diff --git a/data/rawdata/tables/sbem-6dpf-1-whole-traces-labels/default.csv b/data/rawdata/tables/sbem-6dpf-1-whole-traces-labels/default.csv
index bef792dc6d75f151485ca21187a552e55627ffbf..306ed78c4d5aa7fb0293730f7c134f9737e00fe0 100644
--- a/data/rawdata/tables/sbem-6dpf-1-whole-traces-labels/default.csv
+++ b/data/rawdata/tables/sbem-6dpf-1-whole-traces-labels/default.csv
@@ -1,405 +1,405 @@
label_id anchor_x anchor_y anchor_z bb_min_x bb_min_y bb_min_z bb_max_x bb_max_y bb_max_z n_points cell_id nucleus_id
-10.0 193.2 149.2 56.6 191.28 146.8 48.5 210.48 153.52 57.1 262.0 1667.0 0.0
-100.0 203.76 156.08 58.8 203.36 147.68 0.2 221.36 161.92 63.2 993.0 1667.0 0.0
-101.0 179.04 200.56 58.2 152.24 188.08 21.2 200.96 210.32 58.3 632.0 1667.0 0.0
-103.0 177.2 193.84 59.4 177.2 186.88 0.2 196.88 208.24 61.2 962.0 1667.0 0.0
-109.0 212.56 177.36 68.6 212.56 177.2 68.6 213.28 179.52 71.1 12.0 1667.0 0.0
-113.0 179.44 182.88 59.1 176.64 177.2 50.8 184.56 188.56 66.1 506.0 1667.0 0.0
-115.0 177.28 181.6 56.9 175.36 164.16 56.2 197.2 187.68 66.8 452.0 1667.0 0.0
-117.0 191.04 193.76 56.2 178.64 186.88 55.7 195.04 195.28 66.4 331.0 1667.0 0.0
-119.0 188.0 193.52 56.5 178.64 186.88 55.5 191.36 194.64 65.4 259.0 1667.0 0.0
-12.0 194.0 148.56 55.4 191.04 148.0 48.1 206.88 154.0 56.2 296.0 1667.0 0.0
-125.0 200.16 178.8 72.4 189.44 177.76 68.9 200.88 222.4 76.6 480.0 1667.0 0.0
-127.0 195.84 184.96 61.1 189.12 184.32 61.1 200.08 219.2 76.1 737.0 1667.0 0.0
-13.0 192.0 175.68 43.1 184.48 175.28 42.9 194.96 191.76 70.7 908.0 1667.0 0.0
-133.0 203.04 172.24 70.3 201.76 168.0 64.8 238.48 179.04 81.7 652.0 1667.0 0.0
-135.0 190.08 178.64 57.2 190.08 159.12 57.1 206.4 178.72 69.1 337.0 1667.0 0.0
-137.0 185.92 192.72 62.0 185.76 191.28 62.0 201.68 212.32 66.4 305.0 1667.0 0.0
-139.0 189.44 195.2 64.5 186.8 192.48 60.5 202.0 212.64 64.6 169.0 1667.0 0.0
-141.0 194.24 181.44 63.8 190.96 180.8 61.5 198.64 209.28 71.7 361.0 1667.0 0.0
-148.0 209.2 190.56 63.3 190.96 182.4 63.3 211.36 218.72 84.7 537.0 1667.0 0.0
-149.0 215.36 194.16 61.9 191.12 179.2 60.7 215.52 218.72 84.2 1050.0 1667.0 0.0
-151.0 192.08 193.44 73.0 190.96 191.84 73.0 207.92 218.8 86.7 250.0 1667.0 0.0
-152.0 202.16 175.52 72.0 198.08 171.12 63.6 237.76 194.48 83.6 775.0 1667.0 0.0
-154.0 213.68 191.44 63.9 201.6 172.24 63.7 238.0 191.68 82.3 492.0 1667.0 0.0
-157.0 205.68 172.16 73.7 203.92 162.72 71.6 238.8 172.56 91.8 450.0 7617.0 0.0
-158.0 207.92 170.24 72.0 207.28 160.64 71.8 235.92 173.36 91.7 394.0 1667.0 0.0
-160.0 200.32 139.6 45.4 180.4 121.92 10.0 207.2 141.6 52.0 431.0 2949.0 0.0
-162.0 206.88 141.84 48.2 181.36 124.56 9.9 209.76 144.4 52.7 565.0 3667.0 0.0
-164.0 205.52 139.92 48.6 182.64 123.6 10.1 208.48 142.0 60.3 606.0 1667.0 0.0
