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Merge pull request #779 from suny-downstate-medical-center/check_cond…
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Check conditions
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@vvbragin
vvbragin authored Oct 11, 2023
2 parents 9633701 + 4a898ad commit f013bc9
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Showing 3 changed files with 72 additions and 154 deletions.
31 changes: 8 additions & 23 deletions netpyne/cell/cell.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,29 +186,8 @@ def recordTraces(self):
conditionsMet = 1

if 'conds' in params:
for (condKey, condVal) in params['conds'].items(): # check if all conditions are met
# choose what to comapare to
if condKey in ['gid']: # CHANGE TO GID
compareTo = self.gid
else:
compareTo = self.tags[condKey]

# check if conditions met
if isinstance(condVal, list) and isinstance(condVal[0], Number):
if compareTo == self.gid:
if compareTo not in condVal:
conditionsMet = 0
break
elif compareTo < condVal[0] or compareTo > condVal[1]:
conditionsMet = 0
break
elif isinstance(condVal, list) and isinstance(condVal[0], basestring):
if compareTo not in condVal:
conditionsMet = 0
break
elif compareTo != condVal:
conditionsMet = 0
break
conditionsMet = self.checkConditions(params['conds'])

if conditionsMet:
try:
ptr = None
Expand Down Expand Up @@ -373,6 +352,12 @@ def recordTraces(self):
# else:
# if sim.cfg.verbose: print ' NOT recording ', key, 'from cell ', self.gid, ' with parameters: ',str(params)


def checkConditions(self, conditions):
from ..sim.utils import checkConditions
return checkConditions(conditions=conditions, against=self.tags, cellGid=self.gid)


def _randomizer(self):
try:
return self.__cellParamsRand
Expand Down
158 changes: 27 additions & 131 deletions netpyne/cell/compartCell.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,19 +90,7 @@ def create(self, createNEURONObj=None):
for propLabel, prop in sim.net.params.cellParams.items(): # for each set of cell properties
conditionsMet = 1
if 'conds' in prop and len(prop['conds']) > 0:
for (condKey, condVal) in prop['conds'].items(): # check if all conditions are met
if isinstance(condVal, list):
if isinstance(condVal[0], Number):
if self.tags.get(condKey) < condVal[0] or self.tags.get(condKey) > condVal[1]:
conditionsMet = 0
break
elif isinstance(condVal[0], basestring):
if self.tags.get(condKey) not in condVal:
conditionsMet = 0
break
elif self.tags.get(condKey) != condVal:
conditionsMet = 0
break
conditionsMet = self.checkConditions(prop['conds'])

elif self.tags['cellType'] != propLabel: # simplified method for defining cell params (when no 'conds')
conditionsMet = False
Expand Down Expand Up @@ -132,32 +120,14 @@ def create(self, createNEURONObj=None):
def modify(self, prop):
from .. import sim

conditionsMet = 1
for (condKey, condVal) in prop['conds'].items(): # check if all conditions are met
if condKey == 'label':
if condVal not in self.tags['label']:
conditionsMet = 0
break
elif isinstance(condVal, list):
if isinstance(condVal[0], Number):
if self.tags.get(condKey) < condVal[0] or self.tags.get(condKey) > condVal[1]:
conditionsMet = 0
break
elif isinstance(condVal[0], basestring):
if self.tags.get(condKey) not in condVal:
conditionsMet = 0
break
elif self.tags.get(condKey) != condVal:
conditionsMet = 0
break
conditionsMet = self.checkConditions(prop['conds'])

if conditionsMet: # if all conditions are met, set values for this cell
if sim.cfg.createPyStruct:
self.createPyStruct(prop)
if sim.cfg.createNEURONObj:
self.createNEURONObj(
prop
) # add sections, mechanisms, synaptic mechanisms, geometry and topolgy specified by this property set
# add sections, mechanisms, synaptic mechanisms, geometry and topolgy specified by this property set
self.createNEURONObj(prop)

def createPyStruct(self, prop):
from .. import sim
Expand Down Expand Up @@ -847,45 +817,28 @@ def modifySynMechs(self, params):

conditionsMet = 1
if 'cellConds' in params:
if conditionsMet:
for (condKey, condVal) in params['cellConds'].items(): # check if all conditions are met
# check if conditions met
if isinstance(condVal, list):
if self.tags.get(condKey) < condVal[0] or self.tags.get(condKey) > condVal[1]:
conditionsMet = 0
break
elif self.tags.get(condKey) != condVal:
conditionsMet = 0
break
conditionsMet = self.checkConditions(params['cellConds'])

if conditionsMet:
for secLabel, sec in self.secs.items():
for synMech in sec['synMechs']:
conditionsMet = 1
if 'conds' in params:
for (condKey, condVal) in params['conds'].items(): # check if all conditions are met
# check if conditions met
if condKey == 'sec':
if condVal != secLabel:
conditionsMet = 0
break
elif isinstance(condVal, list) and isinstance(condVal[0], Number):
if synMech.get(condKey) < condVal[0] or synMech.get(condKey) > condVal[1]:
conditionsMet = 0
break
elif isinstance(condVal, list) and isinstance(condVal[0], basestring):
if synMech.get(condKey) not in condVal:
conditionsMet = 0
break
elif synMech.get(condKey) != condVal:
conditionsMet = 0
break
# first check if section matches
secLabelInConds = params['conds'].get('sec')
if secLabelInConds and (secLabelInConds != secLabel):
# skip to next section
break

