OpenMatriX 0.1.0 → 0.2.0

checksums.yaml

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data/Debian-HOWTO.md

@@ -0,0 +1,56 @@
+# Debian Installation and Use Howto
+
+This how-to MAY be applicable to other linux distros.  This was written while making stuff work
+on a Debian Jessie virtual machine that was upgraded from Debian Wheezy.
+
+# Prep
+
+First off, remove the included hdf5 distro.  You need 1.8.15, Jessie stable comes
+with 1.8.13.  And make sure you have 64 bit Debian.  THIS WILL NOT WORK WITH A
+32 BIT OPERATING SYSTEM.
+
+```
+sudo apt-get remove libhdf5-dev
+```
+
+Download the source for hdf5 ans szip from hdf5's webpage and un-tar it, compile, test, and install it:
+```
+wget http://www.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz
+gunzip szip-2.1.tar.gz
+tar -xf szip-2.1.tar
+rm szip-2.1.tar
+cd szip-2.1
+./configure --prefix=/usr/local/hdf5
+make
+sudo make install
+
+wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.15-patch1.tar
+tar -xf hdf5-1.8.15-patch1.tar
+rm hdf5-1.8.15-patch1.tar
+cd hdf5-1.8.15-patch1
+./configure --prefix=/usr/local/hdf5 --enable-cxx --with-szlib=/usr/local/hdf5/lib
+make
+make check
+sudo make install
+sudo make check-install
+```
+
+At this time, there should be necessary .so files in /usr/local/hdf5/lib.  You need these in the linker
+path.  To add them:
+```
+cd /etc/ld.so.conf.d
+sudo touch hdf5.conf
+```
+Add (only) the line /usr/local/hdf5/lib to hdf5.conf (use whatever editor you like).  
+Then, reload the linker:
+```
+sudo ldconfig
+```
+
+# Landing
+
+Install Ruby and Rails:
+```
+sudo apt-get install ruby
+sudo apt-get install rubygems
+gem install rails

data/README.md

@@ -1,6 +1,14 @@
 # OpenMatriX
 
-OpenMatriX is a Ruby Gem to read (Open Matrix files)[https://sites.google.com/site/openmodeldata/]. This was built for use on the web and to eventually have APIs that can return values from a matrix.
+OpenMatriX is a Ruby Gem to read [Open Matrix files](https://sites.google.com/site/openmodeldata/). This was built for use on the web and to eventually have APIs that can return values from a matrix.
+
+## Requirements
+
+Windows: This has only been tested on Windows 7-64 bit.
+
+Linux: a 64-bit version is REQUIRED.  This has been tested on a 32-bit Debian VM
+and it would not work due to addressing issues, however it DOES work on a 64-bit
+Debian VM.
 
 ## Installation
 
@@ -22,25 +30,30 @@ Or install it yourself as:
 
 ```ruby
 # Open file
-# OMX::OMXFile.new(filename)
+# file_obj = OMX::OMXFile.new(filename)
 file = OMX::OMXFile.new('filename.omx')
 
 # Get the attributes from the file
+# att_obj = OMX::OMXAttr(file_obj)
 at = OMX::OMXAttr.new(file)
 puts "Version: #{at.getVersion()}"
 puts "Zones: #{at.getZones()}"
 
 # Get the tables from the file
+# table_obj = OMX::OMXTables.new(file_obj)
 t = OMX::OMXTables.new(file)
 puts "Tables: #{t.getNTables()}"
 puts "Table Names: #{t.getTableNames()}"
 
 # Get data from the file
-# OMX::OMXData.new(file,"Tablename", nZones)
+# data_object = OMX::OMXData.new(file_obj,"Tablename", number_of_zones)
 tt = OMX::OMXData.new(file,"DIST",at.getZones())
-puts tt.getJ(5)
+puts tt.getI(zone) # Returns array of all J from zone
+puts tt.getJ(zone) # Returns array of all I to zone
+puts tt.getIJ(i,j) # Returns value at i,j
 
 # Close the file
+# file_obj.close()
 file.close()
 ```
 

data/lib/OpenMatriX.rb

@@ -113,6 +113,8 @@ module OMX
     ffi_lib H5Library.library_path
     attach_function :group_open, :H5Fopen, [H5Types.hid_t, :string, H5Types.hid_t], H5Types.hid_t
     attach_function :get_type, :H5Iget_type, [H5Types.hid_t], H5Types.hid_t
+    attach_variable :h5P_CLS_GROUP_ACCESS_ID, :H5P_CLS_GROUP_ACCESS_ID_g, :int
+    attach_variable :h5P_CLS_LINK_ACCESS_ID_g, :H5P_CLS_LINK_ACCESS_ID_g, :int
     #
     # Object for wrapping an OMX file. Basic usage:
     #     file = OMX::OMXFile.new('filename.omx')
@@ -217,46 +219,63 @@ module OMX
       extend  FFI::Library
       ffi_lib H5Library.library_path
 