-166.0 199.76 137.12 47.0 180.0 125.92 6.9 205.44 142.0 57.5 599.0 2949.0 0.0
-167.0 209.52 144.48 47.2 183.36 124.8 9.9 209.76 144.56 47.3 424.0 3667.0 0.0
-169.0 199.04 143.68 42.1 187.44 137.28 11.1 202.48 143.76 42.2 138.0 2949.0 0.0
-171.0 186.16 182.96 61.9 174.08 129.6 8.7 208.8 193.68 66.9 938.0 1667.0 0.0
-173.0 207.04 147.28 54.0 182.48 135.84 8.4 211.12 154.88 57.8 722.0 1667.0 0.0
-176.0 196.96 144.32 48.5 182.48 135.36 5.4 203.92 146.4 53.3 624.0 1667.0 0.0
-178.0 206.72 147.84 52.7 177.68 121.2 6.6 207.92 186.64 63.9 1074.0 1667.0 0.0
-179.0 172.72 193.92 55.8 136.32 163.28 11.6 182.0 194.64 63.5 611.0 1667.0 0.0
-181.0 161.6 187.76 43.7 139.04 167.52 6.9 166.64 191.6 52.0 718.0 1667.0 0.0
-183.0 161.28 188.64 46.3 140.48 167.12 14.0 164.64 189.04 48.4 733.0 1667.0 0.0
-187.0 176.08 189.76 56.7 136.16 164.96 11.0 177.12 191.68 57.4 752.0 1667.0 0.0
-189.0 158.24 187.68 40.5 136.0 164.72 11.5 184.72 194.16 66.8 805.0 1667.0 0.0
-191.0 184.16 187.12 62.1 138.08 167.12 12.7 184.24 195.92 62.7 841.0 1667.0 0.0
-193.0 186.96 192.4 70.7 136.48 166.16 10.2 205.44 193.76 72.4 856.0 1667.0 0.0
-195.0 161.6 185.04 49.9 138.24 160.24 15.6 162.96 187.2 50.0 485.0 1667.0 0.0
-197.0 163.12 184.32 46.3 135.92 165.36 13.7 163.68 187.52 48.5 546.0 1667.0 0.0
-199.0 158.64 188.48 38.9 136.64 165.44 9.2 163.6 188.96 53.2 555.0 1667.0 0.0
-201.0 187.84 165.84 34.9 138.64 165.52 15.3 188.08 187.76 49.3 924.0 1667.0 0.0
-203.0 186.32 167.44 34.5 143.36 166.96 10.8 186.88 189.36 48.8 1249.0 1667.0 0.0
-205.0 133.76 174.0 57.6 133.6 170.88 6.5 160.48 192.0 57.7 744.0 4374.0 0.0
-207.0 206.8 143.04 54.2 141.6 143.04 6.5 209.68 195.6 67.1 1341.0 1667.0 0.0
-209.0 178.08 191.44 55.6 167.2 191.44 53.1 179.84 219.28 71.9 415.0 1667.0 0.0
-21.0 203.68 173.44 67.8 203.6 166.0 63.4 224.96 175.76 69.4 669.0 1667.0 0.0
-211.0 209.76 184.72 52.5 167.44 181.44 47.4 212.08 215.2 60.8 1058.0 1667.0 0.0
-213.0 202.24 183.84 59.7 163.84 176.08 51.5 206.8 225.68 65.2 1044.0 1667.0 0.0
-215.0 191.76 187.92 61.9 169.52 185.68 50.8 194.0 216.72 64.2 817.0 1667.0 0.0
-216.0 206.56 192.08 61.0 164.4 184.08 49.4 208.08 225.36 68.5 1273.0 1667.0 0.0
-218.0 213.36 190.64 58.2 163.2 183.68 50.6 216.64 218.08 68.1 1043.0 1667.0 0.0
-220.0 181.44 190.88 52.5 163.52 190.16 51.9 181.68 224.96 67.4 584.0 1667.0 0.0
-222.0 192.8 182.32 51.9 166.08 177.28 40.7 198.0 210.64 68.0 1816.0 1667.0 0.0
-223.0 170.0 198.32 55.3 166.72 195.68 50.1 173.2 218.96 60.7 274.0 1667.0 0.0
-225.0 191.68 183.76 60.4 169.28 183.44 51.3 191.84 217.92 60.5 847.0 1667.0 0.0
-226.0 168.0 195.28 53.1 159.76 195.28 53.1 169.84 225.12 65.9 266.0 1667.0 0.0
-228.0 193.92 191.2 50.9 152.96 166.96 43.2 211.36 223.2 60.6 1836.0 1667.0 0.0
