Class: Mspire::Imzml::Writer
- Inherits:
-
Object
- Object
- Mspire::Imzml::Writer
- Defined in:
- lib/mspire/imzml/writer.rb,
lib/mspire/imzml/writer/commandline.rb
Defined Under Namespace
Modules: Commandline
Constant Summary collapse
- DEFAULTS =
{ mz_data_type: :float, mz_precision: 64, intensity_data_type: :float, intensity_precision: 32, }
Instance Method Summary collapse
- #create_file_description(source_files, config) ⇒ Object
- #create_referenceable_params_by_id_hash ⇒ Object
- #experiment_hash_to_cvs(hash) ⇒ Object
-
#image_hash_to_cvs(hash) ⇒ Object
converts image related hash values to an array of loose describe! params.
-
#write(mzml_filenames, config = {}) ⇒ Object
mzml_filenames can each be a partial or relative path by default the file will write to the same directory and basename.
-
#write_binary(filename, spectra_iterator, config) ⇒ Object
returns an array of DataArrayInfo pairs.
-
#write_data_array(fh, values, dtype = :float, precision = 32) ⇒ Object
Integer values (dtype=:int) may be stored with precision = 8, 16, 32, 64 .
-
#x_y_positions(config) ⇒ Object
returns an array with x, y pairs in the correct order accounts for scan_pattern, scan_type, linescan_direction, linescan_sequence and shots_per_position.
Instance Method Details
#create_file_description(source_files, config) ⇒ Object
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# File 'lib/mspire/imzml/writer.rb', line 216 def create_file_description(source_files, config) Mspire::Mzml::FileDescription.new do |fd| fd.file_content = Mspire::Mzml::FileContent.new.describe_many!( [ 'MS:1000579', # MS1 Spectrum config[:profile] ? 'MS:1000128' : 'MS:1000127', ['IMS:1000080', "{"+config[:uuid_hyphenated]+"}"], ['IMS:1000091', config[:ibd_sha1]], (config[:data_structure] == :processed) ? 'IMS:1000031' : 'IMS:1000030', ] ) fd.source_files.replace(source_files) if [:name, :organization, :address, :email].any? {|key| config[key] } contact = Mspire::Mzml::Contact.new [ [:name, 'MS:1000586'], [:organization, 'MS:1000590'], [:address, 'MS:1000587'], [:email, 'MS:1000589'] ].each do |key, accession| contact.describe!(accession, config[key]) if config[key] end fd.contacts << contact end end end |
#create_referenceable_params_by_id_hash ⇒ Object
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# File 'lib/mspire/imzml/writer.rb', line 242 def create_referenceable_params_by_id_hash # m/z array and no compression (because we'll ref peaks in different # file) rparms = { :mz_array => [ ["MS:1000514", "MS:1000040"], # m/z array, units = m/z "MS:1000576", # no compression ["IMS:1000101", true], # external data 'MS:1000523' # 64-bit float ], :intensity_array => [ ["MS:1000515", "MS:1000131"], # intensity array, units = number of counts "MS:1000576", # no compression ["IMS:1000101", true], # external data 'MS:1000521' # 32-bit float ], :scan1 => [ # this should probably be ascertained from the mzml file: "MS:1000093", # increasing m/z scan # "MS:1000095" # linear # <- this should probably be gathered # from mzml (leave outfor now) # could include the filter string here in future ], :spectrum1 => [ "MS:1000579", # MS1 spectrum ["MS:1000511", 1], # ms level - default implementation uses 0 but I disagree... "MS:1000127", # centroid spectrum "MS:1000130" # <- positive scan ]}.map do |id, list| Mspire::Mzml::ReferenceableParamGroup.new(id).describe_many!(list) end Hash[ rparms.map {|prm_group_obj| [prm_group_obj.id, prm_group_obj]} ] end |
#experiment_hash_to_cvs(hash) ⇒ Object
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# File 'lib/mspire/imzml/writer.rb', line 154 def experiment_hash_to_cvs(hash) cvs = { :matrix_solution_concentration => "MS:1000835", :matrix_solution => "MS:1000834", :solvent => 'IMS:1001211', :solvent_flowrate => 'IMS:1001213', :spray_voltage => 'IMS:1001212', :target_material => 'IMS:10000202' }.map do |key,cv_acc| [cv_acc, hash[key]] if hash[key] end.compact mats = hash[:matrix_application_types] if mats app_types = mats.map do |typ| case typ.to_s when 'sprayed' ; 'MS:1000838' when 'precoated' ; 'MS:1000839' when 'printed' ; 'MS:1000837' when 'drieddroplet' ; 'MS:1000836' else ; raise "invalid matrix_application_type" end end cvs.push(*app_types) end cvs end |
#image_hash_to_cvs(hash) ⇒ Object
converts image related hash values to an array of loose describe! params
