metamri 0.2.25 → 0.2.26

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 92932063e1a8a63e45c8b74c92adfbd4def00b09
-  data.tar.gz: 467f2328d0aee4538b0cd03c68e98b8a8599c7b9
+  metadata.gz: 5af9adf7949a97f8a098295e8f05aeac91d61fd2
+  data.tar.gz: 4c9475178d5a518b07ec5b4fce88bb9b7d28eec4
 SHA512:
-  metadata.gz: 9de4f0f131ad11edd2c8a9e99c22efeb8c0e243e14fb8a23ec3c373e7fa537cceabc3dc837310dd35704c7d77a674b8f136fc455adf490e4227c2d1ced991419
-  data.tar.gz: bf1ade09fe6571e22d4c6f71efb3305e28bb01b528e87e5c9212bf6e8aab3fd8f2d5d4289c3d45323c941a2f77fb394b73b7e42a0fffa7329c24e3651b465542
+  metadata.gz: 161d4cd4c8dd011e8455fdab16591d7a84a83c095999722bbb0cc2d1094ffb24b9c14b6c8671f771047376d6fbdb1f1f4f610feffd2758d1ad3915b6bb442258
+  data.tar.gz: f34510cc2c7ed1280745a3bb6fef604c857786e92ef20d2f229fdff38975e00d2460aade4bf2a42c62ccc21b81a144dd41d9435a4bc45b1e8c825bccac9c3580

data/VERSION

@@ -1 +1 @@
-0.2.25
+0.2.26

data/bin/import_visit.rb

@@ -49,7 +49,7 @@ require 'metamri'
 def import_visit(raw_directory, scan_procedure_codename, database)
   log = Logger.new(File.basename(raw_directory))  
   v = VisitRawDataDirectory.new(raw_directory, scan_procedure_codename)
-  puts "+++ Importing #{v.visit_directory} as part of #{v.scan_procedure_name} +++"
+  puts "|||+++ Importing #{v.visit_directory} as part of #{v.scan_procedure_name} +++"
   begin
     v.scan
     v.db_insert!(database)

data/lib/metamri/core_additions.rb

@@ -128,6 +128,29 @@ class Pathname
     end
   end
 
+
+    def each_scanner_archive_summary
+    entries.each do |leaf|
+      next unless leaf.to_s =~ /^ScanArchive.*(.h5.json)$/
+      branch = self + leaf
+      next if branch.symlink?
+        lc = branch.local_copy
+        begin
+          yield lc
+        rescue StandardError => e
+          case $LOG.level
+          when Logger::DEBUG
+            raise e
+          else
+            puts "#{e}"
+          end
+        ensure
+          lc.delete
+        end
+    end
+  end
+
+
   
   def first_dicom
     entries.each do |leaf|

data/lib/metamri/raw_image_dataset.rb

@@ -47,6 +47,12 @@ class RawImageDataset
   attr_reader :dicom_taghash
   # Array of Read Error Strings
   attr_reader :read_errors
+  # head coil
+  attr_reader :mri_coil_name  
+  # staion name
+  attr_reader :mri_station_name 
+  # mri model name
+  attr_reader :mri_manufacturer_model_name  
 
   
   # * dir: The directory containing the files.
@@ -113,6 +119,12 @@ class RawImageDataset
     
     @image_uid  = @raw_image_files.first.image_uid
     validates_metainfo_for :image_uid if pfile?
+
+    @mri_coil_name  = @raw_image_files.first.mri_coil_name
+
+    @mri_station_name  = @raw_image_files.first.mri_station_name
+
+    @mri_manufacturer_model_name   = @raw_image_files.first.mri_manufacturer_model_name 
     
