expcalc 0.1.1

checksums.yaml

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+SHA256:
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+  data.tar.gz: a7a7067ec190eba6e97a4afcd6dc76a1abf6ce5caf07b49a3371c9d531beaa82
+SHA512:
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data/.github/workflows/main.yml

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+name: Ruby
+
+on: [push,pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: 3.0.1
+    - name: Run the default task
+      run: |
+        gem install bundler -v 2.2.15
+        bundle install
+        bundle exec rake

data/.gitignore

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+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status

data/.rspec

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+--format documentation
+--color
+--require spec_helper

data/.rubocop.yml

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+AllCops:
+  TargetRubyVersion: 2.4
+
+Style/StringLiterals:
+  Enabled: true
+  EnforcedStyle: double_quotes
+
+Style/StringLiteralsInInterpolation:
+  Enabled: true
+  EnforcedStyle: double_quotes
+
+Layout/LineLength:
+  Max: 120

data/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at seoanezonjic@hotmail.com. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior,  harassment of an individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 2.0,
+available at https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

data/Gemfile

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+# frozen_string_literal: true
+
+source "https://rubygems.org"
+
+# Specify your gem's dependencies in expcalc.gemspec
+gemspec
+
+gem "rake", "~> 13.0"
+
+gem "rspec", "~> 3.0"
+
+gem "rubocop", "~> 1.7"

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2022 seoanezonjic
+
+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.

data/README.md

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+# Expcalc
+
+Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/expcalc`. To experiment with that code, run `bin/console` for an interactive prompt.
+
+TODO: Delete this and the text above, and describe your gem
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'expcalc'
+```
+
+And then execute:
+
+    $ bundle install
+
+Or install it yourself as:
+
+    $ gem install expcalc
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and the created tag, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/expcalc. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [code of conduct](https://github.com/[USERNAME]/expcalc/blob/master/CODE_OF_CONDUCT.md).
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+
+## Code of Conduct
+
+Everyone interacting in the Expcalc project's codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[USERNAME]/expcalc/blob/master/CODE_OF_CONDUCT.md).

data/Rakefile

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+# frozen_string_literal: true
+
+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+require "rubocop/rake_task"
+
+RuboCop::RakeTask.new
+
+task default: %i[spec rubocop]

data/bin/console

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+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+require "bundler/setup"
+require "expcalc"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/expcalc.gemspec

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+# frozen_string_literal: true
+
+require_relative "lib/expcalc/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "expcalc"
+  spec.version       = Expcalc::VERSION
+  spec.authors       = ["seoanezonjic"]
+  spec.email         = ["seoanezonjic@hotmail.com"]
+
+  spec.summary       = "Gem to expand ruby math capabilities"
+  spec.description   = "To expand ruby math operations this gem call to others such as Numo:narray and others and implements methods onto them to deal with our needs"
+  spec.homepage      = "https://github.com/seoanezonjic/expcalc"
+  spec.license       = "MIT"
+  spec.required_ruby_version = Gem::Requirement.new(">= 2.4.0")
+
+  #spec.metadata["allowed_push_host"] = "TODO: Set to 'http://mygemserver.com'"
+
+  spec.metadata["homepage_uri"] = spec.homepage
+  spec.metadata["source_code_uri"] = spec.homepage
+  #spec.metadata["changelog_uri"] = "TODO: Put your gem's CHANGELOG.md URL here."
+
+  # Specify which files should be added to the gem when it is released.
+  # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
+  spec.files = Dir.chdir(File.expand_path(__dir__)) do
+    `git ls-files -z`.split("\x0").reject { |f| f.match(%r{\A(?:test|spec|features)/}) }
+  end
+  spec.bindir        = "bin"
+  spec.executables   = spec.files.grep(%r{\Abin/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency "cmath", ">= 1.0.0"
+  spec.add_dependency "numo-linalg", ">= 0.1.5"
+  spec.add_dependency "numo-narray", ">= 0.9.1.9"
+  spec.add_dependency "pp", ">= 0.1.0"
+  spec.add_dependency "pycall", ">= 1.3.1"
+  spec.add_dependency "npy", ">= 0.2.0"
+
+  # For more information and examples about making a new gem, checkout our
+  # guide at: https://bundler.io/guides/creating_gem.html
+end

data/lib/expcalc/array_expansion.rb

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+class Array
+
+	def mean
+		return self.inject(0){|sum, n | sum + n}.fdiv(self.length)
+	end
+
+	def standard_deviation
+		x_mean = self.mean
+		variance = self.inject(0){|sum, n | sum + (n - x_mean)**2 }.fdiv(self.length)
+		return Math.sqrt(variance)
+	end
+
+	def get_quantiles(position=0.5)
+	  self.sort!
+	  n_items = self.size
+	  quantile_coor = n_items * position - 1
+	  if n_items % 2 == 0
+	    quantile_value = (self[quantile_coor.to_i] + self[quantile_coor.to_i + 1]).fdiv(2)   
+	  else
+	    quantile_value = self[quantile_coor.ceil]
+	  end
+	  return quantile_value
+	end
+end

