bioroebe 0.10.80

data/lib/bioroebe/electron_microscopy/fix_pos_file.rb

@@ -0,0 +1,102 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::ElectronMicroscopy::FixPosFile
+#
+# This class will attempt to fix a .pos file.
+# =========================================================================== #
+# 'bioroebe/fix_pos_file.rb'
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+module ElectronMicroscopy
+
+class FixPosFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::FixPosFile
+
+  require 'bioroebe/electron_microscopy/parse_coordinates.rb'
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      fix_this_pos_file = nil,
+      run_already       = true
+    )
+    reset
+    set_fix_this_pos_file(
+      fix_this_pos_file
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    super()
+    set_fix_this_pos_file
+    # ======================================================================= #
+    # === @namespace
+    # ======================================================================= #
+    @namespace = NAMESPACE
+  end
+
+  # ========================================================================= #
+  # === set_fix_this_pos_file
+  # ========================================================================= #
+  def set_fix_this_pos_file(i = nil)
+    @fix_this_pos_file = i
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    if File.exist? @fix_this_pos_file
+      dataset = File.read(@fix_this_pos_file)
+      unless dataset.include? '_pickingMicrographState' # In this case we assume it to be incorrect.
+        parse_coordinates = ParseCoordinates.new(@fix_this_pos_file)
+        _ = '# XMIPP_STAR_1 *
+#
+data_header
+loop_
+ _pickingMicrographState
+ _autopickPercent
+ _cost
+Manual         50     0.000000
+data_particles
+loop_
+ _xcoor
+ _ycoor'+N
+        coordinates = parse_coordinates.coordinates?
+        # If we wish to sort this dataset, we can do, but this did lead
+        # to an error:
+        # coordinates.sort_by! {|x_axis, y_axis|
+        #   x_axis.to_i 
+        # }
+        coordinates.each {|x_axis, y_axis|
+          _ << '    '+x_axis.to_s.rjust(6)+'     '+y_axis.to_s.rjust(6)+N
+        }
+      end
+      new_file = File.dirname(@fix_this_pos_file)+
+                '/fixed_coordinates_'+File.basename(@fix_this_pos_file)
+      opnn; e 'Now storing new dataset into '+sfile(new_file)+'.'
+      write_what_into(_, new_file)
+    else
+      opnn; no_file_exists_at(@fix_this_pos_file)
+    end
+  end
+
+end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::ElectronMicroscopy::FixPosFile.new(ARGV)
+end

data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb

@@ -0,0 +1,122 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# ============================================================================= #
+# === Bioroebe::ElectronMicroscopy::GenerateEm2emFile
+#
+# This class can generate a _em2em.dff file.
+# ============================================================================= #
+# require 'bioroebe/electron_microscopy/generate_em2em_file.rb'
+# ============================================================================= #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+module ElectronMicroscopy
+
+class GenerateEm2emFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::GenerateEm2emFile
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === NAME_OF_NEW_FILE
+  # ========================================================================= #
+  NAME_OF_NEW_FILE = '_em2em.dff'
+
+  # ========================================================================= #
+  # === initialize
+  #
+  # We require a .tif as input file.
+  # 
+  # To invoke this class, do:
+  #
+  #   gen2 1_36kx_01.tif
+  #   gen2 1_36kx_02.tif
+  #   gen2 1_36kx_03.tif
+  #
+  # ========================================================================= #
+  def initialize(
+      name_of_input_tif_file = '1_36kx_02.tif',
+      run_already            = true
+    )
+    reset
+    set_tif_file(
+      name_of_input_tif_file
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @namespace
+    # ======================================================================= #
+    @namespace = NAMESPACE
+    # ======================================================================= #
+    # === @name_of_new_file
+    # ======================================================================= #
+    @name_of_new_file = NAME_OF_NEW_FILE
+  end
+
+  # ========================================================================= #
+  # === set_tif_file
+  # ========================================================================= #
+  def set_tif_file(i)
+    if i.is_a? Array
+      i = i.first
+    end
+    i = i.to_s
+    @tif_file = i
+  end
+
+  # ========================================================================= #
+  # === save_dataset
+  # ========================================================================= #
+  def save_dataset
+    write_what_into(@_, @name_of_new_file)
+  end
+
+  # ========================================================================= #
+  # === setup_dataset
+  #
+  # Fill up the ivar @_.
+  # ========================================================================= #
+  def setup_dataset
+    @_ = 
+'INP_2D_OR_3D:  2D
+FORMAT_INP:  TIFF
+FORMAT_OUT:  MRC
+IMPORT_2D_NO_EXTENSION:
+OUTPUT_2D_INPUT_TYPE:  STACK_OF_IMAGES
+OUTPUT_2D_SET_ROOTNAME:
+ASK_SCALE_DENS:  YES
+KEEP_TYPE:  RETAIN_TYPE
+SINGLE_LOC_EXP_2D:  SINGLE_IMAGE_FILE
+IMPORT_A_2D_SET:  NO
+IMPORT_ONE_2D_WITH_EXT_TIFF:  '+@tif_file+'
+OUTPUT_SINGLE_2D_WITH_EXTENSION:  '+
+  @tif_file.gsub(/#{File.extname(@tif_file)}/,'')+'.mrc
+REVERSE_WANTED:  YES
+NAME_OPTION_SINGLE:  NAME_OF_IMPORT_FILE'
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    setup_dataset
+    opnn; e "Next generating file `#{sfile(@name_of_new_file)}`."
+    save_dataset
+  end
+
+end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::ElectronMicroscopy::GenerateEm2emFile.new(ARGV)
+end # em2

