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Fix black issues
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Stijn van Dorp committed Jun 11, 2024
1 parent 09604f8 commit 7482583
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Showing 7 changed files with 172 additions and 156 deletions.
104 changes: 55 additions & 49 deletions bluepyemodel/icselector/icselector.py
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
"""# ICSELECTOR
""" ICSELECTOR
Select a set of NEURON mechanisms, parameters and bounds from corresponding
genes. Gene names can be selected from a file mapping genes to different
ME-T types. Corresponding channels are selected from a file mapping channels
Expand Down Expand Up @@ -39,45 +39,51 @@ def get_cmd_args():
usage = "%(prog)s"
parser = ArgumentParser(
description="Retrieve a list of NEURON mechanisms associated with provided genes.",
usage=usage)
usage=usage,
)
parser.add_argument(
'--ic_map',
dest='ic_map_path',
"--ic_map",
dest="ic_map_path",
type=str,
help="Path to .json file containing gene to channel mapping.")
help="Path to .json file containing gene to channel mapping.",
)
parser.add_argument(
'--gene_map',
dest='gene_map_path',
"--gene_map",
dest="gene_map_path",
type=str,
help="Path to .csv file containing met-type to gene mapping.")
help="Path to .csv file containing met-type to gene mapping.",
)
parser.add_argument(
'--keys',
"--keys",
type=str,
nargs='+',
help='Optional list of keywords to filter genes.')
nargs="+",
help="Optional list of keywords to filter genes.",
)
parser.add_argument(
'--mode',
"--mode",
type=str,
choices=['genetic', 'generic', 'mixed'],
default='mixed',
help='Model types to include.')
choices=["genetic", "generic", "mixed"],
default="mixed",
help="Model types to include.",
)
parser.add_argument(
'--status',
"--status",
type=str,
choices=['stable', 'latest'],
default='latest',
help='Model version to include.')
choices=["stable", "latest"],
default="latest",
help="Model version to include.",
)

args = parser.parse_args()
return vars(args)


class ICSelector():
""" Selects NEURON mechanisms, with parameters, value bounds, and
class ICSelector:
"""Selects NEURON mechanisms, with parameters, value bounds, and
distributions. Uses reference files for MET-type to gene mapping,
gene to channel mapping, and channel to parameter mapping. """
gene to channel mapping, and channel to parameter mapping."""

def __init__(self, ic_map_path, gene_map_path=None, mode='mixed', status='latest'):
def __init__(self, ic_map_path, gene_map_path=None, mode="mixed", status="latest"):
"""
Args:
ic_map_path (str): path to ic_mapping file (.json)
Expand All @@ -92,11 +98,11 @@ def __init__(self, ic_map_path, gene_map_path=None, mode='mixed', status='latest
else:
self._gene_selector = None

with open(ic_map_path, mode='r', encoding="utf-8") as fid:
with open(ic_map_path, mode="r", encoding="utf-8") as fid:
ic_map = json.load(fid)
self._misc_parameters = ic_map['misc_parameters']
self._gene_to_ic = ic_map['genes']
self._distributions = ic_map['distributions']
self._misc_parameters = ic_map["misc_parameters"]
self._gene_to_ic = ic_map["genes"]
self._distributions = ic_map["distributions"]
self._model_selector = ModelSelector(ic_map)
self.set_status(status)
self.set_mode(mode)
Expand All @@ -107,7 +113,7 @@ def set_status(self, status):
Args:
status (str): 'stable' or 'latest'
"""
if status in ['stable', 'latest']:
if status in ["stable", "latest"]:
self._model_selector.status = status

def set_mode(self, mode):
Expand All @@ -117,7 +123,7 @@ def set_mode(self, mode):
mode (str): 'generic', 'genetic', or 'mixed'
"""

if mode in ['genetic', 'generic', 'mixed']:
if mode in ["genetic", "generic", "mixed"]:
self._model_selector.mode = mode

def _get_channel_name(self, gene_name):
Expand Down Expand Up @@ -155,12 +161,12 @@ def __set_parameters_from_gene(self, gene_name):
"""

info = self._gene_selector.get(gene_name)
channel_name = info['channel']
channel_name = info["channel"]
mech = self.get(channel_name)
if mech:
mech.set_from_gene_info(info)
else:
logging.warning('Could not determine mechanism for gene %s', gene_name)
logging.warning("Could not determine mechanism for gene %s", gene_name)

def _set_parameters_from_ttype(self):
"""Copy parameters from selected genes to mechanims."""
Expand All @@ -175,19 +181,19 @@ def _select_genes_from_ttype(self, key_words):
"""

