Update neuron trace extraction

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
 

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)
 

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()