can i use OR-tools for TSP with partial distance matrix (for a huge set of nodes)? - optimization

i'm trying to solve tsp with OR-tools for a problem of something like 80,000 nodes, the problem is, I need a huge distance matrix that takes to much memory ,so its infeasible and i don't get a solution.
so:
is there an option to work with partial distance matrix in or-tools?
if not is there a way to improve my code?
is there another external solver that can work for this task in python?
import math
from collections import namedtuple
import random
import time
from collections import namedtuple
from sklearn.metrics.pairwise import euclidean_distances
import numpy as np
import numba
from scipy.spatial import distance_matrix
from sklearn.metrics.pairwise import euclidean_distances
from math import sqrt
Point = namedtuple("Point", ['x', 'y'])
def solve_it(input_data):
# Modify this code to run your optimization algorithm
global POINTS
# parse the input
lines = input_data.split('\n')
nodeCount = int(lines[0])
points = []
for i in range(1, nodeCount+1):
line = lines[i]
parts = line.split()
points.append(Point(float(parts[0]), float(parts[1])))
#2.routing with or tools
def dist_matrix(nodeCount,points):
data=[]
for k in range(len(points)):
data.append([int(points[k].x),int(points[k].y)])
D=euclidean_distances(data, data)
return D
def create_data_model(D):
"""Stores the data for the problem."""
data = {}
data['distance_matrix'] = D # yapf: disable
data['num_vehicles'] = 1
data['depot'] = 0
return data
def print_solution(manager, routing, solution):
index = routing.Start(0)
plan_output = []#Route for vehicle 0:\n'
route_distance = 0
while not routing.IsEnd(index):
plan_output.append(manager.IndexToNode(index))
index = solution.Value(routing.NextVar(index))
return plan_output
def or_main(nodeCount,points):
from ortools.constraint_solver import routing_enums_pb2
from ortools.constraint_solver import pywrapcp
"""Entry point of the program."""
# Instantiate the data problem.
global sol
D=dist_matrix(nodeCount,points)
data = create_data_model(D)
# Create the routing index manager.
manager = pywrapcp.RoutingIndexManager(len(data['distance_matrix']),
data['num_vehicles'], data['depot'])
# Create Routing Model.
routing = pywrapcp.RoutingModel(manager)
def distance_callback(from_index, to_index):
"""Returns the distance between the two nodes."""
# Convert from routing variable Index to distance matrix NodeIndex.
from_node = manager.IndexToNode(from_index)
to_node = manager.IndexToNode(to_index)
return data['distance_matrix'][from_node][to_node]
transit_callback_index = routing.RegisterTransitCallback(distance_callback)
# Define cost of each arc.
routing.SetArcCostEvaluatorOfAllVehicles(transit_callback_index)
# Setting first solution heuristic.
search_parameters = pywrapcp.DefaultRoutingSearchParameters()
search_parameters.local_search_metaheuristic = (
routing_enums_pb2.LocalSearchMetaheuristic.GUIDED_LOCAL_SEARCH)
k = 100
if nodeCount <= 100:
k = 30
elif 100 <= nodeCount <= 1000:
k = 300
elif nodeCount > 1000:
k = 17000
search_parameters.time_limit.seconds =k
search_parameters.log_search = True
# Solve the problem.
solution = routing.SolveWithParameters(search_parameters)
# #print solution on console.
if solution:
sol=print_solution(manager, routing, solution)
return sol
######################################################################
solution=or_main(nodeCount,points)
# calculate the length of the tour
obj = length(points[solution[-1]], points[solution[0]])
for index in range(0, nodeCount-1):
obj += length(points[solution[index]], points[solution[index+1]])
# prepare the solution in the specified output format
output_data = '%.2f' % obj + ' ' + str(0) + '\n'
output_data += ' '.join(map(str, solution))
return output_data
if __name__ == '__main__':
import sys
if len(sys.argv) > 1:
file_location = sys.argv[1].strip()
with open(file_location, 'r') as input_data_file:
input_data = input_data_file.read()
#print(solve_it(input_data))
else:
print('This test requires an input file. Please select one from the data directory. (i.e. python solver.py ./data/tsp_51_1)')

