def gen_eddy_outputname(self):
fn = self.txt_output_eddy.get()
if fn == '' or '_rigid.nii.gz' in fn:
fn = filename_wo_ext(self.txt_dwi.get()) + '_eddy_unwarped.nii.gz'
else:
fn = filename_wo_ext(self.txt_dwi.get()) + '_rigid.nii.gz'
self.reset_entry(self.txt_output_eddy, fn)
def get_dwi_filenames(self):
'''
:return: [('from', 'to'), ('from', 'to')]
'''
filename_from = self.text_from.get()
filename_to = self.text_to.get()
if self.is_dw.get():
rtn = [ [filename_from, filename_to] ]
filename_b_from = filename_wo_ext(filename_from)
filename_b_to = filename_wo_ext(filename_to)
rtn.append( [filename_b_from+'.bval', filename_b_to+'.bval'] )
rtn.append( [filename_b_from+'.bvec', filename_b_to+'.bvec'] )
return rtn
return []
def run_topup(self):
dependency = [
self.txt_b0,
self.txt_b0mask,
]
if not self.check_dependency(dependency):
return
working = self.txt_working.get()
fn_b0 = os.path.join(working, self.txt_b0.get())
fn_b0mask = os.path.join(working, self.txt_b0mask.get())
fn_b0masked = filename_wo_ext(fn_b0) + '_masked.nii.gz'
fn_out = os.path.join(working, self.prefix() + 'topup')
run_command('fslmaths %s -mas %s %s' % (fn_b0, fn_b0mask, fn_b0masked))
topup_command = [self.txt_topup_app.get()]
if self.txt_topup_config.get() != '':
topup_command.append('--config=%s' % self.txt_topup_config.get())
topup_command.append('--datain=%s' %
(os.path.join(working,
self.prefix() + 'acqparams.txt')))
topup_command.append('--imain=%s' % fn_b0masked)
topup_command.append('--out=%s' % fn_out)
topup_command.append('--iout=%s_warped' % fn_out)
topup_command.append('--fout=%s_field' % fn_out)
topup_command.append('--logout=%s_log' % fn_out)
topup_command.append('1> %s_topup_log.out' % self.txt_subject.get())
cmd = ' '.join(topup_command)
append_text(self.log, cmd, 'run_topup')
run_command(cmd)
print 'Done: TOPUP'
tkMessageBox.showinfo(self.title, 'Done: TOPUP')
def set_filenames(filename):
filename_woext = filename_wo_ext(filename)
filename_wodir = os.path.basename(filename_woext)
filename_fltd = '%s_mask_base_filtered' % filename_wodir
filename_mask = '%s_mask' % filename_wodir
return filename, filename_fltd, filename_mask
def __init__(self,
parent,
filename=None,
filename_roi=None,
filename_csv=None,
dirname=None,
obj_return_value=None):
Frame.__init__(self, parent)
self.parent = parent
self.obj_return_value = obj_return_value
# check filenames
if filename is None or not os.path.isfile(filename):
if dirname is not None:
filename = tkFileDialog.askopenfilename(initialdir=dirname)
else:
filename = tkFileDialog.askopenfilename()
if not os.path.isfile(filename):
parent.destroy()
return
if filename_roi is None or not os.path.isfile(filename_roi):
if dirname is not None:
filename_roi = tkFileDialog.askopenfilename(initialdir=dirname)
else:
filename_roi = tkFileDialog.askopenfilename()
if not os.path.isfile(filename_roi):
parent.destroy()
return
if dirname is None:
self.dirname = os.path.dirname(filename)
else:
self.dirname = dirname
if filename_csv is None:
filename_csv = os.path.join(
self.dirname,
filename_wo_ext(os.path.basename(filename)) + '.csv')
self.filename = filename
self.filename_roi = filename_roi
self.filename_csv = filename_csv
self.dat = nib.load(filename).get_data()
self.shape = self.dat.shape
print self.shape
dz = self.shape[2]
df = self.shape[-1]
self.badenc = np.zeros((dz, df), dtype=np.int16)
self.prev = np.zeros((dz, df), dtype=np.int16)
self.z = 0
self.initUI()
self.run()
def update_parameter(self):
if self.parameter_values.has_key('subject'):
self.reset_entry(self.txt_subject,
self.parameter_values['subject'])
if self.parameter_values.has_key('dwi'):
self.reset_entry(self.txt_dwi, self.parameter_values['dwi'])
self.reset_entry(
self.txt_bval,
filename_wo_ext(self.parameter_values['dwi']) + '.bval')
self.reset_entry(
self.txt_bvec,
filename_wo_ext(self.parameter_values['dwi']) + '.bvec')
if self.parameter_values.has_key('b0'):
self.reset_entry(self.txt_b0, self.parameter_values['b0'])
if self.parameter_values.has_key('working'):
self.reset_entry(self.txt_working,