data/lib/bioroebe/electron_microscopy/parse_coordinates.rb

@@ -0,0 +1,197 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# ========================================================================= #
+# === Bioroebe::ElectronMicroscopy::ParseCoordinates
+#
+# This class will parse a coordinate files.
+#
+# Usage example:
+#
+#   Bioroebe::ElectronMicroscopy/ParseCoordinates.new
+#
+# ========================================================================= #
+# require 'bioroebe/electron_microscopy/parse_coordinates.rb'
+# ========================================================================= #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+module ElectronMicroscopy
+
+class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::ParseCoordinates.new
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === DEFAULT_FILE
+  # ========================================================================= #
+  DEFAULT_FILE = 'test_coordinates.pos'
+
+  # ========================================================================= #
+  # === DEFAULT_RUN_MODE
+  # ========================================================================= #
+  DEFAULT_RUN_MODE = true
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      i           = nil,
+      run_already = DEFAULT_RUN_MODE
+    )
+    reset
+    set_file(i)
+    case run_already
+    when :be_quiet
+      be_silent
+      run_already = DEFAULT_RUN_MODE
+    end
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @namespace
+    # ======================================================================= #
+    @namespace = NAMESPACE
+    # ======================================================================= #
+    # === @dataset
+    # ======================================================================= #
+    @dataset = nil
+    # ======================================================================= #
+    # === @be_verbose
+    # ======================================================================= #
+    @be_verbose = true
+    clear_coordinates
+  end
+
+  # ========================================================================= #
+  # === dataset?
+  # ========================================================================= #
+  def dataset?
+    @dataset
+  end; alias dataset dataset? # === dataset
+
+  # ========================================================================= #
+  # === set_file
+  # ========================================================================= #
+  def set_file(
+      i = DEFAULT_FILE
+    )
+    i = i.first if i.is_a? Array
+    i = DEFAULT_FILE if i.nil?
+    i = i.to_s.dup
+    if be_verbose?
+      opnn; e "Next assigning to the file #{sfile(i)}."
+    end
+    @file = i
+  end
+
+  # ========================================================================= #
+  # === parse_x_y_coordinate
+  #
+  # This method will parse x/y coordinates.
+  # ========================================================================= #
+  def parse_x_y_coordinate(line)
+    line = line.split('  ').map(&:strip)
+    line.reject!(&:empty?)
+    x = line[0]
+    y = line[1]
+    return [x,y]
+  end
+
+  # ========================================================================= #
+  # === grab_dataset
+  # ========================================================================= #
+  def grab_dataset(
+      use_this_file = file?
+    )
+    if File.exist? use_this_file
+      @dataset = File.readlines(use_this_file).map(&:strip)
+    else
+      no_file_exists_at(use_this_file)
+    end
+  end
+
+  # ========================================================================== #
+  # === file?
+  # ========================================================================== #
+  def file?
+    @file
+  end
+
+  # ========================================================================= #
+  # === no_file?
+  # ========================================================================= #
+  def no_file?(
+      i = file?
+    )
+    !File.exist?(i)
+  end
+
+  # ========================================================================= #
+  # === report_stats
+  # ========================================================================= #
+  def report_stats
+    _ = file?
+    if no_file?
+      opnn; e 'No statistics can be reported because there is'
+      opnn; e 'no file at `'+sfile(_)+'`.'
+    else
+      opnn; e "We have #{sfancy(@array_coordinates.size.to_s)} "\
+              "coordinates in #{sfile(_)}."
+    end
+  end
+
+  # ========================================================================= #
+  # === clear_coordinates
+  # ========================================================================= #
+  def clear_coordinates
+    @array_coordinates = []
+  end
+
+  # ========================================================================= #
+  # === determine_coordinates
+  # ========================================================================= # 
+  def determine_coordinates
+    clear_coordinates
+    @dataset.each {|line|
+      next unless line.include? '   '
+      coordinates = parse_x_y_coordinate(line)
+      @array_coordinates << coordinates
+    } if @dataset
+    # @array_coordinates.sort!
+    # For some reason, sorting this dataset is not working for xmipp.
+  end
+
+  # ========================================================================= #
+  # === coordinates?
+  #
+  # Return the coordinates.
+  # ========================================================================= #
+  def coordinates?
+    @array_coordinates
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    grab_dataset
+    determine_coordinates
+    report_stats # Show some information about our dataset in question.
+  end
+
+end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::ElectronMicroscopy::ParseCoordinates.new(ARGV)
+end # parsecoordinates