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# File 'lib/mspire/imzml/writer.rb', line 105 def image_hash_to_cvs(hash) cvs = [] cvs << case hash[:data_structure].to_sym when :processed ; 'IMS:1000031' when :continuous ; 'IMS:1000030' else ; raise ":data_structure must be :processed or :continuous" end cvs << case hash[:scan_pattern].to_sym when :meandering ; 'IMS:1000410' when :random ; 'IMS:1000412' when :flyback ; 'IMS:1000413' else ; raise ":scan_pattern must be :meandering, :random or :flyback" end cvs << case hash[:scan_type].to_sym when :horizontal ; 'IMS:1000480' when :vertical ; 'IMS:1000481' else ; raise ":scan_type must be :horizontal or :vertical" end cvs << case hash[:linescan_direction].to_s when 'left-right' ; 'IMS:1000402' when 'right-left' ; 'IMS:1000403' when 'bottom-up' ; 'IMS:1000400' when 'top-down' ; 'IMS:1000401' when 'none' ; 'IMS:1000404' else ; raise ":linescan_direction unacceptable" end cvs << case hash[:linescan_sequence].to_s when 'top-down' ; 'IMS:1000493' when 'bottom-up' ; 'IMS:1000492' when 'left-right' ; 'IMS:1000491' when 'right-left' ; 'IMS:1000490' else ; raise "linescan_sequence unacceptable" end max_pix_dims = hash[:max_dimensions_pixels].split(/x/i) cvs.push *['IMS:1000042', 'IMS:1000043'].zip(max_pix_dims).to_a real_dims = hash[:max_dimensions_microns].split(/x/i) cvs.push *['IMS:1000044', 'IMS:1000045'].zip(real_dims).map {|pair| [*pair, "UO:0000017"] } pix_dims = hash[:pixel_size].split(/x/i) cvs.push *["IMS:1000046", "IMS:1000047"].zip(pix_dims).map {|pair| [*pair, "UO:0000017"] } cvs end |
#write(mzml_filenames, config = {}) ⇒ Object
mzml_filenames can each be a partial or relative path by default the file will write to the same directory and basename
contact:
:name => name of the person or organization
:address => address of the person or organization
:url => url of person or organization
:email => email of person or organization
:organization => home institution of contact
experiment:
:solvent => the solvent used
:solvent_flowrate => flowrate of the solvent (ml/min)
:spray_voltage => spray voltage in kV
:target_material => the material the target is made of
editing:
:trim_files => determines min # spectra in file and lops
off the ends of other files.
general:
:omit_zeros => remove zero values
:combine => use this outfile base name to combine files
also works on single files to rename them.
MUST be present if more than one mzml given.
imaging:
:data_structure => :processed or :continuous
:scan_pattern => meandering random flyback
:scan_type => horizontal or vertical
:linescan_direction => scan_direction.join('|')
:linescan_sequence => scan_sequence.join('|')
:max_dimensions_pixels => maximum X by Y pixels (e.g. 300x100)
:shots_per_position => number of spectra per position
:pixel_size => X by Y of a single pixel in microns (μm)
:max_dimensions_microns => maximum X by Y in microns (e.g. 25x20)
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# File 'lib/mspire/imzml/writer.rb', line 308 def write(mzml_filenames, config={}) base = config[:combine] || mzml_filenames.first.chomp(File.extname(mzml_filenames.first)) config[:imzml_filename] = base + ".imzML" config[:ibd_filename] = base + ".ibd" uuid_with_hyphens = UUID.new.generate config[:uuid_hyphenated] = uuid_with_hyphens config[:uuid] = uuid_with_hyphens.gsub('-','') if config[:trim_files] config[:trim_to] = mzml_filenames.map {|fn| Mspire::Mzml.open(fn, &:size) }.min end sourcefile_id_parallel_to_spectra = [] sourcefile_ids = [] all_spectra_iter = Enumerator.new do |yielder| mzml_filenames.each_with_index do |mzml_filename,i| sourcefile_id = "source_file_#{i}" sourcefile_ids << sourcefile_id Mspire::Mzml.open(mzml_filename) do |mzml| enumerates_spectra = # handle SIM files "MS:1001472", "selected ion monitoring chromatogram" if mzml.file_description.file_content.fetch_by_acc('MS:1001472') # handle normal mzml files mz_ars = [] its_ars = [] mzml.each_chromatogram.each do |chromatogram,i| next unless chromatogram.fetch_by_acc('MS:1001472') target_mz = chromatogram.precursor.isolation_window.fetch_by_acc('MS:1000827').to_f its = chromatogram.intensities mz_ars << Array.new(its.size, target_mz) its_ars << its end mz_ars.transpose.zip(its_ars.transpose).map {|mzs, its| Mspire::Spectrum.new([mzs, its]) } else # normal mzml file with spectra mzml end enumerates_spectra.each_with_index do |spec,i| break if config[:trim_to] && (i >= config[:trim_to]) sourcefile_id_parallel_to_spectra << sourcefile_id yielder << spec end end end end