From d5656cdecc443506887f9deb5010688f0d5093b7 Mon Sep 17 00:00:00 2001
From: Constantin Pape <c.pape@gmx.net>
Date: Thu, 17 Oct 2019 14:17:22 +0200
Subject: [PATCH] Add check for validation data
---
analysis/validation/check_validation.py | 47 +++++++++++++++++++
scripts/segmentation/validation/eval_cells.py | 22 ++++++---
2 files changed, 63 insertions(+), 6 deletions(-)
create mode 100644 analysis/validation/check_validation.py
diff --git a/analysis/validation/check_validation.py b/analysis/validation/check_validation.py
new file mode 100644
index 0000000..7e59d72
--- /dev/null
+++ b/analysis/validation/check_validation.py
@@ -0,0 +1,47 @@
+import h5py
+from heimdall import view, to_source
+
+
+def check_cell_evaluation():
+ from scripts.segmentation.validation.eval_cells import (eval_slice,
+ get_ignore_seg_ids,
+ get_bounding_box)
+
+ praw = '../../data'
+ pseg = '../../data'
+ pann = '../../data'
+
+ table_path = '../../data'
+ ignore_seg_ids = get_ignore_seg_ids(table_path)
+
+ with h5py.File(pseg, 'r') as fseg, h5py.File(pann, 'r') as fann:
+ ds_seg = fseg['t00000/s00/0/cells']
+ ds_ann = fann['xy/']
+
+ print("Run evaluation ...")
+ res, masks = eval_slice(ds_seg, ds_ann, ignore_seg_ids, min_radius=16,
+ return_maksks=True)
+ fm, fs = masks['false_merges'], masks['false_splits']
+ print()
+ print("Eval result")
+ print(res)
+ print()
+
+ print("Load raw data ...")
+ bb = get_bounding_box(ds_ann)
+ with h5py.File(praw, 'r') as f:
+ raw = f['t00000/s00/1/cells'][bb]
+
+ print("Load seg data ...")
+ seg = ds_seg[bb].squeeze()
+
+ view(to_source(raw, name='raw'), to_source(seg, name='seg'),
+ to_source(fm, name='merges'), to_source(fs, name='splits'))
+
+
+# def check_nucleus_evaluation():
+# eval_nuclei()
+
+
+if __name__ == '__main__':
+ check_cell_evaluation()
diff --git a/scripts/segmentation/validation/eval_cells.py b/scripts/segmentation/validation/eval_cells.py
index 4332632..7560650 100644
--- a/scripts/segmentation/validation/eval_cells.py
+++ b/scripts/segmentation/validation/eval_cells.py
@@ -5,16 +5,22 @@ from elf.io import open_file, is_dataset
from .evaluate_annotations import evaluate_annotations, merge_evaluations
-def eval_slice(ds_seg, ds_ann, ignore_seg_ids, min_radius):
- ds_seg.n_threads = 8
- ds_ann.n_threads = 8
-
- attrs = ds_ann.attrs
+def get_bounding_box(ds):
+ attrs = ds.attrs
start, stop = attrs['starts'], attrs['stops']
bb = tuple(slice(sta, sto) for sta, sto in zip(start, stop))
+ return bb
+
+
+def eval_slice(ds_seg, ds_ann, ignore_seg_ids, min_radius,
+ return_masks=False):
+ ds_seg.n_threads = 8
+ ds_ann.n_threads = 8
+ bb = get_bounding_box(ds_ann)
annotations = ds_ann[:]
seg = ds_seg[bb].squeeze()
+ assert annotations.shape == seg.shape
seg_eval = vigra.analysis.labelImageWithBackground(seg)
@@ -28,7 +34,8 @@ def eval_slice(ds_seg, ds_ann, ignore_seg_ids, min_radius):
bg_annotations = annotations == 3
return evaluate_annotations(seg_eval, fg_annotations, bg_annotations,
- this_ignore_ids, min_radius=min_radius)
+ this_ignore_ids, min_radius=min_radius,
+ return_masks=return_masks)
def get_ignore_seg_ids(table_path, ignore_names=['cuticle', 'neuropil', 'yolk']):
@@ -55,8 +62,11 @@ def eval_cells(seg_path, seg_key,
def visit_annotation(name, node):
nonlocal eval_res
if is_dataset(node):
+ print("Evaluating:", name)
res = eval_slice(ds_seg, node, ignore_seg_ids, min_radius)
eval_res = merge_evaluations(res, eval_res)
+ else:
+ print("Group:", name)
g.visititems(visit_annotation)
--
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