From 54026e2f6e356e1ec2ca649e717d282ed963abbb Mon Sep 17 00:00:00 2001
From: Constantin Pape <c.pape@gmx.net>
Date: Thu, 17 Oct 2019 16:10:24 +0200
Subject: [PATCH] Update cell seg evaluation
---
analysis/validation/eval_cell_segmentation.py | 63 ++++++++++
.../validation/eval_nucleus_segmentation.py | 0
scripts/segmentation/validation/eval_cells.py | 2 +-
.../validation/refine_annotations.py | 116 ++++++++++++++++++
4 files changed, 180 insertions(+), 1 deletion(-)
create mode 100644 analysis/validation/eval_cell_segmentation.py
create mode 100644 analysis/validation/eval_nucleus_segmentation.py
create mode 100644 scripts/segmentation/validation/refine_annotations.py
diff --git a/analysis/validation/eval_cell_segmentation.py b/analysis/validation/eval_cell_segmentation.py
new file mode 100644
index 0000000..b8f6470
--- /dev/null
+++ b/analysis/validation/eval_cell_segmentation.py
@@ -0,0 +1,63 @@
+# TODO shebang
+import argparse
+import os
+from scripts.segmentation.validation import eval_cells, get_ignore_seg_ids
+
+ANNOTATIONS = '../../data/rawdata/evaluation/validation_annotations.h5'
+BASELINES = '../../data/rawdata/evaluation/baseline_cell_segmentations.h5'
+
+
+def eval_seg(path, key, table):
+ ignore_ids = get_ignore_seg_ids(table)
+ fm, fs, tot = eval_cells(path, key, ANNOTATIONS,
+ ignore_seg_ids=ignore_ids)
+ print("Evaluation yields:")
+ print("False merges:", fm)
+ print("False splits:", fs)
+ print("Total number of annotations:", tot)
+
+
+def eval_baselines():
+ names = ['lmc', 'mc', 'curated_lmc', 'curated_mc']
+ # TODO still need to compute region tables for the baselines
+ tables = ['',
+ '',
+ '',
+ '']
+ results = {}
+ for name, table in zip(names, tables):
+ ignore_ids = get_ignore_seg_ids(table)
+ fm, fs, tot = eval_cells(path, key, ANNOTATIONS,
+ ignore_seg_ids=ignore_ids)
+ results[name] = (fm, fs, tot)
+
+ for name in names:
+ print("Evaluation of", name, "yields:")
+ print("False merges:", fm)
+ print("False splits:", fs)
+ print("Total number of annotations:", tot)
+
+
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument("path", type=str, help="Path to segmentation that should be validated.")
+ parser.add_argument("table", type=str, help="Path to table with region/semantic assignments")
+ parse.add_argument("--key", type=str, default="t00000/s00/0/cells", help="Segmentation key")
+ parser.add_argument("--baselines", type=int, default=0,
+ help="Whether to evaluate the baseline segmentations (overrides path)")
+ args = parser.parse_args()
+
+ baselines = bool(args.baselines)
+ if baselines:
+ eval_baselines()
+ else:
+ path = args.path
+ table = args.table
+ key = args.key
+ assert os.path.exists(path), path
+ eval_seg(path, key, table)
+
+
+if __name__ == '__main__':
+ main()
diff --git a/analysis/validation/eval_nucleus_segmentation.py b/analysis/validation/eval_nucleus_segmentation.py
new file mode 100644
index 0000000..e69de29
diff --git a/scripts/segmentation/validation/eval_cells.py b/scripts/segmentation/validation/eval_cells.py
index 908d407..91bd7d2 100644
--- a/scripts/segmentation/validation/eval_cells.py
+++ b/scripts/segmentation/validation/eval_cells.py
@@ -52,7 +52,7 @@ def to_scores(eval_res):
n = float(eval_res['n_annotations'] - eval_res['n_unmatched'])
n_splits = eval_res['n_splits']
n_merges = eval_res['n_merged_annotations']
- return n_merges / n, n_splits / n
+ return n_merges / n, n_splits / n, n
def eval_cells(seg_path, seg_key,
diff --git a/scripts/segmentation/validation/refine_annotations.py b/scripts/segmentation/validation/refine_annotations.py
