diff --git a/scripts/export/extract_neuron_traces.py b/scripts/export/extract_neuron_traces.py index 9274984b1a262da6597e35230a7f115b4b2c803b..79187739bbfa8f52298bf0c997d6580171281508 100644 --- a/scripts/export/extract_neuron_traces.py +++ b/scripts/export/extract_neuron_traces.py @@ -4,7 +4,7 @@ from glob import glob import numpy as np import h5py -import elf.skeletion.io as skio +import elf.skeleton.io as skio from skimage.draw import circle from pybdv import convert_to_bdv @@ -96,7 +96,7 @@ def make_seg_and_scale(traces, reference_vol_path, reference_scale, seg_out_path res = get_resolution(reference_scale) # the circle radius we write out - radius = 10 + radius = 5 max_id = np.iinfo('int16').max diff --git a/segmentation/cell_segmentation.py b/segmentation/cell_segmentation.py index 763f95cf4fcbc9107f23f9605baa1922262a6ea8..40f78e6d18fc7238a3b5ea5e3b00320e8dbf2790 100644 --- a/segmentation/cell_segmentation.py +++ b/segmentation/cell_segmentation.py @@ -9,7 +9,7 @@ def run_workflow(): target = 'slurm' use_curated_affs = False - use_lmc = False + use_lmc = True workflow(use_curated_affs, use_lmc, target) diff --git a/segmentation/neuron_traces.py b/segmentation/neuron_traces.py index 1e0b1bd45bcfd794d9da6af1a21b89a151733991..63c657fb87f4e58edf67ec8e77e8d733b51cb233 100644 --- a/segmentation/neuron_traces.py +++ b/segmentation/neuron_traces.py @@ -3,13 +3,13 @@ from scripts.export import extract_neuron_traces def export_test_traces(): - folder = '' - ref_path = '' - seg_out_path = '' - table_out_path = '' + folder = '/g/kreshuk/data/arendt/platyneris_v1/tracings' + ref_path = '../data/rawdata/sbem-6dpf-1-whole-raw.h5' + seg_out_path = './sbem-6dpf-1-whole-traces.xml' + table_out_path = './sbem-6dpf-1-whole-traces-table-default.xml' tmp_folder = './tmp_traces' extract_neuron_traces(folder, ref_path, seg_out_path, table_out_path, tmp_folder) if __name__ == '__main__': - export_test_traces + export_test_traces()