WIP: refactoring hard coded parts in renaming cells in HNN #702
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Glad to see you got everything setup @wagdy88! Next step is to start working through |
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Then, you could refactor the logic for assigning a cell's position within the column according to |
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hnn_core/network.py
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| @@ -387,20 +403,19 @@ def __init__(self, params, add_drives_from_params=False, | |||
| # cell counts, real and artificial | |||
| self._n_cells = 0 # used in tests and MPIBackend checks | |||
| self.pos_dict = dict() | |||
| self.cell_types = dict() | |||
| # COMMENTED By WAGDY #self.cell_types = dict() | |||
hnn_core/network.py
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| #if cell_name == "L2_basket": | ||
| # self.gid_ranges[cell_name] = range(0,35) | ||
| # elif cell_name == 'L2_pyramidal' | ||
| # ..... | ||
| # if self.gid_ranges[cell_name] |
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Remove unless you have a plan for this later.
hnn_core/network.py
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| Args: | ||
| original_name (string): The original cell | ||
| name in the network to be changed | ||
| new_name (string): The desired new cell name in the network |
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Follow same format as is elsewhere in the repo for readability.
hnn_core/network.py
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| def __init__(self, params, add_drives_from_params=False, | ||
| legacy_mode=False): | ||
| # Save the parameters used to create the Network | ||
| _validate_type(params, dict, 'params') | ||
| self._params = params | ||
| # Update the cell names -if needed |
| @@ -363,7 +378,8 @@ def __init__(self, params, add_drives_from_params=False, | |||
| stacklevel=1) | |||
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| # Source dict of names, first real ones only! | |||
| cell_types = { | |||
| # adding self before cell_types to make it an instance attribute | |||
| self.cell_types = { | |||
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We may want to consider turning this into an OrderedDict to be explicit about order mattering here. Either that or we need to find a way to make order at this point irrelevant.
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Resolved in conversation with @wagdy88: our solution will be to maintain the original order of Network.gid_ranges after renaming, but not necessarily Network.cell_types or Network.pos_dict.
hnn_core/viz.py
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| cell_types = cell_response._cell_type_names | ||
| cell_type_colors = ['r', 'b', 'g', 'w'] | ||
| # Ensure cell_types list matches the size of cell_type_colors dictionary | ||
| if len(cell_types) != len(cell_type_colors): | ||
| raise ValueError("cell_types list must " | ||
| "match the number of items in cell_type_colors.") | ||
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| cell_types = ['L2_basket', 'L2_pyramidal', 'L5_basket', 'L5_pyramidal'] | ||
| cell_type_colors = {'L5_pyramidal': 'r', 'L5_basket': 'b', | ||
| 'L2_pyramidal': 'g', 'L2_basket': 'w'} | ||
| # Create a new dictionary with the new keys and old values | ||
| new_cell_type_colors = dict(zip(cell_types, cell_type_colors)) |
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Maybe we should use a default colormap here and ask users to enter a dict of colors if they want a specific cell_type -> color mapping. @ntolley wdyt?
hnn_core/viz.py
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| # re-arranged cell_colors to match old colors dictionary | ||
| cell_colors = ['m', 'c', 'r', 'b'] | ||
| colors = dict(zip(net.cell_types.keys(), cell_colors)) | ||
| cell_markers = ['x', '^', 'x', '^'] | ||
| markers = dict(zip(net.cell_types.keys(), cell_markers)) |
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Same here as in plot_spikes_raster.
| # WAGDY: could try to create a dictionary | ||
| # of src_cell and target_cell and then a | ||
| # function that takes default cell names | ||
| # from this dictionary and overrides it | ||
| # with user cell names |
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removing hard coding in _create_cell_coords function and linking this with __init__ in class Network fixing the _create_cell_coords refactoring _create_cell_coords refactoring _create_cell_coords contd removing cell_name from 466 argument correcting styling error and fixing self.post_dict in class network making different corrections in network fixed line 463 working with line 465 network.py still working with line 407 adding a space added self before cell_types commented line 404 and added self to cell_types to make it an attribute to instance network de-indenting line 115 for pos_dict to get input from the whole code de-indenting lines 103 thru 115 in network corrected names of cells to match cell.name added a comment on the plan lines 81 thru 86 in network_models changing cell name to L2_basket added a rename_cell function and _rename_basket subfunction WIP making some re-organizing of comments to rename_cell function rename is working with gid_ranges ordered, still working on visualization fixing a typo modified rename function to order cell_types items visualization raster working and colors matching fixing extra white spaces etc... . Updating plot cell function WIP maintain original order in net.gid_ranges only modify net.gid_ranges in loop to simplify rename_cell cleaning up code modifying the discription removing extra lines fixed color_map in plot_raster marker set to o for all cells adding tests aethetic modification correct elif or error correcting a typo correcting pytests updating pytest fixing network tests cell-repsonse test _add_cell-type
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Work in Progress to refactor the hard-coded parts in the code for renaming cells in HNN.