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Minimal updates to work with modelspec v0.3 - onnx examples use floats #476

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Aug 14, 2023
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Minimal updates to work with modelspec v0.3 - onnx examples use floats #476

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2b398e6
Modelspec>=0.3
pgleeson Aug 8, 2023
5ad2579
Minimal updates to work with modelspec v0.3 - onnx examples use floats
pgleeson Aug 9, 2023
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13 changes: 13 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -278,3 +278,16 @@ Thumbs.db #thumbnail cache on Windows
/examples/NeuroML/arm64
/examples/MDF/RNN/iaf.net
/examples/MDF/RNN/iaf.net2
/examples/NeuroML/PyNN/All*
/examples/NeuroML/PyNN/*dat
/examples/NeuroML/PyNN/*.png
/examples/NeuroML/PyNN/*.1
/examples/NeuroML/PyNN/InputWeights*
/examples/NeuroML/PyNN/OneCell*
/examples/NeuroML/PyNN/Sim*
/examples/NeuroML/PyNN/LEMS_Sim*
/examples/NeuroML/PyNN/HH*
/examples/NeuroML/PyNN/arm64
/examples/NeuroML/PyNN/*.pkl
*_code.gen.c
/examples/NeuroML/PyNN/Net1*
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2 changes: 1 addition & 1 deletion examples/NeuroML/FN__lems.xml
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Original file line number Diff line number Diff line change
@@ -54,5 +54,5 @@
</OnEvent>
</Dynamics>
</ComponentType>
<Component id="fn" type="fnCell" initial_w="0" initial_v="-1" a_v="-0.3333333333333333" b_v="0" c_v="1" d_v="1" e_v="-1" f_v="1" time_constant_v="1" a_w="1" b_w="-0.8" c_w="0.7" time_constant_w="12.5" threshold_exc="-1.0" mode="1" uncorrelated_activity="0" Iext="0" threshold="-1"/>
<Component id="fn" type="fnCell" initial_w="0.0" initial_v="-1" a_v="-0.3333333333333333" b_v="0.0" c_v="1.0" d_v="1" e_v="-1.0" f_v="1.0" time_constant_v="1.0" a_w="1.0" b_w="-0.8" c_w="0.7" time_constant_w="12.5" threshold_exc="-1.0" mode="1.0" uncorrelated_activity="0.0" Iext="0" threshold="-1.0"/>
</Lems>
6 changes: 4 additions & 2 deletions examples/ONNX/ab.json
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Original file line number Diff line number Diff line change
@@ -11,7 +11,8 @@
"shape": [
2,
3
]
],
"type": "float"
}
},
"parameters": {
@@ -38,7 +39,8 @@
"shape": [
2,
3
]
],
"type": "float"
}
},
"parameters": {
Binary file modified examples/ONNX/ab.png
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2 changes: 2 additions & 0 deletions examples/ONNX/ab.yaml
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Original file line number Diff line number Diff line change
@@ -10,6 +10,7 @@ ONNX Model:
shape:
- 2
- 3
type: float
parameters:
B:
value: 1.0
@@ -27,6 +28,7 @@ ONNX Model:
shape:
- 2
- 3
type: float
parameters:
B:
value: 5.0
15 changes: 10 additions & 5 deletions examples/ONNX/abc.json
