IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Question

IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Closed this issue 7 years ago · 6 comments

I was following the readme.md and when I was executing this
(cluster_assignment, cluster_MRFs) = TICC_solver.solve(window_size = 10,number_of_clusters = 5, lambda_parameter = 11e-2, beta = 400, maxIters = 70, threshold = 2e-5, write_out_file = True, input_file = "data.csv", prefix_string = "output_folder/")
it throws me error:
IndexError: only integers, slices (:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices

I am using anaconda python 2.7 with cvxpy and snap just installed today.

Answer 1 · 2017-09-22T13:57:02.000Z

Hmmm, can you copy-paste the full error trace so I can try to see where it occurred? Thanks!

Answer 2 · 2017-09-22T16:09:51.000Z

Hi David,

So what I did is:
$python ./paper\ code/generate_synthetic_data.py
$cp ./paper\ code/Synthetic\ Data\ Matrix\ rand_seed\ =[0,1]\ generated2.csv ../data.csv
$python test.py

where test.py is just two lines:
mport TICC_solver as TICC
(cluster_assignment, cluster_MRFs) = TICC.solve(window_size = 10,number_of_clusters = 5, lambda_parameter = 11e-2, beta = 400, maxIters = 100, threshold = 2e-5, write_out_file = False, input_file = "data.csv", prefix_string = "output_folder/")

Then this is the stdout:

ITERATION ### 0
completed INITIALIZATION
OPTIMIZATION for Cluster # 0 DONE!!!
OPTIMIZATION for Cluster # 1 DONE!!!
OPTIMIZATION for Cluster # 2 DONE!!!
OPTIMIZATION for Cluster # 3 DONE!!!
OPTIMIZATION for Cluster # 4 DONE!!!
length of the cluster 0 ------> 2
length of the cluster 1 ------> 145
length of the cluster 2 ------> 186
length of the cluster 3 ------> 119
length of the cluster 4 ------> 139
UPDATED THE OLD COVARIANCE
beginning with the smoothening ALGORITHM
length of cluster # 0 --------> 0
length of cluster # 1 --------> 0
length of cluster # 2 --------> 591
length of cluster # 3 --------> 0
length of cluster # 4 --------> 0
Done writing the figure
Traceback (most recent call last):
File "test_TICC.py", line 2, in
(cluster_assignment, cluster_MRFs) = TICC.solve(window_size = 10,number_of_clusters = 5, lambda_parameter = 11e-2, beta = 400, maxIters = 100, threshold = 2e-5, write_out_file = False, input_file = "data.csv", prefix_string = "output_folder/")
File "/home/local/ASUAD/rguo12/Downloads/TICC-master/TICC_solver.py", line 1626, in solve
true_confusion_matrix = compute_confusion_matrix(num_clusters,clustered_points,sorted_training_idx)
File "/home/local/ASUAD/rguo12/Downloads/TICC-master/TICC_solver.py", line 1335, in compute_confusion_matrix
true_confusion_matrix[num,cluster] += 1
IndexError: only integers, slices (:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices

