def main():
file_path = "Simple.json"
data = convert_states_to_stateful_parameters("../" + file_path)
# print(data)
with open("Translated_" + file_path, "w") as fp:
json.dump(data, fp, indent=4)
if "-run" in sys.argv:
verbose = True
mod_graph = load_mdf("Translated_%s" % file_path).graphs[0]
eg = EvaluableGraph(mod_graph, verbose)
mod_graph_old = load_mdf("../" + file_path).graphs[0]
eg_old = EvaluableGraph(mod_graph_old, verbose)
format = FORMAT_NUMPY
eg.evaluate(array_format=format)
eg_old.evaluate(array_format=format)
print(
"New file output value>>>",
eg.enodes["processing_node"].evaluable_outputs["output_1"].
curr_value,
)
print(
"Old file output value>>>",
eg_old.enodes["processing_node"].evaluable_outputs["output_1"].
curr_value,
)
def main():
dt = 0.01
file_path = "States.json"
data = convert_states_to_stateful_parameters("../" + file_path, dt)
with open("Translated_" + file_path, "w") as fp:
json.dump(data, fp, indent=4)
if "-run" in sys.argv:
verbose = True
mod_graph = load_mdf("Translated_%s" % file_path).graphs[0]
eg = EvaluableGraph(mod_graph, verbose)
mod_graph_old = load_mdf("../" + file_path).graphs[0]
eg_old = EvaluableGraph(mod_graph_old, verbose)
duration = 2
t = 0
recorded = {}
times = []
s = []
s_old = []
while t <= duration:
print("====== Evaluating at t = %s ======" % (t))
# levels.append(eg.enodes['sine_node'].evaluable_stateful_parameters['level'].curr_value)
# t+=args.dt
# print("time first>>>",type(t))
t = float(
eg.enodes["sine_node"].evaluable_parameters["time"].curr_value)
# times.append(float(eg.enodes['sine_node'].evaluable_parameters['time'].curr_value))
times.append(t)
if t == 0:
eg_old.evaluate() # replace with initialize?
else:
eg_old.evaluate(time_increment=dt)
s_old.append(eg_old.enodes["sine_node"].
evaluable_outputs["out_port"].curr_value)
eg.evaluate()
s.append(eg.enodes["sine_node"].evaluable_outputs["out_port"].
curr_value)
# t+=dt
print(s_old[:10], s[:10], times[:10])
import matplotlib.pyplot as plt
plt.plot(times, s)
plt.show()
plt.savefig("translated_levelratesineplot.jpg")
def main(example_file: str,
array_format: str = FORMAT_NUMPY,
verbose: bool = False):
"""
Main entry point for execution engine.
Args:
example_file: The MDF file to execute.
array_format: The format of arrays to use. Allowed values: 'numpy' or 'tensorflow'.
verbose: Whether to print output to standard out during execution.
"""
from modeci_mdf.utils import load_mdf, print_summary
mod_graph = load_mdf(example_file).graphs[0]
if verbose:
print("Loaded Graph:")
print_summary(mod_graph)
print("------------------")
eg = EvaluableGraph(mod_graph, verbose)
eg.evaluate(array_format=array_format)
return eg
def convert_mdf_file_to_onnx(input_file: str):
"""
Converter from MDF to ONNX. Takes in a JSON/ONNX file and generates ONNX files.
Args:
input_file: The input file path to the MDF file. Output files are generated in same
directory with -m2o.onnx extensions.