+      class H5GInfoT < FFI::Struct
+        layout :storType, :int,
+          :nLinks, H5Types.hsize_t,
+          :maxCOrder, :int,
+          :mounted, H5Types.hbool_t
+      end
+
+      def cast_to_H5GInfoT pointer
+        H5GInfoT.new pointer
+      end
+
+      class H5_index < FFI::Struct
+        layout :idxUnk, :int,
+          :idxName, :string,
+          :idxOrder, :int,
+          :nIdx, :int
+      end
+
+      def cast_to_H5_index pointer
+        H5_index.new pointer
+      end
+
       #hid_t H5Dopen( hid_t loc_id, const char *name )
-      attach_function :gOpen, :H5Gopen1, [H5Types.hid_t, :string], H5Types.hid_t
+      attach_function :gOpen, :H5Gopen2, [H5Types.hid_t, :string, H5Types.hid_t], H5Types.hid_t
 
-      #herr_t H5Gget_num_objs(hid_t loc_id, hsize_t* num_obj)
-      attach_function :nTables, :H5Gget_num_objs, [H5Types.hid_t, :pointer], H5Types.herr_t
+      #herr_t H5Gget_info( hid_t group_id, H5G_info_t *group_info )
+      attach_function :nTables, :H5Gget_info, [H5Types.hid_t, H5GInfoT], H5Types.herr_t
 
-      #ssize_t H5Gget_objname_by_idx(hid_t loc_id, hsize_t idx, char *name, size_t size )
-      attach_function :tNames, :H5Gget_objname_by_idx, [H5Types.hid_t, :int, :pointer, :int], :int
+      #ssize_t H5Lget_name_by_idx( hid_t loc_id, const char *group_name, H5_index_t index_field, H5_iter_order_t order, hsize_t n, char *name, size_t size, hid_t lapl_id )
+      attach_function :tNames2, :H5Lget_name_by_idx, [H5Types.hid_t, :string, :int, :int, :int, :pointer, :int, :int ], :int
 
       def initialize(file)
         @id = file.id
-        @gId = gOpen(@id, "data")
+        @gId = gOpen(@id, "data",0)
       end
 
       # A function to return the number of matrix tables. Returns an integer value
       # of the number of tables in the matrix
       def getNTables()
-        nObjs = FFI::MemoryPointer.new(H5Types.hsize_t)
-        nT = nTables(@gId, nObjs)
-        return(nObjs.read_int())
-      end
-
-      # A function to get the table info... kind of a useless function for now
-      # TODO: Can this be removed?
-      def getTableInfo()
-        sb = Statbuf.new
-        oi = tInfo(@id, "data", 0, sb)
-        puts sb[:nlink]
-        return(oi)
+        h5gi = cast_to_H5GInfoT(FFI::MemoryPointer.new :char, H5GInfoT.size)
+        op = nTables(@gId,h5gi)
+        return(h5gi[:nLinks])
       end
 
       # A function to get the table names. Returns a string array of table names.
       def getTableNames()
         nT = self.getNTables()-1
+        gName = FFI::MemoryPointer.new(:string)
+
+        pl = createpl(OMX::h5P_CLS_LINK_ACCESS_ID_g)
 
+        # Note from okiAndrew: this seems seriously kludgy, but it works.
         tN ||= []
         for t in 0..nT
-          tName = FFI::MemoryPointer.new(:string)
-          tno = tNames(@gId,t,tName,100)
-          tN << tName.read_string()
+          tn2o = tNames2(@gId, ".", 0, t, 0, gName, 20, pl)
+          #puts "gName = #{gName.read_string()}"
+          tN << gName.read_string()
         end
         return(tN)
       end

data/lib/OpenMatriX/version.rb

@@ -1,3 +1,3 @@
 module OpenMatriX
-  VERSION = "0.1.0"
+  VERSION = "0.2.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: OpenMatriX
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Andrew Rohne
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2015-10-21 00:00:00.000000000 Z
+date: 2015-11-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -90,6 +90,7 @@ files:
 - ".gitignore"
 - ".rspec"
 - ".travis.yml"
+- Debian-HOWTO.md
 - Gemfile
 - LICENSE.md
 - OpenMatriX.gemspec
@@ -119,7 +120,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.5
+rubygems_version: 2.4.8
 signing_key: 
 specification_version: 4
 summary: Open Matrix support for Ruby