I am new to Python, coming from MATLAB, and long ago from C. I have written a script in MATLAB which simulates sediment transport in rivers as a Markov Process. The code randomly places circles of a random diameter within a rectangular area of a specified dimension. The circles are non-uniform is size, drawn randomly from a specified range of sizes. I do not know how many times I will step through the circle placement operation so I use a while loop to complete the process. In an attempt to be more community oriented, I am translating the MATLAB script to Python. I used the online tool OMPC to get started, and have been working through it manually from the auto-translated version (was not that helpful, which is not surprising). To debug the code as I go, I use the
MATLAB generated results to generally compare and contrast against results in Python. It seems clear to me that I have declared variables in a way that introduces problems as calculations proceed in the script. Here are two examples of consistent problems between different instances of code execution. First, the code generated what I think are arrays within arrays because the script is returning results which look like:
array([[ True]
[False]], dtype=bool)
This result was generated for the following code snippet at the overlap_logix operation:
CenterCoord_Array = np.asarray(CenterCoordinates)
Diameter_Array = np.asarray(Diameter)
dist_check = ((CenterCoord_Array[:,0] - x_Center) ** 2 + (CenterCoord_Array[:,1] - y_Center) ** 2) ** 0.5
radius_check = (Diameter_Array / 2) + radius
radius_check_update = np.reshape(radius_check,(len(radius_check),1))
radius_overlap = (radius_check_update >= dist_check)
# Now actually check the overalp condition.
if np.sum([radius_overlap]) == 0:
# The new circle does not overlap so proceed.
newCircle_Found = 1
debug_value = 2
elif np.sum([radius_overlap]) == 1:
# The new circle overlaps with one other circle
overlap = np.arange(0,len(radius_overlap), dtype=int)
overlap_update = np.reshape(overlap,(len(overlap),1))
overlap_logix = (radius_overlap == 1)
idx_true = overlap_update[overlap_logix]
radius = dist_check(idx_true,1) - (Diameter(idx_true,1) / 2)
A similar result for the same run was produced for variables:
radius_check_update
radius_overlap
overlap_update
Here is the same code snippet for the working MATLAB version (as requested):
distcheck = ((Circles.CenterCoordinates(1,:)-x_Center).^2 + (Circles.CenterCoordinates(2,:)-y_Center).^2).^0.5;
radius_check = (Circles.Diameter ./ 2) + radius;
radius_overlap = (radius_check >= distcheck);
% Now actually check the overalp condition.
if sum(radius_overlap) == 0
% The new circle does not overlap so proceed.
newCircle_Found = 1;
debug_value = 2;
elseif sum(radius_overlap) == 1
% The new circle overlaps with one other circle
temp = 1:size(radius_overlap,2);
idx_true = temp(radius_overlap == 1);
radius = distcheck(1,idx_true) - (Circles.Diameter(1,idx_true)/2);
In the Python version I have created arrays from lists to more easily operate on the contents (the first two lines of the code snippet). The array within array result and creating arrays to access data suggests to me that I have incorrectly declared variable types, but I am not sure. Furthermore, some variables have a size, for example, (2L,) (the numerical dimension will change as circles are placed) where there is no second dimension. This produces obvious problems when I try to use the array in an operation with another array with a size (2L,1L). Because of these problems I started reshaping arrays, and then I stopped because I decided these were hacks because I had declared one, or more than one variable incorrectly. Second, for the same run I encountered the following error:
TypeError: 'numpy.ndarray' object is not callable
for the operation:
radius = dist_check(idx_true,1) - (Diameter(idx_true,1) / 2)
which occurs at the bottom of the above code snippet. I have posted the entire script at the following link because it is probably more useful to execute the script for oneself:
https://github.com/smchartrand/MarkovProcess_Bedload
I have set-up the code to run with some initial parameter values so decisions do not need to be made; these parameter values produce the expected results in the MATLAB-based script, which look something like this when plotted:
So, I seem to specifically be having issues with operations on lines 151-165, depending on the test value np.sum([radius_overlap]) and I think it is because I incorrectly declared variable types, but I am really not sure. I can say with confidence that the Python version and the MATLAB version are consistent in output through the first step of the while loop, and code line 127 which is entering the second step of the while loop. Below this point in the code the above documented issues eventually cause the script to crash. Sometimes the script executes to 15% complete, and sometimes it does not make it to 5% - this is due to the random nature of circle placement. I am preparing the code in the Spyder (Python 2.7) IDE and will share the working code publicly as a part of my research. I would greatly appreciate any help that can be offered to identify my mistakes and misapplications of python coding practice.
