spectrum.rb in imzml-0.1.1

- old
+ new

@@ -1,52 +1,52 @@
 module ImzML
-  
+
   class Spectrum
-    
+
     class BinaryData
-      
+
       # Binary data types, always little endian
       BINARY_TYPE_8BIT_INTEGER = "IMS:1100000"
       BINARY_TYPE_16BIT_INTEGER = "IMS:1100001"
       BINARY_TYPE_32BIT_INTEGER = "MS:1000519"
       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
           "C"
         when :int16
@@ -61,67 +61,68 @@
           "E"
         end
 
         # 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
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