linregmc 0.0.1__tar.gz → 0.0.2__tar.gz

linregmc-0.0.2/LICENSE

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2025, Pär Söderhjelm
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

linregmc-0.0.2/PKG-INFO

@@ -0,0 +1,22 @@
+Metadata-Version: 2.3
+Name: linregmc
+Version: 0.0.2
+Summary: Linear regression with Monte Carlo error analysis
+License: MIT
+Author: Pär Söderhjelm
+Requires-Python: >=3.12,<4.0
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: numpy (>=1.23,<2.0)
+Description-Content-Type: text/markdown
+
+# linregmc package  (Linear regression with Monte Carlo error analysis)
+
+This package is a single module which contains four functions:<br>
+addnoise        - introduce noise in the data based on known experimental precision<br>
+linreg          - perform multiple linear regressions and calculate goodness-of-fit<br>
+confidence      - get confidence intervals, plot distributions etc.<br>
+linconf         - do all the steps in succession, including possible transformation of the data<br>
+

linregmc-0.0.2/README.md

@@ -0,0 +1,7 @@
+# linregmc package  (Linear regression with Monte Carlo error analysis)
+
+This package is a single module which contains four functions:<br>
+addnoise        - introduce noise in the data based on known experimental precision<br>
+linreg          - perform multiple linear regressions and calculate goodness-of-fit<br>
+confidence      - get confidence intervals, plot distributions etc.<br>
+linconf         - do all the steps in succession, including possible transformation of the data<br>

linregmc-0.0.2/pyproject.toml

@@ -0,0 +1,27 @@
+[tool.poetry]
+name = "linregmc"
+version = "0.0.2"
+description = "Linear regression with Monte Carlo error analysis"
+authors = ["Pär Söderhjelm"]
+license = "MIT"
+readme = "README.md"
+packages = [
+    { include = "linregmc", from = "src" }
+]
+
+
+[tool.poetry.dependencies]
+python = "^3.12"
+numpy = "^1.23"
+
+[tool.poetry.group.dev.dependencies]
+myst-nb = "^1.3.0"
+sphinx-autoapi = "^3.6.0"
+
+[tool.poetry.group.docs.dependencies]
+sphinx = "^7.0"
+sphinx-rtd-theme = "^3.0.2"
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"

