From 3f26a0b4550210094b6aa99d2f04aaddd041e01e Mon Sep 17 00:00:00 2001
From: Argyris Z <azardilis@gmail.com>
Date: Mon, 6 Jul 2020 12:19:53 +0100
Subject: [PATCH] TV convert functions + more types
---
common/common/lin.py | 32 ++++++++++++++++++++++++++++++++
common/common/seg.py | 30 +++++++++++++++++++++---------
2 files changed, 53 insertions(+), 9 deletions(-)
diff --git a/common/common/lin.py b/common/common/lin.py
index 3a93172..1825c7f 100644
--- a/common/common/lin.py
+++ b/common/common/lin.py
@@ -6,6 +6,7 @@ from common.seg import (Tissue,
Vec3,
readDataT1,
readGeomT1,
+ readGeomIm,
readRess,
geneNms,
readDataT1Im)
@@ -361,6 +362,37 @@ def mkSeriesIm0(dataDir: str,
return tss, linss
+def mkSeriesGeomIm(dataDir: str,
+ fid: int = 1,
+ ft: Callable[[int], bool] = lambda x: True):
+ d = join(dataDir, "FM{fid}".format(fid=fid))
+ linDataLoc = join(dataDir, "FM{fid}/tracking_data".format(fid=str(fid)))
+ ressFn = join(dataDir, "FM{fid}/resolutions.txt".format(fid=str(fid)))
+
+ ress = readRess(ressFn.format(fid=str(fid)))
+ tpoints = [t for t in sorted(ress.keys()) if ft(t)]
+
+ lins = mkLinsSeries1(readLins1(linDataLoc))
+ tss = dict()
+ linss = dict()
+
+ for t in tpoints:
+ print(t)
+ tss[t] = readGeomIm(d, t)
+
+ for t1, t2 in zip(tpoints, tpoints[1:]):
+ print(t1, t2)
+ linss[(t1, t2)] = mergeLinss(list(map(lambda x: x[1],
+ between(lins, t1, t2))))
+
+ return tss, linss
+
+
+def writeSeriesGeomTV(tss: Dict[int, Tissue], d: str):
+ for t, ts in tss.items():
+ seg.writeTV(ts, d, "{t}h".format(t=str(t)))
+
+
###################################
def invertMap(ln):
iLin = [list(zip(ds, repeat(m, len(ds)))) for m, ds in ln.items()]
diff --git a/common/common/seg.py b/common/common/seg.py
index bd2d9fc..13c7567 100644
--- a/common/common/seg.py
+++ b/common/common/seg.py
@@ -3,6 +3,8 @@ import ast # type: ignore
from tifffile import TiffFile # type: ignore
from copy import deepcopy # type: ignore
from typing import Tuple, Dict, TypeVar, Callable, List, Set, Iterator
+from numpy import ndarray
+from os.path import join
T = TypeVar('T')
@@ -374,7 +376,7 @@ class Tissue():
ns=repr(nids))
return "\n".join([toTVNeighCell(cid, neighs)
- for cid, neighs in self.neighs.items()])
+ for cid, neighs in self.neighs.items() if cid != 1])
def toTV(self) -> Tuple[str, str]:
return (self.toTVGeom(), self.toTVNeigh())
@@ -500,7 +502,9 @@ def readImage(fseg: str):
return seg
-def readImageRegionPoints(fseg, res=[1, 1, 1], d=2):
+def readImageRegionPoints(fseg: str,
+ res: List[float] = [1, 1, 1],
+ d: int = 3) -> Dict[int, ndarray]:
from skimage.measure import regionprops # type: ignore
cell_regions = dict()
@@ -509,8 +513,12 @@ def readImageRegionPoints(fseg, res=[1, 1, 1], d=2):
cellsSeg = regionprops(seg)
for cregion in cellsSeg:
- cell_regions[cregion.label] = np.multiply(cregion.coords[:, :d],
- res[:d])
+ cid = int(cregion.label)
+ if cid != 1:
+ coords = cregion.coords[:, [2, 1, 0]]
+ coords_: ndarray = np.multiply(coords,
+ res[:d])
+ cell_regions[cid] = coords_
return cell_regions
@@ -519,15 +527,19 @@ def mergePoints(cell_regions, cids):
return np.vstack(tuple([cell_regions[cid] for cid in cids]))
-def getCellRegions(fid=1, ft=lambda t: True, d=2):
- segFn = "../data/FM{fid}/segmentation_tiffs/{t}h_segmented.tif"
- ressFn = "../data/FM{fid}/resolutions.txt"
+def getCellRegions(d: str,
+ fid: int = 1,
+ ft: Callable[[int], bool] = lambda t: True,
+ dim: int = 3) -> Dict[int, Dict[int, ndarray]]:
+
+ segFn = join(d, "FM{fid}/segmentation_tiffs/{t}h_segmented.tif")
+ ressFn = join(d, "FM{fid}/resolutions.txt")
ress = readRess(ressFn.format(fid=str(fid)))
tpoints = [t for t in sorted(ress.keys()) if ft(t)]
fsegs = dict([(t, segFn.format(fid=fid, t=str(t))) for t in tpoints])
- return dict([(t, readImageRegionPoints(fn, res=ress[t], d=d))
+ return dict([(t, readImageRegionPoints(fn, res=ress[t], d=dim))
for t, fn in fsegs.items()])
@@ -558,7 +570,7 @@ def writeOrg(fnGeom, fnNeigh, ts):
def writeTV(ts, d, lab):
- from os.path import join
+
fnGeom = "{lab}_segmented_tvformat_volume_position.txt".format(lab=lab)
fnNeigh = "{lab}_segmented_tvformat_neighbors.txt".format(lab=lab)
--
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