问题

I am trying to export a myokit model to python file using a myokit.formats.python.PythonExporter from here: https://myokit.readthedocs.io/en/stable/api_formats/python.html?highlight=export python# The code is like this:

model1, protocol, x = myokit.load('dn-1985-if-gna.mmt')
sim = myokit.Simulation(model1, protocol)

exporter= myokit.formats.python.PythonExporter()
exporter.model('dn-1985-if-gna_py.mmt', model1)

And I get the NotImplemented Error:

NotImplementedError: 

I suppose that I am possibly not creating the correct class object, but I have also tried this:

exporter = myokit.formats.python.PythonExporter
exporter.model('dn-1985-if-gna_py.mmt', model1)

The error is:

TypeError: model() missing 1 required positional argument: 'model'

P.S. I have tried a couple of models, for example, this .mmt file https://dropmefiles.com/e3xjm

model1, protocol, x = myokit.load('dn-1985-if-gna.mmt')
sim = myokit.Simulation(model1, protocol)

exporter= myokit.formats.python.PythonExporter()
exporter.model('dn-1985-if-gna_py.mmt, model1)

NotImplementedError                       Traceback (most recent call last)
c:\More_Program_Files\Coding\Jupyter_files23_cellml_myokit23_07_04_myokit_tut.ipynb Cell 48 in ()
      1 exporter= myokit.formats.python.PythonExporter()
----> 2 a = exporter.model('dn-1985-if-gna_copy_py.mmt', sim)

File c:\More_Program_Files\Anaconda3\lib\site-packages\myokit\formats\__init__.py:61, in Exporter.model(self, path, model)
     54 def model(self, path, model):
     55     """
     56     Exports a :class:`myokit.Model`.
     57 
     58     The output will be stored in the **file** ``path``. A
     59     :class:`myokit.ExportError` will be raised if any errors occur.
     60     """
---> 61     raise NotImplementedError

NotImplementedError: 

exporter= myokit.formats.python.PythonExporter
exporter.model('dn-1985-if-gna_py.mmt', model1)

TypeError                                 Traceback (most recent call last)
c:\More_Program_Files\Coding\Jupyter_files23_cellml_myokit23_07_04_myokit_tut.ipynb Cell 48 in ()
      1 exporter= myokit.formats.python.PythonExporter
----> 2 exporter.model('dn-1985-if-gna_copy_py.mmt', model)

TypeError: model() missing 1 required positional argument: 'model'

答案1

得分: 1

这是您提供的Python代码的翻译：

#!/usr/bin/env python
#
# 生成日期：2023年5月13日02:47:17
#

import math

#
# 组件和变量
#

class CEngine(object):
    def __init__(self):
        self.time = None
        self.pace = None

        self._constants()
        self.init()
    def _constants(self):
        """
        设置常量值
        """
    def init(self):
        """
        将状态变量重置为其初始值
        """
    def update(self):
        """
        重新计算当前时间和状态的所有值
        """
        c_engine.pace = engine.pace
        c_engine.time = engine.time

class CIk1(object):
    def __init__(self):
        self.IK1 = None

        self._constants()
        self.init()
    def _constants(self):
        """
        设置常量值
        """
    def init(self):
        """
        将状态变量重置为其初始值
        """
    def update(self):
        """
        重新计算当前时间和状态的所有值
        """
        self.IK1 = 0.35 * (4.0 * (math.exp(0.04 * (c_membrane.V + 85.0)) - 1.0) / (math.exp(0.08 * (c_membrane.V + 53.0)) + math.exp(0.04 * (c_membrane.V + 53.0))) + 0.2 * (c_membrane.V + 23.0) / (1.0 - math.exp((-0.04) * (c_membrane.V + 23.0))))

class CIna(object):
    def __init__(self):
        self.gNaBar = None
        self.gNaC = None
        self.ENa = None
        self.INa = None
        self.m = None
        self.d_m = None
        self.ina_m_alpha = None
        self.ina_m_beta = None
        self.h = None
        self.d_h = None
        self.ina_h_alpha = None
        self.ina_h_beta = None
        self.j = None
        self.d_j = None
        self.ina_j_alpha = None
        self.ina_j_beta = None

