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Commit 8352d3c5 authored by Simon Oehrl's avatar Simon Oehrl
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Merge branch 'feature/Fix_neuron_properties' into 'develop'

Feature/fix neuron properties

See merge request VR-Group/in-situ-pipeline/access-node!6
parents 733c0f17 84931aeb
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1 merge request!6Feature/fix neuron properties
Pipeline #163401 passed
2.4.8
\ No newline at end of file
2.4.13
\ No newline at end of file
......@@ -26,7 +26,7 @@ def connect_to_database():
def arbor_get_attributes(): # noqa: E501
"""Retrieves the list of all attributes.
"""Retrieves a list of all attributes.
# noqa: E501
......@@ -44,7 +44,7 @@ def arbor_get_attributes(): # noqa: E501
def arbor_get_cell_ids(): # noqa: E501
"""Retrieves the list of all cell ids.
"""Retrieves a list of all cell ids.
# noqa: E501
......@@ -98,7 +98,7 @@ def arbor_get_measurements(attribute, probe_ids=None, _from=None, to=None, offse
# noqa: E501
:param attribute: The attribute to query (e.g., 'V_m' for the membrane potential)
:param attribute: The attribute to query
:type attribute: str
:param probe_ids: A list of probes ids queried for data.
:type probe_ids: List[int]
......@@ -108,7 +108,7 @@ def arbor_get_measurements(attribute, probe_ids=None, _from=None, to=None, offse
:type to: float
:param offset: The offset into the result.
:type offset: int
:param limit: The maximum of entries to be result.
:param limit: The maximum of entries to be returned.
:type limit: int
:rtype: ArborMeasurement
......@@ -151,7 +151,7 @@ def arbor_get_measurements(attribute, probe_ids=None, _from=None, to=None, offse
def arbor_get_probes(attribute=None): # noqa: E501
"""Retrieves the list of all probes for a given attribute (optional).
"""Retrieves a list of all probes for a given attribute (optional).
# noqa: E501
......@@ -187,7 +187,7 @@ def arbor_get_probes(attribute=None): # noqa: E501
def arbor_get_simulation_time_info(): # noqa: E501
"""Retrieves simulation time information.
"""Retrieves simulation time information(begin, current, end).
# noqa: E501
......
......@@ -26,7 +26,7 @@ def connect_to_database():
def nest_get_gids(): # noqa: E501
"""Retrieves the list of all GID.
"""Retrieves a list of all gids.
# noqa: E501
......@@ -44,7 +44,7 @@ def nest_get_gids(): # noqa: E501
def nest_get_gids_in_population(population_id): # noqa: E501
"""Retrieves the list of all neuron IDs within the population.
"""Retrieves the list of all neuron ids within the population.
# noqa: E501
......@@ -96,19 +96,19 @@ def nest_get_multimeter_info(): # noqa: E501
def nest_get_multimeter_measurements(multimeter_id, attribute, _from=None, to=None, gids=None, offset=None, limit=None): # noqa: E501
"""Retrieves the measurements for a multimeter, attribute and GIDS (optional).
"""Retrieves the measurements for a multimeter, attribute and gids (optional).
# noqa: E501
:param multimeter_id: The multimeter to query
:type multimeter_id:
:type multimeter_id: int
:param attribute: The attribute to query (e.g., 'V_m' for the membrane potential)
:type attribute: str
:param _from: The start time (including) to be queried.
:type _from: float
:param to: The end time (excluding) to be queried.
:type to: float
:param gids: A list of GIDs queried for spike data.
:param gids: A list of gids queried for spike data.
:type gids: List[int]
:param offset: The offset into the result.
:type offset: int
......@@ -174,7 +174,7 @@ def nest_get_neuron_properties(gids=None): # noqa: E501
# noqa: E501
:param gids: A list of GIDs queried for properties.
:param gids: A list of gids queried for properties.
:type gids: List[int]
:rtype: List[NestNeuronProperties]
......@@ -208,7 +208,7 @@ def nest_get_neuron_properties(gids=None): # noqa: E501
def nest_get_populations(): # noqa: E501
"""Retrieves the list of all population IDs.
"""Retrieves a list of all population IDs.
# noqa: E501
......@@ -226,7 +226,7 @@ def nest_get_populations(): # noqa: E501
def nest_get_simulation_time_info(): # noqa: E501
"""Retrieves simulation time information.
"""Retrieves simulation time information (begin, current, end).
# noqa: E501
......@@ -253,7 +253,7 @@ def nest_get_simulation_time_info(): # noqa: E501
def nest_get_spikes(_from=None, to=None, gids=None, offset=None, limit=None): # noqa: E501
"""Retrieves the spikes for the given simulation steps (optional) and GIDS (optional).
"""Retrieves the spikes for the given simulation steps (optional) and gids (optional).
# noqa: E501
......@@ -261,11 +261,11 @@ def nest_get_spikes(_from=None, to=None, gids=None, offset=None, limit=None): #
:type _from: float
:param to: The end time (excluding) to be queried.
:type to: float
:param gids: A list of GIDs queried for spike data.
:param gids: A list of gids queried for spike data.