data/lib/expcalc/nmatrix_expansion.rb

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+require 'nmatrix'
+require 'nmatrix/lapacke'
+require 'cmath'
+require 'time'
+require 'npy'
+#require 'pp'
+
+class NMatrix
+	def div(second_mat) #Matrix division A/B => A.dot(B.pinv) #https://stackoverflow.com/questions/49225693/matlab-matrix-division-into-python
+		return self.dot(second_mat.pinv)
+	end
+
+	def div_by_vector(vector, by=:col)
+		new_matrix =  NMatrix.zeros(self.shape, dtype: self.dtype)
+		if by == :col
+			self.cols.times do |n|
+				vector.each_with_indices do |val, i, j|
+					new_matrix[i, n] = self[i, n].fdiv(val)
+				end
+			end
+		elsif by == :row
+
+		end
+		return new_matrix
+	end
+
+	def frobenius_norm
+		fro = 0.0
+		self.each do |value|
+			fro += value.abs ** 2
+		end
+		return fro ** 0.5
+	end
+
+	def  max_norm #https://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.norm.html, ord parameter = 1
+		sums = self.abs.sum(1)
+		return sums.max[0, 0]
+	end
+
+	def vector_product(vec_b)
+		product = 0.0
+		self.each_with_indices do |val, i, j|
+			product += val * vec_b[i, j]
+		end
+		return product
+	end
+
+	def vector_self_product
+		product = 0.0
+		self.each_stored_with_indices do |val, i, j|
+			product +=  val ** 2
+		end
+		return product
+	end
+
+	def max_eigenvalue(n=100, error = 10e-12) # do not set error too low or the eigenvalue cannot stabilised around the real one
+		max_eigenvalue = 0.0
+		length = self.cols
+		v = NMatrix.random([self.cols, 1], dtype: self.dtype)
+		# http://web.mit.edu/18.06/www/Spring17/Power-Method.pdf 
+		#IMPLEMENTATION PROBLEM: RESULTS ARE TOO VARIABLE
+		last_max_eigenvalue = nil
+		n.times do
+			v = self.dot(v) # calculate the matrix-by-vector product Mv
+			v = v / v.frobenius_norm # calculate the norm and normalize the vector
+			max_eigenvalue = v.vector_product(self.dot(v)) / v.vector_self_product #Rayleigh quotient 
+			# Rayleigh quotient: lambda = vMv/vv
+			# v is a vector so vv is inner product of one vector with self (use vector_self_product); 
+			# Mv gives a vector, so vMv is the inner product of two different vectors (use vector_product)
+			break if !last_max_eigenvalue.nil? && last_max_eigenvalue - max_eigenvalue <= error
+			last_max_eigenvalue = max_eigenvalue
+		end
+		return max_eigenvalue
+	end
+
+	def min_eigenvalue(n=100, error = 10e-12)
+		return  self.invert.max_eigenvalue(n, error)
+	end
+
+	def expm
+		return compute_py_method{|mat| expm(mat)}
+		#return compute_py_method(self){|mat| expm(mat)}
+		##################################################
+		# matlab pade aproximation 
+		################################################
+		### toolbox/matlab/demos/expmdemo1.m (Golub and Van Loan, Matrix Computations, Algorithm 11.3-1.)		
+		
+		#fraction, exponent = Math.frexp(max_norm)
+		#s = [0, exponent+1].max
+		#a = self/2**s
+
+		## Pade approximation for exp(A)
+		#x = a
+		#c = 0.5
+		#ac = a*c
+		#e = NMatrix.identity(a.shape, dtype: a.dtype) + ac
+		#d = NMatrix.identity(a.shape, dtype: a.dtype) - ac
+		#q = 6
+		#p = true
+		#(2..q).each do |k|
+		#	c = c * (q-k+1) / (k*(2*q-k+1))
+		#	x = a.dot(x)
+		#	cX =  x * c
+		#	e = e + cX
+		#	if p
+		#		d = d + cX
+		#	else
+		#		d = d - cX
+		#	end
+		#	p = !p
+		#end
+		#e = d.solve(e) #solve
+
+		## Undo scaling by repeated squaring
+		#(1..s).each do
+		#	e = e.dot(e) 
+		#end
+		#return e
+
+		###################################
+		## Old python Pade aproximation
+		###################################
+		#### Pade aproximation: https://github.com/rngantner/Pade_PyCpp/blob/master/src/expm.py
+		#a_l1 = max_norm
+		#n_squarings = 0
+		#if self.dtype == :float64 || self.dtype == :complex128
+		#	if a_l1 < 1.495585217958292e-002
+		#		u,v = _pade3(self)
+	        #elsif a_l1 < 2.539398330063230e-001
+		#		u,v = _pade5(self)
+	        #elsif a_l1 < 9.504178996162932e-001
+		#		u,v = _pade7(self)
+	        #elsif a_l1 < 2.097847961257068e+000
+		#		u,v = _pade9(self)
+		#	else
+		#		maxnorm = 5.371920351148152
+		#		n_squarings = [0, Math.log2(a_l1 / maxnorm).ceil].max
+		#		mat = self / 2**n_squarings
+		#		u,v = _pade13(mat)
+		#	end
+		#elsif self.dtype == :float32 || self.dtype == :complex64
+		#	if a_l1 < 4.258730016922831e-001
