Merge pull request #47 from natacha-beck/bb_hdf-5

BrainBrowser read directly HDF5 file

userfiles/minc1_file/minc1_file.rb

@@ -33,5 +33,11 @@ def self.pretty_type #:nodoc:
     "Minc1 File"
   end
 
+  # Overwrite the method in order to
+  # call the "volume_viewer_loader" of MincFile
+  def view_path(partial_name=nil)
+     MincFile.view_path(partial_name)
+  end
+
 end
 

userfiles/minc2_file/minc2_file.rb

@@ -37,5 +37,11 @@ def has_minctools?(min_version=[2,0,0],which_tools=["mincinfo", "minctoraw"])  #
     super
   end
 
+  # Overwrite the method in order to
+  # call the "volume_viewer_loader" of MincFile
+  def view_path(partial_name=nil)
+     MincFile.view_path(partial_name)
+  end
+
 end
 

userfiles/minc_file/minc_file.rb

@@ -37,6 +37,7 @@ class MincFile < SingleFile
 
   has_content :method => :get_headers_to_json, :type => :text
   has_content :method => :get_raw_data,        :type => :text
+  has_content :method => :raw_content,         :type => :text
 
   def self.file_name_pattern #:nodoc:
     /\.mi?nc(\.gz|\.Z|\.gz2)?$/i
@@ -115,6 +116,15 @@ def get_raw_data #:nodoc:
     @raw_data = IO.popen("minctoraw -byte -unsigned -normalize #{escaped_path}") { |fh| fh.readlines.join }
   end
 
+  #For content
+  def raw_content
+    if self.name =~ /(\.gz|\.Z|\.gz2)$/i
+      IO.popen("gunzip -c #{self.cache_full_path.to_s.bash_escape}") { |fh| fh.readlines.join }
+    else
+      File.open(self.cache_full_path, "r").read
+    end
+  end
+
   def minc_get_data #:nodoc:
     @data ||= self.raw_data.unpack('v*') #Unpack is used here to convert 4 byte(char) to a short unsigned integer
   end

userfiles/minc_file/views/_volume_viewer_loader.html.erb

@@ -18,8 +18,8 @@ viewer.loadVolumes({
       volumes: [
         {
           type: "minc",
-          header_url:   "<%= content_userfile_path(@userfile) + "?content_loader=get_headers_to_json" %>",
-          raw_data_url: "<%= content_userfile_path(@userfile) + "?content_loader=get_raw_data" %>",
+          header_url:   "",
+          raw_data_url: "<%= content_userfile_path(@userfile) + "?content_loader=raw_content" %>",
         },
       ],
       complete: function() {