:type gids: List[int]
:param offset: The offset into the result.
:type offset: int
:param limit: The maximum of entries to be result.
:param limit: The maximum of entries to be returned.
:type limit: int
:rtype: Spikes
......@@ -316,7 +316,7 @@ def nest_get_spikes_by_population(population_id, _from=None, to=None, offset=Non
:type to: float
:param offset: The offset into the result.
:type offset: int
:param limit: The maximum of entries to be result.
:param limit: The maximum of entries to be returned.
:type limit: int
:rtype: Spikes
......
......@@ -6,7 +6,6 @@ from datetime import date, datetime # noqa: F401
from typing import List, Dict # noqa: F401
from access_node.models.base_model_ import Model
from access_node.models.multimeter_info_inner import MultimeterInfoInner # noqa: F401,E501
from access_node import util
......
......@@ -100,7 +100,7 @@ class MultimeterMeasurement(Model):
def values(self) -> List[float]:
"""Gets the values of this MultimeterMeasurement.
This array contains the measured values for each probe and time to get the value for probe n at time t you have to use the index n * length(simulation_times) + t # noqa: E501
This array contains the measured values for each gid and time to get the value for gid n at time t you have to use the index n * length(simulation_times) + t # noqa: E501
:return: The values of this MultimeterMeasurement.
:rtype: List[float]
......@@ -111,7 +111,7 @@ class MultimeterMeasurement(Model):
def values(self, values: List[float]):
"""Sets the values of this MultimeterMeasurement.
This array contains the measured values for each probe and time to get the value for probe n at time t you have to use the index n * length(simulation_times) + t # noqa: E501
This array contains the measured values for each gid and time to get the value for gid n at time t you have to use the index n * length(simulation_times) + t # noqa: E501
:param values: The values of this MultimeterMeasurement.
:type values: List[float]
......
......@@ -63,11 +63,11 @@ paths:
type: "integer"
format: "uint64"
responses:
200:
"200":
description: "Operation successful."
schema:
$ref: "#/definitions/Spikes"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -77,20 +77,23 @@ paths:
get:
tags:
- "arbor"
summary: "Retrieves the list of all cell ids."
summary: "Retrieves a list of all cell ids."
operationId: "arbor_get_cell_ids"
produces:
- "application/json"
parameters: []
responses:
200:
"200":
description: "Operation successful."
schema:
type: "array"
items:
type: "integer"
format: "uint64"
400:
example:
- 1
- 2
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -100,7 +103,7 @@ paths:
get:
tags:
- "arbor"
summary: "Retrieves the list of all probes for a given attribute (optional)."
summary: "Retrieves a list of all probes for a given attribute (optional)."
operationId: "arbor_get_probes"
produces:
- "application/json"
......@@ -111,13 +114,13 @@ paths:
required: false
type: "string"
responses:
200:
"200":
description: "Operation successful."
schema:
type: "array"
items:
$ref: "#/definitions/Probe"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -127,13 +130,13 @@ paths:
get:
tags:
- "arbor"
summary: "Retrieves the list of all attributes."
summary: "Retrieves a list of all attributes."
operationId: "arbor_get_attributes"
produces:
- "application/json"
parameters: []
responses:
200:
"200":
description: "Operation successful."
schema:
type: "array"
......@@ -142,7 +145,7 @@ paths:
example:
- "Voltage"
- "Current"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -161,7 +164,7 @@ paths:
parameters:
- name: "attribute"
in: "query"
description: "The attribute to query (e.g., 'V_m' for the membrane potential)"
description: "The attribute to query"
required: true
type: "string"
- name: "probe_ids"
......@@ -192,16 +195,16 @@ paths:
format: "uint64"
- name: "limit"
in: "query"
description: "The maximum of entries to be result."
description: "The maximum of entries to be returned."
required: false
type: "integer"
format: "uint64"
responses:
200:
"200":
description: "Operation successful."
schema:
$ref: "#/definitions/ArborMeasurement"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -211,17 +214,17 @@ paths:
get:
tags:
- "arbor"
summary: "Retrieves simulation time information."
summary: "Retrieves simulation time information(begin, current, end)."
operationId: "arbor_get_simulation_time_info"
produces:
- "application/json"
parameters: []
responses:
200:
"200":
description: "Operation successful."
schema:
$ref: "#/definitions/SimulationTimeInfo"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -245,13 +248,13 @@ paths:
type: "integer"
format: "uint64"
responses:
200:
"200":
description: "Operation successful."
schema:
type: "array"
items:
$ref: "#/definitions/ArborCellProperties"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -261,17 +264,17 @@ paths:
get:
tags:
- "nest"
summary: "Retrieves simulation time information."
summary: "Retrieves simulation time information (begin, current, end)."
operationId: "nest_get_simulation_time_info"
produces:
- "application/json"
parameters: []
responses:
200:
"200":
description: "Operation successful."
schema:
$ref: "#/definitions/SimulationTimeInfo"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -281,20 +284,25 @@ paths:
get:
tags:
- "nest"
summary: "Retrieves the list of all GID."
summary: "Retrieves a list of all gids."