linregmc-0.0.2/src/linregmc/linregmc.py

@@ -0,0 +1,313 @@
+import numpy as np
+from numpy.matlib import repmat,randn
+
+def addnoise(yinp,ysiginp,nmc=10000,distrib='normal'):	
+	"""Adds noise to an array of data points (or a single value).
+	
+	Creates a matrix of nmc vectors with the mean values of y but with
+	added random noise of standard deviation ysig. 
+	You might want to initialize the random number generator in forehand.
+	
+	
+	Parameters
+	----------
+	y : array
+	    data vector
+	ysig : array
+	    standard deviation vector (same length as y, or a single value)
+	nmc : int, default 10000
+	    number of Monte Carlo copies
+	distrib : str, default 'normal'
+	    'norm'/'normal' gives normal distribution
+	    'lognorm'/'lognormal' give lognormal distribution (useful for example if negative results are unphysical)
+	
+	Returns
+	-------
+	array
+		the data vector with added noise
+		(always two-dimensional, but only one column if y was a single value)
+	
+	Examples
+	--------
+	>>> y = np.array([1.2, 2.3, 3.7])
+	>>> ysig = np.array([0.1, 0.3, 0.2])
+	>>> y1 = addnoise(y, ysig)  # different stdev for the three points, normal distribution
+	>>> y1.shape  # (10000, 3)
+	>>> y2 = addnoise(y, 0.2, 1000, distrib='lognorm')   # same stdev for the three points, lognormal distribution
+	>>> y2.shape  # (1000, 3)
+	>>> y3 = addnoise(1.5, 0.2) # only one point
+	>>> y3.shape  # (10000, 1)   
+	"""
+	
+	
+	yinp = np.asarray(yinp)
+	ysiginp = np.asarray(ysiginp)
+	if np.ndim(yinp)>1 or np.ndim(ysiginp)>1:
+		raise Exception('y and ysig must not have higher dimension than 1.')
+	if np.size(ysiginp) == 1:
+		ysiginp = ysiginp*np.ones(np.size(yinp))  #If ysiginp is a scalar, turn it into a vector with identical elements
+	if np.size(yinp) != np.size(ysiginp):
+		raise Exception('y and ysig must have the same length.')
+
+	n=np.size(yinp)
+	y=yinp.reshape((1,n))
+	ysig=ysiginp.reshape((1,n))
+	if distrib.lower() in ('norm' ,'normal'):
+		
+		return np.array(repmat(y,nmc,1)) + np.array(repmat(ysig,nmc,1))*np.array(randn(nmc,n))
+	elif  distrib.lower() in ('lognorm','lognormal'):
+			mu = np.log(y**2/np.sqrt(ysig**2+y**2))  # mu of lognormal dist
+			sigma = np.sqrt(np.log(ysig**2/y**2+1))  # sigma of lognormal dist
+			return np.exp(np.array(randn(nmc,n))*np.array(repmat(sigma,nmc,1)) + np.array(repmat(mu,nmc,1)))
+	else:
+		raise Exception('Distribution named "' + distrib + '" is not recognized.')
+
+
+def linreg(xinp, yinp, plot = False):
+	"""Performs linear fitting ax+b=y with error analysis using a Monte Carlo approach.
+	
+	Parameters
+	----------
+	xinp : array
+	    an NM x N matrix: the NX data sets of x values (N data points)
+	yinp : array
+	    an NY x N matrix: the NY data sets of y values (N data points)
+		NX and NY need not be the same. In particular one may use a
+		single data set (without added noise) for one of them.
+		The number of fits equals NM = max(NX,NY) and if there are less data
+		sets for one of x or y, they are just cyclically reused.
+	plot : boolean, default False
+	    an optional argument that specifies whether to plot the chi2 distribution
+	    to visualize the "goodness-of-fit".
+	
+	Returns
+	-------
+	pp  : array (2 elements)
+		single-fit value of each parameter (can be used as the result)
+	psig  : array (2 elements)
+		standard deviation of each parameter
+	pchi : float
+		goodness-of-fit, i.e. probability of chi>chi0
+	pmc  : array
+		a (NM x 2 matrix, the fitted parameters for all data sets
+		
+	Examples
+	--------
+	>>> x = np.array([0.1, 0.2, 0.3])
+	>>> y = np.array([1.2, 2.3, 3.7])
+	>>> y_mc=addnoise(y, 0.1)
+	>>> pp,psig,pchi2,pmc = linreg(x, y_mc)	
+	>>> print(pp)   #[12.517 -0.102]