        self._constants()
        self.init()
    def _constants(self):
        """
        设置常量值
        """
        self.ENa = 50.0
        self.gNaBar = 4.0
        self.gNaC = 0.003
    def init(self):
        """
        将状态变量重置为其初始值
        """
        self.m = 0.01
        self.h = 0.99
        self.j = 0.98
    def update(self):
        """
        重新计算当前时间和状态的所有值
        """
        self.ina_h_alpha = 0.126 * math.exp((-0.25) * (c_membrane.V + 77.0))
        self.ina_h_beta = 1.7 / (1.0 + math.exp((-0.082) * (c_membrane.V + 22.5)))
        self.d_h = self.ina_h_alpha * (1.0 - self.h) - self.ina_h_beta * self.h
        self.ina_j_alpha = 0.055 * math.exp((-0.25) * (c_membrane.V + 78.0)) / (1.0 + math.exp((-0.2) * (c_membrane.V + 78.0)))
        self.ina_j_beta = 0.3 / (1.0 + math.exp((-0.1) * (c_membrane.V + 32.0)))
        self.d_j = self.ina_j_alpha * (1.0 - self.j) - self.ina_j_beta * self.j
        self.ina_m_alpha = (c_membrane.V + 47.0) / (1.0 - math.exp((-0.1) * (c_membrane.V + 47.0)))
        self.ina_m_beta = 40.0 * math.exp((-0.056) * (c_membrane.V + 72.0))
        self.d_m = self.ina_m_alpha * (1.0 - self.m) - self.ina_m_beta * self.m
        self.INa = (self.gNaBar * self.m ** 3.0 * self.h * self.j + self.gNaC) * (c_membrane.V - self.ENa)

class CIsi(object):
    def __init__(self):
        self.gsBar = None
        self.Es = None
        self.Isi = None
        self.d = None
        self.d_d = None
        self.isi_d_alpha = None
        self.isi_d_beta = None
        self.f = None
        self.d_f = None
        self.isi_f_alpha = None
        self.isi_f_beta = None
        self.Cai = None
        self.d_cai = None

        self._constants()
        self.init()
    def _constants(self):
        """
        设置常量值
        """
        self.gsBar = 0.09
    def init(self):
        """
        将状态变量重置为其初始值
        """
        self.d = 0.003
        self.f = 0.99
        self.Cai = 2e-07
    def update(self):
        """
        重新计算当前时间和状态的所有值
        """
        self.Es = (-82.3) - 13.0287 * math.log(self.Cai)
        self.isi_d_alpha = 0.095 * math.exp((-0.01) * (c_membrane.V + (-5.0))) / (math.exp((-0.072) * (c_membrane.V + (-5.0))) + 1.0)
        self.isi_d_beta = 0.07 * math.exp((-0.017) * (c_membrane.V + 44.0)) / (math.exp(0.05 * (c_membrane.V + 44.0)) + 1.0)
        self.d_d = self.isi_d_alpha * (1.0 - self.d) - self.isi_d_beta * self.d
        self.isi_f_alpha = 0.012 * math.exp((-0.008) * (c_membrane.V + 28.0)) / (math.exp(0.15 * (c_membrane.V + 28.0)) + 1.0)
        self.isi_f_beta = 0.0065 * math.exp((-0.02) * (c_membrane.V + 30.0)) / (math.exp((-0.2) * (c_membrane.V + 30.0)) + 1.0)
        self.d_f = self.isi_f_alpha * (1.0 - self.f) - self.isi_f_beta

<details>
<summary>英文:</summary>

I have never used this library before so there could be a lot of mistakes in my comment but hopefully it might show you the correct path.

