dicoms 1.0.0 → 1.2.0

data/lib/dicoms/stats.rb

@@ -1,6 +1,5 @@
 class DicomS
   def stats(dicom_directory, options = {})
-    # TODO: compute histogram of levels
     dicom_files = find_dicom_files(dicom_directory)
     if dicom_files.empty?
       raise "ERROR: no se han encontrado archivos DICOM en: \n #{dicom_directory}"
@@ -24,7 +23,8 @@ class DicomS
       n: n,
       min: mins.min,
       next_min: next_mins.min,
-      max: maxs.max
+      max: maxs.max,
+      histogram: compute_histogram(dicom_directory, options)
     }
   end
 end

data/lib/dicoms/support.rb

@@ -1,6 +1,26 @@
 require 'matrix'
 
 class DicomS
+  class Error < RuntimeError
+    def initialize(code, *args)
+      @code = code
+      super *args
+    end
+    attr_reader :code
+  end
+
+  class UnsupportedDICOM < Error
+    def initialize(*args)
+      super 'unsupported_dicom', *args
+    end
+  end
+
+  class InvaliddDICOM < Error
+    def initialize(*args)
+      super 'invalid_dicom', *args
+    end
+  end
+
   USE_SLICE_Z = false
   METADATA_TYPES = {
     # Note: for axisx, axisy, axisz decode_vector should be used
@@ -141,7 +161,7 @@ class DicomS
       ny = dicom.num_rows # dicom.rows.value.to_i
 
       unless dicom.samples_per_pixel.value.to_i == 1
-        raise "Invalid DICOM format"
+        raise InvalidDICOM, "Invalid image format"
       end
       Settings[
         dx: dx, dy: dy, x: x, y: y, z: z,
@@ -169,7 +189,7 @@ class DicomS
       file = File.basename(name)
       number_pattern = /\d+/
       match = number_pattern.match(file)
-      raise "Invalid DICOM file name" unless match
+      raise UnsupportedDICOM, "Invalid DICOM file name" unless match
       number = match[0]
       file = file.sub(number_pattern, "%d")
       if match.begin(0) == 0
@@ -345,5 +365,31 @@ class DicomS
       ts = DICOM::LIBRARY.uid(dicom.transfer_syntax)
       ts.name if ts.compressed_pixels?
     end
+
+    def terminal_size
+      if $stdout.respond_to?(:tty?) && $stdout.tty? && $stdout.respond_to?(:winsize)
+        $stdout.winsize
+      else
+        size = [ENV['LINES'] || ENV['ROWS'], ENV['COLUMNS']]
+        if size[1].to_i > 0
+          size
+        else
+          if defined?(Readline) && Readline.respond_to?(:get_screen_size)
+            size = Readline.get_screen_size
+            if size[1].to_i > 0
+              size
+            elsif ENV['ANSICON'] =~ /\((.*)x(.*)\)/
+              size = [$2, $1]
+              if size[1].to_i > 0
+                size
+              else
+                [27, 80]
+              end
+            end
+          end
+        end
+      end
+    end
+
   end
 end

data/lib/dicoms/transfer.rb

@@ -17,6 +17,12 @@ class DicomS
   # values which are mapped to the output limits.
   # These values may be raw or rescaled depending on the min_max_rescaled? method
   #
+  # Derived classes should also provide a method
+  #
+  #     transfer_rescaled_pixels(dicom, data, min, max)
+  #
+  # To apply the transfer conversion to data which has been only rescaled
+  #
   class Transfer
     USE_DATA = false
 
@@ -70,8 +76,8 @@ class DicomS
       when :unsigned
         min, max = Transfer.min_max_limits(dicom)
         if min < 0
-          min = 0
           max -= min
+          min = 0
         end
         [min, max]
       else
@@ -96,6 +102,7 @@ class DicomS
     def initialize(options = {})
       @center = options[:center]
       @width  = options[:width]
+      @float_arith = options[:float] || FLOAT_MAPPING
       super options
     end
 
@@ -116,6 +123,14 @@ class DicomS
       map_to_output dicom, data, min, max
     end
 