Related

passing panda dataframe data to functions and its not outputting the results

In my code, I am trying to extract data from csv file to use in the function, but it doesnt output anything, and gives no error. My code works because I tried it with just numpy array as inputs. not sure why it doesnt work with panda.
import numpy as np
import pandas as pd
import os
# change the current directory to the directory where the running script file is
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# finding best fit line for y=mx+b by iteration
def gradient_descent(x,y):
m_iter = b_iter = 1 #starting point
iteration = 10000
n = len(x)
learning_rate = 0.05
last_mse = 10000
#take baby steps to reach global minima
for i in range(iteration):
y_predicted = m_iter*x + b_iter
#mse = 1/n*sum([value**2 for value in (y-y_predicted)]) # cost function to minimize
mse = 1/n*sum((y-y_predicted)**2) # cost function to minimize
if (last_mse - mse)/mse < 0.001:
break
# recall MSE formula is 1/n*sum((yi-y_predicted)^2), where y_predicted = m*x+b
# using partial deriv of MSE formula, d/dm and d/db
dm = -(2/n)*sum(x*(y-y_predicted))
db = -(2/n)*sum((y-y_predicted))
# use current predicted value to get the next value for prediction
# by using learning rate
m_iter = m_iter - learning_rate*dm
b_iter = b_iter - learning_rate*db
print('m is {}, b is {}, cost is {}, iteration {}'.format(m_iter,b_iter,mse,i))
last_mse = mse
#x = np.array([1,2,3,4,5])
#y = np.array([5,7,8,10,13])
#gradient_descent(x,y)
df = pd.read_csv('Linear_Data.csv')
x = df['Area']
y = df['Price']
gradient_descent(x,y)
My code works because I tried it with just numpy array as inputs. not sure why it doesnt work with panda.
Well no, your code also works with pandas dataframes:
df = pd.DataFrame({'Area': [1,2,3,4,5], 'Price': [5,7,8,10,13]})
x = df['Area']
y = df['Price']
gradient_descent(x,y)
Above will give you the same output as with numpy arrays.
Try to check what's in Linear_Data.csv and/or add some print statements in the gradient_descent function just to check your assumptions. I would suggest to first of all add a print statement before the condition with the break statement:
print(last_mse, mse)
if (last_mse - mse)/mse < 0.001:
break

could not convert string to float in python

i try to analysis the Principle Component from cvs file but when i run the code i get this error
C:\Users\Lenovo\Desktop>python pca.py
ValueError: could not convert string to float: Annee;NET;INT;SUB;LMT;DCT;IMM;EXP;VRD
this is my cvs file
i try to remove any space and any think
this is my python script, i don't know what i miss
Note: i run this code under python2.7
from sklearn.externals import joblib
import numpy as np
import glob
import os
import time
import numpy
my_matrix = numpy.loadtxt(open("pca.csv","rb"),delimiter= ",",skiprows=0)
def pca(dataMat, r, autoset_r=False, autoset_rate=0.9):
"""
purpose: principal components analysis
"""
print("Start to do PCA...")
t1 = time.time()
meanVal = np.mean(dataMat, axis=0)
meanRemoved = dataMat - meanVal
# normData = meanRemoved / np.std(dataMat)
covMat = np.cov(meanRemoved, rowvar=0)
eigVals, eigVects = np.linalg.eig(np.mat(covMat))
eigValIndex = np.argsort(-eigVals)
if autoset_r:
r = autoset_eigNum(eigVals, autoset_rate)
print("autoset: take top {} of {} features".format(r, meanRemoved.shape[1]))
r_eigValIndex = eigValIndex[:r]
r_eigVect = eigVects[:, r_eigValIndex]
lowDDataMat = meanRemoved * r_eigVect
reconMat = (lowDDataMat * r_eigVect.T) + meanVal
t2 = time.time()
print("PCA takes %f seconds" %(t2-t1))
joblib.dump(r_eigVect, './pca_args_save/r_eigVect.eig')
joblib.dump(meanVal, './pca_args_save/meanVal.mean')
return lowDDataMat, reconMat
def autoset_eigNum(eigValues, rate=0.99):
eigValues_sorted = sorted(eigValues, reverse=True)
eigVals_total = eigValues.sum()
for i in range(1, len(eigValues_sorted)+1):
eigVals_sum = sum(eigValues_sorted[:i])
if eigVals_sum / eigVals_total >= rate:
break
return i
It seemed that NumPy has some problem parsing your index row to float.
Try setting skiprows = 1 in your np.readtxt command in order to skip the table header.

