def export(self):
from tifffile import imsave
from pyqtgraph import FileDialog
start_doc = getattr(self.catalog, self.stream).metadata['start']
if 'FileName' in start_doc:
current_dir = str(Path(start_doc['FileName']).parent)
current_name = Path(start_doc['FileName']).stem
elif 'sample_name' in start_doc:
current_dir = str(
Path.home()) # sample name is usually just te file stem
current_name = Path(start_doc['sample_name']).stem
else:
current_dir = Path.home()
current_name = 'xicamNCEM_output'
# Get a file path to save to in current directory
fd = FileDialog()
fd.setNameFilter("TIF (*.tif)")
fd.setDirectory(current_dir)
fd.selectFile(current_name)
fd.setFileMode(FileDialog.AnyFile)
fd.setAcceptMode(FileDialog.AcceptSave)
if fd.exec_():
file_names = fd.selectedFiles()[0]
outPath = Path(file_names)
else:
return
if outPath.suffix != '.tif':
outPath = outPath.with_suffix('.tif')
scale0, units0 = self._get_physical_size()
# Avoid overflow in field of view later
if units0[0] == 'm':
units0 = ['um', 'um']
scale0 = [ii * 1e6 for ii in scale0]
# Change scale from pixel to 1/pixel
FOV = [1 / ii for ii in scale0]
# Add units to metadata for Imagej type output
metadata = {'unit': units0[0]}
# Get the data and change to float
image = self.xarray[self.currentIndex, :, :].astype('f')
imsave(outPath, image, imagej=True, resolution=FOV, metadata=metadata)
