ValueError: could not broadcast input array from shape (2) into shape (5) [closed]

+1 vote

I was implementing gillespie algorithm and when i ran the code it gave me a value error saying can't broadcast input array from shape(2) into shape(5). Can anyone please help me out?

import multiprocessing
import numpy as np
import scipy.stats as st
import numba
import matplotlib.pyplot as plt
import seaborn as sns

simple_update = np.array([[-1,1,0,0,0],
                         [1,-1,0,0,0],
                         [0,-1,1,0,0],
                         [0,1,-1,0,0],
                         [0,0,-1,1,0],
                         [0,0,1,-1,0],
                         [0,0,0,-1,1],
                         [0,0,0,1,-1]], dtype = np.int)

def simple_propensity(params, population):

    alpha_1,alpha_2,alpha_3,alpha_4,beta_1,beta_2,beta_3,beta_4 = params

    C0,C1,C2,C3,O = population

    return np.array([alpha_1*C0,
                    beta_1*C1,
                    alpha_2*C1,
                    beta_2*C2,
                    alpha_3*C2,
                    beta_3*C3,
                    alpha_4*C3,
                    beta_4*O])

def sample_discrete(probs):
    q = np.random.randn()

    # Find index
    i = 0
    p_sum = 0.0
    while p_sum < q:
        p_sum += probs[i]
        i += 1
    return i - 1

def gillespie_draw(params, propensity_func, population):

    props = propensity_func(params, population)

    # Sum of propensities
    props_sum = props.sum()

    # Compute time
    time = np.random.exponential(1.0 / props_sum)

    # Compute discrete probabilities of each reaction
    rxn_probs = props / props_sum

    # Draw reaction from this distribution
    rxn = sample_discrete(rxn_probs)

    return rxn, time
def gillespie_ssa(params, propensity_func, update, population_0,
                  time_points):

    pop_out = np.empty((len(time_points), update.shape[1]), dtype=np.int)

    # Initialize and perform simulation
    i_time = 1
    i = 0
    t = time_points[0]
    population = population_0.copy()
    pop_out[0,:] = population
    while i < len(time_points):
        while t < time_points[i_time]:
            # draw the event and time step
            event, dt = gillespie_draw(params, propensity_func, population)

            # Update the population
            population_previous = population.copy()
            population += update[event,:]

            # Increment time
            t += dt

        # Update the index
        i = np.searchsorted(time_points > t, True)

        # Update the population
        pop_out[i_time:min(i,len(time_points))] = population_previous

        # Increment index
        i_time = i

    return pop_out

# Specify parameters for calculation
params = np.array([10, 10, 0.4])
time_points = np.linspace(0, 50, 101)
population_0 = np.array([0, 0])
n_simulations = 100

# Seed random number generator for reproducibility
np.random.seed(42)

# Initialize output array
pops = np.empty((n_simulations, len(time_points), 2))

# Run the calculations
for i in range(n_simulations):
    pops[i,:,:] = gillespie_ssa(params, simple_propensity, simple_update,population_0, time_points)

fig, ax = plt.subplots(1, 2, figsize=(14, 5))

for i in range(n_simulations):
    ax[0].plot(time_points, pops[i,:,0], '-', lw=0.3, alpha=0.2,
               color=sns.color_palette()[0])
# Set up subplots
fig, ax = plt.subplots(1, 2, figsize=(14, 5))

for i in range(n_simulations):
    ax[0].plot(time_points, pops[i,:,0], '-', lw=0.3, alpha=0.2,
               color=sns.color_palette()[0])
# Plot protein trajectories
for i in range(n_simulations):
    ax[1].plot(time_points, pops[i,:,1], 'k-', lw=0.3, alpha=0.2,
               color=sns.color_palette()[0])

ax[0].set_xlabel('time')
ax[1].set_xlabel(' time')
ax[0].set_ylabel('number of subunits')
ax[1].set_ylabel('number of calcium')
plt.tight_layout()
closed with the note: other
Dec 23, 2019 in Python by anonymous
• 130 points

reshown Jan 13 by Kalgi 247 views
Hello

Which line is giving you this error?
in the gillespie_ssa function

pop_out[0,:] = population
Hi @Satyam, did you solve the issue?

Related Questions In Python

0 votes
1 answer
+3 votes
2 answers

how to print array integer without [] bracket in python like result = 1,2,3,4,5

Hey @abhijmr.143, you can print array integers ...READ MORE

answered Aug 4, 2018 in Python by Omkar
• 68,880 points

edited Aug 8, 2018 by Omkar 1,707 views
0 votes
1 answer

I'm using Python 2.7 to convert an XML response (from a REST call to Atlassian Fisheye) into an HTML table.

You don't have a template matching tabularQueryResult in your ...READ MORE

answered Oct 4, 2018 in Python by Priyaj
• 57,510 points
69 views
0 votes
1 answer

How to have values from a List1 into Columns Names and List 2 Values as Index for an Empty DataFrame

Try like this, it will give you ...READ MORE

answered Jul 10, 2019 in Python by Cherukuri
• 32,440 points
77 views
+1 vote
2 answers
0 votes
1 answer
0 votes
1 answer
+1 vote
2 answers

how can i count the items in a list?

Syntax :            list. count(value) Code: colors = ['red', 'green', ...READ MORE

answered Jul 6, 2019 in Python by Neha
• 330 points

edited Jul 8, 2019 by Kalgi 556 views