data/lib/bioroebe/electron_microscopy/read_file_xmd.rb

@@ -0,0 +1,282 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === ElectronMicroscopy::ReadFileXMD
+#
+# This class will read in a single .xmd file. The other file called
+# 'read_all_xmd_files.rb' will read it all .xmd files, respectively.
+#
+# If you need to batch-process several .xmd files, then you will have
+# to run a loop yourself.
+#
+# We will have the body and the header available for every .xmd file.
+# =========================================================================== #
+# require '/home/kumar/Robert/electron_microscopy/read_file_xmd.rb'
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+module ElectronMicroscopy
+
+class ReadFileXMD < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::ReadFileXMD
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === initialize
+  #
+  # The first argument passed to this class here should be the .xmd file
+  # in question.
+  # ========================================================================= #
+  def initialize(
+      this_xmd_file = nil,
+      run_already   = true
+    )
+    reset # Set to default.
+    set_this_xmd_file(this_xmd_file)
+    case run_already
+    when :dont_run_yet
+      run_already = false
+    end
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @namespace
+    # ======================================================================= #
+    @namespace = NAMESPACE
+    # ======================================================================= #
+    # === @header
+    # ======================================================================= #
+    @header = nil
+    # ======================================================================= #
+    # === @body
+    # ======================================================================= #
+    @body   = nil
+    set_be_verbose
+    # ======================================================================= #
+    # === @dataset
+    # ======================================================================= #
+    @dataset = nil
+    set_prepend_this_to_the_mrc_file_path
+  end
+
+  # ========================================================================= #
+  # === _
+  # ========================================================================= #
+  def _
+    @this_xmd_file
+  end
+
+  # ========================================================================= #
+  # === set_this_xmd_file
+  # ========================================================================= #
+  def set_this_xmd_file(i)
+    i = i.first if i.is_a? Array
+    i = i.to_s
+    @this_xmd_file = i
+    # Next, check if the file exists:
+    if File.exist? @this_xmd_file
+      @dataset = File.readlines(@this_xmd_file)
+    else
+      unless @this_xmd_file.empty?
+        opn; e 'The file at '+sfile(_)+' does not exist.'
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === this_xmd_file?
+  # ========================================================================= #
+  def this_xmd_file?
+    @this_xmd_file
+  end; alias this_xmd_file this_xmd_file? # === this_xmd_file
+
+  # ========================================================================= #
+  # === try_to_determine_the_header
+  # ========================================================================= #
+  def try_to_determine_the_header
+    if @dataset
+      @header = @dataset[0,9]
+      sanitize_header
+    end
+  end
+
+  # ========================================================================= #
+  # === try_to_determine_the_body
+  # ========================================================================= #
+  def try_to_determine_the_body
+    if @dataset
+      @body = @dataset[9..-1] # Should be an Array.
+    end
+  end
+
+  # ========================================================================= #
+  # === header?
+  # ========================================================================= #
+  def header?
+    @header
+  end; alias header header? # === header
+
+  # ========================================================================= #
+  # === file?
+  #
+  # This gives us colourized output.
+  # ========================================================================= #
+  def file?
+    sfile(_)
+  end
+
+  # ========================================================================= #
+  # === report_what_we_will_do
+  # ========================================================================= #
+  def report_what_we_will_do
+    if be_verbose?
+      opnn; e "We will next read in the data from the file #{file?}"
+    end
+  end
+
