From 305c6d659553b8149c55e1d2598131ab14e9c757 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Mon, 28 Oct 2019 13:11:46 +0100
Subject: [PATCH] Update segmentation export
---
data/postprocess.json | 2 +-
scripts/export/export_segmentation.py | 33 +++++++++++++++++----------
scripts/export/to_bdv.py | 3 ++-
3 files changed, 24 insertions(+), 14 deletions(-)
diff --git a/data/postprocess.json b/data/postprocess.json
index d22735c..d83f671 100644
--- a/data/postprocess.json
+++ b/data/postprocess.json
@@ -1 +1 @@
-{"sbem-6dpf-1-whole-segmented-cells-labels": {"boundary_path": "/g/kreshuk/data/arendt/platyneris_v1/data.n5", "boundary_key": "volumes/affinities/s1", "min_segment_size": 88604, "label_segmentation": true}}
\ No newline at end of file
+{"sbem-6dpf-1-whole-segmented-cells-labels": {"boundary_path": "/g/kreshuk/data/arendt/platyneris_v1/data.n5", "boundary_key": "volumes/affinities/s1", "max_segment_number": 32700, "label_segmentation": false}}
diff --git a/scripts/export/export_segmentation.py b/scripts/export/export_segmentation.py
index df64f95..4fbe9dc 100644
--- a/scripts/export/export_segmentation.py
+++ b/scripts/export/export_segmentation.py
@@ -6,7 +6,7 @@ import z5py
from cluster_tools.downscaling import DownscalingWorkflow
from paintera_tools import serialize_from_commit, postprocess
from paintera_tools import set_default_shebang as set_ptools_shebang
-from .to_bdv import to_bdv
+from .to_bdv import to_bdv, check_max_id
from .map_segmentation_ids import map_segmentation_ids
from ..default_config import write_default_global_config, get_default_shebang
from ..files import get_postprocess_dict
@@ -73,15 +73,20 @@ def export_segmentation(paintera_path, paintera_key, folder, new_folder, name, r
tmp_key = 'seg'
tmp_key0 = os.path.join(tmp_key, 's0')
+ # set correct shebang for paintera tools
+ set_ptools_shebang(get_default_shebang())
+
# run post-processing if specified for this segmentation name
pp_dict = get_postprocess_dict()
run_postprocessing = name in pp_dict
-
if run_postprocessing:
pp_config = pp_dict[name]
boundary_path = pp_config['boundary_path']
boundary_key = pp_config['boundary_key']
- min_segment_size = pp_config['min_segment_size']
+
+ min_segment_size = pp_config.get('min_segment_size', None)
+ max_segment_number = pp_config.get('max_segment_number', None)
+
label_segmentation = pp_config['label_segmentation']
tmp_postprocess = os.path.join(tmp_folder, 'postprocess_paintera')
postprocess(paintera_path, paintera_key,
@@ -89,15 +94,19 @@ def export_segmentation(paintera_path, paintera_key, folder, new_folder, name, r
tmp_folder=tmp_postprocess,
target=target, max_jobs=max_jobs,
n_threads=16, size_threshold=min_segment_size,
- label=label_segmentation)
-
- # set correct shebang for paintera tools
- set_ptools_shebang(get_default_shebang())
-
- # NOTE map_to_background is needed for cilia, nee some way to enable it automatically
- # export segmentation from paintera commit for all scales
- serialize_from_commit(paintera_path, paintera_key, tmp_path, tmp_key0, tmp_folder,
- max_jobs, target, relabel_output=True) # , map_to_background=[1])
+ target_number=max_segment_number,
+ label=label_segmentation,
+ output_path=tmp_path, output_key=tmp_key0)
+
+ else:
+ # NOTE map_to_background is needed for cilia, need some way to enable it automatically
+ # export segmentation from paintera commit for all scales
+ serialize_from_commit(paintera_path, paintera_key, tmp_path, tmp_key0, tmp_folder,
+ max_jobs, target, relabel_output=True) # , map_to_background=[1])
+
+ # check for overflow
+ print("Check max-id @", tmp_path, tmp_key0)
+ check_max_id(tmp_path, tmp_key0)
# downscale the segemntation
scale_factors = get_scale_factors(paintera_path, paintera_key)
diff --git a/scripts/export/to_bdv.py b/scripts/export/to_bdv.py
index 479b1c3..4a39eaf 100644
--- a/scripts/export/to_bdv.py
+++ b/scripts/export/to_bdv.py
@@ -2,6 +2,7 @@ import os
import json
import luigi
+import numpy as np
import h5py
import z5py
from cluster_tools.downscaling import PainteraToBdvWorkflow
@@ -12,7 +13,7 @@ def check_max_id(path, key):
with z5py.File(path) as f:
attrs = f[key].attrs
max_id = attrs['maxId']
- if max_id > 32000:
+ if max_id > np.iinfo('int16').max:
print("Max-id:", max_id, "does not fit int16")
raise RuntimeError("Uint16 overflow")
else:
--
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