self.parameter_values['working'],
force=True)
def __init__(self, parent, filename=None, filename_csv=None, dirname=None, obj_return_value=None):
Frame.__init__(self, parent)
self.parent = parent
self.obj_return_value = obj_return_value
# check filenames
if filename is None or not os.path.isfile(filename):
if dirname is not None:
filename = tkFileDialog.askopenfilename(initialdir=dirname)
else:
filename = tkFileDialog.askopenfilename()
if not os.path.isfile(filename):
parent.destroy()
return
if dirname is None:
self.dirname = os.path.dirname(filename)
else:
self.dirname = dirname
if filename_csv is None:
filename_csv = os.path.join(self.dirname, filename_wo_ext(os.path.basename(filename)) + '.csv')
self.filename = filename
self.filename_csv = filename_csv
n_slices = 0
n_frames = 0
with open(filename) as f:
line = f.readline()
while True:
line = f.readline()
if not line:
break
slice, frame = [int(tmp) for tmp in line.strip().split(',')[:2]]
if n_slices < slice:
n_slices = slice
if n_frames < frame:
n_frames = frame
n_slices += 1
n_frames += 1
self.shape = (n_slices, n_frames)
#self.distance_x = np.zeros( self.shape, dtype=float )
#self.distance_y = np.zeros( self.shape, dtype=float )
#self.distance = np.zeros( self.shape, dtype=float )
self.values = np.zeros( (n_slices, n_frames, 3), dtype=float )
self.badenc = np.zeros( self.shape, dtype=np.int16 )
self.prev = np.zeros( self.shape, dtype=np.int16 )
self.z = 0
self.initUI()
self.run()
def set_appa(self):
filename_from = self.text_from.get()
basename_from = os.path.basename(filename_from)
basename_b_from = filename_wo_ext(basename_from)
if 'pa' in basename_b_from.lower():
self.direction.set('PA')
elif 'ap' in basename_b_from.lower():
self.direction.set('AP')
else:
pass
def run_md_mask(self):
if not os.path.isfile(
os.path.join(self.txt_working.get(), self.txt_dwi_dti.get())):
sys.stderr.write('File not exist: %s\n' % self.txt_dwi_dti.get())
return
working = self.txt_working.get()
if os.path.isfile(os.path.join(working, self.txt_dti_value.get())):
fn_md = filename_wo_ext(self.txt_dti_value.get()) + '_MD.nii.gz'
else:
fn_md = filename_wo_ext(self.txt_dwi_dti.get()) + '_dti_MD.nii.gz'
fn_mask = create_md_mask(os.path.join(working, fn_md),
fn_out=None,
thr_min=0.1,
thr_max=1.1)
print 'Done: Making MD mask'
self.reset_entry(self.txt_md_mask, os.path.basename(fn_mask))
def get_b0_filename(self):
'''
:return: [('from', 'to')]
'''
filename_from = self.text_from.get()
filename_to = self.text_to.get()
ext = extname(filename_to)
if self.is_b0.get():
if self.is_dw.get():
filename_to = '%s_B0%s' % (filename_wo_ext(filename_to), ext)
return [ [filename_from, filename_to] ]
return []
def add_one(self, text=''):
a_dwi = self.A_DWI(self, self.frame, text=text, row=self.len, column=0)
fn_bval = filename_wo_ext(text) + '.bval'
if os.path.isfile(fn_bval):
a_dwi.is_b0.set(False)
a_dwi.is_dw.set(True)
else:
a_dwi.is_b0.set(True)
a_dwi.is_dw.set(False)
a_dwi.set_appa()
a_dwi.set_filename_to()
self.len += 1
self.lst_dwi.append(a_dwi)
def run_dti_outlier(self):
import outlier_4dfp_gui
root = Tk()
working = self.txt_working.get()
filename = os.path.join(
working,
filename_wo_ext(self.txt_dwi_dti.get()) + '_res.nii.gz')
filename_roi = os.path.join(working, self.txt_md_mask.get())
filename_csv = os.path.join(working, self.txt_dti_outlier.get())
if filename_csv == '':
filename_csv = filename_wo_ext(filename) + '.csv'
print filename, filename_roi, filename_csv
app = outlier_4dfp_gui.Outlier4dfp(
root,
filename=filename,
filename_roi=filename_roi,
filename_csv=filename_csv,
dirname=working,
obj_return_value=self.txt_dti_outlier)
root.mainloop()
def gen_dti_value_outputname(self):
fn = filename_wo_ext(self.txt_dti_value.get()) + '.csv'
self.reset_entry(self.txt_output_dti_value, fn)
def gen_dti_name(self):
self.reset_entry(self.txt_dti,
filename_wo_ext(self.txt_dwi_dti.get()) + '_dti')
def gen_reg_outputname(self):
fn = filename_wo_ext(self.txt_dwi_eddy.get()) + '_xenc.nii.gz'
self.reset_entry(self.txt_output_reg, fn)