Thanks,

Answer 3 · 2017-09-22T17:37:40.000Z

Can you try setting the beta to 5 (instead of 400) So run the following instead: (cluster_assignment, cluster_MRFs) = TICC.solve(window_size = 10,number_of_clusters = 5, lambda_parameter = 11e-2, beta = 5, maxIters = 100, threshold = 2e-5, write_out_file = False, input_file = "data.csv", prefix_string = "output_folder/") On Sep 22, 2017 9:10 AM, "Ruocheng Guo" <notifications@github.com> wrote: Hi David, So what I did is: $python ./paper\ code/generate_synthetic_data.py $cp ./paper\ code/Synthetic\ Data\ Matrix\ rand_seed\ =[0,1]\ generated2.csv ../data.csv $python test.py where test.py is just two lines: mport TICC_solver as TICC (cluster_assignment, cluster_MRFs) = TICC.solve(window_size = 10,number_of_clusters = 5, lambda_parameter = 11e-2, beta = 400, maxIters = 100, threshold = 2e-5, write_out_file = False, input_file = "data.csv", prefix_string = "output_folder/") Then this is the stdout: ITERATION ### 0 completed INITIALIZATION OPTIMIZATION for Cluster # 0 DONE!!! OPTIMIZATION for Cluster # 1 DONE!!! OPTIMIZATION for Cluster # 2 DONE!!! OPTIMIZATION for Cluster # 3 DONE!!! OPTIMIZATION for Cluster # 4 DONE!!! length of the cluster 0 ------> 2 length of the cluster 1 ------> 145 length of the cluster 2 ------> 186 length of the cluster 3 ------> 119 length of the cluster 4 ------> 139 UPDATED THE OLD COVARIANCE beginning with the smoothening ALGORITHM length of cluster # 0 --------> 0 length of cluster # 1 --------> 0 length of cluster # 2 --------> 591 length of cluster # 3 --------> 0 length of cluster # 4 --------> 0 Done writing the figure Traceback (most recent call last): File "test_TICC.py", line 2, in (cluster_assignment, cluster_MRFs) = TICC.solve(window_size = 10,number_of_clusters = 5, lambda_parameter = 11e-2, beta = 400, maxIters = 100, threshold = 2e-5, write_out_file = False, input_file = "data.csv", prefix_string = "output_folder/") File "/home/local/ASUAD/rguo12/Downloads/TICC-master/TICC_solver.py", line 1626, in solve true_confusion_matrix = compute_confusion_matrix(num_ clusters,clustered_points,sorted_training_idx) File "/home/local/ASUAD/rguo12/Downloads/TICC-master/TICC_solver.py", line 1335, in compute_confusion_matrix true_confusion_matrix[num,cluster] += 1 IndexError: only integers, slices (:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices Thanks, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQcjqvwolaxOkYcuvn2s9IS8_ZRWc8axks5sk9vQgaJpZM4PgIq2> .

Answer 4 · 2017-09-22T20:26:33.000Z

Thanks for your reply.
I just used your code and the same error it throws.

In [1]: import TICC_solver as TICC

In [2]: (cluster_assignment, cluster_MRFs) = TICC.solve(window_size =
...: 10,number_of_clusters = 5, lambda_parameter = 11e-2, beta = 5, maxIters
...: =
...: 100, threshold = 2e-5, write_out_file = False, input_file = "data.csv",
...: prefix_string = "output_folder/")
lam_sparse 0.11
switch_penalty 5
num_cluster 5
num stacked 10
completed getting the data

ITERATION ### 0
completed INITIALIZATION
OPTIMIZATION for Cluster # 0 DONE!!!
OPTIMIZATION for Cluster # 1 DONE!!!
OPTIMIZATION for Cluster # 2 DONE!!!
OPTIMIZATION for Cluster # 3 DONE!!!
OPTIMIZATION for Cluster # 4 DONE!!!
length of the cluster 0 ------> 2
length of the cluster 1 ------> 145
length of the cluster 2 ------> 186
length of the cluster 3 ------> 119
length of the cluster 4 ------> 139
UPDATED THE OLD COVARIANCE
beginning with the smoothening ALGORITHM
length of cluster # 0 --------> 2
length of cluster # 1 --------> 78
length of cluster # 2 --------> 234
length of cluster # 3 --------> 146
length of cluster # 4 --------> 131
Done writing the figure

IndexError Traceback (most recent call last)
in ()
2 10,number_of_clusters = 5, lambda_parameter = 11e-2, beta = 5, maxIters =
3 100, threshold = 2e-5, write_out_file = False, input_file = "data.csv",
----> 4 prefix_string = "output_folder/")

/home/local/ASUAD/rguo12/Downloads/TICC-master/TICC_solver.pyc in solve(window_size, number_of_clusters, lambda_parameter, beta, maxIters, threshold, write_out_file, input_file, prefix_string)
1624 print "Done writing the figure"
1625
-> 1626 true_confusion_matrix = compute_confusion_matrix(num_clusters,clustered_points,sorted_training_idx)
1627
1628 ####TEST SETS STUFF

/home/local/ASUAD/rguo12/Downloads/TICC-master/TICC_solver.pyc in compute_confusion_matrix(num_clusters, clustered_points_algo, sorted_indices_algo)
1333 #CASE E : ABCABC
1334 num = (int(sorted_indices_algo[point]/seg_len) %num_clusters)
-> 1335 true_confusion_matrix[num,cluster] += 1
1336
1337 ##CASE D : ABABABAB

IndexError: only integers, slices (:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices

Answer 5 · 2017-09-23T10:59:16.000Z

I'm running the exact code that you are, and it's working on my machine (Anaconda Python 2.7).

That bug refers to an array index being a non-integer. Can you replace line 1335 with: "true_confusion_matrix[int(num),int(cluster)] += 1" and let us know if that works?

Answer 6 · 2017-09-24T21:16:42.000Z

It works! Thank you for the help!