multiple instances of function/variable `ps` for different purposes

[ambarb]

"ps" is used for different things in the code base.

• instance 1, related to peak center
  ps = based on original peak stats ; used in collection environment. may be useful in analysis.
• instance 2, related to aged g2 from two-time
  ps =
• instance 3a, get_timepixel_data comment on line 36
  ps =
• instance 3b, get_pvlist_from_post internal variable that is returned
  ps =
• instance 4, speckle modules with variable
  ps = Poission distribution. Docstring is good. no clarification needed

Instance 1

pyCHX/pyCHX/chx_generic_functions.py

Lines 996 to 1006 in 6e991bb

	def ps( y,shift=.5, replot=True, logplot='off', x= None):
	'''
	Dev 16, 2018
	Modified ps() function in 95-utilities.py
	function to determine statistic on line profile (assumes either peak or erf-profile)
	Input:
	y: 1D array, the data for analysis
	shift: scale for peak presence (0.5 -> peak has to be taller factor 2 above background)
	replot: if True, will plot data (if error func) with the fit and peak/cen/com position
	logplot: if on, will plot in log scale
	x: if not None, give x-data

There are notes in code to @mrakitin .
Is this used in analysis to not have to fit to find the center of a peak?
It seems it was associated with a Bluesky profile file. Is this new one used in bluesky?
What does "ps" mean in this context? peak stats? peak scaling?

Instance 2

show_g12q_aged_g2()

pyCHX/pyCHX/Two_Time_Correlation_Function.py

Lines 599 to 621 in 6e991bb

	ax1 = plt.subplot(gs[1])
	linS1 = [ [0]*len(age_center ), np.int_(age_center - slice_width//2 ) ]
	linS2 = [ [0]*len(age_center ), np.int_(age_center + slice_width//2 ) ]
	linE1 = [ np.int_(age_center - slice_width//2 ), [0]*len(age_center) ]
	linE2 = [ np.int_(age_center + slice_width//2 ), [0]*len(age_center) ]
	linC = [ [0]*len(age_center ), np.int_(age_center ) ]
	for i in range( len(age_center ) ):
	ps = linS1[1][i]
	pe = linE1[0][i]
	if ps>=N:s0=ps - N;s1=N
	else:s0=0;s1=ps
	e0 = s1;e1=s0
	#if pe>=N:e0=N;e1=pe - N
	#else:e0=pe;e1=0
	ps = linS2[1][i]
	pe = linE2[0][i]
	if ps>=N:S0=ps - N;S1=N
	else:S0=0;S1=ps
	#if pe>=N:e0=N;E1=pe - N
	#else:E0=pe;E1=0
	E0=S1;E1=S0

Instance(s) 3

in xpcs_timepixelmodule in 2 functions

pyCHX/pyCHX/xpcs_timepixel.py

Lines 25 to 36 in 6e991bb

	def get_timepixel_data( data_dir, filename, time_unit= 1 ):
	'''give a csv file of a timepixel data, return x,y,t
	x, pos_x in pixel
	y, pos_y in pixel
	t, arrival time
	time_unit, t*time_unit will convert to second, in reality, this value is 6.1e-12
	return x,y,t (in second, starting from zero)
	'''
	data = pds.read_csv( data_dir + filename )
	#'#Col', ' #Row', ' #ToA',
	#return np.array( data['Col'] ), np.array(data['Row']), np.array(data['GlobalTimeFine']) #*6.1 #in ps

"ps" is photon statitisics?

pyCHX/pyCHX/xpcs_timepixel.py

Lines 50 to 72 in 6e991bb

	def get_pvlist_from_post( p, t, binstep=100, detx=256, dety=256 ):
	'''YG.DEV@CHX Nov, 2017 to get a pos, val list of phonton hitting detector by giving
	p (photon hit pos_x * detx + y (photon hit pos_y), t (photon hit time), and the time bin
	The most important function for timepix
	Input:
	p: array, int64, coordinate-x * det_x + coordinate-y
	t: list, int64, photon hit time
	binstep: int, binstep (in t unit) period
	detx,dety: int/int, the detector size in x and y
	Output:
	positions: int array, (x*detx +y)
	vals: int array, counts of that positions
	counts: int array, counts of that positions in each binstep
	'''
	v = ( t - t[0])//binstep
	L= np.max( v ) + 1
	arr = np.ravel_multi_index( [ p, v ], [detx * dety,L ] )
	uval, ind, count = np.unique( arr, return_counts=True, return_index=True)
	ind2 = np.lexsort( ( p[ind], v[ind] ) )
	ps = (p[ind])[ind2]
	vs = count[ind2]
	cs = np.bincount(v[ind])
	return ps,vs,cs

"ps" is photon positions

Instance 4

in speckle* modules for fit_xsvs1. "ps" is Poisson distribution

[mrakitin]

Regarding Andi's question - I believe it stands for "peak stats". I recognize some of my code, but not everything. It looks like it is an extended version of the one from BEC.

…

-------- Original message -------- From: Andi Barbour <notifications@github.com> Date: 2/9/21 18:05 (GMT-05:00) To: NSLS-II/pyCHX <pyCHX@noreply.github.com> Cc: "Rakitin, Maksim" <mrakitin@bnl.gov>, Assign <assign@noreply.github.com> Subject: [NSLS-II/pyCHX] when / how is ps used (#60) "ps" is used for different things in the code base. * instance 1, related to peak center * instance 2, related to aged g2 from two-time * instance 3a, get_timepixel_data comment on line 36 * instance 3b, get_pvlist_from_post internal variable that is returned * instance 4, speckle modules with variable for Poission distribution = ps Instance 1 https://github.com/NSLS-II/pyCHX/blob/6e991bb1eb06d8fe1bc8f684ebfcec581ee57aba/pyCHX/chx_generic_functions.py#L996-L1006 There are notes in code to @mrakitin<https://github.com/mrakitin> . Is this used in analysis to not have to fit to find the center of a peak? It seems it was associated with a Bluesky profile file. Is this new one used in bluesky? What does "ps" mean in this context? peak stats? peak scaling? Instance 2 show_g12q_aged_g2() https://github.com/NSLS-II/pyCHX/blob/6e991bb1eb06d8fe1bc8f684ebfcec581ee57aba/pyCHX/Two_Time_Correlation_Function.py#L599-L621 Instance(s) 3 in xpcs_timepixelmodule in 2 functions https://github.com/NSLS-II/pyCHX/blob/6e991bb1eb06d8fe1bc8f684ebfcec581ee57aba/pyCHX/xpcs_timepixel.py#L25-L36 "ps" is photon statitisics? https://github.com/NSLS-II/pyCHX/blob/6e991bb1eb06d8fe1bc8f684ebfcec581ee57aba/pyCHX/xpcs_timepixel.py#L50-L72 "ps" is photon positions Instance 4 in speckle* modules for fit_xsvs1. "ps" is Poisson distribution — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub<#60>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADEY4WFJGR3YGHPPWHIQQCDS6G5T3ANCNFSM4XL4BW4A>.