From e4dbeb4d5767ccbea4958052e120d37499e67336 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Wed, 4 Sep 2019 17:02:05 +0200
Subject: [PATCH] Update cilia attributes WIP
---
analysis/cilia.py | 155 ++++++++++++++++++++++---
scripts/attributes/cilia_attributes.py | 13 ++-
2 files changed, 151 insertions(+), 17 deletions(-)
diff --git a/analysis/cilia.py b/analysis/cilia.py
index 2e589dd..913a4de 100644
--- a/analysis/cilia.py
+++ b/analysis/cilia.py
@@ -1,37 +1,166 @@
+import json
+from concurrent import futures
+
import numpy as np
import h5py
import pandas as pd
-from scipy.ndimage.morphology import binary_dilation
-from heimdall import view
+
+from heimdall import view, to_source
+from elf.skeleton import skeletonize
from scripts.attributes.cilia_attributes import (compute_centerline,
- load_seg,
+ get_bb, load_seg,
make_indexable)
-def view_centerline(obj, resolution):
- path = compute_centerline(obj, [res * 1000 for res in resolution])
+# NOTE the current paths don't look that great.
+# probably need to play with the teasar parameters a bit to improve this
+def view_centerline(raw, obj, path, compare_skeleton=False):
path = make_indexable(path)
- cline = np.zeros(obj.shape, dtype='bool')
- cline = binary_dilation(cline, iterations=2)
- view(obj.astype('uint32'), cline.astype('uint32'))
+ cline = np.zeros(obj.shape, dtype='uint32')
+ cline[path] = 1
+
+ if compare_skeleton:
+ coords, _ = skeletonize(obj)
+ coords = make_indexable(coords)
+ skel = np.zeros(obj.shape, dtype='uint32')
+ skel[coords] = 1
+
+ view(raw, obj.astype('uint32'), cline, skel)
+ else:
+ view(raw, obj.astype('uint32'), cline)
-def check_lens():
+def check_lens(cilia_ids=None, compare_skeleton=False):
path = '../data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-cilia-labels.h5'
+ path_raw = '../data/rawdata/sbem-6dpf-1-whole-raw.h5'
table = '../data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/default.csv'
table = pd.read_csv(table, sep='\t')
table.set_index('label_id')
+ with open('precomputed_cilia.json') as f:
+ skeletons = json.load(f)
+
+ if cilia_ids is None:
+ cilia_ids = range(len(table))
+
resolution = [.025, .01, .01]
- with h5py.File(path) as f:
+ with h5py.File(path, 'r') as f, h5py.File(path_raw, 'r') as fr:
ds = f['t00000/s00/0/cells']
+ dsr = fr['t00000/s00/0/cells']
- for cid in range(len(table)):
+ for cid in cilia_ids:
if cid in (0, 1, 2):
continue
+
+ print(cid)
+ obj_path = skeletons[cid]
+ if obj_path is None:
+ print("Skipping cilia", cid)
+ continue
+ print(len(obj_path))
+
+ bb = get_bb(table, cid, resolution)
+ raw = dsr[bb]
+ obj = ds[bb] == cid
+ view_centerline(raw, obj, obj_path, compare_skeleton)
+
+
+def precompute():
+ path = '../data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-cilia-labels.h5'
+ table = '../data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/default.csv'
+ table = pd.read_csv(table, sep='\t')
+ table.set_index('label_id')
+
+ resolution = [.025, .01, .01]
+ with h5py.File(path) as f:
+ ds = f['t00000/s00/0/cells']
+
+ def precomp(cid):
+ if cid in (0, 1, 2):
+ return
+ print(cid)
obj = load_seg(ds, table, cid, resolution)
- view_centerline(obj, resolution)
+ if obj.sum() == 0:
+ return
+ path = compute_centerline(obj, [res * 1000 for res in resolution])
+ return path
+
+ n_cilia = len(table)
+ with futures.ThreadPoolExecutor(16) as tp:
+ tasks = [tp.submit(precomp, cid) for cid in range(n_cilia)]
+ # tasks = [tp.submit(precomp, cid) for cid in (3, 4, 5)]
+ results = [t.result() for t in tasks]
+
+ with open('precomputed_cilia.json', 'w') as f:
+ json.dump(results, f)
+
+
+def grid_search():