+  # ========================================================================= #
+  # === body?
+  #
+  # The body of the .xmd file.
+  # ========================================================================= #
+  def body?
+    @body
+  end; alias body body? # === body
+
+  # ========================================================================= #
+  # === sanitize_body
+  #
+  # This method will do two things:
+  #
+  #   (1) It will chop off the trailing 1 (if it can be found)
+  #   (2) It will chop off the leading string that includes the
+  #       @ character.
+  #   (3) It will eliminate an existing trailing newlines, and
+  #       then .strip on the result.
+  #   (4) It will also replace the relative path to the .stk file
+  #       with an absolute path. (This is experimental for now)
+  #
+  # ========================================================================= #
+  def sanitize_body
+    # ======================================================================= #
+    # @body is an Array.
+    # ======================================================================= #
+    @body.map! {|entry|
+      entry = entry.dup if entry.frozen?
+      entry.chomp!
+      entry = entry[(entry.index('@')+1)..-1] if entry.include? '@'
+      entry.strip!
+      entry.chop! if entry.end_with? '1'
+      # ===================================================================== #
+      # Next, we modify the path to the .mrc file in question.
+      # The line may look like so: "1_36kx_15.stk ./1_36kx_15.mrc"
+      # ===================================================================== #
+      if entry.include? '.mrc'
+        entry.sub!(/\.\/(.+\.mrc)/,
+          @prepend_this_to_the_mrc_file_path+'\\1')
+      end
+      # ===================================================================== #
+      # if entry.include?('.stk') and ! entry.start_with?('/home')
+      #   entry[0,0] = '/home/kumar/Robert/'
+      # end
+      # ===================================================================== #
+      entry.strip!
+      entry
+    } if @body
+  end
+
+  # ========================================================================= #
+  # === set_prepend_this_to_the_mrc_file_path
+  # ========================================================================= #
+  def set_prepend_this_to_the_mrc_file_path(i = '')
+    i = i.to_s.dup
+    @prepend_this_to_the_mrc_file_path = i
+  end; alias set_path_to_mrc_file set_prepend_this_to_the_mrc_file_path # === set_path_to_mrc_file
+
+  # ========================================================================= #
+  # === body?
+  # ========================================================================= #
+  def body?
+    @body
+  end
+
+  # ========================================================================= #
+  # === sanitize_header
+  #
+  # Next we will sanitize the @header variable.
+  # ========================================================================= #
+  def sanitize_header(i = @header)
+    if i.is_a? String
+      i = i.split(N)
+    end
+    i[3..-1] = '
+_rlnImageName #1
+_rlnMicrographName #2
+_rlnCoordinateX #3
+_rlnCoordinateY #4
+'
+    @header = i
+    return i
+  end
+
+  # ========================================================================= #
+  # === show_body
+  # ========================================================================= #
+  def show_body
+    pp body?
+  end
+
+  # ========================================================================= #
+  # === report                                                   (report tag)
+  # ========================================================================= #
+  def report
+    opnn; e 'The header subsection of this .xmd file is:'
+    pp @header
+    if @body
+      opnn; e 'The body subsection has '+@body.size.to_s+' entries.'
+    else
+      opnn; e 'No body has been found. Has a .xmd file been '\
+              'passed to this class?'
+    end
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    report_what_we_will_do
+    try_to_determine_the_header
+    try_to_determine_the_body
+    sanitize_body
+  end
+
+  # ========================================================================= #
+  # === ReadFileXMD.sanitize_header
+  #
+  # Pass an array to us here.
+  # ========================================================================= #
+  def self.sanitize_header(i)
+    _ = new(nil, :dont_run_yet)
+    result = _.sanitize_header(i)
+    return result
+  end
+
+end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  _ = Bioroebe::ElectronMicroscopy::ReadFileXMD.new(ARGV)
+  _.report
+  _.show_body
+end # readxmd