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Original file line number Diff line number Diff line change
@@ -11,7 +11,8 @@
"shape": [
2,
3
]
],
"type": "float"
}
},
"parameters": {
@@ -37,13 +38,15 @@
"B_loop_count": {
"shape": [
1
]
],
"type": "float"
},
"onnx_Loop_3": {
"shape": [
2,
3
]
],
"type": "float"
}
},
"parameters": {
@@ -58,7 +61,8 @@
"shape": [
2,
3
]
],
"type": "float"
}
},
"parameters": {
@@ -124,7 +128,8 @@
"x_3": {
"shape": [
1
]
],
"type": "float"
}
},
"parameters": {
5 changes: 5 additions & 0 deletions examples/ONNX/abc.yaml
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Original file line number Diff line number Diff line change
@@ -10,6 +10,7 @@ ONNX Model:
shape:
- 2
- 3
type: float
parameters:
B:
value: 1.0
@@ -26,10 +27,12 @@ ONNX Model:
B_loop_count:
shape:
- 1
type: float
onnx_Loop_3:
shape:
- 2
- 3
type: float
parameters:
body:
value:
@@ -42,6 +45,7 @@ ONNX Model:
shape:
- 2
- 3
type: float
parameters:
B:
value: 10.0
@@ -80,6 +84,7 @@ ONNX Model:
x_3:
shape:
- 1
type: float
parameters:
B:
value: 100.0
21 changes: 14 additions & 7 deletions examples/ONNX/abcd.json
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Original file line number Diff line number Diff line change
@@ -11,7 +11,8 @@
"shape": [
1,
1
]
],
"type": "float"
}
},
"parameters": {
@@ -42,7 +43,8 @@
"shape": [
1,
1
]
],
"type": "float"
}
},
"parameters": {
@@ -73,7 +75,8 @@
"shape": [
1,
1
]
],
"type": "float"
}
},
"parameters": {
@@ -104,7 +107,8 @@
"shape": [
1,
1
]
],
"type": "float"
}
},
"parameters": {
@@ -135,7 +139,8 @@
"shape": [
1,
1
]
],
"type": "float"
}
},
"parameters": {
@@ -166,7 +171,8 @@
"shape": [
1,
1
]
],
"type": "float"
}
},
"parameters": {
@@ -197,7 +203,8 @@
"shape": [
1,
1
]
],
"type": "float"
}
},
"parameters": {
7 changes: 7 additions & 0 deletions examples/ONNX/abcd.yaml
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Original file line number Diff line number Diff line change
@@ -10,6 +10,7 @@ ONNX Model:
shape:
- 1
- 1
type: float
parameters:
A:
value:
@@ -28,6 +29,7 @@ ONNX Model:
shape:
- 1
- 1
type: float
parameters:
B:
value:
@@ -46,6 +48,7 @@ ONNX Model:
shape:
- 1
- 1
type: float
parameters:
A:
value:
@@ -64,6 +67,7 @@ ONNX Model:
shape:
- 1
- 1
type: float
parameters:
B:
value:
@@ -82,6 +86,7 @@ ONNX Model:
shape:
- 1
- 1
type: float
parameters:
A:
value:
@@ -100,6 +105,7 @@ ONNX Model:
shape:
- 1
- 1
type: float
parameters:
B:
value:
@@ -118,6 +124,7 @@ ONNX Model:
shape:
- 1
- 1
type: float
parameters:
B:
value:
8 changes: 4 additions & 4 deletions examples/ONNX/simple_ab.py
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Original file line number Diff line number Diff line change
@@ -86,16 +86,16 @@ def main():
), # Makes sure test of this doesn't fail on Windows on GitHub Actions
)
if "-run" in sys.argv:
verbose = True
verbose = False