+ path = '../data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-cilia-labels.h5'
+ table = '../data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/default.csv'
+ table = pd.read_csv(table, sep='\t')
+ table.set_index('label_id')
+
+ label_id = 11
+
+ penalty_scales = [1000, 2500, 5000, 10000]
+ penalty_exponents = [2, 4, 8, 16]
+
+ resolution = [.025, .01, .01]
+ with h5py.File(path) as f:
+ ds = f['t00000/s00/0/cells']
+
+ def precomp(cid, penalty_scale, penalty_exponent):
+ print("scale:", penalty_scale, "exponent:", penalty_exponent)
+ obj = load_seg(ds, table, cid, resolution)
+ path = compute_centerline(obj, [res * 1000 for res in resolution],
+ penalty_scale=penalty_scale, penalty_exponent=penalty_exponent)
+ return {'penalty_scale': penalty_scale, 'penalty_exponent': penalty_exponent, 'path': path}
+
+ with futures.ThreadPoolExecutor(16) as tp:
+ tasks = [tp.submit(precomp, label_id, penalty_scale, penalty_exponent)
+ for penalty_scale in penalty_scales for penalty_exponent in penalty_exponents]
+ results = [t.result() for t in tasks]
+
+ with open('grid_search.json', 'w') as f:
+ json.dump(results, f)
+
+
+def eval_gridsearch():
+ with open('grid_search.json') as f:
+ results = json.load(f)
+
+ path_raw = '../data/rawdata/sbem-6dpf-1-whole-raw.h5'
+ path = '../data/0.5.1/segmentations/sbem-6dpf-1-whole-segmented-cilia-labels.h5'
+ table = '../data/0.5.1/tables/sbem-6dpf-1-whole-segmented-cilia-labels/default.csv'
+ table = pd.read_csv(table, sep='\t')
+ table.set_index('label_id')
+
+ label_id = 11
+
+ resolution = [.025, .01, .01]
+ with h5py.File(path, 'r') as f, h5py.File(path_raw, 'r') as fr:
+ ds = f['t00000/s00/0/cells']
+ dsr = fr['t00000/s00/0/cells']
+ bb = get_bb(table, label_id, resolution)
+
+ raw = dsr[bb]
+ obj = (ds[bb] == label_id).astype('uint32')
+
+ sources = [to_source(raw, name='raw'), to_source(obj, name='mask')]
+ for res in results:
+ line = np.zeros_like(obj)
+ path = make_indexable(res['path'])
+ line[path] = 1
+ name = '%i_%i' % (res['penalty_scale'], res['penalty_exponent'])
+ sources.append(to_source(line, name=name))
+
+ view(*sources)
if __name__ == '__main__':
- check_lens()
+ # precompute()
+ # grid_search()
+
+ check_lens([11], compare_skeleton=True)
+ # eval_gridsearch()
diff --git a/scripts/attributes/cilia_attributes.py b/scripts/attributes/cilia_attributes.py
index 1db20e1..57e4355 100644
--- a/scripts/attributes/cilia_attributes.py
+++ b/scripts/attributes/cilia_attributes.py
@@ -17,8 +17,10 @@ def get_mapped_cell_ids(cilia_ids, manual_mapping_table_path):
return cell_ids
-def compute_centerline(obj, resolution, return_teasar=False):
- teasar = Teasar(obj, resolution)
+def compute_centerline(obj, resolution, penalty_scale=1000, penalty_exponent=16,
+ return_teasar=False):
+ teasar = Teasar(obj, resolution,
+ penalty_scale=penalty_scale, penalty_exponent=penalty_exponent)
src = teasar.root_node
target = np.argmax(teasar.distances)
path = teasar.get_path(src, target)
@@ -31,17 +33,20 @@ def make_indexable(path):
return tuple(np.array([p[i] for p in path], dtype='uint64') for i in range(3))
-def load_seg(ds, base_table, cid, resolution):
+def get_bb(base_table, cid, resolution):
# get the row for this cilia id
row = base_table.loc[cid]
-
# compute the bounding box
bb_min = (row.bb_min_z, row.bb_min_y, row.bb_min_x)
bb_max = (row.bb_max_z, row.bb_max_y, row.bb_max_x)
bb = tuple(slice(int(mi / re), int(ma / re))
for mi, ma, re in zip(bb_min, bb_max, resolution))
+ return bb
+
+def load_seg(ds, base_table, cid, resolution):
# load segmentation from the bounding box and get foreground
+ bb = get_bb(base_table, cid, resolution)
obj = ds[bb] == cid
return obj
--
GitLab