# then check the rest of conds
synMechConds = deepcopy(params['conds'])
synMechConds.pop('sec')
conditionsMet = sim.utils.checkConditions(synMechConds, against=synMech)

if conditionsMet: # if all conditions are met, set values for this cell
exclude = ['conds', 'cellConds'] + SynMechParams.reservedKeys()
for synParamName, synParamValue in {
k: v for k, v in params.items() if k not in exclude
}.items():
paramsToModify = {k: v for k, v in params.items() if k not in exclude}
for synParamName, synParamValue in paramsToModify.items():
if sim.cfg.createPyStruct:
synMech[synParamName] = synParamValue
if sim.cfg.createNEURONObj:
Expand Down Expand Up @@ -1198,59 +1151,22 @@ def modifyConns(self, params):
conditionsMet = 1

if 'conds' in params:
for (condKey, condVal) in params['conds'].items(): # check if all conditions are met
# choose what to comapare to
if condKey in ['postGid']:
compareTo = self.gid
else:
compareTo = conn.get(condKey)
conds = params['conds']

# check if conditions met
if isinstance(condVal, list) and isinstance(condVal[0], Number):
if compareTo < condVal[0] or compareTo > condVal[1]:
conditionsMet = 0
break
elif isinstance(condVal, list) and isinstance(condVal[0], basestring):
if compareTo not in condVal:
conditionsMet = 0
break
elif compareTo != condVal:
conditionsMet = 0
break
# `conds` may contain `postGid` key, which is deprecated in favour of having `gid` key in `postConds`,
# but for backward compatibility, try to detect it here and replace with `gid`, so checkConditions() can process it:
if 'postGid' in conds:
conds['gid'] = conds.pop('postGid')
conditionsMet = sim.utils.checkConditions(conds, against=conn, cellGid=self.gid)

if conditionsMet and 'postConds' in params:
for (condKey, condVal) in params['postConds'].items(): # check if all conditions are met
# check if conditions met
if isinstance(condVal, list) and isinstance(condVal[0], Number):
if self.tags.get(condKey) < condVal[0] or self.tags.get(condKey) > condVal[1]:
conditionsMet = 0
break
elif isinstance(condVal, list) and isinstance(condVal[0], basestring):
if self.tags.get(condKey) not in condVal:
conditionsMet = 0
break
elif self.tags.get(condKey) != condVal:
conditionsMet = 0
break
conditionsMet = self.checkConditions(params['postConds'])

if conditionsMet and 'preConds' in params:
try:
cell = sim.net.cells[conn['preGid']]

if cell:
for (condKey, condVal) in params['preConds'].items(): # check if all conditions are met
# check if conditions met
if isinstance(condVal, list) and isinstance(condVal[0], Number):
if cell.tags.get(condKey) < condVal[0] or cell.tags.get(condKey) > condVal[1]:
conditionsMet = 0
break
elif isinstance(condVal, list) and isinstance(condVal[0], basestring):
if cell.tags.get(condKey) not in condVal:
conditionsMet = 0
break
elif cell.tags.get(condKey) != condVal:
conditionsMet = 0
break
conditionsMet = cell.checkConditions(params['preConds'])
except:
pass
# print('Warning: modifyConns() does not yet support conditions of presynaptic cells when running parallel sims')
Expand Down Expand Up @@ -1279,34 +1195,14 @@ def modifyStims(self, params):
conditionsMet = 1
if 'cellConds' in params:
if conditionsMet:
for (condKey, condVal) in params['cellConds'].items(): # check if all conditions are met
# check if conditions met
if isinstance(condVal, list):
if self.tags.get(condKey) < condVal[0] or self.tags.get(condKey) > condVal[1]:
conditionsMet = 0
break
elif self.tags.get(condKey) != condVal:
conditionsMet = 0
break
conditionsMet = self.checkConditions(params['cellConds'])

if conditionsMet == 1:
for stim in self.stims:
conditionsMet = 1

if 'conds' in params:
for (condKey, condVal) in params['conds'].items(): # check if all conditions are met
# check if conditions met
if isinstance(condVal, list) and isinstance(condVal[0], Number):
if stim.get(condKey) < condVal[0] or stim.get(condKey) > condVal[1]:
conditionsMet = 0
break
elif isinstance(condVal, list) and isinstance(condVal[0], basestring):
if stim.get(condKey) not in condVal:
conditionsMet = 0
break
elif stim.get(condKey) != condVal:
conditionsMet = 0
break
conditionsMet = sim.utils.checkConditions(params['conds'], against=stim)

if conditionsMet: # if all conditions are met, set values for this cell
if stim['type'] == 'NetStim': # for netstims, find associated netcon
Expand Down
37 changes: 37 additions & 0 deletions netpyne/sim/utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1017,6 +1017,43 @@ def clearAll():
gc.collect()


def checkConditions(conditions, against, cellGid=None):

conditionsMet = 1
for (condKey, condVal) in conditions.items():

# gid matching will be processed in specific way
gidCompare = False
if (cellGid is not None) and (condKey == 'gid'):
compareTo = cellGid
gidCompare = True

else:
compareTo = against.get(condKey)

if isinstance(condVal, list):
if isinstance(condVal[0], Number):
if gidCompare:
if compareTo not in condVal:
conditionsMet = 0
break
elif compareTo < condVal[0] or compareTo > condVal[1]:
conditionsMet = 0
break
elif isinstance(condVal[0], basestring):
if compareTo not in condVal:
conditionsMet = 0
break
elif isinstance(compareTo, list): # e.g. to match 'label', which may be list
if condVal not in compareTo:
conditionsMet = 0
break
elif compareTo != condVal:
conditionsMet = 0
break
return conditionsMet


# ------------------------------------------------------------------------------
# Create a subclass of json.JSONEncoder to convert numpy types in Python types
# ------------------------------------------------------------------------------
Expand Down

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