def _on_pos_changed(self, current, previous):
w = str(self.pos_table.item(current.row(), 1).text())
p = str(self.pos_table.item(current.row(), 2).text())
coord = cellh5.CH5PositionCoordinate(self.ch5file.plate, w, p)
pos = self.ch5file.get_position_from_coord(coord)
self.cur_pos = pos
self.cur_w = w
self.cur_p = p
self.cur_coord = coord
self.update_event_table(coord)
def _to_ch5_coord(self, plate, well, site):
return cellh5.CH5PositionCoordinate(plate, well, site)
if isStatic:
timePoints = None
else:
timePoints = analyse_each_cell(pool, minSegLen, elongationRegions, cellRois, mitosisDir)
if ch5:
description = ("cell", "cell_shape_features")
with cellh5write.CH5FileWriter(mitosisDir + "mitosisAnalysis.ch5") as cfw:
for cellNb in [k.split("_")[0] for k in elongationRegions.keys()]:
cdata = list()
for c in chs:
cdata.append(tifffile.imread(fluoDir + cropImgs + str(cellNb) + "_" + c + ".tif"))
cdata = np.array(cdata)
while len(cdata.shape) < 5:
cdata = np.expand_dims(cdata, axis=0)
shape = cdata.shape
cpw = cfw.add_position(cellh5.CH5PositionCoordinate(pos, date, cellNb))
crw = cpw.add_label_image(shape=shape, dtype=np.int16)
for c in range(shape[0]):
for t in range(shape[1]):
for z in range(shape[2]):
crw.write(cdata[c,t,z,:,:], c=c, t=t, z=z)
crw.finalize()
regObjs = list()
cow_cell = cpw.add_region_object('cell')
for t in range(shape[2]):
cow_cell.write(t=t, object_labels=np.array([cellNb]))
cow_cell.finalize()
regObjs.append(cow_cell)