Returns:
NoneType
"""
import os
# Load the MDF model from file - this is not used anymore
mdf_model = load_mdf(input_file)
# print("Loaded MDF file from ", mdf_model_file)
onnx_models = mdf_to_onnx(mdf_model)
for onnx_model in onnx_models:
out_filename = (
f"{os.path.splitext(input_file)[0]}_{onnx_model.graph.name}-m2o.onnx"
)
onnx.save(onnx_model, out_filename)
print("ONNX output saved in ", out_filename)
def test_abc():
base_path = Path(__file__).parent
filename = "examples/ONNX/abc_basic-mdf.json"
file_path = (base_path / "../../.." / filename).resolve()
# Load the MDF model
mdf_model = load_mdf(str(file_path))
# Test input
test_input = np.array([[0, 0, 0], [1, 1, 1]], dtype=np.float32)
# Get the result of MDF execution
mdf_executable = EvaluableGraph(mdf_model.graphs[0], verbose=False)
mdf_executable.evaluate(initializer={"input": test_input})
mdf_output = mdf_executable.enodes["Cos_2"].evaluable_outputs[
"_3"].curr_value
# Get the translated ONNX model
onnx_models = mdf_to_onnx(mdf_model)
# Bluffing onnx that our model is 13 when it is actually 15. This is needed for older onnxruntime
# installations to run this model. See https://github.com/onnx/onnx/issues/3205
onnx_models[0].opset_import[0].version = 13
# Get the result of running the ONNX model
session = backend.prepare(onnx_models[0])
onnx_output = session.run(
test_input) # run returns a list with the actual result and type
onnx_res_output = np.array(onnx_output[0])
assert np.array_equal(onnx_res_output, mdf_output)
def test_ab():
base_path = Path(__file__).parent
filename = "examples/ONNX/ab.json"
file_path = (base_path / "../../.." / filename).resolve()
# Load the MDF model
mdf_model = load_mdf(str(file_path))
# Test input
test_input = np.array([[0, 0, 0], [1, 1, 1]], 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_output = mdf_executable.enodes["Mul_3"].evaluable_outputs[
"_4"].curr_value
# Get the translated ONNX model
onnx_models = mdf_to_onnx(mdf_model)
# Bluffing onnx that our model is 13 when it is actually 15. This is needed for older onnxruntime
# installations to run this model. See https://github.com/onnx/onnx/issues/3205
onnx_models[0].opset_import[0].version = 13
# Get the result of running the ONNX model
session = backend.prepare(onnx_models[0])
onnx_output = session.run(
test_input) # run returns a list with the actual result and type
onnx_res_output = np.array(onnx_output[0])
# print(f"Output calculated by onnxruntime: {onnx_res_output} and MDF: {mdf_output.astype(float)}")
assert np.array_equal(onnx_res_output, mdf_output)
def test_no_input_ports_to_json(tmpdir):
"""Test the edge case of exporting a model to JSON when it has a node with no input ports"""
mod = Model(id="ABCD")
mod_graph = Graph(id="abcd_example")
mod.graphs.append(mod_graph)
input_node = Node(id="input0")
input_node.parameters.append(Parameter(id="input_level", value=10.0))
op1 = OutputPort(id="out_port")
op1.value = "input_level"
input_node.output_ports.append(op1)
mod_graph.nodes.append(input_node)
tmpfile = f"{tmpdir}/test.json"
mod.to_json_file(tmpfile)
# FIXME: Doesn't seem like we have any methods for deserialization. Just do some quick and dirty checks
# This should really be something like assert mod_graph == deserialized_mod_graph
import json
with open(tmpfile) as f:
data = json.load(f)
print(data)
assert (data["ABCD"]["graphs"]["abcd_example"]["nodes"]["input0"]
["parameters"]["input_level"]["value"] == 10.0)
mod_graph2 = load_mdf(tmpfile)
print(mod_graph2)
assert mod_graph2.graphs[0].nodes[0].parameters[0].value == 10.0
def _generate_scripts_from_json(model_input):
"""
Helper function to parse MDF objects from MDF json representation as well
as load the h5 weights for large weight matrices. Uses MDF scheduler to
determine proper ordering of nodes, and calls `build_script`.
Returns dictionary of scripts where key = name of mdf model, value is string
representation of script.