I downloaded a sample `br-1977.mmt` model from the documentation and I used this following script to export the python code.

```python
import myokit

model = myokit.load(&quot;./br-1977.mmt&quot;)

print(model)
# (&lt;Model(Beeler-Reuter-1977)&gt;, &lt;myokit._protocol.Protocol object at 0x7fd77bb52bd0&gt;, &quot;import matplotlib.pyplot as plt\nimport myokit\n\n#\n# This example file plots a single AP using the model develope by Beeler\n# and Reuter.\n#\n\n# Get model and protocol, create simulation\nm = get_model()\np = get_protocol()\ns = myokit.Simulation(m, p)\n\n# Run simulation\nd = s.run(1000)\n\n# Display the result\nplt.figure()\nplt.plot(d[&#39;engine.time&#39;], d[&#39;membrane.V&#39;])\nplt.show()\n\n&quot;)

exporter = myokit.formats.python.PythonExporter()
exporter.runnable(model=model[0], path=&quot;./br-1977&quot;)

Here the loaded model is a tuple, so I passed the first item from the tuple as it seemed to be the model object required by the function.

And I got this as the generated code.

#!/usr/bin/env python
#
# Generated on 2023-05-13 02:47:17
#
import math

#
# Components and variables
#

class CEngine(object):
    def __init__(self):
        self.time = None
        self.pace = None

        self._constants()
        self.init()
    def _constants(self):
        """
        Sets the constant values
        """
    def init(self):
        """
        Resets the state variables to their initial values
        """
    def update(self):
        """
        Re-calculates all values for the current time and state
        """
        c_engine.pace = engine.pace
        c_engine.time = engine.time

class CIk1(object):
    def __init__(self):
        self.IK1 = None

        self._constants()
        self.init()
    def _constants(self):
        """
        Sets the constant values
        """
    def init(self):
        """
        Resets the state variables to their initial values
        """
    def update(self):
        """
        Re-calculates all values for the current time and state
        """
        self.IK1 = 0.35 * (4.0 * (math.exp(0.04 * (c_membrane.V + 85.0)) - 1.0) / (math.exp(0.08 * (c_membrane.V + 53.0)) + math.exp(0.04 * (c_membrane.V + 53.0))) + 0.2 * (c_membrane.V + 23.0) / (1.0 - math.exp((-0.04) * (c_membrane.V + 23.0))))

class CIna(object):
    def __init__(self):
        self.gNaBar = None
        self.gNaC = None
        self.ENa = None
        self.INa = None
        self.m = None
        self.d_m = None
        self.ina_m_alpha = None
        self.ina_m_beta = None
        self.h = None
        self.d_h = None
        self.ina_h_alpha = None
        self.ina_h_beta = None
        self.j = None
        self.d_j = None
        self.ina_j_alpha = None
        self.ina_j_beta = None

        self._constants()
        self.init()
    def _constants(self):
        """
        Sets the constant values
        """
        self.ENa = 50.0
        self.gNaBar = 4.0
        self.gNaC = 0.003
    def init(self):
        """
        Resets the state variables to their initial values
        """
        self.m = 0.01
        self.h = 0.99
        self.j = 0.98
    def update(self):
        """
        Re-calculates all values for the current time and state
        """
        self.ina_h_alpha = 0.126 * math.exp((-0.25) * (c_membrane.V + 77.0))
        self.ina_h_beta = 1.7 / (1.0 + math.exp((-0.082) * (c_membrane.V + 22.5)))
        self.d_h = self.ina_h_alpha * (1.0 - self.h) - self.ina_h_beta * self.h
        self.ina_j_alpha = 0.055 * math.exp((-0.25) * (c_membrane.V + 78.0)) / (1.0 + math.exp((-0.2) * (c_membrane.V + 78.0)))
        self.ina_j_beta = 0.3 / (1.0 + math.exp((-0.1) * (c_membrane.V + 32.0)))
        self.d_j = self.ina_j_alpha * (1.0 - self.j) - self.ina_j_beta * self.j
        self.ina_m_alpha = (c_membrane.V + 47.0) / (1.0 - math.exp((-0.1) * (c_membrane.V + 47.0)))