-230.0 206.08 157.2 54.2 200.8 137.2 52.9 239.52 179.36 65.6 1201.0 1667.0 0.0
-232.0 203.68 173.36 64.8 197.92 138.48 52.6 240.32 187.84 66.2 1179.0 1667.0 0.0
-234.0 197.28 175.28 61.9 196.72 144.0 51.9 234.08 178.32 63.9 1321.0 1667.0 0.0
-236.0 200.64 182.4 60.5 195.6 143.28 52.3 241.84 183.6 65.1 1230.0 1667.0 0.0
-238.0 210.56 156.0 56.5 208.08 144.64 54.7 224.0 156.08 64.0 203.0 1667.0 0.0
-240.0 211.44 170.56 55.6 200.32 143.6 53.2 230.88 174.64 65.1 756.0 1667.0 0.0
-242.0 210.96 180.16 66.7 199.28 138.96 52.1 240.24 195.68 67.3 1475.0 1667.0 0.0
-244.0 209.92 156.88 55.8 209.84 132.64 55.4 227.52 157.28 58.8 251.0 1667.0 0.0
-246.0 210.8 147.12 57.3 209.28 135.68 54.9 229.6 148.48 59.0 189.0 1667.0 0.0
-248.0 199.44 172.32 41.0 197.36 128.8 39.5 225.76 178.88 60.3 1364.0 1667.0 0.0
-249.0 201.36 177.36 64.7 200.16 138.72 53.6 241.36 198.16 69.6 1140.0 1667.0 0.0
-251.0 200.48 170.56 67.4 198.72 136.16 53.5 225.52 176.08 68.4 1452.0 1667.0 0.0
-253.0 205.04 160.48 59.2 201.36 124.88 54.0 232.32 162.24 59.5 759.0 1667.0 0.0
-255.0 203.6 176.48 45.5 194.0 132.64 39.2 223.12 178.24 60.3 1277.0 1667.0 0.0
-257.0 208.64 158.48 54.9 194.08 140.8 41.4 226.64 177.36 63.1 1867.0 1667.0 0.0
-259.0 163.36 187.44 51.2 156.56 164.64 4.9 173.6 187.68 53.4 804.0 1667.0 0.0
-26.0 211.28 152.32 0.6 208.16 151.84 0.1 223.92 171.84 37.5 538.0 14.0 0.0
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-263.0 163.76 185.6 45.9 152.4 162.64 4.2 169.36 188.16 46.0 833.0 1667.0 0.0
-265.0 169.92 180.72 52.4 156.96 163.6 5.7 173.84 185.36 52.5 723.0 1667.0 0.0
-269.0 164.16 190.48 51.8 157.12 167.76 10.1 172.72 192.96 51.9 536.0 1667.0 0.0
-271.0 158.88 187.68 45.4 153.68 161.76 4.9 174.96 192.88 57.6 811.0 1667.0 0.0
-273.0 162.32 186.16 38.5 156.0 168.72 9.6 169.12 189.92 41.1 282.0 1667.0 0.0
-275.0 161.36 183.36 46.8 156.4 164.08 4.8 176.88 184.8 56.5 786.0 1667.0 0.0
-277.0 163.12 190.0 41.6 155.68 167.68 7.8 169.12 190.88 42.0 411.0 1667.0 0.0
-279.0 163.04 191.36 42.1 155.76 168.56 12.4 170.56 191.44 42.7 472.0 1667.0 0.0
-281.0 162.16 193.84 45.3 154.56 163.76 4.8 178.08 195.28 48.3 589.0 1667.0 0.0
-283.0 162.8 193.52 42.1 157.12 168.24 9.7 174.8 193.6 43.5 502.0 1667.0 0.0
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-289.0 213.36 178.32 57.5 202.24 158.08 54.2 226.24 197.52 72.3 690.0 1667.0 0.0
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-3.0 209.36 179.68 56.8 209.04 164.64 56.8 220.8 179.76 68.8 499.0 1667.0 0.0
-30.0 215.92 148.96 0.2 212.0 148.8 0.2 227.04 165.84 61.3 1331.0 4.0 0.0
-301.0 228.72 150.08 82.8 221.44 150.08 68.2 234.48 158.96 84.6 140.0 8349.0 0.0