+	>>> pmc.shape   # (10000, 2)	
+	"""
+
+	if np.ndim(xinp) == 1:
+		x=xinp.reshape((1,np.size(xinp)))
+	else:
+		x= xinp
+	if np.ndim(yinp) == 1:
+		y=yinp.reshape((1,np.size(yinp)))
+	else:
+		y=yinp
+	if np.size(x,1) != np.size(y,1):
+		raise Exception('Number of columns in x and y must be equal')
+	N=np.size(x,1)
+	n=1 #always linear fit
+	
+	#Perform single fit to get the base chi2 value
+	xs=np.median(x, axis=0)
+	ys=np.median(y, axis=0)   #Reproduces original data points independent of distribution
+	sig=np.std(x, axis=0)+np.std(y, axis=0)  #This only makes sense if either x or y is a single set
+	
+	Xt=np.stack((xs, np.ones(N)), axis=1)
+	X=np.stack((xs/sig, np.ones(N)/sig), axis=1)
+	Y=ys/sig
+	pp=np.linalg.lstsq(X,Y, rcond=None)[0]    
+	chi2 = sum((Y - np.matmul(X,pp))**2)
+	subtract=ys - np.matmul(Xt,pp)
+	
+	
+	xn=np.size(x,0)
+	yn=np.size(y,0)
+	nmc = max(xn,yn)
+	pmc = np.zeros((nmc,n+1)) 
+	chi2mc = np.zeros(nmc)
+	for i in range(nmc):
+		X=np.stack((x[i%xn,:]/sig,np.ones(N)/sig),axis=1)
+		Y=(y[i%yn,:]-subtract)/sig
+		p=np.linalg.lstsq(X,Y, rcond=None)[0] 
+		pmc[i,:]=p
+		chi2mc[i] = sum((Y - np.matmul(X,p))**2)
+	
+	pmean = np.mean(pmc,0)    #This is not used, as the single fit (pp) is returned for compatibility with the MATLAB script
+	psig = np.std(pmc,0)
+	
+	#Compute pchi2
+	pchi2=sum(chi2mc>chi2)/nmc
+	
+	if plot:
+		import matplotlib.pyplot as plt
+		fig, ax = plt.subplots(1, 1, figsize=(4, 2))
+		counts,*_=ax.hist(chi2mc,bins=50)
+		ycent=0.5*max(counts)
+		ax.plot([chi2,chi2],[0,ycent],'r-')
+		ax.set_yticks([])
+		ax.set_xlabel(r"$\chi^2$")
+		plt.show()
+		
+	return (pp,psig,pchi2,pmc)
+
+
+#
+	
+
+def confidence(X, level=0.683, plot=False):
+	"""Statistical analysis of the data in matrix X.
+	
+	It is assumed that the number of data points are large; all properties
+	are calculated from the data itself.
+	
+	Parameters
+	----------
+	X : array
+	    data matrix. Data in columns. For example, if X contains data
+	    from two measurements, data for measurement 1 is in column 1
+	    and measurement 2 in columns 2.
+	    If only one column, a 1d-array is also acceptable
+	level : float, default 0.683
+	    desired confidence level
+	plot : boolean, default False
+	    an optional boolean specifying whether to plot histograms for each column
+	    where a general statistic is shown as a red errorbar (median +/- stdev)
+	    and the confidence intervals are shown with black lines.
+	    The red markers at the bottom show the simpler (median +/- err) 
+	    interval which should normally coincide with the confidence interval
+	    unless the distribution is skew (in which case the confidence interval is more reliable).
+	    If X has exactly two columns, a scatter plot showing possible correlation between
+	    the two columns is also produced.
+	
+	Returns
+	-------
+	err : float
+	    estimated error in the columns based on selected confidence level.
+	confint : list
+	    a list of tuples (low, high), the confidence interval for each input column
+	    (pconf*100% of values are found within this interval around median) 
+	    If the input x was a 1d-array, a single tuple is returned instead of a list
+
+	Examples
+	--------
+	>>> x = np.array([0.1, 0.2, 0.3])
+	>>> y = np.array([1.2, 2.3, 3.7])
+	>>> y_mc=addnoise(y, 0.1)
+	>>> pp,psig,pchi2,pmc = linreg(x, y_mc)
+	>>> err,confint = confidence(pmc, 0.95)
+	>>> print(err)    # gives [1.364 0.296]
+	>>> print(confint)    # gives [(11.16, 13.88), (-0.401, 0.190)]
+	
+	"""
+
+	onedim = (np.ndim(X) == 1)
+	
+	if onedim:  #convert to matrix, then convert back to onedim at the end
+		X=X.reshape((np.size(X),1))
+	
+	if level <= 0 or level >= 1:
+		raise Exception("levvel must be 0 < level < 1.")