operationId: "nest_get_gids"
produces:
- "application/json"
parameters: []
responses:
200:
"200":
description: "Operation successful."
schema:
type: "array"
items:
type: "integer"
format: "uint64"
400:
example:
- 1
- 2
- 3
- 15
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -311,20 +319,20 @@ paths:
parameters:
- name: "gids"
in: "query"
description: "A list of GIDs queried for properties."
description: "A list of gids queried for properties."
required: false
type: "array"
items:
type: "integer"
format: "uint64"
responses:
200:
"200":
description: "Operation successful."
schema:
type: "array"
items:
$ref: "#/definitions/NestNeuronProperties"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -334,20 +342,24 @@ paths:
get:
tags:
- "nest"
summary: "Retrieves the list of all population IDs."
summary: "Retrieves a list of all population IDs."
operationId: "nest_get_populations"
produces:
- "application/json"
parameters: []
responses:
200:
"200":
description: "Operation successful."
schema:
type: "array"
items:
type: "integer"
format: "uint64"
400:
example:
- 1
- 2
- 3
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -358,7 +370,7 @@ paths:
tags:
- "nest"
summary: "Retrieves the spikes for the given simulation steps (optional) and\
\ GIDS (optional)."
\ gids (optional)."
operationId: "nest_get_spikes"
consumes:
- "application/json"
......@@ -379,7 +391,7 @@ paths:
format: "double"
- name: "gids"
in: "query"
description: "A list of GIDs queried for spike data."
description: "A list of gids queried for spike data."
required: false
type: "array"
items:
......@@ -393,16 +405,16 @@ paths:
format: "uint64"
- name: "limit"
in: "query"
description: "The maximum of entries to be result."
description: "The maximum of entries to be returned."
required: false
type: "integer"
format: "uint64"
responses:
200:
"200":
description: "Operation successful."
schema:
$ref: "#/definitions/Spikes"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -446,16 +458,16 @@ paths:
format: "uint64"
- name: "limit"
in: "query"
description: "The maximum of entries to be result."
description: "The maximum of entries to be returned."
required: false
type: "integer"
format: "uint64"
responses:
200:
"200":
description: "Operation successful."
schema:
$ref: "#/definitions/Spikes"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -473,11 +485,11 @@ paths:
- "application/json"
parameters: []
responses:
200:
"200":
description: "Operation successful."
schema:
$ref: "#/definitions/MultimeterInfo"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -487,7 +499,7 @@ paths:
get:
tags:
- "nest"
summary: "Retrieves the measurements for a multimeter, attribute and GIDS (optional)."
summary: "Retrieves the measurements for a multimeter, attribute and gids (optional)."
operationId: "nest_get_multimeter_measurements"
consumes:
- "application/json"
......@@ -498,8 +510,8 @@ paths:
in: "query"
description: "The multimeter to query"
required: true
type: "number"
format: "integer"
type: "integer"
format: "uint64"
- name: "attribute"
in: "query"
description: "The attribute to query (e.g., 'V_m' for the membrane potential)"
......@@ -519,7 +531,7 @@ paths:
format: "double"
- name: "gids"
in: "query"
description: "A list of GIDs queried for spike data."
description: "A list of gids queried for spike data."
required: false
type: "array"
items:
......@@ -538,11 +550,11 @@ paths:
type: "integer"
format: "uint64"
responses:
200:
"200":
description: "Operation successful."
schema:
$ref: "#/definitions/MultimeterMeasurement"
400:
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -552,7 +564,7 @@ paths:
get:
tags:
- "nest"
summary: "Retrieves the list of all neuron IDs within the population."
summary: "Retrieves the list of all neuron ids within the population."
operationId: "nest_get_gids_in_population"
produces:
- "application/json"
......@@ -564,14 +576,17 @@ paths:
type: "integer"
format: "uint64"
responses:
200:
"200":
description: "Operation successful."
schema:
type: "array"
items:
type: "integer"
format: "uint64"
400:
example:
- 1
- 2
"400":
description: "Operation failed."
schema:
type: "string"
......@@ -594,11 +609,11 @@ definitions:
format: "uint64"
example:
simulation_times:
- 0.8008281904610115
- 0.8008281904610115
- 0.8
- 0.9
gids:
- 6.027456183070403
- 6.027456183070403
- 1
- 2
MultimeterInfo:
type: "array"
items:
......@@ -607,6 +622,10 @@ definitions:
- id: 0
attributes:
- "V_m"
gids:
- 1
- 2
- 3
MultimeterMeasurement:
type: "object"
properties:
......@@ -724,7 +743,9 @@ definitions:
type: "object"
properties: {}
example:
population: "pop1"
gid: 1
properties:
population: 2
position:
- 0.1
- 0.1
......@@ -742,9 +763,9 @@ definitions:
type: "number"
format: "double"
example:
current: 1.4658129805029452
start: 0.8008281904610115
end: 6.027456183070403
current: 2.1
start: 0.1
end: 4.5
MultimeterInfo_inner:
properties:
id:
......@@ -759,3 +780,4 @@ definitions:
items:
type: "integer"
format: "uint64"
\ No newline at end of file
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