new file mode 100644
index 0000000..f58df90
--- /dev/null
+++ b/scripts/segmentation/validation/refine_annotations.py
@@ -0,0 +1,116 @@
+import os
+import json
+import vigra
+import numpy as np
+import napari
+from heimdall import view, to_source
+from elf.io import open_file
+
+from .eval_cells import get_bounding_box
+from .evaluate_annotations import evaluate_annotations
+
+
+def compute_masks(seg, labels, ignore_seg_ids):
+
+ seg_eval = vigra.analysis.labelImageWithBackground(seg)
+
+ if ignore_seg_ids is None:
+ this_ignore_ids = None
+ else:
+ ignore_mask = np.isin(seg, ignore_seg_ids)
+ this_ignore_ids = np.unique(seg_eval[ignore_mask])
+
+ fg_annotations = np.isin(labels, [1, 2]).astype('uint32')
+ bg_annotations = labels == 3
+
+ min_radius = 16
+ _, masks = evaluate_annotations(seg_eval, fg_annotations, bg_annotations,
+ this_ignore_ids, min_radius=min_radius,
+ return_masks=True)
+ return masks['merges'], masks['splits']
+
+
+def refine(seg_path, seg_key, ignore_seg_ids,
+ orientation, slice_id,
+ project_folder,
+ annotation_path='/g/arendt/...',
+ raw_path='/g/arendt/...',
+ raw_key='t00000/s00/1/cells'):
+
+ label_path = os.path.join(project_folder, 'labels.npy')
+ fm_path = os.path.join(project_folder, 'fm.npy')
+ fs_path = os.path.join(project_folder, 'fs.npy')
+ bb_path = os.path.join(project_folder, 'bounding_box.json')
+
+ if os.path.exists(project_folder):
+ print("Load from existing project")
+ labels = np.load(label_path) if os.path.exists(label_path) else None
+ fm = np.load(fm_path) if os.path.exists(fm_path) else None
+ fs = np.load(fs_path) if os.path.exists(fs_path) else None
+
+ with open_file(annotation_path, 'r') as fval:
+ ds = fval[orientation][str(slice_id)]
+ bb = get_bounding_box(ds)
+ ds.n_threads = 8
+ if labels is None:
+ labels = ds[:]
+
+ starts = [b.start for b in bb]
+ stops = [b.stop for b in bb]
+
+ with open_file(seg_path, 'r') as f:
+ ds = f[seg_key]
+ ds.n_threads = 8
+ seg = ds[bb].squeeze().astype('uint32')
+
+ with open_file(raw_path, 'r') as f:
+ ds = f[raw_key]
+ ds.n_threads = 8
+ raw = ds[bb].squeeze()
+
+ assert labels.shape == seg.shape
+ if fm is None:
+ assert fs is None
+ fm, fs = compute_masks(seg, labels, ignore_seg_ids)
+ else:
+ assert fs is not None
+
+ with napari.gui_qt():
+ viewer = view(to_source(raw, name='raw'), to_source(labels, name='labels'),
+ to_source(seg, name='seg'), to_source(fm, name='merges'),
+ to_source(fs, name='splits'), return_viewer=True)
+
+ @viewer.bind_key('s')
+ def save_labels(viewer):
+ print("Saving state ...")
+ layers = viewer.layers
+ os.makedirs(project_folder, exist_ok=True)
+
+ labels = layers['labels'].data
+ np.save(label_path, labels)
+
+ fm = layers['merges'].data
+ np.save(fm_path, fm)
+
+ fs = layers['splits'].data
+ np.save(fs_path, fs)
+
+ with open(bb_path, 'w') as f:
+ json.dump({'starts': starts, 'stops': stops}, f)
+ print("... done")
+
+
+def export_refined(project_folder, out_path, out_key):
+
+ print("Export", project_folder, "to", out_path, out_key)
+ label_path = os.path.join(project_folder, 'labels.npy')
+ labels = np.load(label_path)
+
+ bb_path = os.path.join(project_folder, 'bounding_box.json')
+ with open(bb_path) as f:
+ bb = json.load(f)
+
+ with open_file(out_path) as out:
+ dso = out.create_dataset(out_key, data=labels, compression='gzip')
+ dso.attrs['starts'] = bb['starts']
+ dso.attrs['stops'] = bb['stops']
--
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