+		#		u,v = _pade3(self)
+		#    elsif a_l1 < 1.880152677804762e+000
+		#		u,v = _pade5(self)
+		#	else
+		#		maxnorm = 3.925724783138660
+		#		n_squarings = [0, Math.log2(a_l1 / maxnorm).ceil].max
+		#		mat = self / 2**n_squarings
+		#		u,v = _pade7(mat)
+		#	end
+		#end
+		#p = u + v
+		#q = -u + v
+		#r = q.solve(p)
+		#n_squarings.times do
+		#	r = r.dot(r)
+		#end
+		#return r
+
+		######################
+		# Exact computing
+		######################
+		#####expm(matrix) = V*diag(exp(diag(D)))/V; V => eigenvectors(right), D => eigenvalues (right). # https://es.mathworks.com/help/matlab/ref/expm.html
+		#eigenvalues, eigenvectors = NMatrix::LAPACK.geev(self, :right)
+		#eigenvalues.map!{|val| Math.exp(val)}
+		#numerator = eigenvectors.dot(NMatrix.diagonal(eigenvalues, dtype: self.dtype))
+		#matrix_exp = numerator.div(eigenvectors)
+		#return matrix_exp
+	end 
+
+	def cosine_normalization
+		normalized_matrix =  NMatrix.zeros(self.shape, dtype: self.dtype)
+		#normalized_matrix =  NMatrix.zeros(self.shape, dtype: :complex64)
+		self.each_with_indices do |val, i, j|
+			norm = val/CMath.sqrt(self[i, i] * self[j,j])
+			#abort("#{norm} has non zero imaginary part" ) if norm.imag != 0
+			normalized_matrix[i, j] = norm#.real
+		end
+		return normalized_matrix
+	end
+	
+
+	private
+	def copy_array_like(ary1, ary2)
+		length = ary2.shape[0] #ruby nmatrix
+		length.times do |i|
+			length.times do |j|
+				ary2[i,j] = ary1[i,j] #python array
+			end
+		end
+	end
+
+	def compute_py_method
+		require 'pycall/import'
+		self.class.class_eval do # To include Pycall into NMatrix
+			include PyCall::Import
+		end
+		#Python
+		pyfrom 'scipy.linalg', import: :expm
+		pyimport :numpy, as: :np
+	
+		b = np.empty(self.shape)
+		STDERR.puts "Start cpy rb in py array #{Time.now}"		
+		copy_array_like(self, b)
+		STDERR.puts "Finish cpy rb in py array #{Time.now}"		
+		a = nil
+		STDERR.puts "Start computing #{Time.now}"		
+		PyCall.without_gvl do
+			a = yield(b) # Code block from ruby with python code
+			#a = expm(b)
+		end
+		##
+		STDERR.puts "Finish computing #{Time.now}"		
+
+		STDERR.puts "Start cpy py in rb array #{Time.now}"		
+		result_matrix =  NMatrix.zeros(self.shape, dtype: self.dtype)
+		copy_array_like(a, result_matrix)
+		STDERR.puts "Finish cpy py in rb array #{Time.now}"		
+		return result_matrix
+	end
+
+	def _pade3(a)
+		b = [120.0, 60.0, 12.0, 1.0]
+		a2 = a.dot(a)
+		ident = NMatrix.identity(a.shape, dtype: a.dtype)
+		u = a.dot(a2 * b[3] + ident * b[1])
+		v = a2 * b[2] + ident * b[0]
+		return u,v 
+	end
+
+	def _pade5(a)
+		b = [30240.0, 15120.0, 3360.0, 420.0, 30.0, 1.0]
+		a2 = a.dot(a)
+		a4 = a2.dot(a2)
+		ident = NMatrix.identity(a.shape, dtype: a.dtype)
+		u = a.dot(a4 * b[5] + a2 * b[3] + ident * b[1])
+		v = a4 * b[4] + a2 * b[2] + ident * b[0]
+		return u,v 
+	end
+
+	def _pade7(a)
+		b = [17297280.0, 8648640.0, 1995840.0, 277200.0, 25200.0, 1512.0, 56.0, 1.0]
+		a2 = a.dot(a)
+		a4 = a2.dot(a2)
+		a6 = a4.dot(a2)	
+		ident = NMatrix.identity(a.shape, dtype: a.dtype)
+		u = a.dot(a6 * b[7] + a4 * b[5] + a2 * b[3] + ident * b[1])
+		v = a6 * b[6] + a4 * b[4] + a2 * b[2] + ident * b[0]
+		return u,v 
+	end
+
+	def _pade9(a)
+		b = [17643225600.0, 8821612800.0, 2075673600.0, 302702400.0, 30270240.0,
+2162160.0, 110880.0, 3960.0, 90.0, 1.0]
+		a2 = a.dot(a)
+		a4 = a2.dot(a2)
+		a6 = a4.dot(a2)	
+		a8 = a6.dot(a2)	
+		ident = NMatrix.identity(a.shape, dtype: a.dtype)
+		u = a.dot(a8 * b[9] + a6 * b[7] + a4 * b[5] + a2 * b[3] + ident * b[1])
+		v = a8 * b[8] + a6 * b[6] + a4 * b[4] + a2 * b[2] + ident * b[0]
+		return u,v 
+	end
+
+	def _pade13(a)
+		b = [64764752532480000.0, 32382376266240000.0, 7771770303897600.0,
+			1187353796428800.0, 129060195264000.0, 10559470521600.0, 670442572800.0,
+			33522128640.0, 1323241920.0, 40840800.0, 960960.0, 16380.0, 182.0, 1.0]
+		a2 = a.dot(a)
+		a4 = a2.dot(a2)
+		a6 = a4.dot(a2)	
+		ident = NMatrix.identity(a.shape, dtype: a.dtype)
+		submat = a6 * b[13] + a4 * b[11] + a2 * b[9]
+		u = a.dot(a6.dot(submat) + a6 * b[7] + a4 * b[5] + a2 * b[3] + ident * b[1])
+		v = a6.dot(a6 * b[12] + a4 * b[10] + a2 * b[8] ) + a6 * b[6] + a4 * b[4] + a2 * b[2] + ident * b[0]
+		return u,v 
+	end
+end

