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[WIP] fix __iter__ #329

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[WIP] fix __iter__ #329

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15 changes: 4 additions & 11 deletions jaxley/modules/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1055,14 +1055,9 @@ def shape(self):

```
network.shape = (num_cells, num_branches, num_compartments)
cell.shape = (num_branches, num_compartments)
branch.shape = (num_compartments,)
cell.shape = (1, num_branches, num_compartments)
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I am not so sure if we should assign dim=1 to cell if you technically have no way to index into it (it is the object being indexed into).

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For consistency, net would also have to have shape=(1,...), which would be odd imo.

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Should be added to #43 when settled.

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Ah, sorry, I had not meant to request a review yet...

Anyways, __iter__ is broken right now, see the PR description. But let's just talk in person this is not an urgent PR

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Went over the recent PRs and thought I'd just do a pass of this one as well, even though you did not request it.

Alright sounds good.

branch.shape = (1, 1, num_compartments,)
```"""
mod_name = self.__class__.__name__.lower()
if "comp" in mod_name:
return (1,)
elif "branch" in mod_name:
return self[:].shape[1:]
return self[:].shape

def _childview(self, index: Union[int, str, list, range, slice]):
Expand All @@ -1087,8 +1082,7 @@ def __getitem__(self, index):
return self._childview(index)

def __iter__(self):
for i in range(self.shape[0]):
yield self[i]
raise NotImplementedError

def _local_inds_to_global(
self, cell_inds: np.ndarray, branch_inds: np.ndarray, comp_inds: np.ndarray
Expand Down Expand Up @@ -1293,8 +1287,7 @@ def __getitem__(self, index):
return self._childview(index)

def __iter__(self):
for i in range(self.shape[0]):
yield self[i]
raise NotImplementedError

def rotate(self, degrees: float, rotation_axis: str = "xy"):
"""Rotate jaxley modules clockwise. Used only for visualization.
Expand Down
8 changes: 8 additions & 0 deletions jaxley/modules/branch.py
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Expand Up @@ -82,6 +82,10 @@ def __getattr__(self, key):
else:
raise KeyError(f"Key {key} not recognized.")

def __iter__(self):
for i in range(self.shape[2]):
yield self[i]

def init_conds(self, params):
conds = self.init_branch_conds(
params["axial_resistivity"], params["radius"], params["length"], self.nseg
Expand Down Expand Up @@ -142,6 +146,10 @@ def __call__(self, index: float):
new_view = super().adjust_view("branch_index", index)
return new_view

def __iter__(self):
for i in range(self.shape[2]):
yield self[i]

def __getattr__(self, key):
assert key in ["comp", "loc"]
compview = CompartmentView(self.pointer, self.view)
Expand Down
8 changes: 8 additions & 0 deletions jaxley/modules/cell.py
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Expand Up @@ -115,6 +115,10 @@ def __getattr__(self, key):
else:
raise KeyError(f"Key {key} not recognized.")

def __iter__(self):
for i in range(self.shape[1]):
yield self[i]

def init_morph(self):
"""Initialize morphology."""
parents = self.comb_parents
Expand Down Expand Up @@ -248,6 +252,10 @@ def __call__(self, index: float):
def __getattr__(self, key):
assert key == "branch"
return BranchView(self.pointer, self.view)

def __iter__(self):
for i in range(self.shape[1]):
yield self[i]

def rotate(self, degrees: float, rotation_axis: str = "xy"):
"""Rotate jaxley modules clockwise. Used only for visualization.
Expand Down
4 changes: 4 additions & 0 deletions jaxley/modules/network.py
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Expand Up @@ -111,6 +111,10 @@ def __getattr__(self, key):
else:
raise KeyError(f"Key {key} not recognized.")

def __iter__(self):
for i in range(self.shape[0]):
yield self[i]

def init_morph(self):
self.nbranches_per_cell = [cell.total_nbranches for cell in self.cells]
self.total_nbranches = sum(self.nbranches_per_cell)
Expand Down
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