     $LOG ||= Logger.new(STDOUT)
   end
@@ -134,7 +146,7 @@ class RawImageDataset
   # transaction at the visit level, or even higher when doing a whole file system
   # scan.
   def db_insert(visit_id)
-    "INSERT INTO image_datasets
+    "INSERT INto image_datasets
     (rmr, series_description, path, timestamp, created_at, updated_at, visit_id, 
     glob, rep_time, bold_reps, slices_per_volume, scanned_file, 'dicom_study_uid')
     VALUES ('#{@rmr_number}', '#{@series_description}', '#{@directory}', '#{@timestamp.to_s}', '#{DateTime.now}', 
@@ -191,7 +203,10 @@ class RawImageDataset
       :scanned_file => @scanned_file,
       :dicom_series_uid => @dicom_series_uid,
       :dicom_taghash => @dicom_taghash,
-      :image_uid => @image_uid
+      :image_uid => @image_uid,
+      :mri_coil_name => @mri_coil_name, 
+      :mri_station_name => @mri_station_name, 
+      :mri_manufacturer_model_name => @mri_manufacturer_model_name
     }.merge attrs
   end
   
@@ -287,7 +302,9 @@ Returns a path to the created dataset as a string if successful.
         @file_count = Dir.open(@directory).reject{ |branch| /(^\.|.yaml$)/.match(branch) }.length
       elsif @raw_image_files.first.pfile?
         @file_count = 1
-      else raise "File not recognized as dicom or pfile."
+      elsif @raw_image_files.first.scan_archive_h5_json?
+        @file_count = 1
+      else raise "File not recognized as dicom or pfile or scan_archive_h5_json."
       end
     end
     return @file_count
@@ -325,6 +342,13 @@ Returns a path to the created dataset as a string if successful.
         else
           relative_dataset_path = image_file.filename
         end
+      when 'scan_archive_h5_json'
+        full_dataset_path = Pathname.new(File.join(directory, image_file.filename))
+        if visit_dir
+          relative_dataset_path = full_dataset_path.relative_path_from(visit_dir)
+        else
+          relative_dataset_path = image_file.filename
+        end
       else raise "Cannot identify #{@raw_image_files.first.filename}"
     end
     
@@ -354,6 +378,10 @@ Returns a path to the created dataset as a string if successful.
   def geifile?
     @raw_image_files.first.geifile?
   end
+
+   def scan_archive_h5_json?
+      @raw_image_files.first.scan_archive_h5_json?
+  end
   
 private
 

data/lib/metamri/raw_image_dataset_resource.rb

@@ -14,10 +14,16 @@ class RawImageDatasetResource < ActiveResource::Base
     # need to stop loading bz2 P files - 15 GB nmprage pfiles taking to long to bunzip2
     # load just P*.7 and have routine job to pbzip2 things up later
     filename = Pathname.new(File.join(path, scanned_file))
-flash "wwwwwwwwwwww filename= #{filename}" if $LOG.level <= Logger::INFO
+flash "wwwwwwwwwwwwZZZZZZ filename= #{filename}" #if $LOG.level <= Logger::INFO
     filename_matches = /P\d{5}.7(.bz2)?/.match(filename)
     filename_matches_non_bz2 = /P\d{5}(.7)?/.match(filename)
     filename_matches_summary = /P\d{5}(.7.summary)?/.match(filename)
+
+    filename_matches_json = /^ScanArchive.*(.h5.json)?/.match(filename)
+    puts "zzzzZZZ filename="+filename
+    if filename_matches_json
+      puts "IIITTTS a json"
+    end
     
     if filename_matches    # Pfile
       if filename_matches[1] # '.bz2' if present, nil if otherwise.

data/lib/metamri/raw_image_file.rb

@@ -4,6 +4,7 @@ require 'rubygems';
 require 'yaml';
 # require 'sqlite3';
 require 'dicom'
+require 'json'
 