+	
+	if np.size(X,1) > np.size(X,0):
+		print("Warning. It appears that your data is not placed column-wise.")
+	
+	N = np.size(X,0) #number of data points
+	n = np.size(X,1)  #number of dimensions (columns)
+	
+	# GUM recommendation. ncut is the complement to pconf, ie the 1-pconf
+	# fraction of points.
+	#ncut = floor((N - floor(level*N+0.5) + 1)/2);   
+	
+	median = np.median(X,0)
+	sig = np.std(X,0)
+	absdiff = abs(X-np.mean(X,0)) #Absolute difference to mean value
+	plow = np.zeros(n)
+	phigh = np.zeros(n)
+	err = np.zeros(n)
+	for j in range(n):
+		tmp=np.sort(X[:,j])
+		plow[j]=tmp[round(max(1,0.5*(1-level)*N))-1]
+		phigh[j]=tmp[round(min(N,1-0.5*(1-level)*N))-1]
+		tmp=np.sort(absdiff[:,j])
+		err[j]=tmp[round(min(N,level*N))-1]
+	
+	if plot:
+		import matplotlib.pyplot as plt
+		import matplotlib.gridspec as gridspec
+		nvar=np.size(X,1)
+		if nvar==2: #Exactly two parameters so produce a scatter plot and histograms
+			fig = plt.figure(figsize=(8, 4.8))
+			gs = gridspec.GridSpec(2, 2, width_ratios=[1.5, 1], height_ratios=[1, 1])
+			# Left square spans both rows
+			ax_left = fig.add_subplot(gs[:, 0])
+			axes = [fig.add_subplot(gs[0, 1]), fig.add_subplot(gs[1, 1])]
+			ax_left.set_aspect('equal')
+			ax_left.scatter(X[:,0],X[:,1],s=0.1)
+			ax_left.set_xlabel('a')
+			ax_left.set_ylabel('b')
+			ax_left.plot([plow[0],plow[0]],[np.min(X[:,1]),np.max(X[:,1])],'k--')
+			ax_left.plot([phigh[0],phigh[0]],[np.min(X[:,1]),np.max(X[:,1])],'k--')
+			ax_left.plot([np.min(X[:,0]),np.max(X[:,0])],[plow[1],plow[1]], 'k--')
+			ax_left.plot([np.min(X[:,0]),np.max(X[:,0])],[phigh[1],phigh[1]], 'k--')
+			
+			ax_left.set_aspect(1.0/ax_left.get_data_ratio(), adjustable='box')
+		else:  #only produce histograms
+			fig, axes = plt.subplots(nrows=nvar, ncols=1, figsize=(4, 2*nvar))
+			if nvar==1: axes=[axes] # fix stupid inconsistency in plt.subplots so that axes is always a list
+		
+		for i,ax in enumerate(axes):
+			counts,*_=ax.hist(X[:,i], bins=50)
+			ycent=0.5*max(counts)
+			ax.errorbar(median[i],ycent,xerr=sig[i],fmt='ro',capsize=5)
+			ax.plot([plow[i],plow[i]]  ,[0,0.8*ycent],'k--')
+			ax.plot([phigh[i],phigh[i]],[0,0.8*ycent],'k--')
+			ax.plot([median[i]-err[i], median[i]-err[i]], [0,0.1*ycent],'r-')
+			ax.plot([median[i]+err[i], median[i]+err[i]], [0,0.1*ycent],'r-')
+			ax.set_xlabel(chr(ord('a')+i))  #Name the variables a,b,c...
+			ax.set_yticks([])
+	
+		plt.tight_layout()
+		plt.show()
+	
+	if onedim:
+		return (err[0], (plow[0], phigh[0])) #simply return scalars
+	else:
+		return (err, list(zip(plow, phigh)))
+
+
+def linconf(xinp, yinp, ysig, nmc=10000, distrib='normal', level=0.683, ytransform=None, restransform=None):
+	"""Performs the full Monte Carlo linear regression with confidence calculation.
+	
+	This is done by applying the following 5 steps in succession:
+	- addnoise to y values
+	- transform y values (skipped if ytransform==None)
+	- linreg (x,y)
+	- calculate a tuple of results from a,b   (skipped if restransform==None)
+	- confidence for each result
+	
+	For detailed description of parameters, see previous functions
+	Returns (reslist, pchi2) where reslist is a list of (result, error, confidenceinterval) for each calculated result
+	"""
+	
+	ymc=addnoise(yinp, ysig, nmc, distrib)
+	if ytransform!=None:
+		ymc = ytransform(ymc)
+	pp,psig,pchi2,pmc=linreg(xinp,ymc)
+	if restransform!=None:
+		results=restransform(pp[0],pp[1])
+		results_mc=restransform(pmc[:,0],pmc[:,1])
+	else:
+		results=(pp[0],pp[1])
+		results_mc=(pmc[:,0],pmc[:,1])
+	rlist=[]
+	for r,rmc in zip(results,results_mc):
+		perr,confint=confidence(rmc, level)
+		rlist.append((r,perr,confint))
+	return (rlist,pchi2)