Trying to take pictures with Coral camera with Coral edgeTPU dev board but it is really slow

To start with, I am not a developer, but a mere automation engineer that have worked a bit with coding in Java, python, C#, C++ and C.
I am trying to make a prototype that take pictures and stores them using a digital pin on the board. Atm I can take pictures using a switch, but it is really slow(around 3 seconds pr image).
My complete system is going to be like this:
A product passes by on a conveyor and a photo cell triggers the board to take an image and store it. If an operator removes a product(because of bad quality) the image is stored in a different folder.
I started with the snapshot function shipped with Mendel and have tried to get rid off the overhead, but the Gstream and pipeline-stuff confuses me a lot.
If someone could help me with how to understand the supplied code, or how to write a minimalistic solution to take an image i would be grateful :)
I have tried to understand and use project-teachable and examples-camera from Google coral https://github.com/google-coral, but with no luck. I have had the best luck with the snapshot tool that uses snapshot.py that are referenced here https://coral.withgoogle.com/docs/camera/datasheet/#snapshot-tool
from periphery import GPIO
import time
import argparse
import contextlib
import fcntl
import os
import select
import sys
import termios
import threading
import gi
gi.require_version('Gst', '1.0')
gi.require_version('GstBase', '1.0')
from functools import partial
from gi.repository import GLib, GObject, Gst, GstBase
from PIL import Image
GObject.threads_init()
Gst.init(None)
WIDTH = 2592
HEIGHT = 1944
FILENAME_PREFIX = 'img'
FILENAME_SUFFIX = '.png'
AF_SYSFS_NODE = '/sys/module/ov5645_camera_mipi_v2/parameters/ov5645_af'
CAMERA_INIT_QUERY_SYSFS_NODE = '/sys/module/ov5645_camera_mipi_v2/parameters/ov5645_initialized'
HDMI_SYSFS_NODE = '/sys/class/drm/card0/card0-HDMI-A-1/status'
# No of initial frames to throw away before camera has stabilized
SCRAP_FRAMES = 1
SRC_WIDTH = 2592
SRC_HEIGHT = 1944
SRC_RATE = '15/1'
SRC_ELEMENT = 'v4l2src'
SINK_WIDTH = 2592
SINK_HEIGHT = 1944
SINK_ELEMENT = ('appsink name=appsink sync=false emit-signals=true '
'max-buffers=1 drop=true')
SCREEN_SINK = 'glimagesink sync=false'
FAKE_SINK = 'fakesink sync=false'
SRC_CAPS = 'video/x-raw,format=YUY2,width={width},height={height},framerate={rate}'
SINK_CAPS = 'video/x-raw,format=RGB,width={width},height={height}'
LEAKY_Q = 'queue max-size-buffers=1 leaky=downstream'
PIPELINE = '''
{src_element} ! {src_caps} ! {leaky_q} ! tee name=t
t. ! {leaky_q} ! {screen_sink}
t. ! {leaky_q} ! videoconvert ! {sink_caps} ! {sink_element}
'''
def on_bus_message(bus, message, loop):
t = message.type
if t == Gst.MessageType.EOS:
loop.quit()
elif t == Gst.MessageType.WARNING:
err, debug = message.parse_warning()
sys.stderr.write('Warning: %s: %s\n' % (err, debug))
elif t == Gst.MessageType.ERROR:
err, debug = message.parse_error()
sys.stderr.write('Error: %s: %s\n' % (err, debug))
loop.quit()
return True
def on_new_sample(sink, snapinfo):
if not snapinfo.save_frame():