 
 # Implements a collection of metadata associated with a raw image file.  In
@@ -23,8 +24,9 @@ class RawImageFile
   RDGEHDR = "rdgehdr"
   PRINTRAW = "printraw"
   PRINTRAW_SUMMARY = "cat"   #"printraw_summary"
+  PRINTRAW_H5_JSON = "cat"
   RUBYDICOM_HDR = "rubydicom"
-  VALID_HEADERS = [DICOM_HDR, PRINTRAW, RDGEHDR, RUBYDICOM_HDR,PRINTRAW_SUMMARY]
+  VALID_HEADERS = [DICOM_HDR, PRINTRAW, RDGEHDR, RUBYDICOM_HDR,PRINTRAW_SUMMARY,PRINTRAW_H5_JSON]
   MONTHS = {
     :jan => "01", :feb => "02", :mar => "03", :apr => "04", :may => "05", 
     :jun => "06", :jul => "07", :aug => "08", :sep => "09", :oct => "10", 
@@ -87,6 +89,12 @@ class RawImageFile
   attr_reader :operator_name
   # Patient "Name", usually StudyID or ENUM
   attr_reader :patient_name
+  # head coil
+  attr_reader :mri_coil_name  
+  # staion name
+  attr_reader :mri_station_name 
+  # mri model name
+  attr_reader :mri_manufacturer_model_name  
   
   # Creates a new instance of the class given a path to a valid image file.
   # 
@@ -108,6 +116,9 @@ class RawImageFile
     if @filename =~ /^P*\.summary/
        @hdr_reader = PRINTRAW_SUMMARY
     end
+    if @filename =~ /^ScanArchive*\.h5.json/
+       @hdr_reader = nil #PRINTRAW_H5_JSON
+    end
     # try to read the header, raise an IOError if unsuccessful
     begin
       @hdr_data, @hdr_reader = read_header(absfilepath)
@@ -152,6 +163,9 @@ class RawImageFile
     return @file_type == "pfile"
   end
 
+ def scan_archive_h5_json?
+    return @file_type == "scan_archive_h5_json"
+  end
 
   # Predicate simply returns true if "dicom" is stored in the img_type instance variable.
   def dicom?
@@ -284,7 +298,7 @@ private
   # Note: The rdgehdr is a binary file; the correct version for your architecture must be installed in the path.
   def read_header(absfilepath)
     tmp_filename= File.basename(absfilepath)
-
+    
     case File.basename(absfilepath)
     when /^P.{5}\.7$|^I\..{3}/
          # check for 
@@ -302,6 +316,22 @@ private
             @current_hdr_reader = nil
             return [ header, PRINTRAW ]
          end
+    when /^ScanArchive_.{10,}\.h5\.json$/
+        json_file = File.read(absfilepath)
+        data_hash = JSON.parse(json_file)
+        ####header ="se_desc =               "+data_hash["SERIES INFORMATION"]["Series Desc"]+"
+####image_uid =             "+data_hash["RHUSER and OPUSER INFORMATION"]["imagehead.image_uid"]+"\n"
+        ## if ( header.chomp != "" )#and   header.length > MIN_HDR_SUMMARY_LENGTH )
+        if !data_hash.nil?
+            @current_hdr_reader = nil
+           # puts data_hash.to_s
+            # FAILING IN HEADER READ - WHERE IS THE HEADER TRYING TO GET READ? NOT STOPING AT PRINTRAW_SUMMARY
+            # CAN THE data_hash be passed instead of the header, and then read in the header_json_reader?
+            return [data_hash, nil] ###PRINTRAW_H5_JSON  ]
+            ###return [ header, PRINTRAW_H5_JSON ]
+         end
+        # need to read json
+        # create header
     when /^P.{5}\.7\.summary/
          # check for 
          @current_hdr_reader = PRINTRAW_SUMMARY
@@ -360,6 +390,7 @@ private
     return "pfile"    if image? and (@filename =~ /^P.....\.7/) != nil
     return "pfile"    if (@filename =~ /^P.....\.7\.summary/) != nil
     return "geifile"  if image? and (@filename =~ /^I\.\d*/) != nil
+    return "scan_archive_h5_json"  if (@filename =~ /^ScanArchive_.{10,}.h5.json/) != nil
     return "dicom"    if image? and (@filename =~ /^P.....\.7/) == nil
     return nil
   end
@@ -368,10 +399,10 @@ private
   # Parses the header data and extracts a collection of instance variables.  If 
   # @hdr_data and @hdr_reader are not already available, this function does nothing.
   def import_hdr
-
     if @hdr_reader == nil
       case @file_type
           when "pfile" then printraw_summary_import
+          when "scan_archive_h5_json" then printraw_scan_archive_h5_json
      end
     else
       raise(IndexError, "No Header Data Available.") if @hdr_data == nil
@@ -713,6 +744,88 @@ puts "printraw_import rrrrrr @image_uid ="+@image_uid .to_s
     @hdr_data = nil
 
