def save_data(self):
"""
Dialog for saving an data as a nifti file
"""
if self.ivm.current_data is None:
QtGui.QMessageBox.warning(self, "No data",
"No current data to save",
QtGui.QMessageBox.Close)
else:
if hasattr(self.ivm.current_data,
"fname") and self.ivm.current_data.fname is not None:
fname = self.ivm.current_data.fname
else:
fname = os.path.join(default_save_dir(),
self.ivm.current_data.name + ".nii")
fname, _ = QtGui.QFileDialog.getSaveFileName(
self,
'Save file',
dir=fname,
filter="NIFTI files (*.nii *.nii.gz)")
if fname != '':
save(self.ivm.current_data, fname)
else: # Cancelled
pass
def run(self, options):
exceptions = list(options.keys())
for k in exceptions: options.pop(k)
for name, qpdata in self.ivm.data.items():
if name in exceptions:
continue
try:
save(qpdata, name, outdir=self.outdir)
except QpException as exc:
self.warn("Failed to save %s: %s" % (name, str(exc)))
except:
import traceback
traceback.print_exc()
def save_roi(self):
"""
Dialog for saving an ROI as a nifti file
"""
if self.ivm.current_roi is None:
QtGui.QMessageBox.warning(self, "No ROI", "No current ROI to save",
QtGui.QMessageBox.Close)
else:
fname, _ = QtGui.QFileDialog.getSaveFileName(
self,
'Save file',
dir=self.default_directory,
filter="NIFTI files (*.nii *.nii.gz)")
if fname != '':
save(self.ivm.current_roi, fname)
else: # Cancelled
pass
def _save(self):
if self.data_list.selected is not None:
name = self.data_list.selected.name
data = self.ivm.data[name]
if hasattr(data, "fname") and data.fname is not None:
fname = data.fname
else:
fname = os.path.join(default_save_dir(), name + ".nii")
fname, _ = QtGui.QFileDialog.getSaveFileName(
self,
'Save file',
dir=fname,
filter="NIFTI files (*.nii *.nii.gz)")
if fname != '':
save(self.ivm.data[name], fname)
else: # Cancelled
pass
def save_output(self, save_folder):
"""
Save process output to a folder
In practice this is very process dependent and this method may well need to be
overridden. The default implementation uses the ``output_data_items()`` to
get the names of the data items the process has created and writes these
plus the logfile to the output folder
"""
data_to_save = self.output_data_items()
self.debug("Data to save: %s", data_to_save)
for d in data_to_save:
qpdata = self.ivm.data.get(d, None)
if qpdata is not None:
save(qpdata, os.path.join(save_folder, d + ".nii"))
logfile = open(os.path.join(save_folder, "logfile"), "w")
logfile.write(self._log)
logfile.close()
def run(self, options):
# Note that output-grid is not a valid data name so will not clash
output_grid = None
output_grid_name = options.pop("output-grid", None)
if output_grid_name is not None:
output_grid_data = self.ivm.data.get(output_grid_name, self.ivm.rois.get(output_grid_name, None))
if output_grid_data is None:
raise QpException("No such data found as source of grid: %s" % output_grid_name)
else:
output_grid = output_grid_data.grid
for name in list(options.keys()):
try:
fname = options.pop(name, name)
qpdata = self.ivm.data.get(name, None)
if qpdata is not None:
save(qpdata, fname, grid=output_grid, outdir=self.outdir)
else:
self.warn("Failed to save %s - no such data or ROI found" % name)
except QpException as exc:
self.warn("Failed to save %s: %s" % (name, str(exc)))
def add(self, data_name):
"""
Add a data item to the working directory from the IVM
"""
fname = os.path.join(self.workdir, data_name)
save(self.ivm.data[data_name], fname)