# === Get genes from gene mapping file
logging.info('\n===============\nGenes Selection\n===============')
logging.info("\n===============\nGenes Selection\n===============")
genes = self._gene_selector.select_from_ttype(key_words)
logging.info(str(self._gene_selector))

# === Map genes to channels
for gene, info in genes.items():
if gene in self._gene_to_ic:
info['channel'] = self._gene_to_ic[gene]
info["channel"] = self._gene_to_ic[gene]

def _select_mechanisms_from_ttype(self):
"""Select mechanisms from previously selected genes."""

logging.info('\n==================\nChannels Selection\n==================')
logging.info("\n==================\nChannels Selection\n==================")
for gene_name in self._gene_selector.selected_genes:
self.select(gene_name)
logging.info(str(self._model_selector))
Expand Down Expand Up @@ -229,12 +235,12 @@ def get_gene_mapping(self):

mechs = self.get_mechanisms()
genes = self._gene_selector.selected_genes
genes = {k: v for k, v in genes.items() if not v['channel'] == 'n/a'}
genes = {k: v for k, v in genes.items() if not v["channel"] == "n/a"}
for k, v in genes.items():
channel = v['channel']
channel = v["channel"]
for a, b in mechs.items():
if channel in b['_mapped_from']:
v['mapped_to'] = a
if channel in b["_mapped_from"]:
v["mapped_to"] = a
return genes

def get_mechanisms(self, selected_only=True):
Expand All @@ -253,7 +259,7 @@ def get_mechanisms(self, selected_only=True):
return mechs

def get_selected_cell_types(self):
""" Get met types selected from the gene mapping table.
"""Get met types selected from the gene mapping table.
Returns:
(list): all selected cell types
Expand All @@ -273,25 +279,25 @@ def _get_cell_config(self):
for mech in mechanisms.values():
config.add_from_mechanism(mech)

logging.info('\n=======================\nParameter Configuration\n=======================')
logging.info("\n=======================\nParameter Configuration\n=======================")

# === Set additional parameters
# misc = self._get_ic_map_entry('misc_parameters')
misc = self._misc_parameters
for name, setting in misc.items():

if 'local' in setting:
if "local" in setting:
# Location to be obtained from mechanism
locations = []
for mech in mechanisms.values():
model = mech.model
if 'read' in model:
reads = model['read']
if "read" in model:
reads = model["read"]
if name in reads:
locs = mech.distribution.get()
locations.extend(locs.keys())
for loc in np.unique(locations):
config.add_parameter(name, loc, setting['local'])
config.add_parameter(name, loc, setting["local"])
else:
for loc, value in setting.items():
config.add_parameter(name, loc, value)
Expand All @@ -300,7 +306,7 @@ def _get_cell_config(self):
return config

def get_cell_config_from_ttype(self, key_words):
""" Get all information related to cell model configuration from
"""Get all information related to cell model configuration from
mechanisms selected based on genetic expression profiles.
Args:
Expand Down Expand Up @@ -330,8 +336,8 @@ def get_cell_config_from_ttype(self, key_words):
# Define distributions
distr_funcs = self._distributions
for distr in distributions:
distr_name = distr['name']
if not distr_name == 'uniform':
distr_name = distr["name"]
if not distr_name == "uniform":
if distr_name in distr_funcs:
d = distr_funcs[distr_name]
for k, v in d.items():
Expand All @@ -348,7 +354,7 @@ def get_cell_config_from_ttype(self, key_words):
def main(*args, **kwargs):
"""Main"""
# === Instantiate
keys = kwargs.pop('keys', None)
keys = kwargs.pop("keys", None)
icselector = ICSelector(*args, **kwargs)