   end
+  def printraw_scan_archive_h5_json
+     #puts "hhhhhhh @hdr_data[SERIES INFORMATION][Series Desc]="+@hdr_data["SERIES INFORMATION"]["Series Desc"] 
+    source_pat =               /hospital [Nn]ame: ([[:graph:]\t ]+)/i
+    num_slices_pat =           /Number of slices in this scan group: ([0-9]+)/i
+    slice_thickness_pat =      /slice thickness \(mm\): ([[:graph:]]+)/i
+    slice_spacing_pat =        /spacing between scans \(mm\??\): ([[:graph:]]+)/i
+    date_pat =                 /actual image date\/time stamp: (.*)\n/i
+    gender_pat =               /Patient Sex: (1|2)/i
+    acquisition_matrix_x_pat = /Image matrix size \- X: ([0-9]+)/i
+    acquisition_matrix_y_pat = /Image matrix size \- Y: ([0-9]+)/i
+    series_description_pat =   /Series Description: ([[:graph:] \t]+)/i
+    recon_diam_pat =           /Display field of view \- X \(mm\): ([0-9]+)/i
+    rmr_number_pat =           /Patient ID for this exam: ([[:graph:]]+)/i
+    bold_reps_pat =            /Number of excitations: ([0-9]+)/i
+    rep_time_pat =             /Pulse repetition time \(usec\): ([0-9]+)/i
+    study_uid_pat =            /Study entity unique ID: ([[:graph:]]+)/i
+    series_uid_pat =           /Series entity unique ID: ([[:graph:]]+)/i
+    image_uid_pat =            /Image unique ID: ([[:graph:]]+)/i    
+
+    @dicom_taghash =  @hdr_data
+    @rmr_number = (@hdr_data["PATIENT INFORMATION"]["PID"]).nil? ? "rmr not found" : (@hdr_data["PATIENT INFORMATION"]["PID"]).strip.chomp
+
+    @source = (@hdr_data["EXAM INFORMATION"]["Hospital Name"]).nil? ? "source not found" : (@hdr_data["EXAM INFORMATION"]["Hospital Name"]).strip.chomp
+ 
+    ####num_slices_pat =~ @hdr_data
+    @num_slices = (@hdr_data["ACQUISITION INFORMATION"]["Nslices"]).strip.chomp
+ 
+    ####slice_thickness_pat =~ @hdr_data
+    @slice_thickness = (@hdr_data["RECONSTRUCTION INFORMATION"][ "Z thick"]).strip.to_f
+   
+
+    ####slice_spacing_pat =~ @hdr_data
+    @slice_spacing = 0 #($1).to_f
+
+    ####date_pat =~ @hdr_data
+
+    v_scan_date_mm_dd_yy = @hdr_data["EXAM INFORMATION"]["Exam Date"] # @hdr_data["ACQUISITION INFORMATION"]["Scan Date"] had 3 digit year???
+    v_scan_time_hh24_min = @hdr_data["ACQUISITION INFORMATION"]["Scan Time"]
+    v_scan_date_mm_dd_yy_array = v_scan_date_mm_dd_yy.split(" ")
