def main_noninteractive():
"""The main routine for running non-interactively."""
global imcftpl
args = parse_arguments()
set_loglevel(args.verbose)
log.info('Running in non-interactive mode.')
log.debug('Python FluoView package file: %s' % fv.__file__)
base = dirname(args.mosaiclog)
fname = basename(args.mosaiclog)
mosaics = fv.FluoViewMosaic(join(base, fname))
log.warn(gen_mosaic_details(mosaics))
if args.templates is not None:
imcftpl = args.templates
code = imagej.gen_stitching_macro_code(mosaics, 'templates/stitching',
path=base, tplpath=imcftpl)
if not args.dryrun:
log.info('Writing stitching macro.')
imagej.write_stitching_macro(code, fname='stitch_all.ijm', dname=base)
log.info('Writing tile configuration files.')
imagej.write_all_tile_configs(mosaics, fixsep=True)
log.info('Launching stitching macro.')
IJ.runMacro(flatten(code))
else:
log.info('Dry-run was selected. Printing generated macro:')
log.warn(flatten(code))
def main():
"""Parse commandline arguments and run parser."""
args = parse_arguments()
set_loglevel(args.verbosity)
dname = dirname(args.mosaic.name)
fname = basename(args.mosaic.name)
if args.out == '':
dout = dname
else:
dout = args.out
mosaic = fv.FluoViewMosaic(args.mosaic.name)
ij.write_all_tile_configs(mosaic, fixsep=args.fixsep)
code = ij.gen_stitching_macro_code(mosaic, 'stitching', path=dname)
ij.write_stitching_macro(code, 'stitch_all.ijm', dout)
def main_interactive():
"""The main routine for running interactively."""
log.info('Running in interactive mode.')
(base, fname) = ui_get_input_file()
if (base is None):
return
log.warn("Parsing project file: %s" % (base + fname))
IJ.showStatus("Parsing experiment file...")
mosaics = fv.FluoViewMosaic(join(base, fname), runparser=False)
IJ.showStatus("Parsing mosaics...")
progress = 0.0
count = len(mosaics.mosaictrees)
step = 1.0 / count
for subtree in mosaics.mosaictrees:
IJ.showProgress(progress)
mosaics.add_mosaic(subtree)
progress += step
IJ.showProgress(progress)
IJ.showStatus("Parsed %i mosaics." % len(mosaics))
dialog = GenericDialog('FluoView OIF / OIB Stitcher')
if len(mosaics) == 0:
msg = ("Couldn't find any (valid) mosaics in the project file.\n"
" \n"
"Please make sure to have all files available!\n"
" \n"
"Will stop now.\n")
log.warn(msg)
dialog.addMessage(msg)
dialog.showDialog()
return
msg = "------------------------ EXPORT OPTIONS ------------------------"
dialog.addMessage(msg)
formats = ["OME-TIFF", "ICS/IDS"]
dialog.addChoice("Export Format", formats, formats[0])
dialog.addCheckbox("separate files by Z slices (OME-TIFF only)?", False)
msg = "------------------------ EXPORT OPTIONS ------------------------"
dialog.addMessage(msg)
dialog.addMessage("")
dialog.addMessage("")
msg = gen_mosaic_details(mosaics)
log.warn(msg)
msg += "\n \nPress [OK] to write tile configuration files\n"
msg += "and continue with running the stitcher."
dialog.addMessage(msg)
dialog.showDialog()
opts = {}
if dialog.getNextChoice() == 'ICS/IDS':
opts['export_format'] = '".ids"'
else:
opts['export_format'] = '".ome.tif"'
if dialog.getNextBoolean() == True:
opts['split_z_slices'] = 'true'
code = imagej.gen_stitching_macro_code(mosaics, 'templates/stitching',
path=base, tplpath=imcftpl, opts=opts)
log.warn("============= generated macro code =============")
log.warn(flatten(code))
log.warn("============= end of generated macro code =============")
if dialog.wasOKed():
log.warn('Writing stitching macro.')
imagej.write_stitching_macro(code, fname='stitch_all.ijm', dname=base)
log.warn('Writing tile configuration files.')
imagej.write_all_tile_configs(mosaics, fixsep=True)
log.warn('Launching stitching macro.')
IJ.runMacro(flatten(code))