# Throw away the frame
return Gst.FlowReturn.OK
sample = sink.emit('pull-sample')
buf = sample.get_buffer()
result, mapinfo = buf.map(Gst.MapFlags.READ)
if result:
imgfile = snapinfo.get_filename()
caps = sample.get_caps()
width = WIDTH
height = HEIGHT
img = Image.frombytes('RGB', (width, height), mapinfo.data, 'raw')
img.save(imgfile)
img.close()
buf.unmap(mapinfo)
return Gst.FlowReturn.OK
def run_pipeline(snapinfo):
src_caps = SRC_CAPS.format(width=SRC_WIDTH, height=SRC_HEIGHT, rate=SRC_RATE)
sink_caps = SINK_CAPS.format(width=SINK_WIDTH, height=SINK_HEIGHT)
screen_sink = FAKE_SINK
pipeline = PIPELINE.format(
leaky_q=LEAKY_Q,
src_element=SRC_ELEMENT,
src_caps=src_caps,
sink_caps=sink_caps,
sink_element=SINK_ELEMENT,
screen_sink=screen_sink)
pipeline = Gst.parse_launch(pipeline)
appsink = pipeline.get_by_name('appsink')
appsink.connect('new-sample', partial(on_new_sample, snapinfo=snapinfo))
loop = GObject.MainLoop()
# Set up a pipeline bus watch to catch errors.
bus = pipeline.get_bus()
bus.add_signal_watch()
bus.connect('message', on_bus_message, loop)
# Connect the loop to the snaphelper
snapinfo.connect_loop(loop)
# Run pipeline.
pipeline.set_state(Gst.State.PLAYING)
try:
loop.run()
except:
pass
# Clean up.
pipeline.set_state(Gst.State.NULL)
while GLib.MainContext.default().iteration(False):
pass
class SnapHelper:
def __init__(self, sysfs, prefix='img', oneshot=True, suffix='jpg'):
self.prefix = prefix
self.oneshot = oneshot
self.suffix = suffix
self.snap_it = oneshot
self.num = 0
self.scrapframes = SCRAP_FRAMES
self.sysfs = sysfs
def get_filename(self):
while True:
filename = self.prefix + str(self.num).zfill(4) + '.' + self.suffix
self.num = self.num + 1
if not os.path.exists(filename):
break
return filename
#def check_af(self):
#try:
# self.sysfs.seek(0)
# v = self.sysfs.read()
# if int(v) != 0x10:
# print('NO Focus')
#except:
# pass
# def refocus(self):
# try:#
# self.sysfs.write('1')
# self.sysfs.flush()
# except:
# pass
def save_frame(self):
# We always want to throw away the initial frames to let the
# camera stabilize. This seemed empirically to be the right number
# when running on desktop.
if self.scrapframes > 0:
self.scrapframes = self.scrapframes - 1
return False
if self.snap_it:
self.snap_it = False
retval = True
else:
retval = False
if self.oneshot:
self.loop.quit()
return retval
def connect_loop(self, loop):
self.loop = loop
def take_picture(snap):
start_time = int(round(time.time()))
run_pipeline(snap)
print(time.time()- start_time)
def main():
button = GPIO(138, "in")
last_state = False
with open(AF_SYSFS_NODE, 'w+') as sysfs:
snap = SnapHelper(sysfs, 'test', 'oneshot', 'jpg')
sysfs.write('2')
while 1:
button_state = button.read()
if(button_state==True and last_state == False):
snap = SnapHelper(sysfs, 'test', 'oneshot', 'jpg')
take_picture(snap)
last_state = button_state
if __name__== "__main__":
main()
sys.exit()
Output is what i expect, but it is slow.
I switched to a USB-webcam and used the pygame library instead.

dask how to define a custom (time fold) function that operates in parallel and returns a dataframe with a different shape