linregmc-0.0.1/.bashlog

@@ -1,42 +0,0 @@
-  522  cd packaging_mclinreg/
-  523  ls
-  527  cd packaging_mclinreg/
-  528  vi README.MD 
-  529  ls
-  530  vi pyproject.toml 
-  531  rm -r dist/
-  549  cd ..
-  550  ls
-  551  vi pyproject.toml 
-  552  vi README.MD 
-  553  vi README.MD 
-  554  ls
-  555  python -m pip install --upgrade build
-  556  python -m build
-  557  python -m pip install --upgrade twine
-  558  python -m twine upload --repository testpypi dist/*
-  568  cd ../packaging_linregmc/
-  569  ls
-  570  vi src
-  576  cd ..
-  577  ls
-  578  cat pyproject.toml 
-  579  python -m build
-  580  ls
-  588  cd ..
-  589  python -m build
-  590  python -m twine upload --repository testpypi dist/*
-  591  vi pyproject.toml 
-  592  python -m build
-  593  ls
-  594  ls dist/
-  595  python -m twine upload --repository testpypi dist/*0.0.2*
-  596  vi src/linregmc/__init__.py 
-  597  vi pyproject.toml 
-  598  python -m build
-  599  python -m twine upload --repository testpypi dist/*0.0.3*
-  603  cd packaging_linregmc/
-  604  rm -r dist
-  605  vi pyproject.toml 
-  606  ls -lt ../linregmc.py 
-  607  cp ../linregmc.py src/linregmc/

linregmc-0.0.1/PKG-INFO

@@ -1,21 +0,0 @@
-Metadata-Version: 2.4
-Name: linregmc
-Version: 0.0.1
-Summary: Linear regression with Monte Carlo error analysis
-Project-URL: Homepage, https://github.com/parsod/BFKdemos
-Author-email: Par Soderhjelm <par.soderhjelm@bpc.lu.se>
-License-Expression: MIT
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3
-Requires-Python: >=3.7
-Description-Content-Type: text/markdown
-
-# linregmc package  (Linear regression with Monte Carlo error analysis)
-
-This package is a single module which contains three functions
-
-createmcdata - introduce noise in the data based on known experimental precision
-linreg       - perform multiple linear regressions and calculate goodness-of-fit
-errconf      - get confidence intervals, plot distributions etc.
-
-TODO: Add detailed documentation here

linregmc-0.0.1/README.MD

@@ -1,9 +0,0 @@
-# linregmc package  (Linear regression with Monte Carlo error analysis)
-
-This package is a single module which contains three functions
-
-createmcdata - introduce noise in the data based on known experimental precision
-linreg       - perform multiple linear regressions and calculate goodness-of-fit
-errconf      - get confidence intervals, plot distributions etc.
-
-TODO: Add detailed documentation here

linregmc-0.0.1/README.md

@@ -1,9 +0,0 @@
-# linregmc package  (Linear regression with Monte Carlo error analysis)
-
-This package is a single module which contains three functions
-
-createmcdata - introduce noise in the data based on known experimental precision
-linreg       - perform multiple linear regressions and calculate goodness-of-fit
-errconf      - get confidence intervals, plot distributions etc.
-
-TODO: Add detailed documentation here

linregmc-0.0.1/pyproject.toml

@@ -1,22 +0,0 @@
-[build-system]
-requires = ["hatchling >= 1.26"]
-build-backend = "hatchling.build"
-
-[project]
-name = "linregmc"
-version = "0.0.1"
-authors = [
-  { name="Par Soderhjelm", email="par.soderhjelm@bpc.lu.se" },
-]
-description = "Linear regression with Monte Carlo error analysis"
-readme = "README.md"
-requires-python = ">=3.7"
-classifiers = [
-    "Programming Language :: Python :: 3",
-    "Operating System :: OS Independent",
-]
-license = "MIT"
-license-files = ["LICEN[CS]E*"]
-
-[project.urls]
-Homepage = "https://github.com/parsod/BFKdemos"

linregmc-0.0.1/src/.bashlog

@@ -1,20 +0,0 @@
-  555  cd src
-  556  mkdir example_package_per
-  560  cd ..
-  532  cd src
-  533  ls
-  534  ls example_package_parsod/
-  535  ln -sf ../../linregmc.py .
-  536  ls
-  537  mv example_package_parsod/ linregmc
-  538  mv linregmc.py linregmc
-  548  cd ..
-  571  cd src/
-  572  ls
-  573  mv linregmc/linregmc.py .
-  574  ls
-  575  mv linregmc ../linregmc_package
-  581  cd src/
-  582  mv ../linregmc_package/ linregmc
-  583  mv linregmc.py linregmc
-  587  cd ..