data/lib/expcalc/numo_expansion.rb

@@ -0,0 +1,367 @@
+#require 'nmatrix'
+#require 'nmatrix/lapacke'
+require 'numo/narray'
+require 'numo/linalg'
+require 'cmath'
+require 'time'
+require 'npy'
+#require 'pp'
+
+# Tb meter leer matrices con npy
+class Hash
+	def get_hash_values_idx
+	  x_names_indx = {}
+	  i = 0
+	  self.each do |k, values|
+	    values.each do |val_id|
+	      query = x_names_indx[val_id]
+	      if query.nil?
+	        x_names_indx[val_id] = i
+	        i += 1
+	      end
+	    end
+	  end
+	  return x_names_indx
+	end
+
+	def to_bmatrix 
+	  x_names_indx = self.get_hash_values_idx
+	  y_names = self.keys
+	  x_names = x_names_indx.keys
+	   # row (y), cols (x)
+	  matrix = Numo::DFloat.zeros(self.length, x_names.length)
+	  i = 0
+	  self.each do |id, items|
+	    items.each do |item_id|
+	      matrix[i, x_names_indx[item_id]] = 1
+	    end
+	    i += 1
+	  end
+	  return matrix, y_names, x_names
+	end
+
+
+	# TODO: Only works if the resulting matrix will be squared. Replace implementacion taking into account to_bmatrix and its output
+	def to_wmatrix
+	  element_names = self.keys
+	  matrix = Numo::DFloat.zeros(element_names.length, element_names.length)
+	  i = 0
+	  self.each do |elementA, relations|
+	    element_names.each_with_index do |elementB, j|
+	      if elementA != elementB
+	        query = relations[elementB]
+	        if !query.nil?
+	          matrix[i, j] = query
+	        else
+	          matrix[i, j] = self[elementB][elementA]
+	        end
+	      end
+	    end
+	    i += 1
+	  end
+	  return matrix, element_names
+	end
+end
+
+module Numo
+	class NArray
+		# TODO: load and save must have exact coherence between load ouput and save input
+		# Take into acount https://github.com/ankane/npy to load and read mats it allows serialize matrices larger than ruby marshal format
+
+		def self.load(input_file, type='txt', splitChar="\t")
+			matrix = nil
+			if type == 'txt' 
+				counter = 0
+				File.open(input_file).each do |line|
+			    	line.chomp!
+		    		row = line.split(splitChar).map{|c| c.to_f }
+		    		if matrix.nil?
+		    			matrix = Numo::DFloat.zeros(row.length, row.length)
+		    		end
+		    		row.each_with_index do |val, i|
+		    			matrix[counter, i] = val if val != 0
+		    		end
+		    		counter += 1
+				end
+			elsif type == 'npy'
+				matrix = Npy.load(input_file)
+			end
+			return matrix
+		end
+
+		def save(matrix_filename, x_axis_names=nil, x_axis_file=nil, y_axis_names=nil, y_axis_file=nil)
+		  File.open(x_axis_file, 'w'){|f| f.print x_axis_names.join("\n") } if !x_axis_names.nil?
+		  File.open(y_axis_file, 'w'){|f| f.print y_axis_names.join("\n") } if !y_axis_names.nil?
+		  Npy.save(matrix_filename, self)
+		end
+
+
+		def div(second_mat) #Matrix division A/B => A.dot(B.pinv) #https://stackoverflow.com/questions/49225693/matlab-matrix-division-into-python
+			return self.dot(second_mat.pinv)
+		end
+
+		def div_by_vector(vector, by=:col)
+			new_matrix =  self.new_zeros
+			if by == :col
+				self.shape.last.times do |n|
+					vector.each_with_indices do |val, i, j|
+						new_matrix[i, n] = self[i, n].fdiv(val)
+					end
+				end
+			elsif by == :row
+
+			end
+			return new_matrix
+		end
+
+		def frobenius_norm
+			fro = 0.0
+			self.each do |value|
+				fro += value.abs ** 2
+			end
+			return fro ** 0.5
+		end
+
+		def  max_norm #https://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.norm.html, ord parameter = 1
+			sums = self.abs.sum(1)
+			return sums.max[0, 0]
+		end
+
+		def vector_product(vec_b)
+			product = 0.0
+			self.each_with_indices do |val, i, j|