I believe I have answered my own question, and maybe it will be of use for someone down the road. The main sources of instruction for me can be found at the following three web pages:
Stackoverflow Question 176011
SciPy FAQ
SciPy NumPy for Matlab users
The third web page was very helpful for me coming from MATLAB. Here is the modified and working python code snippet which relates to the original snippet provided above:
dist_check = ((CenterCoordinates[0,:] - x_Center) ** 2 + (CenterCoordinates[1,:] - y_Center) ** 2) ** 0.5
radius_check = (Diameter / 2) + radius
radius_overlap = (radius_check >= dist_check)
# Now actually check the overalp condition.
if np.sum([radius_overlap]) == 0:
# The new circle does not overlap so proceed.
newCircle_Found = 1
debug_value = 2
elif np.sum([radius_overlap]) == 1:
# The new circle overlaps with one other circle
overlap = np.arange(0,len(radius_overlap[0]), dtype=int).reshape(1, len(radius_overlap[0]))
overlap_logix = (radius_overlap == 1)
idx_true = overlap[overlap_logix]
radius = dist_check[idx_true] - (Diameter[0,idx_true] / 2)
In the end it was clear to me that it was more straightforward for this example to use numpy arrays vs. lists to store results for each iteration of filling the rectangular area. For the corrected code snippet this means I initialized the variables:
CenterCoordinates, and
Diameter
as numpy arrays whereas I initialized them as lists in the posted question. This made a few mathematical operations more straightforward. I was also incorrectly indexing into variables with parentheses () as opposed to the correct method using brackets []. Here is an example of a correction I made which helped the code execute as envisioned:
Incorrect: radius = dist_check(idx_true,1) - (Diameter(idx_true,1) / 2)
Correct: radius = dist_check[idx_true] - (Diameter[0,idx_true] / 2)
This example also shows that I had issues with array dimensions which I corrected variable by variable. I am still not sure if my working code is the most pythonic or most efficient way to fill a rectangular area in a random fashion, but I have tested it about 100 times with success. The revised and working code can be downloaded here:
Working Python Script to Randomly Fill Rectangular Area with Circles
Here is an image of a final results for a successful run of the working code:
The main lessons for me were (1) numpy arrays are more efficient for repetitive numerical calculations, and (2) dimensionality of arrays which I created were not always what I expected them to be and care must be practiced when establishing arrays. Thanks to those who looked at my question and asked for clarification.
Related
I am new to reinforcement learning. I had recently learned about approximate q learning, or feature-based q learning, in which you describe states by features to save space. I have tried to implement this in a simple grid game. Here, the agent is supposed to learn to not go into a firepit(signaled by an f) and to instead eat up as much dots as possible. Here is the grid used:
...A
.f.f
.f.f
...f
Here A signals the agent's starting location. Now, when implementing, I set up two features. One was 1/((distance to closest dot)^2), and the other was (distance to firepit) + 1. When the agent enters a firepit, the program returns with a reward of -100. If it goes to a non firepit position that was already visited(and thus there is no dot to be eaten), the reward is -50. If it goes to an unvisited dot, the reward is +500. In the above grid, no matter what the initial weights are, the program never learns the correct weight values. Specifically, in the output, the first training session gains a score(how many dots it ate) of 3, but for all other training sessions, the score is just 1 and the weights converge to an incorrect value of -125 for weight 1(distance to firepit) and 25 for weight 2(distance to unvisited dot). Is there something specifically wrong with my code or is my understanding of approximate q learning incorrect?
I have tried to play around with the rewards that the environment is giving and also with the initial weights. None of these have fixed the problem.
Here is the link to the entire program: https://repl.it/repls/WrongCheeryInterface
Here is what is going on in the main loop:
while(points != NUMPOINTS){
bool playerDied = false;
if(!start){
if(!atFirepit()){
r = 0;
if(visited[player.x][player.y] == 0){
points += 1;
r += 500;
}else{
r += -50;
}
}else{
playerDied = true;
r = -100;
}
}
//Update visited
visited[player.x][player.y] = 1;
if(!start){
//This is based off the q learning update formula
pairPoint qAndA = getMaxQAndAction();
double maxQValue = qAndA.q;
double sample = r;
if(!playerDied && points != NUMPOINTS)
sample = r + (gamma2 * maxQValue);
double diff = sample - qVal;
updateWeights(player, diff);
}
// checking end game condition
if(playerDied || points == NUMPOINTS) break;
pairPoint qAndA = getMaxQAndAction();
qVal = qAndA.q;
int bestAction = qAndA.a;
//update player and q value
player.x += dx[bestAction];
player.y += dy[bestAction];
start = false;
}
I would expect that both weights would still be positive, but one of them is negative(the one giving distance to the firepit).
I also expected the program to learn overtime that it is bad to enter a firepit and also bad, but not as bad, to go to an unvisited dot.
