def handle(self, *args, **options):
pipeline = marker_pipeline('260714_s13_7OFMC9VV_', '-zcomp-zedge-7OFMC9VV', 's13_ch-zcomp-primary-7OFMC9VV', 's13_ch-zedge')
out_path = '/Volumes/transport/data/puzzle/260714/pipelines/test.cppipe'
# pipeline = region_pipeline('s14_ch-zbf-regionprimary-8C3WCS1E', 's14_ch-zbf')
with open(out_path, 'w+') as f:
f.write(pipeline)
def save_marker_pipeline(self, series_name=None, primary_channel_name=None, secondary_channel_name=None):
# 1. make unique key
unique = random_string()
unique_key = '{}{}-{}'.format(primary_channel_name, secondary_channel_name, unique)
# 2. format and save file
pipeline_text = marker_pipeline('{}_s{}_{}_'.format(self.name, series_name, unique), unique_key, primary_channel_name, secondary_channel_name)
with open(os.path.join(self.pipeline_path, 'markers.cppipe'), 'w+') as open_pipeline_file:
open_pipeline_file.write(pipeline_text)
return unique, unique_key
def save_marker_pipeline(self, series_name=None, primary_channel_name=None, secondary_channel_name=None, threshold_correction_factor=1.2, background=True, unique='', unique_key=''):
# format and save file
pipeline_text = marker_pipeline('{}_s{}_{}_'.format(self.name, series_name, unique), unique_key, 's{}_ch{}'.format(series_name, primary_channel_name), 's{}_ch{}'.format(series_name, secondary_channel_name), threshold_correction_factor=threshold_correction_factor, background=background)
with open(os.path.join(self.pipeline_path, 'markers.cppipe'), 'w+') as open_pipeline_file:
open_pipeline_file.write(pipeline_text)