linregmc-0.0.1/src/linregmc/.bashlog

@@ -1,15 +0,0 @@
-  557  cd example_package_per/
-  558  echo -n >__init__.py
-  559  vi example.py
-  539  cd linregmc/
-  540  ls
-  541  ls -lt
-  542  rm example.py 
-  543  vi __init__.py 
-  544  ls
-  545  rm linregmc.py 
-  546  cp ../../../linregmc.py .
-  547  ls
-  584  cd linregmc/
-  585  ls
-  586  vi __init__.py

linregmc-0.0.1/src/linregmc/linregmc.py

@@ -1,253 +0,0 @@
-import numpy as np
-from numpy.matlib import repmat,randn
-
-def addnoise(yinp,ysiginp,nmc=10000,distrib='normal'):
-
-	#      function ymc = createmcdata(y,ysig,nmc,distrib)
-	#
-	# Creates a matrix ymc of nmc vectors with the mean values of y but with
-	# added random noise of standard deviation ysig. 
-	#
-	#     y       data vector
-	#     ysig    standard deviation vector (same length as y)
-	#     nmc     number of Monte Carlo copies
-	#     distrib 'norm'/'normal' gives normal distribution
-	#             'lognorm'/'lognormal' give lognormal distribution (useful for example 
-	#             if negative results are unphysical)
-	#
-	#
-	#  You might want to initialize the random number generator in forehand.
-	#
-
-	yinp = np.asarray(yinp)
-	ysiginp = np.asarray(ysiginp)
-	if np.ndim(yinp)>1 or np.ndim(ysiginp)>1:
-		raise Exception('y and ysig must not have higher dimension than 1.')
-	if np.size(ysiginp) == 1:
-		ysiginp = ysiginp*np.ones(np.size(yinp))  #If ysiginp is a scalar, turn it into a vector with identical elements
-	if np.size(yinp) != np.size(ysiginp):
-		raise Exception('y and ysig must have the same length.')
-
-	n=np.size(yinp)
-	y=yinp.reshape((1,n))
-	ysig=ysiginp.reshape((1,n))
-	if distrib.lower() in ('norm' ,'normal'):
-		
-		return np.array(repmat(y,nmc,1)) + np.array(repmat(ysig,nmc,1))*np.array(randn(nmc,n))
-	elif  distrib.lower() in ('lognorm','lognormal'):
-			mu = np.log(y**2/np.sqrt(ysig**2+y**2))  # mu of lognormal dist
-			sigma = np.sqrt(np.log(ysig**2/y**2+1))  # sigma of lognormal dist
-			return np.exp(np.array(randn(nmc,n))*np.array(repmat(sigma,nmc,1)) + np.array(repmat(mu,nmc,1)))
-	else:
-		raise Exception('Distribution named "' + distrib + '" is not recognized.')
-
-
-def linreg(xinp, yinp, plot = False):
-	#This is the new (2024) weighted-fit version (similar to MATLAB linregmc) that only handles linear fits
-	#and does NOT do confidence intervals, as these can be done by mcerrconf
-	
-    #Performs linear fitting ax+b=y with error analysis 
-    #using a Monte Carlo approach.
-    
-    #Input arguments:
-    #  x : a NX x N matrix: the NX data sets of x values (N data points)
-    #  y : a NY x N matrix: the NY data sets of y values (N data points)
-    #      NX and NY need not be the same. In particular one may use a
-    #      single data set (without added noise) for one of them.
-    #      The number of fits equals max(NX,NY) and if there are less data
-    #      sets for one of x or y, they are just cyclically reused.
-    #Return values:
-    #  pp    (2 elements): single-fit value of each parameter (can be used as the result)
-    #  psig  (2 elements): standard deviation of each parameter
-    #  pchi  : probability of chi>chi0
-    #  pmc   : a NX x (n+1) maxtrix, the fitted parameters for all data sets
-	
-
-    if np.ndim(xinp) == 1:
-        x=xinp.reshape((1,np.size(xinp)))
-    else:
-        x= xinp
-    if np.ndim(yinp) == 1:
-        y=yinp.reshape((1,np.size(yinp)))
-    else:
-        y=yinp
-    if np.size(x,1) != np.size(y,1):
-        raise Exception('Number of columns in x and y must be equal')
-    N=np.size(x,1)
-    n=1 #always linear fit
-
-	#Perform single fit to get the base chi2 value
-    xs=np.median(x, axis=0)