"""
file_dir = os.path.dirname(model_input)
model = load_mdf(model_input)
scripts = {}
for graph in model.graphs:
nodes = graph.nodes
# Read weights.h5 if exists
if "weights.h5" in os.listdir(file_dir):
weight_dict = h5py.File(os.path.join(file_dir, "weights.h5"), "r")
# Hack to fix problem with HDF5 parameters
for node in graph.nodes:
if node.parameters:
for param in node.parameters:
param_key = param.id
param_val = param.value
if param_key in ["weight", "bias"
] and type(param_val) == str:
# Load and reassign
array = weight_dict[param_val][:]
# np.set_printoptions(threshold=sys.maxsize)
param.value = array
evaluable_graph = EvaluableGraph(graph, verbose=False)
enodes = evaluable_graph.enodes
edges = evaluable_graph.ordered_edges
try:
conditions = evaluable_graph.conditions
except AttributeError:
conditions = {}
# Use edges and nodes to construct execution order
execution_order = []
for idx, edge in enumerate(edges):
if idx == 0:
execution_order.append(edge.sender)
execution_order.append(edge.receiver)
# Build script
script = build_script(nodes, execution_order, conditions=conditions)
scripts[graph.id] = script
return scripts
def test_graph_types(tmpdir):
r"""
Test whether types saved in parameters are the same after reloading
"""
mod = Model(id="Test0")
mod_graph = Graph(id="test_example")
mod.graphs.append(mod_graph)
node0 = Node(id="node0")
mod_graph.nodes.append(node0)
p_int = 2
node0.parameters.append(Parameter(id="p_int", value=p_int))
p_float = 2.0
node0.parameters.append(Parameter(id="p_float", value=p_float))
p_bool = False
node0.parameters.append(Parameter(id="p_bool", value=p_bool))
p_str = "p_int + p_float"
node0.parameters.append(Parameter(id="p_str", value=p_str))
p_str2 = "2"
node0.parameters.append(Parameter(id="p_str2", value=p_str2))
p_list = ["2", 2, "two"]
node0.parameters.append(Parameter(id="p_list", value=p_list))
p_dict = {"a": 3, "w": {"b": 3, "x": True, "y": [2, 2, 2, 2]}}
node0.parameters.append(Parameter(id="p_dict", value=p_dict))
p_dict_tuple = {"y": (4, 44)} # will change to {'y': [4, 44]}
node0.parameters.append(Parameter(id="p_dict_tuple", value=p_dict_tuple))
print(mod)
tmpfile = f"{tmpdir}/test.json"
mod.to_json_file(tmpfile)
mod_graph2 = load_mdf(tmpfile)
print(f"Saved to {tmpfile}: {mod_graph2}")
new_node0 = mod_graph2.graphs[0].nodes[0]
for p in [p.id for p in node0.parameters]:
print("Testing {}, is {} = {}?".format(
p,
new_node0.get_parameter(p).value, eval(p)))
assert type(new_node0.get_parameter(p).value) == type(eval(p))
# Type will be same for tuple containing dict, but tuple will have been converetd to dict...
if not p == "p_dict_tuple":
assert new_node0.get_parameter(p).value == eval(p)
def main():
"""Takes count.lisp, converts to MDF, and runs using the scheduler."""
file_name = os.path.dirname(os.path.realpath(__file__)) + "/count.lisp"
print(file_name)
mod = actr_to_mdf(file_name)
mdf_graph = load_mdf(file_name[:-5] + ".json").graphs[0]
eg = EvaluableGraph(graph=mdf_graph, verbose=False)
term = False
goal = {}
retrieval = {}
while not term:
eg.evaluate(initializer={"goal_input": goal, "dm_input": retrieval})
term = (eg.enodes["check_termination"].
evaluable_outputs["check_output"].curr_value)
goal = (eg.enodes["fire_production"].
evaluable_outputs["fire_prod_output_to_goal"].curr_value)
retrieval = (
eg.enodes["fire_production"].