+				product += val * vec_b[i, j]
+			end
+			return product
+		end
+
+		def vector_self_product
+			product = 0.0
+			self.each_stored_with_indices do |val, i, j|
+				product +=  val ** 2
+			end
+			return product
+		end
+
+		def max_eigenvalue(n=100, error = 10e-15) # do not set error too low or the eigenvalue cannot stabilised around the real one
+			max_eigenvalue = 0.0
+			length = self.shape.last
+			v = Numo::DFloat.new(length).rand
+			# http://web.mit.edu/18.06/www/Spring17/Power-Method.pdf 
+			last_max_eigenvalue = nil
+			n.times do
+				v = Numo::Linalg.dot(self, v) 
+				v = v / Numo::Linalg.norm(v) 
+				max_eigenvalue = Numo::Linalg.dot(v, Numo::Linalg.dot(self, v)) / Numo::Linalg.dot(v,v) #Rayleigh quotient
+				break if !last_max_eigenvalue.nil? && (last_max_eigenvalue - max_eigenvalue).abs <= error
+				last_max_eigenvalue = max_eigenvalue
+			end
+			return max_eigenvalue
+		end
+
+		def min_eigenvalue(n=100, error = 10e-12)
+			return  Numo::Linalg.inv(self).max_eigenvalue(n, error)
+		end
+
+		def expm
+			return compute_py_method{|mat| expm(mat)}
+			#return compute_py_method(self){|mat| expm(mat)}
+			##################################################
+			# matlab pade aproximation 
+			################################################
+			### toolbox/matlab/demos/expmdemo1.m (Golub and Van Loan, Matrix Computations, Algorithm 11.3-1.)		
+			
+			#fraction, exponent = Math.frexp(max_norm)
+			#s = [0, exponent+1].max
+			#a = self/2**s
+
+			## Pade approximation for exp(A)
+			#x = a
+			#c = 0.5
+			#ac = a*c
+			#e = NMatrix.identity(a.shape, dtype: a.dtype) + ac
+			#d = NMatrix.identity(a.shape, dtype: a.dtype) - ac
+			#q = 6
+			#p = true
+			#(2..q).each do |k|
+			#	c = c * (q-k+1) / (k*(2*q-k+1))
+			#	x = a.dot(x)
+			#	cX =  x * c
+			#	e = e + cX
+			#	if p
+			#		d = d + cX
+			#	else
+			#		d = d - cX
+			#	end
+			#	p = !p
+			#end
+			#e = d.solve(e) #solve
+
+			## Undo scaling by repeated squaring
+			#(1..s).each do
+			#	e = e.dot(e) 
+			#end
+			#return e
+
+			###################################
+			## Old python Pade aproximation
+			###################################
+			#### Pade aproximation: https://github.com/rngantner/Pade_PyCpp/blob/master/src/expm.py
+			#a_l1 = max_norm
+			#n_squarings = 0
+			#if self.dtype == :float64 || self.dtype == :complex128
+			#	if a_l1 < 1.495585217958292e-002
+			#		u,v = _pade3(self)
+		        #elsif a_l1 < 2.539398330063230e-001
+			#		u,v = _pade5(self)
+		        #elsif a_l1 < 9.504178996162932e-001
+			#		u,v = _pade7(self)
+		        #elsif a_l1 < 2.097847961257068e+000
+			#		u,v = _pade9(self)
+			#	else
+			#		maxnorm = 5.371920351148152
+			#		n_squarings = [0, Math.log2(a_l1 / maxnorm).ceil].max
+			#		mat = self / 2**n_squarings
+			#		u,v = _pade13(mat)
+			#	end
+			#elsif self.dtype == :float32 || self.dtype == :complex64
+			#	if a_l1 < 4.258730016922831e-001
+			#		u,v = _pade3(self)
+			#    elsif a_l1 < 1.880152677804762e+000
+			#		u,v = _pade5(self)
+			#	else
+			#		maxnorm = 3.925724783138660
+			#		n_squarings = [0, Math.log2(a_l1 / maxnorm).ceil].max
+			#		mat = self / 2**n_squarings
+			#		u,v = _pade7(mat)
+			#	end
+			#end
+			#p = u + v
+			#q = -u + v
+			#r = q.solve(p)
+			#n_squarings.times do
+			#	r = r.dot(r)
+			#end
+			#return r
+
+			######################
+			# Exact computing
+			######################
+			#####expm(matrix) = V*diag(exp(diag(D)))/V; V => eigenvectors(right), D => eigenvalues (right). # https://es.mathworks.com/help/matlab/ref/expm.html
+			#eigenvalues, eigenvectors = NMatrix::LAPACK.geev(self, :right)