        self.ina_m_beta = 40.0 * math.exp((-0.056) * (c_membrane.V + 72.0))
        self.d_m = self.ina_m_alpha * (1.0 - self.m) - self.ina_m_beta * self.m
        self.INa = (self.gNaBar * self.m ** 3.0 * self.h * self.j + self.gNaC) * (c_membrane.V - self.ENa)

class CIsi(object):
    def __init__(self):
        self.gsBar = None
        self.Es = None
        self.Isi = None
        self.d = None
        self.d_d = None
        self.isi_d_alpha = None
        self.isi_d_beta = None
        self.f = None
        self.d_f = None
        self.isi_f_alpha = None
        self.isi_f_beta = None
        self.Cai = None
        self.d_cai = None

        self._constants()
        self.init()
    def _constants(self):
        """
        Sets the constant values
        """
        self.gsBar = 0.09
    def init(self):
        """
        Resets the state variables to their initial values
        """
        self.d = 0.003
        self.f = 0.99
        self.Cai = 2e-07
    def update(self):
        """
        Re-calculates all values for the current time and state
        """
        self.Es = (-82.3) - 13.0287 * math.log(self.Cai)
        self.isi_d_alpha = 0.095 * math.exp((-0.01) * (c_membrane.V + (-5.0))) / (math.exp((-0.072) * (c_membrane.V + (-5.0))) + 1.0)
        self.isi_d_beta = 0.07 * math.exp((-0.017) * (c_membrane.V + 44.0)) / (math.exp(0.05 * (c_membrane.V + 44.0)) + 1.0)
        self.d_d = self.isi_d_alpha * (1.0 - self.d) - self.isi_d_beta * self.d
        self.isi_f_alpha = 0.012 * math.exp((-0.008) * (c_membrane.V + 28.0)) / (math.exp(0.15 * (c_membrane.V + 28.0)) + 1.0)
        self.isi_f_beta = 0.0065 * math.exp((-0.02) * (c_membrane.V + 30.0)) / (math.exp((-0.2) * (c_membrane.V + 30.0)) + 1.0)
        self.d_f = self.isi_f_alpha * (1.0 - self.f) - self.isi_f_beta * self.f
        self.Isi = self.gsBar * self.d * self.f * (c_membrane.V - self.Es)
        self.d_cai = (-1e-07) * self.Isi + 0.07 * (1e-07 - self.Cai)

class CIx1(object):
    def __init__(self):
        self.Ix1 = None
        self.x1 = None
        self.d_x1 = None
        self.ix1_x1_alpha = None
        self.ix1_x1_beta = None

        self._constants()
        self.init()
    def _constants(self):
        """
        Sets the constant values
        """
    def init(self):
        """
        Resets the state variables to their initial values
        """
        self.x1 = 0.0004
    def update(self):
        """
        Re-calculates all values for the current time and state
        """
        self.Ix1 = self.x1 * 0.8 * (math.exp(0.04 * (c_membrane.V + 77.0)) - 1.0) / math.exp(0.04 * (c_membrane.V + 35.0))
        self.ix1_x1_alpha = 0.0005 * math.exp(0.083 * (c_membrane.V + 50.0)) / (math.exp(0.057 * (c_membrane.V + 50.0)) + 1.0)
        self.ix1_x1_beta = 0.0013 * math.exp((-0.06) * (c_membrane.V + 20.0)) / (math.exp((-0.04) * (c_membrane.V + 333.0)) + 1.0)
        self.d_x1 = self.ix1_x1_alpha * (1.0 - self.x1) - self.ix1_x1_beta * self.x1

class CStimulus(object):
    def __init__(self):
        self.amplitude = None
        self.IStim = None

        self._constants()
        self.init()
    def _constants(self):
        """
        Sets the constant values
        """
        self.amplitude = 25.0
    def init(self):
        """
        Resets the state variables to their initial values
        """
    def update(self):
        """
        Re-calculates all values for the current time and state
        """
        self.IStim = c_engine.pace * self.amplitude

class CMembrane(object):
    def __init__(self):
        self.C = None
        self.V = None
        self.d_v = None

        self._constants()
        self.init()
    def _constants(self):
        """
        Sets the constant values
        """
        self.C = 1.0
    def init(self):
        """
        Resets the state variables to their initial values