evaluable_outputs["fire_prod_output_to_retrieval"].curr_value)
print("Final Goal:")
print(eg.enodes["goal_buffer"].evaluable_outputs["goal_output"].curr_value)
from modeci_mdf.utils import load_mdf, print_summary
verbose = True
if len(sys.argv) < 3:
print(
"Usage:\n\n python graphviz.py MDF_JSON_FILE level [%s]\n\n" %
NO_VIEW +
"where level = 1, 2 or 3. Include %s to supress viewing generated graph on render\n"
% NO_VIEW)
exit()
example = sys.argv[1]
view = NO_VIEW not in sys.argv
model = load_mdf(example)
mod_graph = model.graphs[0]
print("------------------")
print("Loaded Graph:")
print_summary(mod_graph)
print("------------------")
# nmllite_file = example.replace('.json','.nmllite.json')
mdf_to_graphviz(mod_graph,
engine=engines["d"],
view_on_render=view,
level=int(sys.argv[2]))
def main():
verbose = True
dt = 5e-05
file_path = "mlp_pure_mdf.json"
data = convert_states_to_stateful_parameters(file_path, dt)
# print(data)
with open("Translated_" + file_path, "w") as fp:
json.dump(data, fp, indent=4)
test_all = "-test" in sys.argv
mod_graph = load_mdf("Translated_%s" % file_path).graphs[0]
# mdf_to_graphviz(mod_graph,view_on_render=not test_all, level=3)
from modelspec.utils import FORMAT_NUMPY, FORMAT_TENSORFLOW
format = FORMAT_TENSORFLOW if "-tf" in sys.argv else FORMAT_NUMPY
eg = EvaluableGraph(mod_graph, verbose=False)
eg.evaluate(array_format=format)
print("Finished evaluating graph using array format %s" % format)
for n in [
"mlp_input_layer",
"mlp_relu_1",
"mlp_hidden_layer_with_relu",
"mlp_output_layer",
]:
out = eg.enodes[n].evaluable_outputs["out_port"].curr_value
print(f"Final output value of node {n}: {out}, shape: {out.shape}")
if "-graph" in sys.argv:
mod.to_graph_image(
engine="dot",
output_format="png",
view_on_render=False,
level=2,
filename_root="mlp_pure_mdf",
only_warn_on_fail=
True, # Makes sure test of this doesn't fail on Windows on GitHub Actions
)
if test_all:
# Iterate on training data, feed forward and log accuracy
imgs = np.load("example_data/imgs.npy")
labels = np.load("example_data/labels.npy")
import torch.nn
matches = 0
imgs_to_test = imgs[:300]
start = time.time()
for i in range(len(imgs_to_test)):
ii = imgs[i, :, :]
target = labels[i]
img = torch.Tensor(ii).view(-1, 14 * 14).numpy()
# plot_img(img, 'Post_%i (%s)'%(i, img.shape))
print("***********\nTesting image %i (label: %s): %s\n%s" %
(i, target, np.array2string(img, threshold=5,
edgeitems=2), img.shape))
# print(mod_graph.nodes[0].parameters['input'])
mod_graph.nodes[0].get_parameter("input").value = img
eg = EvaluableGraph(mod_graph, verbose=False)
eg.evaluate(array_format=format)
for n in ["mlp_output_layer"]:
out = eg.enodes[n].evaluable_outputs["out_port"].curr_value
print("Output of evaluated graph: %s %s (%s)" %
(out, out.shape, type(out).__name__))
prediction = np.argmax(out)
match = target == int(prediction)
if match:
matches += 1
print(
f"Target: {target}, prediction: {prediction}, match: {match}")
t = time.time() - start
print(
"Matches: %i/%i, accuracy: %s%%. Total time: %.4f sec (%.4fs per run)"
% (
matches,
len(imgs_to_test),
(100.0 * matches) / len(imgs_to_test),
t,
t / len(imgs_to_test),
))
def main():
dt = 5e-05
file_path = "FN.mdf.json"
data = convert_states_to_stateful_parameters("../" + file_path, dt)
# print(data)
with open("Translated_" + file_path, "w") as fp:
json.dump(data, fp, indent=4)
if "-run" in sys.argv:
verbose = True
mod_graph = load_mdf("Translated_%s" % file_path).graphs[0]
eg = EvaluableGraph(mod_graph, verbose)
mod_graph_old = load_mdf("../" + file_path).graphs[0]
eg_old = EvaluableGraph(mod_graph_old, verbose)
duration = 0.1
t = 0
recorded = {}
times = []
s = []
vv = []
ww = []
vv_old = []
ww_old = []
while t <= duration + dt:
print("====== Evaluating at t = %s ======" % (t))
vv.append(
float(
eg.enodes["FNpop_0"].evaluable_parameters["V"].curr_value))
ww.append(
float(
eg.enodes["FNpop_0"].evaluable_parameters["W"].curr_value))
# levels.append(eg.enodes['sine_node'].evaluable_stateful_parameters['level'].curr_value)
# print("time first>>>",type(t))
t = float(
eg.enodes["FNpop_0"].evaluable_parameters["time"].curr_value)
times.append(t)
if t == 0:
eg_old.evaluate() # replace with initialize?