+			#eigenvalues.map!{|val| Math.exp(val)}
+			#numerator = eigenvectors.dot(NMatrix.diagonal(eigenvalues, dtype: self.dtype))
+			#matrix_exp = numerator.div(eigenvectors)
+			#return matrix_exp
+		end 
+
+		def cosine_normalization
+			normalized_matrix =  NMatrix.zeros(self.shape, dtype: self.dtype)
+			#normalized_matrix =  NMatrix.zeros(self.shape, dtype: :complex64)
+			self.each_with_indices do |val, i, j|
+				norm = val/CMath.sqrt(self[i, i] * self[j,j])
+				#abort("#{norm} has non zero imaginary part" ) if norm.imag != 0
+				normalized_matrix[i, j] = norm#.real
+			end
+			return normalized_matrix
+		end
+		
+
+		private
+		def copy_array_like(ary1, ary2)
+			length = ary2.shape[0] #ruby numo::array
+			length.times do |i|
+				length.times do |j|
+					ary2[i,j] = ary1[i,j] #python array
+				end
+			end
+		end
+
+		def compute_py_method
+			require 'pycall/import'
+			self.class.class_eval do # To include Pycall into Numo::array
+				include PyCall::Import
+			end
+			#Python
+			pyfrom 'scipy.linalg', import: :expm
+			pyimport :numpy, as: :np
+		
+			b = np.empty(self.shape)
+			start = Time.now
+			copy_array_like(self, b)
+			STDERR.puts "Time cpy rb in py array #{(Time.now - start)/60}"		
+
+			a = nil
+			start = Time.now
+			PyCall.without_gvl do
+				a = yield(b) # Code block from ruby with python code
+				#a = expm(b)
+			end
+			##
+			STDERR.puts "Time computing #{(Time.now - start)/60}"		
+
+			start = Time.now
+			result_matrix =  self.new_zeros
+			copy_array_like(a, result_matrix)
+			STDERR.puts "Time cpy py in rb array #{(Time.now - start)/60}"
+			return result_matrix
+		end
+
+		def _pade3(a)
+			b = [120.0, 60.0, 12.0, 1.0]
+			a2 = a.dot(a)
+			ident = NMatrix.identity(a.shape, dtype: a.dtype)
+			u = a.dot(a2 * b[3] + ident * b[1])
+			v = a2 * b[2] + ident * b[0]
+			return u,v 
+		end
+
+		def _pade5(a)
+			b = [30240.0, 15120.0, 3360.0, 420.0, 30.0, 1.0]
+			a2 = a.dot(a)
+			a4 = a2.dot(a2)
+			ident = NMatrix.identity(a.shape, dtype: a.dtype)
+			u = a.dot(a4 * b[5] + a2 * b[3] + ident * b[1])
+			v = a4 * b[4] + a2 * b[2] + ident * b[0]
+			return u,v 
+		end
+
+		def _pade7(a)
+			b = [17297280.0, 8648640.0, 1995840.0, 277200.0, 25200.0, 1512.0, 56.0, 1.0]
+			a2 = a.dot(a)
+			a4 = a2.dot(a2)
+			a6 = a4.dot(a2)	
+			ident = NMatrix.identity(a.shape, dtype: a.dtype)
+			u = a.dot(a6 * b[7] + a4 * b[5] + a2 * b[3] + ident * b[1])
+			v = a6 * b[6] + a4 * b[4] + a2 * b[2] + ident * b[0]
+			return u,v 
+		end
+
+		def _pade9(a)
+			b = [17643225600.0, 8821612800.0, 2075673600.0, 302702400.0, 30270240.0,
+	2162160.0, 110880.0, 3960.0, 90.0, 1.0]
+			a2 = a.dot(a)
+			a4 = a2.dot(a2)
+			a6 = a4.dot(a2)	
+			a8 = a6.dot(a2)	
+			ident = NMatrix.identity(a.shape, dtype: a.dtype)
+			u = a.dot(a8 * b[9] + a6 * b[7] + a4 * b[5] + a2 * b[3] + ident * b[1])
+			v = a8 * b[8] + a6 * b[6] + a4 * b[4] + a2 * b[2] + ident * b[0]
+			return u,v 
+		end
+
+		def _pade13(a)
+			b = [64764752532480000.0, 32382376266240000.0, 7771770303897600.0,
+				1187353796428800.0, 129060195264000.0, 10559470521600.0, 670442572800.0,
+				33522128640.0, 1323241920.0, 40840800.0, 960960.0, 16380.0, 182.0, 1.0]
+			a2 = a.dot(a)
+			a4 = a2.dot(a2)
+			a6 = a4.dot(a2)	
+			ident = NMatrix.identity(a.shape, dtype: a.dtype)
+			submat = a6 * b[13] + a4 * b[11] + a2 * b[9]
+			u = a.dot(a6.dot(submat) + a6 * b[7] + a4 * b[5] + a2 * b[3] + ident * b[1])
+			v = a6.dot(a6 * b[12] + a4 * b[10] + a2 * b[8] ) + a6 * b[6] + a4 * b[4] + a2 * b[2] + ident * b[0]
+			return u,v 
+		end
+	end
+end

