TV convert functions + more types

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()]

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)