diff --git a/io/cells.py b/io/cells.py
index d16efbb9f8c77b5c742b5cbfb82385cde08c4576..1ff1c7972294c8b06d4d4f739ba3ed858f4fefcc 100644
--- a/io/cells.py
+++ b/io/cells.py
@@ -11,19 +11,12 @@ from scipy import ndimage
from scipy.sparse.base import isdense
from utils_find_1st import cmp_equal, find_1st
-# def cell_factory(store, type="hdf5"):
-# if type == "hdf5":
-# return CellsHDF(store)
-# else:
-# raise TypeError(
-# "Could not get cells for type {}:" "valid types are matlab and hdf5"
-# )
-
class Cells:
- """An object that gathers information about all the cells in a given
+ """
+ An object that gathers information about all the cells in a given
trap.
- This is the abstract object, used for type testing
+ This is the abstract object, used for type testing.
"""
def __init__(self):
@@ -55,15 +48,32 @@ class Cells:
def hdf(cls, fpath):
return CellsHDF(fpath)
- # @classmethod
- # def mat(cls, path):
- # return CellsMat(matObject(store))
class CellsHDF(Cells):
def __init__(
self, filename: Union[str, PosixPath], path: str = "cell_info"
):
+ '''
+ Extracts information from an h5 file.
+
+ The h5 file is organised as
+
+ 'cell_info', which contains 'angles', 'cell_label', 'centres', 'edgemasks', 'ellipse_dims', 'mother_assign', 'mother_assign_dynamic', 'radii', 'timepoint', 'trap'
+
+ 'extraction', which contains, for example, 'GFP', 'GFP_bgsub', 'general'
+
+ 'last_state', which contains information on the last state processed by BABY to enable resuming analyses
+
+ 'modifiers', which contains 'merges', 'picks'
+
+ 'postprocessing', which contains, for example, 'births', 'bud_metric', 'dsignal', 'experiment_wide', 'lineage', 'lineage_merged', 'savgol'
+
+ 'trap_info', which contains 'drifts', 'trap_locations'
+
+ # timepoint is a linear array of cell_ids for all cells for each trap for each time point
+
+ '''
self.filename = filename
self.cinfo_path = path
self._edgem_indices = None
@@ -71,36 +81,42 @@ class CellsHDF(Cells):
self._tile_size = None
def __getitem__(self, item: str):
+ '''
+ Defines attributes from the h5 file, which can then be accessed like items in a dictionary.
+
+ Data is accessed from /cinfo_path in the h5 file via _fetch.
+
+ Alan: is cells[X] and cells._X better than cells.X?
+ '''
if item == "edgemasks":
return self.edgemasks
- _item = "_" + item
- if not hasattr(self, _item):
- setattr(self, _item, self._fetch(item))
- return getattr(self, _item)
+ else:
+ _item = "_" + item
+ if not hasattr(self, _item):
+ # define from the h5 file
+ setattr(self, _item, self._fetch(item))
+ return getattr(self, _item)
def _get_idx(self, cell_id: int, trap_id: int):
+ # returns boolean array of time points where both the cell with cell_id and the trap with trap_id exist
return (self["cell_label"] == cell_id) & (self["trap"] == trap_id)
- def _fetch(self, path: str):
+ def _fetch(self, item: str):
+ # get data from /cinfo_path in h5 file
with h5py.File(self.filename, mode="r") as f:
- return f[self.cinfo_path][path][()]
+ return f[self.cinfo_path][item][()]
@property
def ntraps(self) -> int:
+ # find the number of traps from the h5 file
with h5py.File(self.filename, mode="r") as f:
- return len(f["/trap_info/trap_locations"][()])
+ return len(f["trap_info/trap_locations"][()])
@property
def traps(self) -> list:
+ # returns a list of traps
return list(set(self["trap"]))
- @property
- def tile_size(self) -> int:
- if self._tile_size is None:
- with h5py.File(self.filename, mode="r") as f:
- self._tile_size == f["trap_info/tile_size"][0]
- return self._tile_size
-
@property
def edgem_indices(self) -> np.array:
if self._edgem_indices is None:
@@ -109,15 +125,15 @@ class CellsHDF(Cells):
return self._edgem_indices
def nonempty_tp_in_trap(self, trap_id: int) -> set:
- # Returns time-points in which cells are available
+ # given a trap_id returns time points in which cells are available
return set(self["timepoint"][self["trap"] == trap_id])
@property
def edgemasks(self):
+ # returns the masks per tile
if self._edgemasks is None:
- edgem_path = "edgemasks/values"
+ edgem_path = "edgemasks"
self._edgemasks = self._fetch(edgem_path)
-
return self._edgemasks
def _edgem_where(self, cell_id, trap_id):
@@ -128,13 +144,13 @@ class CellsHDF(Cells):
def labels(self):
"""
Return all cell labels in object
- We use mother_assign to list traps because it is the only propriety that appears even
- when no cells are found"""
+ We use mother_assign to list traps because it is the only property that appears even
+ when no cells are found
+ """
return [self.labels_in_trap(trap) for trap in self.traps]
def where(self, cell_id, trap_id):
"""
- Returns
Parameters
----------
cell_id: int
@@ -182,13 +198,14 @@ class CellsHDF(Cells):
def group_by_traps(self, traps, data):
# returns a dict with traps as keys and labels as value
+ # Alan: what is data?
iterator = groupby(zip(traps, data), lambda x: x[0])
d = {key: [x[1] for x in group] for key, group in iterator}
d = {i: d.get(i, []) for i in self.traps}
return d
def labels_in_trap(self, trap_id):
- # Return set of cell ids in a trap.
+ # return set of cell ids for a given trap
return set((self["cell_label"][self["trap"] == trap_id]))
def labels_at_time(self, timepoint):