data/lib/expcalc/pvalue_expansion.rb

@@ -0,0 +1,153 @@
+# TODO: Make a pull request to https://rubygems.org/gems/ruby-statistics, with all the statistic code implemented here.
+#to cmpute fisher exact test
+#Fisher => http://www.biostathandbook.com/fishers.html
+# TODO:NetAnalyzer when performs hyper simple metric use Rubystats::FishersExactTest, compare results and mody implementation.
+def get_fisher_exact_test(listA, listB, all_elements_count, tail ='two_sided', weigths=nil, partial_weigths=true)
+	#puts '-', listA.inspect, listB.inspect, '-'
+	listA_listB = listA & listB
+	listA_nolistB = listA - listB
+	nolistA_listB = listB - listA
+	if weigths.nil?
+		listA_listB_count = listA_listB.length
+		listA_nolistB_count = listA_nolistB.length
+		nolistA_listB_count = nolistA_listB.length
+		nolistA_nolistB_count = all_elements_count - (listA | listB).length
+	else
+		# Fisher exact test weigthed as proposed in Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
+		# https://academic.oup.com/bioinformatics/article/22/13/1600/193669
+		listA_listB_count = listA_listB.map{|i| weigths[i]}.inject(0){|sum, n| sum + n}.ceil
+		listA_nolistB_count = listA_nolistB.map{|i| weigths[i]}.inject(0){|sum, n| sum + n}.ceil
+		nolistA_listB_count = nolistA_listB.map{|i| weigths[i]}.inject(0){|sum, n| sum + n}.ceil
+
+		if partial_weigths
+			nolistA_nolistB_count = all_elements_count - (listA | listB).length
+			all_elements_count = nolistA_nolistB_count + listA_listB_count + listA_nolistB_count + nolistA_listB_count
+		else
+			nolistA_nolistB_count = (weigths.keys - (listA | listB)).map{|i| weigths[i]}.inject(0){|sum, n| sum + n}.ceil
+			all_elements_count = weigths.values.inject(0){|sum, n| sum + n}.ceil
+		end
+	end
+	#puts [listA_listB_count, listA_nolistB_count, nolistA_listB_count, nolistA_nolistB_count, all_elements_count].inspect
+	if tail == 'two_sided'
+		accumulated_prob = get_two_tail(listA_listB_count, listA_nolistB_count, nolistA_listB_count, nolistA_nolistB_count, all_elements_count)
+	elsif tail == 'less' 
+		accumulated_prob = get_less_tail(listA_listB_count, listA_nolistB_count, nolistA_listB_count, nolistA_nolistB_count, all_elements_count)
+	end
+	return accumulated_prob
+end
+
+def get_two_tail(listA_listB_count, listA_nolistB_count, nolistA_listB_count, nolistA_nolistB_count, all_elements_count)
+	#https://www.sheffield.ac.uk/polopoly_fs/1.43998!/file/tutorial-9-fishers.pdf
+	accumulated_prob = 0
+	ref_prob = compute_hyper_prob(
+		listA_listB_count, 
+		listA_nolistB_count, 
+		nolistA_listB_count, 
+		nolistA_nolistB_count, 
+		all_elements_count
+	)
+	accumulated_prob += ref_prob
+	[listA_listB_count, nolistA_nolistB_count].min.times do |n| #less
+		n += 1
+		prob = compute_hyper_prob(
+			listA_listB_count - n, 
+			listA_nolistB_count + n, 
+			nolistA_listB_count + n, 
+			nolistA_nolistB_count - n, 
+			all_elements_count
+		)
+		prob <= ref_prob ? accumulated_prob += prob : break
+	end
+
+	[listA_nolistB_count, nolistA_listB_count].min.times do |n| #greater
+		n += 1
+		prob = compute_hyper_prob(
+			listA_listB_count + n, 
+			listA_nolistB_count - n, 
+			nolistA_listB_count - n, 
+			nolistA_nolistB_count + n, 
+			all_elements_count
+		)
+		accumulated_prob += prob if prob <= ref_prob
+	end
+
+	return accumulated_prob
+end
+
+def get_less_tail(listA_listB_count, listA_nolistB_count, nolistA_listB_count, nolistA_nolistB_count, all_elements_count)
+	accumulated_prob = 0
+	[listA_listB_count, nolistA_nolistB_count].min.times do |n|
+		accumulated_prob += compute_hyper_prob(
+			listA_listB_count - n, 
+			listA_nolistB_count + n, 
+			nolistA_listB_count + n, 
+			nolistA_nolistB_count - n, 
+			all_elements_count
+		)
+	end
+	return accumulated_prob
+end
+
+def compute_hyper_prob(a, b, c, d, n)
+	# https://en.wikipedia.org/wiki/Fisher%27s_exact_test
+	binomA = binom(a + b, a)
+	binomC = binom(c + d, c)
+	divisor = binom(n, a + c)
+	return (binomA * binomC).fdiv(divisor)
+end
+
+def binom(n,k)
+	if k > 0 && k < n
+		res = (1+n-k..n).inject(:*)/(1..k).inject(:*)
+	else
+		res = 1
+	end
+end
+
+#to cmpute adjusted pvalues
+#https://rosettacode.org/wiki/P-value_correction#Ruby
+def get_benjaminiHochberg_pvalues(arr_pvalues)
+	n = arr_pvalues.length
+	arr_o = order(arr_pvalues, true)
+	arr_cummin_input = []
+	(0..(n - 1)).each do |i|
+		arr_cummin_input[i] = (n / (n - i).to_f) * arr_pvalues[arr_o[i]]
+	end
+	arr_ro = order(arr_o)
+	arr_cummin = cummin(arr_cummin_input)
+	arr_pmin = pmin(arr_cummin)
+	return arr_pmin.values_at(*arr_ro)
+end
+
+def order(array, decreasing = false)
+	if decreasing == false
+		array.sort.map { |n| array.index(n) }
+	else
+		array.sort.map { |n| array.index(n) }.reverse
+	end
+end
+
+def cummin(array)
+	cumulative_min = array.first
+	arr_cummin = []
+	array.each do |p|
+		cumulative_min = [p, cumulative_min].min
+		arr_cummin << cumulative_min
+	end
+	return arr_cummin
+end
+
+def pmin(array)
+	x = 1
+	pmin_array = []
+	array.each_index do |i|
+		pmin_array[i] = [array[i], x].min
+		abort if pmin_array[i] > 1
+	end
+	return pmin_array
+end
+
+
+class Pvalue
+
+end