I am trying to implement a time fold function to be 'map'ed to various partitions of a dask dataframe which in turn changes the shape of the dataframe in question (or alternatively produces a new dataframe with the altered shape). This is how far I have gotten. The result 'res' returned on compute is a list of 3 delayed objects. When I try to compute each of them in a loop (last tow lines of code) this results in a "TypeError: 'DataFrame' object is not callable" After going through the examples for map_partitions, I also tried altering the input DF (inplace) in the function with no return value which causes a similar TypeError with NoneType. What am I missing?
Also, looking at the visualization (attached) I feel like there is a need for reducing the individually computed (folded) partitions into a single DF. How do I do this?
#! /usr/bin/env python
# Start dask scheduler and workers
# dask-scheduler &
# dask-worker --nthreads 1 --nprocs 6 --memory-limit 3GB localhost:8786 --local-directory /dev/shm &
from dask.distributed import Client
from dask.delayed import delayed
import pandas as pd
import numpy as np
import dask.dataframe as dd
import math
foldbucketsecs=30
periodicitysecs=15
secsinday=24 * 60 * 60
chunksizesecs=60 # 1 minute
numts = 5
start = 1525132800 # 01/05
end = 1525132800 + (3 * 60) # 3 minute
c = Client('127.0.0.1:8786')
def fold(df, start, bucket):
return df
def reduce_folds(df):
return df
def load(epoch):
idx = []
for ts in range(0, chunksizesecs, periodicitysecs):
idx.append(epoch + ts)
d = np.random.rand(chunksizesecs/periodicitysecs, numts)
ts = []
for i in range(0, numts):
tsname = "ts_%s" % (i)
ts.append(tsname)
gts.append(tsname)
res = pd.DataFrame(index=idx, data=d, columns=ts, dtype=np.float64)
res.index = pd.to_datetime(arg=res.index, unit='s')
return res
gts = []
load(start)
cols = len(gts)
idx1 = pd.DatetimeIndex(start=start, freq=('%sS' % periodicitysecs), end=start+periodicitysecs, dtype='datetime64[s]')
meta = pd.DataFrame(index=idx1[:0], data=[], columns=gts, dtype=np.float64)
dfs = [delayed(load)(fn) for fn in range(start, end, chunksizesecs)]
from_delayed = dd.from_delayed(dfs, meta, 'sorted')
nfolds = int(math.ceil((end - start)/foldbucketsecs))
cprime = nfolds * cols
gtsnew = []
for i in range(0, cprime):
gtsnew.append("ts_%s,fold=%s" % (i%cols, i/cols))
idx2 = pd.DatetimeIndex(start=start, freq=('%sS' % periodicitysecs), end=start+foldbucketsecs, dtype='datetime64[s]')
meta = pd.DataFrame(index=idx2[:0], data=[], columns=gtsnew, dtype=np.float64)
folded_df = from_delayed.map_partitions(delayed(fold)(from_delayed, start, foldbucketsecs), meta=meta)
result = c.submit(reduce_folds, folded_df)
c.gather(result).visualize(filename='/usr/share/nginx/html/svg/df4.svg')
res = c.gather(result).compute()
for f in res:
f.compute()
Never mind! It was my fault, instead of wrapping my function in delayed I simply passed it to the map_partitions call like so and it worked.
folded_df = from_delayed.map_partitions(fold, start, foldbucketsecs, nfolds, meta=meta)

how to use Apache Commons Math Optimization in Jython?

