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Remove unused 'test' entries in the example pyr.json #51

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merged 5 commits into from
Sep 25, 2023
Merged

Remove unused 'test' entries in the example pyr.json #51

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fb40e3b
remove test entry in pyr.json
Sep 15, 2023
f945f4b
plotting: highlight labels in red for scores greater than 5.
Sep 15, 2023
517cfc0
plotting: add SCORE_THRESHOLD
Sep 18, 2023
80acfed
remove duplicate entry in pyr.json
ilkilic Sep 25, 2023
ff1128e
remove highlight feature labels
ilkilic Sep 25, 2023
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6 changes: 5 additions & 1 deletion bluepyemodel/emodel_pipeline/emodel_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -243,9 +243,13 @@ def plot(self, only_validated=False, load_from_local=False):
record_ions_and_currents=self.access_point.pipeline_settings.plot_currentscape,
)

chkp_paths = glob.glob("./checkpoints/**/*.pkl", recursive=True)
if not chkp_paths:
raise ValueError("The checkpoints directory is empty, or there are no .pkl files.")

# Filter the checkpoints to plot
checkpoint_paths = []
for chkp_path in glob.glob("./checkpoints/**/*.pkl", recursive=True):
for chkp_path in chkp_paths:
if self.access_point.emodel_metadata.emodel not in chkp_path:
continue
if (
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4 changes: 3 additions & 1 deletion bluepyemodel/emodel_pipeline/plotting.py
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Expand Up @@ -333,6 +333,8 @@ def evolution_parameters_density(

def scores(model, figures_dir="./figures", write_fig=True):
"""Plot the scores of a model"""
SCORE_THRESHOLD = 5.0

make_dir(figures_dir)

score = list(model.scores.values()) + list(model.scores_validation.values())
Expand All @@ -345,7 +347,7 @@ def scores(model, figures_dir="./figures", write_fig=True):
axs[0, 0].barh(pos, score, height=0.7, align="center", color="gray")

for p, s in zip(pos, score):
if s > 5.0:
if s > SCORE_THRESHOLD:
axs[0, 0].text(5.15, p - 0.25, s="{:.1f}".format(s), color="red", fontsize=8)

axs[0, 0].set_xlabel("z-score")
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1 change: 1 addition & 0 deletions examples/emodel_pipeline_local_python/README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,7 @@ Finally, the different steps of the pipeline can be run with the commands:
pipeline.extract_efeatures()
pipeline.optimise(seed=1)
pipeline.store_optimisation_results()
pipeline.validation()
pipeline.plot(only_validated=False)