data_info_pairs = write_binary(config[:ibd_filename], all_spectra_iter, config) xy_positions_array = x_y_positions(config) unless data_info_pairs.size == xy_positions_array.size STDERR.puts "Input Error! The number of calculated scans must equal the number of actual scans!" STDERR.puts "The number of calculated positions: #{xy_positions_array.size}" STDERR.puts "The number of actual scans: #{data_info_pairs.size}" raise end config[:ibd_sha1] = Digest::SHA1.hexdigest(IO.read(config[:ibd_filename])) source_files = mzml_filenames.zip(sourcefile_ids).map do |mzml_filename, source_file_id| sfile = Mspire::Mzml::SourceFile[ mzml_filename ] sfile.id = source_file_id sfile.describe! 'MS:1000584' sfile.describe! 'MS:1000569', Digest::SHA1.hexdigest(IO.read(mzml_filename)) sfile end sourcefile_id_to_sourcefile = Hash[ source_files.group_by(&:id).map {|k,v| [k,v.first] } ] imzml_obj = Mspire::Mzml.new do |imzml| imzml.id = UUID.new.generate.gsub('-','') imzml.cvs = Mspire::Mzml::CV::DEFAULT_CVS imzml.file_description = create_file_description(source_files, config) rparms_by_id = create_referenceable_params_by_id_hash warn "using positive scan in every case but need to get this from original mzml!" imzml.referenceable_param_groups = rparms_by_id.values # skip sample list for now mspire_software = Mspire::Mzml::Software.new("mspire", Mspire::VERSION).describe!("MS:1000799") imzml.software_list << mspire_software scan_setting_params = image_hash_to_cvs( config ) scan_setting_params.push *experiment_hash_to_cvs( config ) imzml.scan_settings_list = [Mspire::Mzml::ScanSettings.new("scansettings1").describe_many!(scan_setting_params)] warn 'todo: need to borrow instrumentConfiguration from original mzml' default_instrument_config = Mspire::Mzml::InstrumentConfiguration.new("borrow_from_mzml") warn 'todo: need to include default softare from mzml in default_instrument_config' #default_instrument_config.software = Software.new( from the mzml file! ) imzml.instrument_configurations << default_instrument_config # this is a generic 'file format conversion' but its the closest we # have for mzml to imzml (which is really mzml to mzml) data_processing_obj = Mspire::Mzml::DataProcessing.new('mzml_to_imzml') data_processing_obj.processing_methods << Mspire::Mzml::ProcessingMethod.new(mspire_software).describe!('MS:1000530') imzml.data_processing_list << data_processing_obj warn "not implemented 'omit_zeros' yet" # low intensity data point removal: "MS:1000594" imzml.run = Mspire::Mzml::Run.new("run1", default_instrument_config) do |run| spectra = [] data_info_pairs.zip(xy_positions_array, sourcefile_id_parallel_to_spectra).each_with_index do |(pair, xy, sourcefile_id),i| # TODO: we should probably copy the id from the orig mzml (e.g. # scan=1) spectrum = Mspire::Mzml::Spectrum.new("spectrum#{i}").describe!(rparms_by_id[:spectrum1]) spectrum.source_file = sourcefile_id_to_sourcefile[sourcefile_id] scan_list = Mspire::Mzml::ScanList.new.describe!('MS:1000795') # no combination scan = Mspire::Mzml::Scan.new.describe_many!([rparms_by_id[:scan1], ["IMS:1000050", xy[0]], ["IMS:1000051", xy[1]]]) scan.instrument_configuration = default_instrument_config spectrum.scan_list = (scan_list << scan) data_arrays = %w(mz intensity).zip(pair).map do |type, data_array_info| rparmgroup = rparms_by_id[(type + "_array").to_sym] # the type is defined in the refparams data_array = Mspire::Mzml::DataArray.new data_array.external = true data_array.describe_many! [rparmgroup, *%w(IMS:1000103 IMS:1000102 IMS:1000104).zip(data_array_info).map.to_a] data_array end spectrum.data_arrays = data_arrays spectra << spectrum end run.spectrum_list = Mspire::Mzml::SpectrumList.new(data_processing_obj, spectra) end # run end # imzml imzml_obj.to_xml(config[:imzml_filename]) end |
#write_binary(filename, spectra_iterator, config) ⇒ Object
returns an array of DataArrayInfo pairs
These must be defined in the config hash with valid values (see write_data_array for what those are):
:mz_data_type
:mz_precision
:intensity_data_type
:intensity_precision
Also recognizes :data_structure (:processed or :continuous). If :continuous, then the first spectrum is used to write the initial m/z and intensity pair, then in every spectrum after that the m/z data (if any) is ignored and only the intensities are written). The return is the same, the data info for each intensity is coupled with the m/z info from the first m/z data.
