From 27cf4bffd428f68badf066288f8c585d75910353 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Mon, 26 Aug 2019 16:14:58 +0200
Subject: [PATCH] Update neuron trace extraction
---
scripts/export/extract_neuron_traces.py | 4 ++--
segmentation/cell_segmentation.py | 2 +-
segmentation/neuron_traces.py | 10 +++++-----
3 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/scripts/export/extract_neuron_traces.py b/scripts/export/extract_neuron_traces.py
index 9274984..7918773 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 763f95c..40f78e6 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 1e0b1bd..63c657f 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()
--
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