-    ys=np.median(y, axis=0)   #Reproduces original data points independent of distribution
-    sig=np.std(x, axis=0)+np.std(y, axis=0)  #This only makes sense if either x or y is a single set
-
-    Xt=np.stack((xs, np.ones(N)), axis=1)
-    X=np.stack((xs/sig, np.ones(N)/sig), axis=1)
-    Y=ys/sig
-    pp=np.linalg.lstsq(X,Y, rcond=None)[0]    
-    chi2 = sum((Y - np.matmul(X,pp))**2)
-    subtract=ys - np.matmul(Xt,pp)
-
-
-    xn=np.size(x,0)
-    yn=np.size(y,0)
-    nmc = max(xn,yn)
-    pmc = np.zeros((nmc,n+1)) 
-    chi2mc = np.zeros(nmc)
-    for i in range(nmc):
-        X=np.stack((x[i%xn,:]/sig,np.ones(N)/sig),axis=1)
-        Y=(y[i%yn,:]-subtract)/sig
-        p=np.linalg.lstsq(X,Y, rcond=None)[0] 
-        pmc[i,:]=p
-        chi2mc[i] = sum((Y - np.matmul(X,p))**2)
-
-    pmean = np.mean(pmc,0)    #This is not used, as the single fit (pp) is returned for compatibility with the MATLAB script
-    psig = np.std(pmc,0)
-    
-    #Compute pchi2
-    pchi2=sum(chi2mc>chi2)/nmc
-
-    if plot:
-        import matplotlib.pyplot as plt
-        fig, ax = plt.subplots(1, 1, figsize=(4, 2))
-        counts,*_=ax.hist(chi2mc,bins=50)
-        ycent=0.5*max(counts)
-        ax.plot([chi2,chi2],[0,ycent],'r-')
-        ax.set_yticks([])
-        ax.set_xlabel(r"$\chi^2$")
-        plt.show()
-        
-    return (pp,psig,pchi2,pmc)
-
-
-
-def confidence(X, level=0.683, plot=False):
-    #
-    # Statistical analysis of the data in matrix X.
-    # It is assumed that the number of data points are large; all properties
-    # are calculated from the data itself. 
-    #
-    #     X       data matrix. Data in columns. For example, if X contains data
-    #             from two measurements, data for measurement 1 is in column 1
-    #             and measurement 2 in columns 2.
-    #             If only one column, a 1d-array is also acceptable
-    #     level   confidence limit of error in err. If not specified, level =
-    #             0.683 is default.
-	#     plot    an optional boolean specifying whether to plot histograms for each column
-	#             where a general statistic is shown as a red errorbar (median +/- stdev)
-    #             and the confidence intervals are shown with black lines.
-	#             The red markers at the bottom show the simpler (median +/- err) 
-	#             interval which should normally coincide with the confidence interval
-	#             unless the distribution is skew (in which case the confidence interval is more reliable).
-	#             If X has exactly two columns, a scatter plot showing possible correlation between
-	#             the two columns is also produced.
-    #
-    # Returns a tuple (err, confint) where
-    #     err            Error in the columns based on selected confidence limit.
-    #     confint        A list of tuples (low, high), the confidence interval for each input column
-	#                    (pconf*100% of values are found within this interval around median) 
-	#                    If the input X was a 1d-array, a single tuple is returned instead of a list
-
-    onedim = (np.ndim(X) == 1)
-    
-    if onedim:  #convert to matrix, then convert back to onedim at the end
-        X=X.reshape((np.size(X),1))
-
-    if level <= 0 or level >= 1:
-        raise Exception("levvel must be 0 < level < 1.")
-
-    if np.size(X,1) > np.size(X,0):
-        print("Warning. It appears that your data is not placed column-wise.")
-
-    N = np.size(X,0) #number of data points
-    n = np.size(X,1)  #number of dimensions (columns)
-    
-    # GUM recommendation. ncut is the complement to pconf, ie the 1-pconf
-    # fraction of points.
-    #ncut = floor((N - floor(level*N+0.5) + 1)/2);   