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-307.0 220.88 159.44 69.2 220.32 158.56 69.2 233.28 163.84 78.6 99.0 7186.0 0.0
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diff --git a/scripts/export/extract_neuron_traces.py b/scripts/export/extract_neuron_traces.py
index 0f24a210940d3e8b647e2659638dba9e79ff6d9e..e660d0303a8c915a445a420f87939e411205b6f2 100644
--- a/scripts/export/extract_neuron_traces.py
+++ b/scripts/export/extract_neuron_traces.py
@@ -35,6 +35,7 @@ def extract_neuron_traces(trace_folder, reference_vol_path,
print("Make table")
table, col_names = make_table(traces, reference_scale, cell_seg_info, nucleus_seg_info)
write_table(table, col_names, table_out_path)
+ return
# make segmentation in tmp location and compy it to the output path
print("Make segmentation")
@@ -51,7 +52,7 @@ def extract_traces(files):
for k, v in skel.items():
# for now, we only extract nodes belonging to
# what's annotated as 'skeleton'. There are also tags for
- # 'soma' and 'synapse'. I am ignorign these for now.
+ # 'soma' and 'synapse'. I am ignoring these for now.
# is_soma = 'soma' in k
# is_synapse = 'synapse' in k
@@ -114,7 +115,6 @@ def write_table(data, col_names, output_path):
def vals_to_coords(vals, res):
coords = np.array(vals)
- coords = coords[::-1]
coords /= res
coords = coords.astype('uint64')
return coords
@@ -143,10 +143,7 @@ def make_table(traces, reference_scale, cell_seg_info, nucleus_seg_info):
bb_min = coords.min(axis=0)
bb_max = coords.max(axis=0) + 1
- # TODO we want the anchor to correspond to node0. I don't know if this
- # is currently extracted correctly in the coordinates
- # attributes:
- # label_id anchor_x anchor_y anchor_z bb_min_x bb_min_y bb_min_z bb_max_x bb_max_y bb_max_z n_points
+ # get spatial attributes
anchor = coords[0].astype('float32') * res / 1000.
bb_min = bb_min.astype('float32') * res / 1000.
bb_max = bb_max.astype('float32') * res / 1000.
@@ -156,6 +153,11 @@ def make_table(traces, reference_scale, cell_seg_info, nucleus_seg_info):
cell_id = dsc[point_slice][0, 0, 0]
nucleus_id = dsn[point_slice][0, 0, 0]
+ # attributes:
+ # label_id
+ # anchor_x anchor_y anchor_z
+ # bb_min_x bb_min_y bb_min_z bb_max_x bb_max_y bb_max_z
+ # n_points cell-id nucleus-id
attributes = [nid, anchor[2], anchor[1], anchor[0],
bb_min[2], bb_min[1], bb_min[0],
bb_max[2], bb_max[1], bb_max[0],
diff --git a/segmentation/neuron_traces.py b/segmentation/neuron_traces.py
index f146f8914b88921dda22789d0ffb08e91a3b0776..ed2924dc67d4de740e3759395502592bcf6cda34 100644
--- a/segmentation/neuron_traces.py
+++ b/segmentation/neuron_traces.py
@@ -51,6 +51,6 @@ def get_cell_ids():
if __name__ == '__main__':
- get_cell_ids()
- # export_traces()
+ # get_cell_ids()
+ export_traces()
# check_extraction()