+    v_scan_time_hh24_min_array = v_scan_time_hh24_min.split(" ")
+    if v_scan_date_mm_dd_yy_array.count > 2 and v_scan_time_hh24_min_array.count > 1
+        v_datetime = "20"+v_scan_date_mm_dd_yy_array[2]+"-"+v_scan_date_mm_dd_yy_array[0]+"-"+v_scan_date_mm_dd_yy_array[1]+"T"+v_scan_time_hh24_min_array[0]+":"+v_scan_time_hh24_min_array[1]
+        @timestamp =   v_datetime.to_datetime 
+    else
+        @timestamp = Datetime.new
+
+    end
+    ####@timestamp = DateTime.parse(v_datetime) 
+    @gender = @hdr_data["PATIENT INFORMATION"]["Sex"] == 1 ? "M" : "F"
+    
+    ####acquisition_matrix_x_pat =~ @hdr_data
+    @acquisition_matrix_x = (@hdr_data["RECONSTRUCTION INFORMATION"]["Xres"]).strip.to_i
+    ####acquisition_matrix_y_pat =~ @hdr_data
+    @acquisition_matrix_y = 0 #####($1).to_i
+    
+    @series_description = (@hdr_data["RHUSER and OPUSER INFORMATION"]["serieshead.se_desc"]).strip.chomp
+    
+    ####recon_diam_pat =~ @hdr_data
+    @reconstruction_diameter = (@hdr_data["RECONSTRUCTION INFORMATION"]["Yres"]).strip.to_i
+    
+    ####bold_reps_pat =~ @hdr_data
+    @bold_reps = 0 ####($1).to_i
+    
+    ####rep_time_pat =~ @hdr_data
+    @rep_time = (@hdr_data["RHUSER and OPUSER INFORMATION"]["imagehead.reptime"]).to_f / 1000000
+    @study_uid = (@hdr_data["RHUSER and OPUSER INFORMATION"]["examhead.study_uid"]).strip.chomp unless @hdr_data["RHUSER and OPUSER INFORMATION"]["examhead.study_uid"].nil?
+    
+
+    @series_uid = @hdr_data["RHUSER and OPUSER INFORMATION"]["serieshead.series_uid"].chomp unless @hdr_data["RHUSER and OPUSER INFORMATION"]["serieshead.series_uid"].nil?
+    
+
+    @image_uid = (@hdr_data["RHUSER and OPUSER INFORMATION"]["imagehead.image_uid"]).strip.chomp unless @hdr_data["RHUSER and OPUSER INFORMATION"]["imagehead.image_uid"].nil?
+    if !@image_uid.nil?
+       @image_uid = "sa"+@image_uid # unique index on uid - same uid may be in dicoms as scan archive
+    end
+
+    @mri_coil_name = @hdr_data["ACQUISITION INFORMATION"]["Coil Name"].chomp unless @hdr_data["ACQUISITION INFORMATION"]["Coil Name"].nil?
+    
+    @mri_station_name = @hdr_data["EXAM INFORMATION"]["System ID"].chomp unless @hdr_data["EXAM INFORMATION"]["System ID"].nil?
+    ####@mri_manufacturer_model_name = ???
+   end 
+
 
