imzml 0.1.0 → 0.1.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f7be2442cc6f7ce7a1503a2a7c5380c9509043b2
-  data.tar.gz: f76e6a4ff83c1335b90389d6ea6348a2df7a3656
+  metadata.gz: 5591dbd65b301f6c008d56453b7cf9f3668b394b
+  data.tar.gz: d1cd802b1ff67f067d60007687fbaab164745b52
 SHA512:
-  metadata.gz: b6fa51fac3db3e0ed575eca4152b184063ab248da7c91989d1726781919119cb6def12d31965d7cea8a1b424d72d66f93da5ee3077b17ef02cc7dd837bc73409
-  data.tar.gz: d56ab3b35465d58974c80d3e7dd8f1037bd13be794261765ffcee13194510d893ea8e684cffd4a06a82614a954c5c74d7c3f79489b8447fde8ba123f9ea4f1b3
+  metadata.gz: bd611f99d401acc47fdab97c0ce6e1a40a61cb6a95f684374656fdc635f9b745adff17e29116ae691b64044df8d174aa1f5453e9038c2fb87fed0c1ac36e8a8e
+  data.tar.gz: 1470bd7d36bfe4e5233d27d799f0702423a58991bf31175aa7c4cc11bd3965f1ada94fa5d17bb19f6e8a0c0f2628960efb3560036b22e340f42e6252d48ad186

data/lib/imzml/metadata/run/spectrum.rb

@@ -1,9 +1,9 @@
 module ImzML
-  
+
   class Spectrum
-    
+
     class BinaryData
-      
+
       # Binary data types, always little endian
       BINARY_TYPE_8BIT_INTEGER = "IMS:1100000"
       BINARY_TYPE_16BIT_INTEGER = "IMS:1100001"
@@ -11,40 +11,40 @@ module ImzML
       BINARY_TYPE_64BIT_INTEGER = "MS:1000522"
       BINARY_TYPE_32BIT_FLOAT = "MS:1000521"
       BINARY_TYPE_64BIT_FLOAT = "MS:1000523"
-      
+
       # A data array of m/z values
       MZ_ARRAY = "MS:1000514"
-      
+
       # A data array of intensity values
       INTENSITY_ARRAY = "MS:1000515"
-      
+
       # Describes how many fields an array contains
       attr_accessor :length
       EXTERNAL_ARRAY_LENGTH = "IMS:1000103"
-    
+
       # The position where the data of an array of a mass spectrum begins
       attr_accessor :offset
       EXTERNAL_OFFSET = "IMS:1000102"
-    
+
       # Describes the length of the written data
       attr_accessor :encoded_length
       EXTERNAL_ENCODED_LENGHT = "IMS:1000104"
-      
+
       # Path to the external binary file
       attr_accessor :filepath
-      
+
       # Binary values type [:int8, :int16, :int32, :int64, :float32, :float64]
       attr_accessor :type
-      
+
       # grabs the actual binary data from disk
       def data(cached = true)
-        
+
         # Return the data from the cache
         return @cached_data if cached && !@cached_data.nil?
-        
+
         # Remove possible data from the cache
         @cached_data = nil
-        
+
         # Switch binary pattern reading type
         pattern = case type
         when :int8
@@ -63,65 +63,66 @@ module ImzML
 
         # Read data based on metadata
         data = IO.binread(@filepath, @encoded_length.to_i, @offset.to_i).unpack("#{pattern}*")
-        
+
         # Save data only if user want's to cache it, saving take some CPU
         @cached_data = data if cached
       end
-      
+
       private
-      
+
       attr_accessor :cached_data
-      
+
     end
-    
+
     # Attributes to describe the position of a spectrum in the image.
-    # 
+    #
     # represented as Point with position x, y
     attr_accessor :position
     POSITION_X = "IMS:1000050"
     POSITION_Y = "IMS:1000051"
-    
+
     # Info about mz binary data
     #
     # Represented by class BinaryData
     attr_accessor :mz_binary
-    
+
     # Info about intensity binary data
     #
     # Represented by class BinaryData
     attr_accessor :intensity_binary
-    
+
     def intensity(at, interval)
-      
+
       # read whole the binary data
       mz_array = mz_binary.data
       intensity_array = intensity_binary.data
-      
+
       default_from, default_to = mz_array.first, mz_array.first
-      
+
+      from = default_from
+      to = default_to
+
       # find designated intensity
-      if !at
-        from = default_from
-        to = default_to
-      else
+      if at
         from = at - interval
         from = default_from if from < 0
         to = at + interval
         to = default_to if to > mz_array.last
       end
-      
+
       # find values in mz array
-      low_value = mz_array.binary_search(from, false)
+      low_value = mz_array.bsearch { |x| x >= from }
       low_index = mz_array.index(low_value)
-      high_value = mz_array.binary_search(to)
+      high_value = mz_array.bsearch { |x| x >= to }
       high_index = mz_array.index(high_value)
-  
+
       # sum all values in subarray
-      intensity_array[low_index..high_index].inject{|sum, x| sum + x}
-      
+      sum = intensity_array[low_index..high_index].inject{|sum, x| sum + x}
+
+      sum
     end
 
-    
+
   end
-  
+
 end

data/lib/imzml/metadata/scan_settings/image.rb

@@ -1,11 +1,16 @@
 module ImzML
-  
+
   class Image
-    
+
+    # Point
     attr_accessor :max_pixel_count
+
+    # Point
     attr_accessor :max_dimension
+
+    # Point
     attr_accessor :pixel_size
-    
+
   end
-  
+
 end

data/lib/imzml/version.rb

@@ -1,5 +1,5 @@
 module ImzML
-  
-  VERSION = "0.1.0"
-  
+
+  VERSION = "0.1.1"
+
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: imzml
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
 platform: ruby
 authors:
 - Ondra Beneš
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-27 00:00:00.000000000 Z
+date: 2014-05-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: minitest
@@ -73,7 +73,6 @@ files:
 - data/imagingMS.obo
 - data/psi-ms.obo
 - data/unit.obo
-- lib/core_ext/array.rb
 - lib/core_ext/string.rb
 - lib/imzml.rb
 - lib/imzml/metadata.rb

data/lib/core_ext/array.rb

@@ -1,23 +0,0 @@
-class Array
-  
-  def binary_search(value, first = true)
-    
-    if (self.size > 2)
-      middle_index = self.size/2
-      middle = self[middle_index]
-
-      if (middle > value)
-        self[0..middle_index].binary_search(value, first)
-      else
-        self[middle_index..self.size].binary_search(value, first)
-      end
-    else
-      if first
-        self.first
-      else
-        self.last
-      end
-    end
-  end
-  
-end