This snippet will likely not be used as such as the different steps of the pipeline are computationally intensive and will be run separately.
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62 changes: 31 additions & 31 deletions examples/emodel_pipeline_local_python/config/params/pyr.json
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Original file line number Diff line number Diff line change
Expand Up @@ -29,18 +29,18 @@
{"name":"celsius", "val":34}
],
"distribution_decay": [
{"name":"constant", "val":[-0.1, 0.0], "test": -0.0054993896903911335}
{"name":"constant", "val":[-0.1, 0.0]}
],
"myelinated": [
{"name":"cm", "val":0.02}
],
"all": [
{"name":"Ra", "val":100},
{"name":"g_pas", "val":[1e-5, 6e-5], "test":5.3926647384073322e-05},
{"name":"e_pas", "val":[-95, -60], "test":-75.862421167964129}
{"name":"g_pas", "val":[1e-5, 6e-5]},
{"name":"e_pas", "val":[-95, -60]}
],
"somadend": [
{"name":"gIhbar_Ih", "val":[0, 2e-4], "test":4.9710877962221885e-06, "dist":"exp",
{"name":"gIhbar_Ih", "val":[0, 2e-4], "dist":"exp",
"__comment": "distribution starts in soma (uniform) and spreads exponentially to dendrites"}
],
"axonal": [
Expand All @@ -49,16 +49,16 @@
{"name":"ek", "val":-90},
{"name":"vshifth_NaTg", "val":10},
{"name":"slopem_NaTg", "val":9},
{"name":"gNaTgbar_NaTg", "val":[0, 1.5], "test":0.45001599746214271},
{"name":"gNap_Et2bar_Nap_Et2", "val":[0, 0.02], "test":0.0074930910112714971},
{"name":"gK_Pstbar_K_Pst", "val":[0, 1], "test":0.41317541509924871},
{"name":"gK_Tstbar_K_Tst", "val":[0, 0.2], "test":0.18323702633195063},
{"name":"gSKv3_1bar_SKv3_1", "val":[0, 1], "test":0.59766537780998541},
{"name":"gCa_HVAbar_Ca_HVA2", "val":[0, 0.001], "test":0.00065484400421279019},
{"name":"gCa_LVAstbar_Ca_LVAst", "val":[0, 0.01], "test":0.0006624110987988748},
{"name":"gSK_E2bar_SK_E2", "val":[0, 0.1], "test":0.0055436826094973947},
{"name":"decay_CaDynamics_DC0", "val":[20, 300], "test": 187.93939189992398},
{"name":"gamma_CaDynamics_DC0", "val":[0.005, 0.05], "test":0.018262044595632514}
{"name":"gNaTgbar_NaTg", "val":[0, 1.5]},
{"name":"gNap_Et2bar_Nap_Et2", "val":[0, 0.02]},
{"name":"gK_Pstbar_K_Pst", "val":[0, 1]},
{"name":"gK_Tstbar_K_Tst", "val":[0, 0.2]},
{"name":"gSKv3_1bar_SKv3_1", "val":[0, 1]},
{"name":"gCa_HVAbar_Ca_HVA2", "val":[0, 0.001]},
{"name":"gCa_LVAstbar_Ca_LVAst", "val":[0, 0.01]},
{"name":"gSK_E2bar_SK_E2", "val":[0, 0.1]},
{"name":"decay_CaDynamics_DC0", "val":[20, 300]},
{"name":"gamma_CaDynamics_DC0", "val":[0.005, 0.05]}
],
"somatic": [
{"name":"cm", "val":1},
Expand All @@ -67,33 +67,33 @@
{"name":"vshiftm_NaTg", "val":13},
{"name":"vshifth_NaTg", "val":15},
{"name":"slopem_NaTg", "val":7},
{"name":"gNaTgbar_NaTg", "val":[0, 0.3], "test":0.22533600162118178},
{"name":"gK_Pstbar_K_Pst", "val":[0, 0.2], "test":0.15029253289238459},
{"name":"gK_Tstbar_K_Tst", "val":[0, 0.1], "test":0.0048028568033722466},
{"name":"gSKv3_1bar_SKv3_1", "val":[0, 1], "test":0.17097147644202285},
{"name":"gCa_HVAbar_Ca_HVA2", "val":[0, 0.001], "test":0.00056391253652122346},
{"name":"gCa_LVAstbar_Ca_LVAst", "val":[0, 0.01], "test":0.0010207881257459726},
{"name":"gSK_E2bar_SK_E2", "val":[0, 0.1], "test":0.079708174678391613},
{"name":"decay_CaDynamics_DC0", "val":[20, 300], "test":104.85544592336207},
{"name":"gamma_CaDynamics_DC0", "val":[0.005, 0.05], "test":0.02349598838420491}
{"name":"gNaTgbar_NaTg", "val":[0, 0.3]},
{"name":"gK_Pstbar_K_Pst", "val":[0, 0.2]},
{"name":"gK_Tstbar_K_Tst", "val":[0, 0.1]},
{"name":"gSKv3_1bar_SKv3_1", "val":[0, 1]},
{"name":"gCa_HVAbar_Ca_HVA2", "val":[0, 0.001]},
{"name":"gCa_LVAstbar_Ca_LVAst", "val":[0, 0.01]},
{"name":"gSK_E2bar_SK_E2", "val":[0, 0.1]},
{"name":"decay_CaDynamics_DC0", "val":[20, 300]},
{"name":"gamma_CaDynamics_DC0", "val":[0.005, 0.05]}
],
"apical": [
{"name":"cm", "val":2},
{"name":"ena", "val":50},
{"name":"ek", "val":-90},
{"name":"gamma_CaDynamics_DC0", "val":[0.005, 0.05], "test":0.0066739787731804143},
{"name":"gamma_CaDynamics_DC0", "val":[0.005, 0.05]},
{"name":"vshiftm_NaTg", "val":6},
{"name":"vshifth_NaTg", "val":6},
{"name":"gNaTgbar_NaTg", "val":[0, 0.1], "test": 0.099937269709686416, "dist":"decay"},
{"name":"gSKv3_1bar_SKv3_1", "val":[0, 0.003], "test":0.0014911639485230455},
{"name":"gCa_HVAbar_Ca_HVA2", "val":[0, 0.0001], "test":2.0449633205094153e-05},
{"name":"gCa_LVAstbar_Ca_LVAst", "val":[0, 0.001], "test":0.00011242611925684145}
{"name":"gNaTgbar_NaTg", "val":[0, 0.1], "dist":"decay"},
{"name":"gSKv3_1bar_SKv3_1", "val":[0, 0.003]},
{"name":"gCa_HVAbar_Ca_HVA2", "val":[0, 0.0001]},
{"name":"gCa_LVAstbar_Ca_LVAst", "val":[0, 0.001]}
],
"basal": [
{"name":"cm", "val":2},
{"name":"gamma_CaDynamics_DC0", "val":[0.005, 0.05], "test":0.04066564973313349},
{"name":"gCa_HVAbar_Ca_HVA2", "val":[0, 0.0001], "test":8.087166736008117e-05},
{"name":"gCa_LVAstbar_Ca_LVAst", "val":[0, 0.001], "test":2.7582661164552104e-05}
{"name":"gamma_CaDynamics_DC0", "val":[0.005, 0.05]},
{"name":"gCa_HVAbar_Ca_HVA2", "val":[0, 0.0001]},
{"name":"gCa_LVAstbar_Ca_LVAst", "val":[0, 0.001]}
]
}
}