
p50 = ""
## create the mask object here
mask_dset = afni_base.afni_name(mask)
for e in range(0, len(echos)):
## make names for the intermediate datasets
cur_echo = afni_base.afni_name(echos[e])
mask_echo = afni_base.afni_name(echos[e])
mask_echo.new_prefix(OutName + "_echo_" + str(e + 1) + "_masked")
mask_echo.new_path(OutFolder)
# mask_scaled_echo = afni_base.afni_name(echos[e])
# mask_scaled_echo.new_prefix(OutName+"_echo_"+str(e+1)+"_masked_scaled")
# mask_scaled_echo.new_path(OutFolder)
# mean_echo = afni_base.afni_name(echos[e])
## verify rename lengths
if new_prefix is not None:
if len(new_prefix) != len(dset_list):
print("\nError: "+str(len(new_prefix))+" prefix(es) do(es) not match "+
str(len(dset_list))+" dataset(s)!!\n")
sys.exit(1)
########################################################################
## go for all
for i in range(0,len(dset_list)):
########################################################################
## check input dataset
## name the dset
dset = afni_base.afni_name(dset_list[i])
## get some info
afni_cmd = ("3dinfo -exists -ni -nj -nk -TR "+dset.rppv())
check_info = subprocess.check_output(afni_cmd,shell=True).split()
## is the input dataset there?
if check_info[0] == "0":
print("\nError: "+dset.pv()+" does not exist or is not loadable!!\n")
sys.exit(1)
########################################################################
## check for the json file and read it in
## automatically find matching .json ad check it
json_file = dset.realp()+dset.prefix+".json"
def process_opts(self):
"""apply each option"""
# ----------------------------------------
# set verb first
self.verb, err = self.user_opts.get_type_opt(int, '-verb')
if err: return 1
if self.verb == None: self.verb = gDEF_VERB
# ----------------------------------------
# required args
self.infiles, err = self.user_opts.get_string_list('-infiles')
if self.infiles == None or err: return 1
# ----------------------------------------
# optional arguments
val, err = self.user_opts.get_string_opt('-kernel')
if err: return 1
if val != None: self.kernel = val
val, err = self.user_opts.get_string_opt('-kernel_file')
if err: return 1
if val != None: self.kfile = val
val, err = self.user_opts.get_string_opt('-mask_dset')
if err: return 1
if val != None: self.maskset = val
# allow use of old method
if self.user_opts.find_opt('-old'): self.stype = 'old'
val, err = self.user_opts.get_string_opt('-outdir')
if err: return 1
if val != None: self.outdir = val
val, err = self.user_opts.get_string_opt('-prefix')
if err: return 1
if val != None: self.prefix = val
self.script, err = self.user_opts.get_string_opt('-script')
if self.script == None or err: return 1
val, err = self.user_opts.get_type_opt(float, '-tr')
if err: return 1
if val != None: self.tr = val
val, err = self.user_opts.get_type_opt(int, '-tr_nup')
if err: return 1
if val != None: self.tr_nup = val
# ----------------------------------------
# check over the inputs
if len(self.infiles) < 1:
print('** missing option -infiles')
return 1
# check over -input as an AFNI dataset
self.aname = BASE.afni_name(self.infiles[0])
if self.aname == None: return 1
if self.verb > 2: self.aname.show()
if self.aname.type == '1D':
if self.tr == None:
print('** -tr is required if the input is in 1D format')
self.reps = UTIL.max_dim_1D(self.infiles[0])
else:
if self.aname.type != 'BRIK':
print("** unknown 'type' for -input '%s'" % self.infiles[0])
err,self.reps,self.tr = \
UTIL.get_dset_reps_tr(self.aname.pv(), verb=self.verb)
if err: return 1
if self.verb > 1:
print('-- using kernel %s, kfile %s, tr = %s, reps = %s' % \
(self.kernel, self.kfile, self.tr, self.reps))
return None
def process_opts(self):
"""apply each option"""
# ----------------------------------------
# set verb first
self.verb, err = self.user_opts.get_type_opt(int, '-verb')
if err: return 1
if self.verb == None: self.verb = gDEF_VERB
# ----------------------------------------
# required args
opt = self.user_opts.find_opt('-dsets')
if opt and opt.parlist:
self.dsets = opt.parlist
self.adsets = [BASE.afni_name(s) for s in opt.parlist]
if len(self.dsets) < 1:
print('** missing input dataets')
return 1
# ----------------------------------------
# optional arguments
self.script, err = self.user_opts.get_string_opt('-script')
if err: return 1
if self.script == None: self.script = '@review_epi_data'
if os.path.isfile(self.script):
print("** script file '%s' already exists, failing..." \
% self.script)
return 1
opt = self.user_opts.find_opt('-windows')
if opt and opt.parlist:
self.windows = opt.parlist
if len(self.windows) < 1:
print('** missing window list')
return 1
# ----------------------------------------
# image coordinates
self.im_size, err = self.user_opts.get_type_list(int,
'-im_size',
2,
'two',
verb=self.verb)
if err: return 1
if not self.im_size: self.im_size = gDEF_IM_SIZE
self.im_xoff, err = self.user_opts.get_type_opt(int, '-im_xoff')
if err: return 1
if not self.im_xoff: self.im_xoff = gDEF_IM_XOFF
self.im_yoff, err = self.user_opts.get_type_opt(int, '-im_yoff')
if err: return 1
if not self.im_yoff: self.im_yoff = gDEF_IM_YOFF
# ----------------------------------------
# graph coordinates
self.gr_size, err = self.user_opts.get_type_list(int,
'-gr_size',
2,
'two',
verb=self.verb)
if err: return 1
if not self.gr_size: self.gr_size = gDEF_GR_SIZE
self.gr_xoff, err = self.user_opts.get_type_opt(int, '-gr_xoff')
if err: return 1
if not self.gr_xoff: self.gr_xoff = gDEF_GR_XOFF
self.gr_yoff, err = self.user_opts.get_type_opt(int, '-gr_yoff')
if err: return 1
if not self.gr_yoff: self.gr_yoff = gDEF_GR_YOFF