def main():
task = SR_EELS_CharacterisationPlugin()
task.setRotation(do_rotate)
settings = SR_EELS_CharacterisationSettings()
settings.path = in_dir
settings.images = task.getImages(settings)
task.performCharacterisation(settings)
flags = 0
if create_jpeg:
flags += SR_EELS_CharacterisationResults.JPEG
if create_plots:
flags += SR_EELS_CharacterisationResults.PLOTS
if create_tiff:
flags += SR_EELS_CharacterisationResults.TIFF
if create_csv:
flags += SR_EELS_CharacterisationResults.CSV
if create_subdir:
final_out_dir = File(out_dir, settings.toString())
else:
final_out_dir = out_dir
task.saveResults(final_out_dir, flags)
def main():
automated_characterisation = AutomatedCharacterisation()
automated_characterisation.create_dataset_list()
settings = SR_EELS_CharacterisationSettings()
settings.stepSize = stepSize
settings.filterRadius = math.sqrt(stepSize)
settings.energyBorderLow = energyBorderLow
settings.energyBorderHigh = energyBorderHigh
settings.energyPosition = energyPosition
settings.polynomialOrder = polynomialOrder
settings.useThresholding = useThresholding
settings.threshold = threshold
finished = skipped = failed = 0
dataset_count = len(automated_characterisation.datasets)
IJ.log('Processing %d datasets.' % (dataset_count,))
count = 0
for dataset in automated_characterisation.datasets:
count += 1
if not os.path.exists(os.path.join(dataset, settings.toString())):
IJ.log('%d/%d Starting to process "%s".' % (count, dataset_count, dataset))
images = ArrayList()
for image in os.listdir(dataset):
if re.search('Cal_\d+\.tif', image):
images.add(image)
settings.images = images
settings.path = File(dataset)
try:
characterisation = SR_EELS_CharacterisationPlugin()
characterisation.performCharacterisation(settings)
results_path = File(settings.path, settings.toString())
characterisation.saveResults(results_path, types)
finished += 1
except RuntimeException:
IJ.log('%d/%d There was an error when processing "%s"!' % (count, dataset_count, dataset))
failed += 1
else:
IJ.log('%d/%d Skipping "%s" as results for "%s" exist.' % (count, dataset_count, dataset, settings.toString()))
skipped += 1
IJ.log('\nFinished automated SR-EELS characterisation:')
IJ.log('Finished: %d\nSkipped: %d\nFailed: %d' % (finished, skipped, failed))