+    # Apply the transfer map to data which has been only rescaled
+    def transfer_rescaled_pixels(dicom, pixels, min, max)
+      # clip pixels to min, max # wouldn't be needed if map_to_output did output clipping...
+      pixels[pixels < min] = min
+      pixels[pixels > max] = max
+      map_to_output dicom, pixels, min, max
+    end
+
     # def image(dicom, min, max)
     #   center = (min + max)/2
     #   width = max - min
@@ -128,7 +143,7 @@ class DicomS
       output_min, output_max = min_max_limits(dicom)
       output_range = output_max - output_min
       input_range  = max - min
-      float_arith = FLOAT_MAPPING || output_range < input_range
+      float_arith = @float_arith || output_range < input_range
       data_type = data.typecode
       data = data.to_type(NArray::SFLOAT) if float_arith
       data.sbt! min
@@ -179,6 +194,7 @@ class DicomS
       @rescale = options[:rescale]
       @ignore_min = options[:ignore_min]
       @extension_factor = options[:extend] || 0.0
+      @float_arith = options[:float] || FLOAT_MAPPING
       super options
     end
 
@@ -196,16 +212,12 @@ class DicomS
       [minimum, maximum]
     end
 
-    def min_max_rescaled?
-      @rescale
-    end
-
-    def processed_data(dicom, min, max)
+    # Apply the transfer map to data which has been only rescaled
+    def transfer_rescaled_pixels(dicom, data, min, max)
       output_min, output_max = min_max_limits(dicom)
       output_range = output_max - output_min
       input_range  = max - min
-      float_arith = FLOAT_MAPPING || output_range < input_range
-      data = dicom_narray(dicom, level: false, remap: @rescale)
+      float_arith = @float_arith || output_range < input_range
       data_type = data.typecode
       data = data.to_type(NArray::SFLOAT) if float_arith
       data.sbt! min
@@ -217,6 +229,15 @@ class DicomS
       data
     end
 
+    def processed_data(dicom, min, max)
+      data = dicom_narray(dicom, level: false, remap: @rescale)
+      transfer_rescaled_pixels dicom, data, min, max
+    end
+
+    def min_max_rescaled?
+      @rescale
+    end
+
     private
 
     def data_range(dicom)
@@ -320,20 +341,7 @@ class DicomS
     end
 
     def min_max(sequence)
-      min_max_limits(sequence.first)
-    end
-
-    def map_to_output(dicom, data, min, max)
-      if @rescale
-        intercept = dicom_rescale_intercept(dicom)
-        slope = dicom_rescale_slope(dicom)
-        if slope != 1 || intercept != 0
-          return super
-        end
-      end
-      data = dicom_narray(dicom)
-      data.add! -min if min < 0
-      data
+      Transfer.min_max_limits(sequence.first)
     end
   end
 end

data/lib/dicoms/version.rb

@@ -1,3 +1,3 @@
 class DicomS
-  VERSION = "1.0.0"
+  VERSION = "1.2.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: dicoms
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.2.0
 platform: ruby
 authors:
 - Javier Goizueta
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2015-09-17 00:00:00.000000000 Z
+date: 2015-10-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: dicom
@@ -94,6 +94,34 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.19'
+- !ruby/object:Gem::Dependency
+  name: solver
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: histogram
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.4
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.4
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -159,7 +187,10 @@ files:
 - lib/dicoms.rb
 - lib/dicoms/cli.rb
 - lib/dicoms/command_options.rb
+- lib/dicoms/explode.rb
 - lib/dicoms/extract.rb
+- lib/dicoms/histogram.rb
+- lib/dicoms/info.rb
 - lib/dicoms/meta_codec.rb
 - lib/dicoms/pack.rb
 - lib/dicoms/progress.rb
@@ -168,6 +199,7 @@ files:
 - lib/dicoms/sequence.rb
 - lib/dicoms/shared_files.rb
 - lib/dicoms/shared_settings.rb
+- lib/dicoms/sigmoid.rb
 - lib/dicoms/stats.rb
 - lib/dicoms/support.rb
 - lib/dicoms/transfer.rb