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# File 'lib/mspire/imzml/writer.rb', line 72 def write_binary(filename, spectra_iterator, config) config = DEFAULTS.merge(config) raise ":data_structure must be :continuous or :processed" unless [:processed, :continuous].include?(config[:data_structure]) (mz_dtype, mz_prec, int_dtype, int_prec) = config.values_at(:mz_data_type, :mz_precision, :intensity_data_type, :intensity_precision) mz_prec_in_bytes = mz_prec / 8 int_prec_in_bytes = int_prec / 8 File.open(filename, 'wb') do |out| out.print [config[:uuid]].pack("H*") if config[:data_structure] == :continuous # write the first m/z and get its info mzs = spectra_iterator.peek.mzs mz_info = Mspire::Imzml::DataArrayInfo.new mzs.size, out.pos, mzs.size * mz_prec_in_bytes write_data_array(out, mzs, mz_dtype, mz_prec) end spectra_iterator.map do |spec| if config[:data_structure] == :processed mzs = spec.mzs mz_info = Mspire::Imzml::DataArrayInfo.new mzs.size, out.pos, mzs.size * mz_prec_in_bytes write_data_array(out, spec.mzs, mz_dtype, mz_prec) end ints = spec.intensities int_info = Mspire::Imzml::DataArrayInfo.new ints.size, out.pos, ints.size * int_prec_in_bytes write_data_array(out, spec.intensities, int_dtype, int_prec) [mz_info, int_info] end end end |
#write_data_array(fh, values, dtype = :float, precision = 32) ⇒ Object
Integer values (dtype=:int) may be stored with precision = 8, 16, 32, 64 . Floating point values may be stored as 32 or 64 bit precision. The byte order is always little endian (intel style).
NOTE: the documentation is not clear whether they want signed or unsigned integers! Right now this outputs signed integers (my educated guess as to what is required)
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# File 'lib/mspire/imzml/writer.rb', line 34 def write_data_array(fh, values, dtype=:float, precision=32) pack_code = case dtype when :float precision == 64 ? 'E*' : 'e*' when :int # using signed!!!! (should these be unsigned??? NOT DOCUMENTED in # imzml resources anywhere!) case precision when 8 ; 'c<*' when 16 ; 's<*' when 32 ; 'l<*' when 64 ; 'q<*' else raise 'precision must be 8, 16, 32, or 64 for dtype==:int' end else raise 'dtype must be :int or :float!' end fh.print values.pack(pack_code) end |
#x_y_positions(config) ⇒ Object
returns an array with x, y pairs in the correct order accounts for scan_pattern, scan_type, linescan_direction, linescan_sequence and shots_per_position
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# File 'lib/mspire/imzml/writer.rb', line 185 def x_y_positions(config) (scan_pattern, scan_type, scan_direction, scan_sequence, shots_per_pos) = config.values_at(:scan_pattern, :scan_type, :linescan_direction, :linescan_sequence, :shots_per_position).map(&:to_s) shots_per_pos = shots_per_pos.to_i #puts "EXAMIN ARGS: " #p [ scan_pattern, scan_type, scan_direction, scan_sequence, shots_per_pos, shots_per_pos] # the true dimensions we need to work off come from the pixel dimensions. (slen, plen) = config[:max_dimensions_pixels].split(/x/i).map(&:to_i) flip = (scan_type == 'vertical') plen, slen = slen, plen if flip pindices = (1..plen).to_a # mindices if linescan_direction is 'horizontal' sindices = (1..slen).to_a # nindices if linescan_direction is 'horizontal' if flip sindices.reverse! if scan_direction == 'bottom-top' || scan_direction == 'right-left' pindices.reverse! if scan_sequence == 'right-left' || scan_sequence == 'bottom-top' end indices = pindices.map do |a| row = sindices.map do |b| flip ? [a,b] : [b,a] end sindices.reverse! if scan_pattern == 'meandering' row end.flatten(1) indices.map {|pair| shots_per_pos.times.map { pair } }.flatten(1) end |