   def printraw_summary_import
     source_pat =               /hospital [Nn]ame: ([[:graph:]\t ]+)/i

data/lib/metamri/version.rb

@@ -1,3 +1,3 @@
 module Metamri
-  VERSION = "0.2.25"
+  VERSION = "0.2.26"
 end

data/lib/metamri/visit_raw_data_directory.rb

@@ -108,6 +108,9 @@ class VisitRawDataDirectory
         dd.each_pfile  { |pf|  # check for p*.7.summary
               @datasets << import_dataset(pf, dd); @datasets.last.print_scan_status if $LOG.level == Logger::INFO }
         dd.first_dicom { |fd| @datasets << import_dataset(fd, dd); @datasets.last.print_scan_status if $LOG.level == Logger::INFO }
+       if (dd.to_s).include?("scan_archives") and (dd.to_s).include?("raw_data")
+         dd.each_scanner_archive_summary { |sa|  @datasets << import_dataset(sa, dd);  @datasets.last.print_scan_status if $LOG.level == Logger::INFO }
+       end
       rescue StandardError => e
         raise(e, "There was an error scaning dataset #{dd}: #{e}")
       end
@@ -192,8 +195,24 @@ Returns an array of the created nifti files.
         
     @datasets.each do |dataset|
       nifti_output_path = output_directory
-      v_basename =File.basename(dataset.directory).gsub(/-/,"").gsub(/_/,"").gsub(/\:/,"").gsub(/\//,"")
-      v_series_description = "."+dataset.series_description.gsub(/ /,"").gsub(/-/,"").gsub(/_/,"").gsub(/\:/,"").gsub(/\//,"")
+      #v_basename =File.basename(dataset.directory).gsub(/-/,"").gsub(/_/,"").gsub(/\:/,"").gsub(/\//,"")
+      #v_series_description = "."+dataset.series_description.gsub(/ /,"").gsub(/-/,"").gsub(/_/,"").gsub(/\:/,"").gsub(/\//,"")
+      # 20171120 addition
+      v_basename =File.basename(dataset.directory)
+      v_series_description = "."+dataset.series_description
+      v_series_description_full_replace = v_series_description
+      # need to get the scan series numbers - take the v_basename/folder name -- replace all the series description stuff
+      # end up with scan series number - add to the end of the series_description to get the nii file nam 
+      if !v_basename.nil?
+        v_basename = v_basename.gsub(/ /,"").gsub(/\-/,"").gsub(/\_/,"").gsub(/\(/,"").gsub(/\)/,"").gsub(/\=/,"").gsub(/\+/,"").gsub(/\'/,"").gsub(/\^/,"").gsub(/\,/,"").gsub(/\:/,"").gsub(/\*/,"star")
+      end
+      if !v_series_description_full_replace.nil?
+          v_series_description_full_replace =  v_series_description_full_replace.gsub(/ /,"").gsub(/\-/,"").gsub(/\_/,"").gsub(/\(/,"").gsub(/\)/,"").gsub(/\=/,"").gsub(/\+/,"").gsub(/\'/,"").gsub(/\^/,"").gsub(/\,/,"").gsub(/\:/,"").gsub(/\*/,"star")
+      end 
+
+#puts "ccccc end v_basename="+v_basename
+#puts "dddd end v_series_description_full_replace="+v_series_description_full_replace
+
       if v_basename.include? v_series_description
            # want the scan series number - e.g. 00001 at the end
            v_tmp_filename =  v_basename.gsub(v_series_description,"")
@@ -371,9 +390,13 @@ Returns an array of the created nifti files.
       tmp_filename = File.basename rawfile.to_s
       tmp_filname_summary_s = (tmp_filename).gsub(/\.bz2/,"").gsub(/\.summary/,"")+".summary"
       tmp_branch_summary_s = original_parent_directory.to_s+"/"+tmp_filname_summary_s
+      tmp_branch_scan_archive_json = original_parent_directory.to_s+"/"+tmp_filename
+
        if File.exist?(tmp_branch_summary_s)
             #branch_summary_pn = Pathname.new(branch_summary_s)
          rawimagefile = RawImageFile.new(tmp_branch_summary_s)
+        elsif File.exists?(tmp_branch_scan_archive_json)
+          rawimagefile = RawImageFile.new(tmp_branch_scan_archive_json)
         else
             rawimagefile = RawImageFile.new(rawfile.to_s)
         end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: metamri
 version: !ruby/object:Gem::Version
-  version: 0.2.25
+  version: 0.2.26
 platform: ruby
 authors:
 - Kristopher J. Kosmatka
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-04-06 00:00:00.000000000 Z
+date: 2018-10-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: dicom
@@ -154,7 +154,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.5.1
+rubygems_version: 2.6.14
 signing_key: 
 specification_version: 4
 summary: MRI metadata