# === Get cell configuration
Expand All @@ -367,7 +373,7 @@ def main(*args, **kwargs):
pprint(genes)


if __name__ == '__main__':
if __name__ == "__main__":
logging.basicConfig(level=logging.DEBUG)
cmd_args = get_cmd_args()
main(**cmd_args)
52 changes: 26 additions & 26 deletions bluepyemodel/icselector/modules/configuration.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,11 @@
class Parameter:
"""Used to exchange configuration information with BPEM."""

name: str # Neuron parameter name, i.e. {param}_{suffix}
value: tuple # Optimization boundaries
location: str # Cell compartment
mechanism: str = '' # Mechanism suffix
distribution: str = '' # Morphology dependent function
name: str # Neuron parameter name, i.e. {param}_{suffix}
value: tuple # Optimization boundaries
location: str # Cell compartment
mechanism: str = "" # Mechanism suffix
distribution: str = "" # Morphology dependent function


class Configuration:
Expand Down Expand Up @@ -46,17 +46,18 @@ def _add_mech_param(self, mech, param):
"""

model = mech.model
suffix = model['suffix']
suffix = model["suffix"]
locations = asdict(mech.distribution)
name = param + '_' + suffix
name = param + "_" + suffix
for comp, distr in locations.items():
if not distr == '':
if not distr == "":
pset = Parameter(
name=name,
value=tuple(mech.get_bounds(param)),
location=comp,
mechanism=suffix,
distribution=distr)
distribution=distr,
)
self._parameters.append(pset)

def add_from_mechanism(self, mech):
Expand All @@ -68,12 +69,12 @@ def add_from_mechanism(self, mech):

model = mech.model

if 'gbar' in model:
param = model['gbar']
if "gbar" in model:
param = model["gbar"]
self._add_mech_param(mech, param)

if 'parameters' in model:
for param in model['parameters']:
if "parameters" in model:
for param in model["parameters"]:
self._add_mech_param(mech, param)

def add_parameter(self, name, location, value):
Expand All @@ -92,35 +93,34 @@ def get_mechanisms(self):
"""Returns a list of mechanisms and compartments to insert them."""

mechanisms = [
{'name': p.mechanism, 'location': p.location}
for p in self._parameters if p.mechanism]
return self._clean_up_list_of_dicts(mechanisms, 'name')
{"name": p.mechanism, "location": p.location} for p in self._parameters if p.mechanism
]
return self._clean_up_list_of_dicts(mechanisms, "name")

def get_parameters(self):
"""Returns a list of configuration parameters."""

params = [asdict(p) for p in self._parameters]
return self._clean_up_list_of_dicts(params, 'mechanism')
return self._clean_up_list_of_dicts(params, "mechanism")

def get_distributions(self):
"""Returns a list of unique distribution definitions used."""

distr = [{'name': p.distribution} for p in self._parameters if p.distribution]
return self._clean_up_list_of_dicts(distr, 'name')
distr = [{"name": p.distribution} for p in self._parameters if p.distribution]
return self._clean_up_list_of_dicts(distr, "name")

def __str__(self):
locations = {}
for param in self._parameters:
if param.location not in locations:
locations[param.location] = []
locations[param.location].append([
param.name, param.value, param.distribution])
out_str = ['\n']
locations[param.location].append([param.name, param.value, param.distribution])
out_str = ["\n"]
for loc, content in locations.items():
out_str.append(f'>>> {loc} <<<')
out_str.append(f">>> {loc} <<<")
for p in content:
if p[2]:
out_str.append(f' {p[0]}, value: {p[1]}, distribution: {p[2]}')
out_str.append(f" {p[0]}, value: {p[1]}, distribution: {p[2]}")
else:
out_str.append(f' {p[0]}, value: {p[1]}')
return '\n'.join(out_str)
out_str.append(f" {p[0]}, value: {p[1]}")
return "\n".join(out_str)
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