        """
        self.V = -84.622
    def update(self):
        """
        Re-calculates all values for the current time and state
        """
        self.d_v = (-(1.0 / self.C)) * (c_ik1.IK1 + c_ix1.Ix1 + c_ina.INa + c_isi.Isi - c_stimulus.IStim)

#
# Engine component
#
class Engine(object):
    """
    Calculates the derivatives in the current state
    """
    def __init__(self):
        self.pace = 0.0
        self.time = 0.0
    def update(self):
        c_engine.update()
        c_ik1.update()
        c_ina.update()
        c_isi.update()
        c_ix1.update()
        c_stimulus.update()
        c_membrane.update()
        # Remaining equations

#
# Create objects, set initial values
#
def init():
    """ (Re-)Initializes the model """
    global c_engine
    global c_ik1
    global c_ina
    global c_isi
    global c_ix1
    global c_stimulus
    global c_membrane
    global engine
    c_engine   = CEngine()
    c_ik1      = CIk1()
    c_ina      = CIna()
    c_isi      = CIsi()
    c_ix1      = CIx1()
    c_stimulus = CStimulus()
    c_membrane = CMembrane()
    engine = Engine()

#
# Update function (rhs function, takes a single step)
#
def update(stepSize):
    """ Calculates all derivatives, update state, advances time """
    engine.update()
    c_membrane.V += stepSize * c_membrane.d_v
    c_ina.m      += stepSize * c_ina.d_m
    c_ina.h      += stepSize * c_ina.d_h
    c_ina.j      += stepSize * c_ina.d_j
    c_isi.d      += stepSize * c_isi.d_d
    c_isi.f      += stepSize * c_isi.d_f
    c_ix1.x1     += stepSize * c_ix1.d_x1
    c_isi.Cai    += stepSize * c_isi.d_cai

#
# State vector returning function
#
def state():
    """ Returns the state vector """
    return [c_membrane.V,
        c_ina.m,
        c_ina.h,
        c_ina.j,
        c_isi.d,
        c_isi.f,
        c_ix1.x1,
        c_isi.Cai]

#
# State vector printing function
#
def print_state():
    """ Prints the current state to the screen """

    f = "{:<10}  {:<20}  {:<20}"
    print("-"*80)
    print(f.format("Name", "State value", "Derivative"))
    f = "{: <10}  {:< 20.13e}  {:< 20.13e}"
    print(f.format("membrane.V", c_membrane.V, c_membrane.d_v))
    print(f.format("ina.m", c_ina.m, c_ina.d_m))
    print(f.format("ina.h", c_ina.h, c_ina.d_h))
    print(f.format("ina.j", c_ina.j, c_ina.d_j))
    print(f.format("isi.d", c_isi.d, c_isi.d_d))
    print(f.format("isi.f", c_isi.f, c_isi.d_f))
    print(f.format("ix1.x1", c_ix1.x1, c_ix1.d_x1))
    print(f.format("isi.Cai", c_isi.Cai, c_isi.d_cai))

#
# Test step function
#
def test_step():
    """ Calculates and prints the initial derivatives """
    init()
    engine.update()
    print_state()

#
# Pacing
#
class Protocol(object):
    """ Holds an ordered set of ProtocolEvent objects """
    def __init__(self):
        super(Protocol, self).__init__()
        self.head = None
    def add(self, e):
        """ Schedules an event """
        if self.head is None:
            self.head = e
            return
        if e.start < self.head.start:
            e.next = self.head
            self.head = e
            return
        f = self.head
        while (f.next is not None) and (e.start > f.next.start):
            f = f.next
        e.next = f.next
        f.next = e
    def pop(self):
        """ Returns the next event """
        e = self.head
        if self.head is not None:
            self.head = self.head.next
        return e
class ProtocolEvent(object):
    def __init__(self, level, start, duration, period=0, multiplier=0):
        super(ProtocolEvent, self).__init__()
        self.level = float(level)
        self.start = float(start)
        self.duration = float(duration)
        if self.duration <= 0:
            raise Exception('Duration must be greater than zero')
        self.period = float(period)
        if self.period < 0:
            raise Exception('multiplier must be zero or greater')
        self.multiplier = int(multiplier)
        if self.multiplier < 0:
            raise Exception('Multiplier must be zero or greater')
        if self.period == 0 and self.multiplier > 0:
            raise Exception('Non-periodic event cannot occur more than once')
        self.next = None

def pacing_protocol():
    pacing = Protocol()
    pacing.add(ProtocolEvent(1.0, 100.0, 0.5, 1000.0, 0))
    return pacing

#
# Solver
#
def beat(stepSmall = 0.005, stepLarge = 0.01):
    """
    Simulates a single beat
    """
    tmin = 0
    tmax = 1000
    # Feedback
    outInt = int(math.ceil(tmax / 10.0))
    outPos = engine.time
    outVal = 0
    # Logging
    logInt = 1
    logPos = engine.time
    log = []
    # Stepsize
    stepSize = stepSmall
    hadPulse = False
    vInit = c_membrane.V
    # Pacing
    pacing = pacing_protocol()
    next = pacing.head
    while next and next.start < tmin:
        next = next.next
    if next.start < tmin:
        next = None
    fire = None
    fireDown = 0
    stopTime = min(next.start, tmin + stepSize)
    print('Starting integration with step sizes ' + str(stepSmall) + ' and ' + str(stepLarge) + '.')
    while engine.time < tmax:
        update(stopTime - engine.time)
        engine.time = stopTime
        # Event over
        if (fire and engine.time >= fireDown):
            engine.pace = 0
            fire = None
        # New event
        if (next and engine.time >= next.start):
            fire = next
            next = next.next
            engine.pace = fire.level
            fireDown = fire.start + fire.duration
            if fire.period > 0:
                if fire.multiplier == 1:
                    fire.period = 0
                else:
                    if fire.multiplier > 1:
                        fire.multiplier -=1
                    fire.start += fire.period
                    pacing.add(fire)
                    next = pacing.head
        # User feedback
        if engine.time >= outPos and outVal < 100:
            print(str(outVal) + "%")
            outVal += 10
            outPos += outInt
        # Logging
        if engine.time >= logPos:
            log.append((engine.time, state()))
            logPos += logInt
        # Step size update
        if fire: # or c_membrane.V > -70:
            if stepSize != stepSmall:
                print("Small steps")
                stepSize = stepSmall
        else:
            if stepSize != stepLarge:
                print("Big steps")
                stepSize = stepLarge
        # Set next time
        stopTime = engine.time + stepSize
        if fire and fireDown < stopTime:
            stopTime = fireDown
        if next and next.start < stopTime:
            stopTime = next.start
        if logPos < stopTime:
            stopTime = logPos
    print("100% done")
    print("t = " + str(engine.time))
    print_state()
    return log

#
# Run if loaded as main script
#
if __name__ == '__main__':
    small = 0.005
    large = 0.01
    go = True
    done = False
    while go:
        go = False
        try:
            init()
            data = beat(small, large)
            done = True
        except ArithmeticError as e:
            print('Arithmetic error occurred')
            y = 'Continue with smaller stepsize? (y/n): '
            try:
                y = raw_input(y)    # Python 2
            except NameError:
                y = input(y)        # Python 3
            if y.lower()[0:1] == 'y':
                small /= 2
                large /= 2
                go = True
    if done:
        print('Showing result...')
        x = []
        y = []
        for time, state in data:
            x.append(time)
            y.append(state[0])
        import matplotlib.pyplot as py
        plot = py.plot(x, y)
        py.show()