Cecile/heterogeneity #72
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…ous cell parameters (cannot use dict_to_h5 with dolfin.Function type)
…and load homogeneous and heterogeneous parameters separately, as two distinct dictionaries) + fix dict_to_h5 function to avoid overwriting h5 files (but require to make all dict_to_h5 calls before any HDF5File.write(...))
finsberg
reviewed
Aug 9, 2022
finsberg
reviewed
Aug 26, 2022
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| if h5file.keys() != "": | ||
| # Creating a temporary h5file and copy to initial file to avoid overwriting | ||
| # FIXME : Is there a more elegant way to do this ? | ||
| if isinstance(h5name, str): | ||
| tmp_name = str(os.path.splitext(h5name)[0]) + "_tmp.h5" | ||
| elif isinstance(h5name, os.PathLike): | ||
| tmp_name = h5name.with_name(f"{h5name.stem}_tmp.h5") | ||
| else: | ||
| logger.error( | ||
| "dict_to_h5 : h5name has wrong type (supported : str / path)", | ||
| ) | ||
|
|
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| with h5pyfile(tmp_name, "w") as h5file_tmp: | ||
| if h5group == "": | ||
| group = h5file_tmp | ||
| else: | ||
| group = h5file_tmp.create_group(h5group) | ||
| for k, v in data.items(): | ||
| group.create_dataset(k, data=v) | ||
| h5file_tmp.copy(group, h5file, name=h5group) |
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Just trying to understand what you want to do here. I check if h5file.keys() != "" which should be equivalent of saying that the file exist, right?
And if it does exist then you copy all the data to a new temporary file?
finsberg
reviewed
Aug 26, 2022
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| # FIXME : Might be worth moving to a dedicated function | ||
| # Update cellmodel in case of heterogeneous tissue |
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Agree, we should move this to a dedicated function.
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Support heterogeneous tissue parametrization from :
{ "scale_ICaL": { "1": 1.02, "2": 1.01 }, "scale_INaL": { "1": 2.3, "2": 2.1 } }