-    
-    median = np.median(X,0)
-    sig = np.std(X,0)
-    absdiff = abs(X-np.mean(X,0)) #Absolute difference to mean value
-    plow = np.zeros(n)
-    phigh = np.zeros(n)
-    err = np.zeros(n)
-    for j in range(n):
-        tmp=np.sort(X[:,j])
-        plow[j]=tmp[round(max(1,0.5*(1-level)*N))-1]
-        phigh[j]=tmp[round(min(N,1-0.5*(1-level)*N))-1]
-        tmp=np.sort(absdiff[:,j])
-        err[j]=tmp[round(min(N,level*N))-1]
-
-    if plot:
-        import matplotlib.pyplot as plt
-        import matplotlib.gridspec as gridspec
-        nvar=np.size(X,1)
-        if nvar==2: #Exactly two parameters so produce a scatter plot and histograms
-            fig = plt.figure(figsize=(8, 4.8))
-            gs = gridspec.GridSpec(2, 2, width_ratios=[1.5, 1], height_ratios=[1, 1])
-            # Left square spans both rows
-            ax_left = fig.add_subplot(gs[:, 0])
-            axes = [fig.add_subplot(gs[0, 1]), fig.add_subplot(gs[1, 1])]
-            ax_left.set_aspect('equal')
-            ax_left.scatter(X[:,0],X[:,1],s=0.1)
-            ax_left.set_xlabel('a')
-            ax_left.set_ylabel('b')
-            ax_left.plot([plow[0],plow[0]],[np.min(X[:,1]),np.max(X[:,1])],'k--')
-            ax_left.plot([phigh[0],phigh[0]],[np.min(X[:,1]),np.max(X[:,1])],'k--')
-            ax_left.plot([np.min(X[:,0]),np.max(X[:,0])],[plow[1],plow[1]], 'k--')
-            ax_left.plot([np.min(X[:,0]),np.max(X[:,0])],[phigh[1],phigh[1]], 'k--')
-            
-            ax_left.set_aspect(1.0/ax_left.get_data_ratio(), adjustable='box')
-        else:  #only produce histograms
-            fig, axes = plt.subplots(nrows=nvar, ncols=1, figsize=(4, 2*nvar))
-            if nvar==1: axes=[axes] # fix stupid inconsistency in plt.subplots so that axes is always a list
-        
-        for i,ax in enumerate(axes):
-            counts,*_=ax.hist(X[:,i], bins=50)
-            ycent=0.5*max(counts)
-            ax.errorbar(median[i],ycent,xerr=sig[i],fmt='ro',capsize=5)
-            ax.plot([plow[i],plow[i]]  ,[0,0.8*ycent],'k--')
-            ax.plot([phigh[i],phigh[i]],[0,0.8*ycent],'k--')
-            ax.plot([median[i]-err[i], median[i]-err[i]], [0,0.1*ycent],'r-')
-            ax.plot([median[i]+err[i], median[i]+err[i]], [0,0.1*ycent],'r-')
-            ax.set_xlabel(chr(ord('a')+i))  #Name the variables a,b,c...
-            ax.set_yticks([])
-
-        plt.tight_layout()
-        plt.show()
-    
-    if onedim:
-        return (err[0], (plow[0], phigh[0])) #simply return scalars
-    else:
-        return (err, list(zip(plow, phigh)))
-
-
-def linconf(xinp, yinp, ysig, nmc=10000, distrib='normal', level=0.683, ytransform=None, restransform=None):
-	#
-	#Performs the full Monte Carlo linear regression with confidence calculation.
-	#by applying the following 5 steps in succession:
-	#   addnoise to y values
-	#   transform y values (skipped if ytransform==None)
-	#   linreg (x,y)
-	#   calculates a tuple of results from a,b   (skipped if restransform==None)
-	#   confidence for each result
-
-	#   For detailed description of parameters, see previous functions
-	#   Returns (reslist, pchi2) where reslist is a list of (result, error, confidenceinterval) for each calculated result
-	
-	ymc=addnoise(yinp, ysig, nmc, distrib)
-	if ytransform!=None:
-		ymc = ytransform(ymc)
-	pp,psig,pchi2,pmc=linreg(xinp,ymc)
-	if restransform!=None:
-		results=restransform(pp[0],pp[1])
-		results_mc=restransform(pmc[:,0],pmc[:,1])
-	else:
-		results=(pp[0],pp[1])
-		results_mc=(pmc[:,0],pmc[:,1])
-	rlist=[]
-	for r,rmc in zip(results,results_mc):
-		perr,confint=confidence(rmc, level)
-		rlist.append((r,perr,confint))
-	return (rlist,pchi2)