Probably not the anwser you want to hear, but:
Have you try to implement the simpler tabular Q-learning before approximate Q-learning? In your setting, with a few states and actions, it will work pefectly. If you are learning, I strongly recommend you to start with the simpler cases in order to get a better understanding/intuition about how Reinforcement Learning works.
Do you know the implications of using approximators instead of learning the exact Q function? In some cases, due to the complexity of the problem (e.g., when the state space is continuous) you should approximate the Q function (or the policy, depending on the algorithm), but this may introduce some convergence problems. Additionally, in you case, you are trying to hand-pick some features, which usually required a depth knowledge of the problem (i.e., environment) and the learning algorithm.
Do you understand the meaning of the hyperparameters alpha and gamma? You can not choose them randomly. Sometimes they are critical to obtain the expected results, not always, depending heavely on the problem and the learning algorithm. In your case, taking a look to the convergence curve of you weights, it's pretty clear that you are using a value of alpha too high. As you pointed out, after the first training session your weigths remain constant.
Therefore, practical recommendations:
Be sure to solve your grid game using a tabular Q-learning algorithm before trying more complex things.
Experiment with different values of alpha, gamma and rewards.
Read more in depth about approximated RL. A very good and accesible book (starting from zero knowledge) is the classical Sutton and Barto's book: Reinforcement Learning: An Introduction, which you can obtain for free and was updated in 2018.
I would like to use a convolution LSTM in my research but I'm having a difficult time figuring out the exact way to implement this class in tensorflow. Here is what I have so far. I get no errors, but I am seriously doubting my implementation. Can anyone confirm if I am doing this correctly?
n_input = 4
x = tf.placeholder(tf.float32,shape=[None,n_input,HEIGHT,WIDTH,2])
y = tf.placeholder(tf.float32,shape=[None,HEIGHT,WIDTH,2])
convLSTM_cell = tf.contrib.rnn.ConvLSTMCell(
conv_ndims=2,
input_shape = [HEIGHT,WIDTH,DEPTH],
output_channels=2,
kernel_shape=[3,3]
)
outputs, states = tf.nn.dynamic_rnn(convLSTM_cell, x, dtype=tf.float32)
weights = tf.Variable(tf.random_normal([3,3,2,2]))
biases = tf.Variable(tf.random_normal([2]))
conv_out = tf.nn.conv2d(outputs[-1],weights,strides=[1,1,1,1],padding='SAME')
out = tf.nn.sigmoid(conv_out + biases)
UPDATE:
printing the size of outputs gives the shape=(?,4,436,1024,2) but I think I want (?,5,436,1024,2) or (?,1,436,1024,2).
UPDATE2:
So according to a fellow lab mate, the 4 outputs corresponds to the lstm outputs for each frame and so it is working correctly. Apparently all I have to do is take output #4 and that is the predicted future time frame.
A stackoverflow confirmation would put my mind at ease on this whole thing.
Yes, you are correct!
The output dimension will match the input dimension. If you actually want the (?,5,436,1024,2) output, you will have to look at the history, state.h. the last four [-4] of it will still correspond to the output.
I have a PID controller working in simulink, but I want to pass it to C++ code. I found how to make a PID with code, something like this:
error = input - refeed;
iError += error * sampleTime;
dError = (error - lastError)/ sampleTime;
//PID Function
output = Kp * error + Ki * iError + Kd * dError;
refeed = output;
lastError = error;
But, that's the only clear thing I got in my research.
I need to know what's the next step, I have the transfer function discretized but I'm not sure about what should I do with the "z" parameters, the times, ...
Is it possible to pass manually a PID controller to C++? How?
The Temperature Control Lab passes a PID output from Python to an Arduino that runs C++ code through a serial USB interface. It is easier to plot values with Python than C++ if you can create an interface for your application. GitHub source code is here.
For the digital control systems, you need to sample the data and execute the controller at every sampling time. z-transform converts the continuous system to the discrete system.
For exampl, if your sampling time is '1', you can express a simple time-series model as below,
y(t) = a1*u(t-1) + a2*u(t-2)
--> y(t) = a1*z^-1*u(t) + a2*z^-2*u(t)
--> y(t) = A(z)u(t), where A(z) = a1*z^-1 + a2*z^-2
a1, a2 = FIR coefficients
However, this time-shift operator 'z^-1' does not appear in your code. It is implicitly expressed with your sampling-time and FOR or DO loop depending on the language that you are using.
