Skip to content

Commit 5137ffd

Browse files
pgleesonpgleeson
committed
More tests on ex1
1 parent 1442bf5 commit 5137ffd

File tree

8 files changed

+70
-11
lines changed

8 files changed

+70
-11
lines changed

‎LEMSexamples/LEMS_NML2_Ex1_HH.xml‎

Lines changed: 1 addition & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@
6767
<Simulation id="sim1" length="150ms" step="0.01ms" target="net1">
6868

6969
<Display id="d1" title="Ex1: Simple HH example: Voltage" timeScale="1ms" xmin="0" xmax="150" ymin="-90" ymax="60">
70-
<Line id="v" quantity="hhpop[0]/v" scale="1mV" color="#ffffff" timeScale="1ms"/>
70+
<Line id="v" quantity="hhpop[0]/v" scale="1mV" color="#000000" timeScale="1ms"/>
7171
</Display>
7272

7373
<Display id="d2" title="Ex1: Simple HH example: rate variables" timeScale="1ms" xmin="0" xmax="150" ymin="-0.1" ymax="1.1">
@@ -77,9 +77,6 @@
7777
<Line id="k_n" quantity="hhpop[0]/kChans/k/n/q" scale="1" color="#0000ff" timeScale="1ms"/>
7878
</Display>
7979

80-
<Display id="d3" title="Ex1: Simple HH example: currents" timeScale="1ms" xmin="0" xmax="150" ymin="-0.01" ymax="0.1">
81-
<Line id="i" quantity="hhpop[0]/pulseGen1/i" scale="1nA" color="#000000" timeScale="1ms"/>
82-
</Display>
8380

8481
<OutputFile id="of0" fileName="results/hh_v.dat">
8582
<OutputColumn id="v" quantity="hhpop[0]/v"/>

‎LEMSexamples/test/.test.ex1.jnml.omt‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,4 +14,4 @@ experiments:
1414
spike detection:
1515
method: threshold
1616
threshold: 0
17-
tolerance: 0
17+
tolerance: 0.00367537498758

‎LEMSexamples/test/.test.ex1.jnmlbrian2.omt‎

Lines changed: 17 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,17 @@
1+
# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
2+
3+
target: ../LEMS_NML2_Ex1_HH.xml
4+
engine: jNeuroML_Brian2
5+
mep: .test.ex1.mep
6+
experiments:
7+
v:
8+
observables:
9+
spike times:
10+
file:
11+
path: ../results/hh_v.dat
12+
columns: [0,1]
13+
scaling: [1000, 1000]
14+
spike detection:
15+
method: threshold
16+
threshold: 0
17+
tolerance: 0.00307936823284

‎LEMSexamples/test/.test.ex1.jnmlnrn.omt‎

Lines changed: 17 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,17 @@
1+
# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
2+
3+
target: ../LEMS_NML2_Ex1_HH.xml
4+
engine: jNeuroML_NEURON
5+
mep: .test.ex1.mep
6+
experiments:
7+
v:
8+
observables:
9+
spike times:
10+
file:
11+
path: ../results/hh_v.dat
12+
columns: [0,1]
13+
scaling: [1000, 1000]
14+
spike detection:
15+
method: threshold
16+
threshold: 0
17+
tolerance: 0

‎LEMSexamples/test/.test.ex1.mep‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,4 +3,4 @@ system: Test Ex0
33
experiments:
44
v:
55
expected:
6-
spike times: [52.27, 68.61, 84.74, 101.04]
6+
spike times: [52.24, 68.5, 84.56, 100.67]

‎LEMSexamples/test/.test.ex1.pylems.omt‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,4 +14,4 @@ experiments:
1414
spike detection:
1515
method: threshold
1616
threshold: 0
17-
tolerance: 0.0069
17+
tolerance: 0.00317871

‎LEMSexamples/test/.test.ex5.jnmlbrian2.omt‎

Lines changed: 28 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
1+
# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
2+
3+
target: ../LEMS_NML2_Ex5_DetCell.xml
4+
engine: jNeuroML_Brian2
5+
mep: .test.ex5.mep
6+
experiments:
7+
v:
8+
observables:
9+
spike times:
10+
file:
11+
path: ../results/ex5_v.dat
12+
columns: [0,1]
13+
scaling: [1000, 1000]
14+
spike detection:
15+
method: threshold
16+
threshold: 0
17+
tolerance: 0.001712
18+
m:
19+
observables:
20+
spike times:
21+
file:
22+
path: ../results/ex5_vars.dat
23+
columns: [0,1]
24+
scaling: [1000, 1]
25+
spike detection:
26+
method: threshold
27+
threshold: 0.9
28+
tolerance: 0.00166

‎NeuroML2CoreTypes/Cells.xml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -586,8 +586,8 @@
586586
<!--<DerivedVariable name="surfaceArea" dimension="area" exposure="surfaceArea" value = "4 * radDist * radDist * 3.14159265" valueCondition="length .eq. 0" valueIfFalse = "2 * radDist * 3.14159265 * length"/>-->
587587

588588
<ConditionalDerivedVariable name="surfaceArea" dimension="area" exposure="surfaceArea">
589-
<Case condition="length .eq. 0" value="4 * radDist * radDist * 3.14159265"/>
590-
<Case condition="length .gt. 0" value="2 * radDist * 3.14159265 * length"/>
589+
<Case condition="length .eq. 0 * LEN" value="4 * radDist * radDist * 3.14159265"/>
590+
<Case condition="length .gt. 0 * LEN" value="2 * radDist * 3.14159265 * length"/>
591591
</ConditionalDerivedVariable>
592592

593593
</Dynamics>
@@ -1052,7 +1052,7 @@
10521052
<DerivedVariable name="initMembPot" dimension="voltage" select="biophysicalProperties/membraneProperties/initMembPotential/value"/>
10531053
<DerivedVariable name="thresh" dimension="voltage" select="biophysicalProperties/membraneProperties/spikeThresh/value"/>
10541054

1055-
<DerivedVariable name="debug" dimension="none" select="biophysicalProperties/membraneProperties/totChanCurrent"/>
1055+
<DerivedVariable name="debug" dimension="none" value="0"/>
10561056

10571057
<!--TODO replace this with just using first segment!!-->
10581058
<DerivedVariable name="surfaceArea" exposure="surfaceArea" dimension="area" select="morphology/segments[*]/surfaceArea" reduce="add"/>
@@ -1133,7 +1133,7 @@
11331133
<DerivedVariable name="initMembPot" dimension="voltage" select="biophysicalProperties2CaPools/membraneProperties2CaPools/initMembPotential/value"/>
11341134
<DerivedVariable name="thresh" dimension="voltage" select="biophysicalProperties2CaPools/membraneProperties2CaPools/spikeThresh/value"/>
11351135

1136-
<DerivedVariable name="debug" dimension="none" select="biophysicalProperties2CaPools/membraneProperties2CaPools/totChanCurrent"/>
1136+
<DerivedVariable name="debug" dimension="none" select="0"/>
11371137

11381138

11391139
<DerivedVariable name="surfaceArea" exposure="surfaceArea" dimension="area" select="morphology/segments[*]/surfaceArea" reduce="add"/>

0 commit comments

Comments
 (0)