data/lib/expcalc/version.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+module Expcalc
+  VERSION = "0.1.1"
+end

data/lib/expcalc.rb

@@ -0,0 +1,11 @@
+# frozen_string_literal: true
+
+require_relative "expcalc/version"
+require_relative "expcalc/numo_expansion"
+require_relative "expcalc/array_expansion"
+require_relative "expcalc/pvalue_expansion"
+
+module Expcalc
+  class Error < StandardError; end
+  # Your code goes here...
+end

metadata

@@ -0,0 +1,150 @@
+--- !ruby/object:Gem::Specification
+name: expcalc
+version: !ruby/object:Gem::Version
+  version: 0.1.1
+platform: ruby
+authors:
+- seoanezonjic
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2022-02-17 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: cmath
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+- !ruby/object:Gem::Dependency
+  name: numo-linalg
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.5
+- !ruby/object:Gem::Dependency
+  name: numo-narray
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.9.1.9
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.9.1.9
+- !ruby/object:Gem::Dependency
+  name: pp
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+- !ruby/object:Gem::Dependency
+  name: pycall
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.3.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.3.1
+- !ruby/object:Gem::Dependency
+  name: npy
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+description: To expand ruby math operations this gem call to others such as Numo:narray
+  and others and implements methods onto them to deal with our needs
+email:
+- seoanezonjic@hotmail.com
+executables:
+- console
+- setup
+extensions: []
+extra_rdoc_files: []
+files:
+- ".github/workflows/main.yml"
+- ".gitignore"
+- ".rspec"
+- ".rubocop.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- expcalc.gemspec
+- lib/expcalc.rb
+- lib/expcalc/array_expansion.rb
+- lib/expcalc/nmatrix_expansion.rb
+- lib/expcalc/numo_expansion.rb
+- lib/expcalc/pvalue_expansion.rb
+- lib/expcalc/version.rb
+homepage: https://github.com/seoanezonjic/expcalc
+licenses:
+- MIT
+metadata:
+  homepage_uri: https://github.com/seoanezonjic/expcalc
+  source_code_uri: https://github.com/seoanezonjic/expcalc
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.4.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.2.15
+signing_key:
+specification_version: 4
+summary: Gem to expand ruby math capabilities
+test_files: []