else:
eg_old.evaluate(time_increment=dt)
vv_old.append(
eg_old.enodes["FNpop_0"].evaluable_parameters["V"].curr_value)
ww_old.append(
eg_old.enodes["FNpop_0"].evaluable_parameters["W"].curr_value)
eg.evaluate()
print("Times>>>", times[:10])
print("Translated file W and V>>>", ww[:10], vv[:10])
print("Old file W and V>>>", ww_old[:10], vv_old[:10])
import matplotlib.pyplot as plt
plt.plot(times, vv, label="V")
plt.plot(times, ww, label="W")
plt.legend()
plt.show()
plt.savefig("translated_FN_stateful_vw_plot.jpg")
def execute(multi=False):
mdf_model = load_mdf("FN.mdf.yaml")
mod_graph = mdf_model.graphs[0]
dt = 0.00005
duration = 0.1
if not multi:
fn_node = mod_graph.nodes[0]
fn_node.get_parameter("initial_v").value = [-1.0]
fn_node.get_parameter("initial_w").value = [0.0]
input = np.array([0])
else:
size = 15
max_amp = 0.5
input = np.array(
[max_amp * (-1 + 2 * i / size) for i in range(size + 1)])
# input = [-0.4,-0.2, 0.,0.2,0.4]
input_node = Node(id="input_node", parameters={"input_level": input})
op1 = OutputPort(id="out_port", value="input_level")
input_node.output_ports.append(op1)
mod_graph.nodes.append(input_node)
fn_node = mod_graph.nodes[0]
fn_node.get_parameter("initial_v").value = np.array([1.0] * len(input))
fn_node.get_parameter("initial_w").value = np.array([0.0] * len(input))
print(fn_node)
e1 = Edge(
id="input_edge",
sender=input_node.id,
sender_port=op1.id,
receiver="FNpop_0",
receiver_port="INPUT",
)
mod_graph.edges.append(e1)
mdf_model.to_graph_image(
engine="dot",
output_format="png",
view_on_render=False,
level=3,
filename_root="FNmulti",
only_warn_on_fail=
True, # Makes sure test of this doesn't fail on Windows on GitHub Actions
)
duration = 0.1
eg = EvaluableGraph(mod_graph, verbose)
# duration= 2
t = 0
times = []
vv = {}
ww = {}
format = FORMAT_TENSORFLOW if "-tf" in sys.argv else FORMAT_NUMPY
while t < duration + 0.00005:
times.append(t)
print("====== Evaluating at t = %s ======" % (t))
if t == 0:
eg.evaluate(array_format=format) # replace with initialize?
else:
eg.evaluate(array_format=format, time_increment=dt)
for i in range(
len(eg.enodes["FNpop_0"].evaluable_parameters["V"].curr_value)
):
if not i in vv:
vv[i] = []
ww[i] = []
v = eg.enodes["FNpop_0"].evaluable_parameters["V"].curr_value[i]
w = eg.enodes["FNpop_0"].evaluable_parameters["W"].curr_value[i]
vv[i].append(v)
ww[i].append(w)
if i == 0:
print(f" Value at {t}: v={v}, w={w}")
t += dt
import matplotlib.pyplot as plt
for vi in vv:
plt.plot(times, vv[vi], label="V %.3f" % input[vi])
plt.plot(times, ww[vi], label="W %.3f" % input[vi])
plt.legend()
if not multi:
plt.savefig("MDFFNrun.png", bbox_inches="tight")
if not "-nogui" in sys.argv:
plt.show()