Troubled by 1 instance of np.flatnonzero

[wgandler]

Hi,

I am troubled by 1 instance of np.flatnonzero. In _ Esum the lines:
if U_k is None:
U_k = np.flatnonzero(indices)
Removing 0 index makes U_k length 1 less than chi2 length, T_inv_k length, and log_p[k] length. I don't see why the zero index is removed.

                                     Sincerely,

                                 William Gandler

[pmelchior]

Hello William. Are you asking about why that selection U_k = np.flatnonzero(indices) is done, or do you have trouble that is caused by this line?

[wgandler]

Dear Peter Melchior, Thank you to replying to my concern. Specifically, I am porting your code to Java for use in the MIPAV medical imaging software at NIH and I noticed that when a zero index was present the line U_k = np.flatnonzero(indices) produced a U_k whose length was 1 less than the chi2 length, T_inv_k length, and log_p[k] length created in the same _ESum module. Also, I could not understand why the zero index would be excluded. Sincerely, William Gandler

…

________________________________ From: Peter Melchior ***@***.***> Sent: Monday, June 6, 2022 11:28 AM To: pmelchior/pygmmis ***@***.***> Cc: Gandler, William (NIH/CIT) [E] ***@***.***>; Author ***@***.***> Subject: [EXTERNAL] Re: [pmelchior/pygmmis] Troubled by 1 instance of np.flatnonzero (Issue #21) Hello William. Are you asking about why that selection U_k = np.flatnonzero(indices) is done, or do you have trouble that is caused by this line? — Reply to this email directly, view it on GitHub<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fpmelchior%2Fpygmmis%2Fissues%2F21%23issuecomment-1147579488&data=05%7C01%7Cilb%40mail.nih.gov%7Cb7935f4637b640617c7c08da47d133f8%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C637901261090493654%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4Eyhd7h%2BtFbsqHzrBQtqrSQtrogJVVmZMuLQ9zIOG5s%3D&reserved=0>, or unsubscribe<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAXMJ77B4GQR5L752HQSAFKDVNYKIXANCNFSM5X245B6Q&data=05%7C01%7Cilb%40mail.nih.gov%7Cb7935f4637b640617c7c08da47d133f8%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C637901261090493654%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=oojGOJsooTGQgL8lmAKMLTkxfs9557DqdGgmgQLJTAo%3D&reserved=0>. You are receiving this because you authored the thread.Message ID: ***@***.***> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

[pmelchior]

I'm not sure how this can happen. The relevant part of the code is this:

pygmmis/pygmmis.py

Lines 993 to 1001 in 87ad02d

	if cutoff is not None:
	indices = chi2 < cutoff
	chi2 = chi2[indices]
	if (covar is not None and covar.shape != (gmm.D, gmm.D)) or R is not None:
	T_inv_k = T_inv_k[indices]
	if U_k is None:
	U_k = np.flatnonzero(indices)
	else:
	U_k = U_k[indices]

The array indices is of type bool, and the first step of setting U_k from its initial value None lists all non-zero (i.e. non-False) elements of indices.

The following code does exactly the same in a nutshell:

test = np.random.rand(10)
indices = test < 0.5
print(indices, np.flatnonzero(indices))