Please see the python code for velocity form of PID controller. Velocity form is a little bit easier to implement because you don't worry about the additional logic for the anti-reset windup.
for i in range(1, ns): #ns = simulation time
# PID Velocity form
e[i] = sp[i] - pv[i]
P[i] = Kc * (e[i] - e[i-1])
I[i] = Kc*delta_t/tauI * (e[i])
D[i] = Kc*tauD/delta_t * (pv[i] - 2*(pv[i-1]) + pv[i-2])
op[i] = op[i-1] + P[i] + I[i] + D[i]
if op[i] < oplo or op[i] > ophi:
# clip output
op[i] = max(oplo,min(ophi,op[i]))
You can also find an example of a PID controller using a GEKKO package in the following link.
https://apmonitor.com/wiki/index.php/Main/GekkoPythonOptimization
Yes it is possible. Have you considered using someone else's code? Or do you want to write it yourself? If you have no problem using allready written code, check out Github. It has a lot of PID projects. For example PID-controller. It has a usage example and you only have to pass in your p, i and d parameters (which you allready got from Matlab).
Good luck!
Basically, you should send the values somewhere. Reading through the comments, you want to make a plot of the output variable in time, so I guess your best bet (and easier way) is to use gnuplot.
Basically, output the data in a text file, then use gnuplot to display it.
I'd like to build and train a multi-layer LSTM model (stateIsTuple=True) in python, and then load and use it in C++. But I'm having a hard time figuring out how to feed and fetch states in C++, mainly because I don't have string names which I can reference.
E.g. I put the initial state in a named scope such as
with tf.name_scope('rnn_input_state'):
self.initial_state = cell.zero_state(args.batch_size, tf.float32)
and this appears in the graph as below, but how can I feed to these in C++?
Also, how can I fetch the current state in C++? I tried the graph construction code below in python but I'm not sure if it's the right thing to do, because last_state should be a tuple of tensors, not a single tensor (though I can see that the last_state node in tensorboard is 2x2x50x128, which sounds like it just concatenated the states as I have 2 layers, 128 rnn size, 50 mini batch size, and lstm cell - with 2 state vectors).
with tf.name_scope('outputs'):
outputs, last_state = legacy_seq2seq.rnn_decoder(inputs, self.initial_state, cell, loop_function=loop if infer else None)
output = tf.reshape(tf.concat(outputs, 1), [-1, args.rnn_size], name='output')
and this is what it looks like in tensorboard
Should I concat and split the state tensors so there is only ever one state tensor going in and out? Or is there a better way?
P.S. Ideally the solution won't involve hard-coding the number of layers (or rnn size). So I can just have four strings input_node_name, output_node_name, input_state_name, output_state_name, and the rest is derived from there.
I managed to do this by manually concatenating the state into a single tensor. I'm not sure if this is wise, since this is how tensorflow used to handle states, but is now deprecating that and switching to tuple states. Instead of setting state_is_tuple=False and risking my code being obsolete soon, I've added extra ops to manually stack and unstack the states to and from a single tensor. Saying that, it works fine both in python and C++.
The key code is:
# setting up
zero_state = cell.zero_state(batch_size, tf.float32)
state_in = tf.identity(zero_state, name='state_in')
# based on https://medium.com/#erikhallstrm/using-the-tensorflow-multilayered-lstm-api-f6e7da7bbe40#.zhg4zwteg
state_per_layer_list = tf.unstack(state_in, axis=0)
state_in_tuple = tuple(
# TODO make this not hard-coded to LSTM
[tf.contrib.rnn.LSTMStateTuple(state_per_layer_list[idx][0], state_per_layer_list[idx][1])
for idx in range(num_layers)]
)
outputs, state_out_tuple = legacy_seq2seq.rnn_decoder(inputs, state_in_tuple, cell, loop_function=loop if infer else None)
state_out = tf.identity(state_out_tuple, name='state_out')
# running (training or inference)
state = sess.run('state_in:0') # zero state
loop:
feed = {'data_in:0': x, 'state_in:0': state}
[y, state] = sess.run(['data_out:0', 'state_out:0'], feed)
Here is the full code if anyone needs it
https://github.com/memo/char-rnn-tensorflow
I'm working on problem 3 of Project Euler using Python, but I can't seem to solve the problem without running into the following error: "OverflowError: range() result has too many items"
I'm wondering if there's a way to increase the allowed range? My code looks as follows:
target = 600851475143
largest_prime_factor = 1
#find largest prime factor of target
for possible_factor in range(2,(target/2)+1):
if target % possible_factor == 0:
is_prime = True
for i in range(2,(possible_factor/2)+1):
if possible_factor % i == 0:
is_prime = False
break
if is_prime:
largest_prime_factor = possible_factor
print largest_prime_factor
If you run into limitations of your computer or language while trying to solve a puzzle problem, or if it takes too long, it is an indication that probably there exists a better way (read: algorithm) to solve the problem. In your case, you do not need to loop to target / 2 + 1 (though that is a good educated upper bound). You only need to go as far as ceil(sqrt(target)).
And, as a sidenote, you can overcome this limitation by using xrange, which will create a generator, instead of range for Python 2, which creates a list. In Python 3, range will return a sequence type instead of a list by default.
Thanks to #Fernando for the clarification in the comments.