verbose = "-v" in sys.argv

from modeci_mdf.execution_engine import EvaluableGraph

eg = EvaluableGraph(mdf_model.graphs[0], verbose=verbose)

print("Evaluating graph...")
test_values = [0, 1, [1, 2], dummy_input.numpy()]
test_values = [0, 1, [1, 2]]
test_values = [0.0, 1.0, [1.0, 2.0], dummy_input.numpy()]
test_values = [0.0, 1.0, [1.0, 2.0]]

for t in test_values:
print("===================\nEvaluating MDF model with input: %s" % t)
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2 changes: 1 addition & 1 deletion setup.cfg
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Original file line number Diff line number Diff line change
@@ -45,7 +45,7 @@ install_requires =
skl2onnx==1.14.0
attrs>=21.1.0
cattrs
modelspec<0.3,>=0.2.6
modelspec<0.4,>=0.3.0
glom

python_requires = >=3.7
5 changes: 4 additions & 1 deletion src/modeci_mdf/execution_engine.py
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Original file line number Diff line number Diff line change
@@ -686,7 +686,10 @@ class EvaluableInput:
def __init__(self, input_port: InputPort, verbose: Optional[bool] = False):
self.verbose = verbose
self.input_port = input_port
self.curr_value = np.full(input_port.shape, 0)
default = 0
if input_port.type and "float" in input_port.type:
default = 0.0
self.curr_value = np.full(input_port.shape, default)

def set_input_value(self, value: Union[str, int, np.ndarray]):
"""Set a new value at input port
17 changes: 14 additions & 3 deletions src/modeci_mdf/interfaces/graphviz/exporter.py
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Original file line number Diff line number Diff line change
@@ -286,12 +286,23 @@ def mdf_to_graphviz(

if node.input_ports and len(node.input_ports) > 0:
for ip in node.input_ports:

additional = ""
if ip.shape is not None:
additional += "shape: %s, " % str(ip.shape)
"""if ip.reduce is not None:
if ip.reduce != "overwrite": # since this is the default...
additional += "reduce: %s, " % str(ip.reduce)"""
if ip.type is not None:
additional += "type: %s, " % str(ip.type)

if len(additional) > 0:
additional = "(%s)" % additional[:-2]

info += "<tr><td>{}{} {}</td></tr>".format(
format_label("IN"),
format_input(ip.id),
"(shape: %s)" % str(ip.shape)
if level >= LEVEL_2 and ip.shape is not None
else "",
additional,
)

if node.parameters and len(node.parameters) > 0:
2 changes: 1 addition & 1 deletion src/modeci_mdf/interfaces/onnx/importer.py
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Original file line number Diff line number Diff line change
@@ -141,7 +141,7 @@ def onnx_node_to_mdf(
for inp in non_constant_inputs:
param_info = onnx_initializer.get(inp, None)
shape = param_info["shape"] if param_info else None
ip = InputPort(id=id_to_port(inp), shape=shape)
ip = InputPort(id=id_to_port(inp), shape=shape, type="float")
mdf_node.input_ports.append(ip)

for out in node.output:
7 changes: 3 additions & 4 deletions tests/interfaces/onnx/test_importer.py
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Original file line number Diff line number Diff line change
@@ -20,13 +20,12 @@ def test_ab():
mdf_model = load_mdf(str(file_path))

# Test input
test_input = np.array([[0, 0, 0], [1, 1, 1]], dtype=np.float32)
test_input = np.array([[0.0, 0.0, 0.0], [1.0, 1.0, 1.0]], dtype=np.float32)

# Get the result of MDF execution
mdf_executable = EvaluableGraph(mdf_model.graphs[0], verbose=False)
# TODO: the int type cast is necessaryf or now because the nodes' parameters are constants and inputs must have
# the same type
mdf_executable.evaluate(initializer={"input": test_input.astype(int)})

mdf_executable.evaluate(initializer={"input": test_input})
mdf_output = mdf_executable.enodes["Mul_3"].evaluable_outputs["_4"].curr_value

# Get the translated ONNX model
12 changes: 12 additions & 0 deletions tests/test_parameters.py
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Original file line number Diff line number Diff line change
@@ -46,6 +46,10 @@
),
### Conditions
(0, {"x": 3}, 1, "x<4", 1, None),
(0, {"x": 3}, 0, "x<1", 1, None),
(0, {"x": 3}, 1, "x==3", 1, None),
(0, {"x": 3}, 1, "x==3 and x<=5", 1, None),
(2, {"x": 3}, 3, "x<4", 3, None),
(0.6, {"x": 3}, 0.6, "x>=4", 1.6, None),
("y+z", {"x": 3, "y": 2, "z": 3}, 3, "x>y", "z", None),
(
@@ -56,6 +60,14 @@
[3, 3],
None,
),
(
numpy.array([0, 0]),
{"x": numpy.array([1, 1]), "y": numpy.array([0, 0])},
numpy.array([1, 1]),
"y<x",
[1, 1],
None,
),
# ([0,0], {"x": 3}, 1, 'x<4', 1, None),
# (0, {}, 1, 'p1>2', 1, None),
# ("x", {"x": 'abc'}, 'abc'),