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Cecile/heterogeneity #72

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4ceffc9
Start heterogeneous tissue implementation : Generate and load mesh ma…
cdaversin Aug 3, 2022
5d632bc
Fix pytest error
cdaversin Aug 4, 2022
e063272
Set heterogeneous parameters in the cellmodel
cdaversin Aug 5, 2022
4ac34f3
Read heterogeneous parameters config from json file
cdaversin Aug 5, 2022
d066de8
Add missing json file + temporary fix save_state call with heterogene…
cdaversin Aug 5, 2022
9d67d3b
Fix save/load state when we have heterogeneous cell parameters (save …
cdaversin Aug 8, 2022
49ae1ca
(Trying to) fix save/load functions tests
cdaversin Aug 8, 2022
58067ec
Update dict_to_h5 function (save/load)
cdaversin Aug 9, 2022
aa691a0
Update dict_to_h5 : use with_name rather than with_suffix
cdaversin Aug 9, 2022
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15 changes: 8 additions & 7 deletions src/simcardems/save_load_functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,14 +41,14 @@ def dict_to_h5(data, h5name, h5group):
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 ?
try:
tmp_name = str(h5name.with_suffix("")) + "_tmp.h5"
except Exception:
pass
try:
if isinstance(h5name, str):
tmp_name = str(os.path.splitext(h5name)[0]) + "_tmp.h5"
except Exception:
pass
elif isinstance(h5name, os.PathLike):
tmp_name = str(h5name.with_suffix("")) + "_tmp.h5"
else:
logger.error(
"dict_to_h5 : h5name has wrong type (supported : str / path)",
)

with h5pyfile(tmp_name, "w") as h5file_tmp:
if h5group == "":
Expand Down Expand Up @@ -153,6 +153,7 @@ def save_state(
list(heterogeneous_params.keys()),
)
# Saving homogeneous parameters (float, int)
print("type path = ", type(path))
dict_to_h5(homogeneous_params, path, "ep/cell_params")
else:
dict_to_h5(solver.ode_solver._model.parameters(), path, "ep/cell_params")
Expand Down