I want to transfer Matlab code to Jython version, and find that the fminsearch in Matlab might be replaced by Apache-Common-Math-Optimization.
I'm coding on the Mango Medical Image script manager, which uses Jython 2.5.3 as coding language. And the Math version is 3.6.1.
Here is my code:
def f(x,y):
return x^2+y^2
sys.path.append('/home/shujian/APPs/Mango/lib/commons-math3-3.6.1.jar')
sys.add_package('org.apache.commons.math3.analysis')
from org.apache.commons.math3.analysis import MultivariateFunction
sys.add_package('org.apache.commons.math3.optim.nonlinear.scalar.noderiv')
from org.apache.commons.math3.optim.nonlinear.scalar.noderiv import NelderMeadSimplex,SimplexOptimizer
sys.add_package('org.apache.commons.math3.optim.nonlinear.scalar')
from org.apache.commons.math3.optim.nonlinear.scalar import ObjectiveFunction
sys.add_package('org.apache.commons.math3.optim')
from org.apache.commons.math3.optim import MaxEval,InitialGuess
sys.add_package('org.apache.commons.math3.optimization')
from org.apache.commons.math3.optimization import GoalType
initialSolution=[2.0,2.0]
simplex=NelderMeadSimplex([2.0,2.0])
opt=SimplexOptimizer(2**(-6), 2**(-10))
solution=opt.optimize(MaxEval(300),ObjectiveFunction(f),simplex,GoalType.MINIMIZE,InitialGuess([2.0,2.0]))
skewParameters2 = solution.getPointRef()
print skewParameters2;
And I got the error below:
TypeError: optimize(): 1st arg can't be coerced to
I'm quite confused about how to use the optimization in Jython and the examples are all Java version.
I've given up this plan and find another method to perform the fminsearch in Jython. Below is the Jython version code:
import sys
sys.path.append('.../jnumeric-2.5.1_ra0.1.jar') #add the jnumeric path
import Numeric as np
def nelder_mead(f, x_start,
step=0.1, no_improve_thr=10e-6,
no_improv_break=10, max_iter=0,
alpha=1., gamma=2., rho=-0.5, sigma=0.5):
'''
#param f (function): function to optimize, must return a scalar score
and operate over a numpy array of the same dimensions as x_start
#param x_start (float list): initial position
#param step (float): look-around radius in initial step
#no_improv_thr, no_improv_break (float, int): break after no_improv_break iterations with
an improvement lower than no_improv_thr
#max_iter (int): always break after this number of iterations.
Set it to 0 to loop indefinitely.
#alpha, gamma, rho, sigma (floats): parameters of the algorithm
(see Wikipedia page for reference)
return: tuple (best parameter array, best score)
'''
# init
dim = len(x_start)
prev_best = f(x_start)
no_improv = 0
res = [[np.array(x_start), prev_best]]
for i in range(dim):
x=np.array(x_start)
x[i]=x[i]+step
score = f(x)
res.append([x, score])
# simplex iter
iters = 0
while 1:
# order
res.sort(key=lambda x: x[1])
best = res[0][1]
# break after max_iter
if max_iter and iters >= max_iter:
return res[0]
iters += 1
# break after no_improv_break iterations with no improvement
print '...best so far:', best
if best < prev_best - no_improve_thr:
no_improv = 0
prev_best = best
else:
no_improv += 1
if no_improv >= no_improv_break:
return res[0]
# centroid
x0 = [0.] * dim
for tup in res[:-1]:
for i, c in enumerate(tup[0]):
x0[i] += c / (len(res)-1)
# reflection
xr = x0 + alpha*(x0 - res[-1][0])
rscore = f(xr)
if res[0][1] <= rscore < res[-2][1]:
del res[-1]
res.append([xr, rscore])
continue
# expansion
if rscore < res[0][1]:
xe = x0 + gamma*(x0 - res[-1][0])
escore = f(xe)
if escore < rscore:
del res[-1]
res.append([xe, escore])
continue
else:
del res[-1]
res.append([xr, rscore])
continue
# contraction
xc = x0 + rho*(x0 - res[-1][0])
cscore = f(xc)
if cscore < res[-1][1]:
del res[-1]
res.append([xc, cscore])
continue
# reduction
x1 = res[0][0]
nres = []
for tup in res:
redx = x1 + sigma*(tup[0] - x1)
score = f(redx)
nres.append([redx, score])
res = nres
And the test example is as below:
def f(x):
return x[0]**2+x[1]**2+x[2]**2
print nelder_mead(f,[3.4,2.3,2.2])
Actually, the original version is for python, and the link below is the source:
https://github.com/fchollet/nelder-mead