ruby-hdf5 0.0.3 → 0.0.4

data/lib/hdf5/ffi_20.rb

@@ -198,39 +198,6 @@ module HDF5
 
     ImaxdivT = Anon_Type_2
 
-    attach_function 'imaxabs', [
-      :intmax_t
-    ], :intmax_t
-
-    attach_function 'imaxdiv', %i[
-      intmax_t
-      intmax_t
-    ], ImaxdivT
-
-    attach_function 'strtoimax', %i[
-      string
-      pointer
-      int
-    ], :intmax_t
-
-    attach_function 'strtoumax', %i[
-      string
-      pointer
-      int
-    ], :uintmax_t
-
-    attach_function 'wcstoimax', %i[
-      pointer
-      pointer
-      int
-    ], :intmax_t
-
-    attach_function 'wcstoumax', %i[
-      pointer
-      pointer
-      int
-    ], :uintmax_t
-
     typedef :pointer, :__gnuc_va_list
 
     typedef :pointer, :va_list
@@ -373,23 +340,6 @@ module HDF5
 
     typedef :__fd_mask, :fd_mask
 
-    attach_function 'select', [
-      :int,
-      FdSet.ptr,
-      FdSet.ptr,
-      FdSet.ptr,
-      Timeval.ptr
-    ], :int
-
-    attach_function 'pselect', [
-      :int,
-      FdSet.ptr,
-      FdSet.ptr,
-      FdSet.ptr,
-      Timespec.ptr,
-      C_SigsetT.ptr
-    ], :int
-
     typedef :__blksize_t, :blksize_t
 
     typedef :__blkcnt_t, :blkcnt_t
@@ -2950,195 +2900,6 @@ module HDF5
 
     FposT = C_FposT
 
-    attach_variable :stdin, :stdin, FILE.ptr
-
-    attach_variable :stdout, :stdout, FILE.ptr
-
-    attach_variable :stderr, :stderr, FILE.ptr
-
-    attach_function 'remove', [
-      :string
-    ], :int
-
-    attach_function 'rename', %i[
-      string
-      string
-    ], :int
-
-    attach_function 'renameat', %i[
-      int
-      string
-      int
-      string
-    ], :int
-
-    attach_function 'fclose', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'tmpfile', [], FILE.ptr
-
-    attach_function 'tmpnam', [
-      :pointer # [:char, 20]
-    ], :string
-
-    attach_function 'tmpnam_r', [
-      :pointer # [:char, 20]
-    ], :string
-
-    attach_function 'tempnam', %i[
-      string
-      string
-    ], :string
-
-    attach_function 'fflush', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'fflush_unlocked', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'fopen', %i[
-      string
-      string
-    ], FILE.ptr
-
-    attach_function 'freopen', [
-      :string,
-      :string,
-      FILE.ptr
-    ], FILE.ptr
-
-    attach_function 'fdopen', %i[
-      int
-      string
-    ], FILE.ptr
-
-    attach_function 'fopencookie', [
-      :pointer,
-      :string,
-      CookieIoFunctionsT
-    ], FILE.ptr
-
-    attach_function 'fmemopen', %i[
-      pointer
-      size_t
-      string
-    ], FILE.ptr
-
-    attach_function 'open_memstream', %i[
-      pointer
-      pointer
-    ], FILE.ptr
-
-    attach_function 'setbuf', [
-      FILE.ptr,
-      :string
-    ], :void
-
-    attach_function 'setvbuf', [
-      FILE.ptr,
-      :string,
-      :int,
-      :size_t
-    ], :int
-
-    attach_function 'setbuffer', [
-      FILE.ptr,
-      :string,
-      :size_t
-    ], :void
-
-    attach_function 'setlinebuf', [
-      FILE.ptr
-    ], :void
-
-    attach_function 'fprintf', [
-      FILE.ptr,
-      :string
-    ], :int
-
-    attach_function 'printf', [
-      :string
-    ], :int
-
-    attach_function 'sprintf', %i[
-      string
-      string
-    ], :int
-
-    attach_function 'vfprintf', [
-      FILE.ptr,
-      :string,
-      :__gnuc_va_list
-    ], :int
-
-    attach_function 'vprintf', %i[
-      string
-      __gnuc_va_list
-    ], :int
-
-    attach_function 'vsprintf', %i[
-      string
-      string
-      __gnuc_va_list
-    ], :int
-
-    attach_function 'snprintf', %i[
-      string
-      size_t
-      string
-    ], :int
-
-    attach_function 'vsnprintf', %i[
-      string
-      size_t
-      string
-      __gnuc_va_list
-    ], :int
-
-    attach_function 'vasprintf', %i[
-      pointer
-      string
-      __gnuc_va_list
-    ], :int
-
-    attach_function '__asprintf', %i[
-      pointer
-      string
-    ], :int
-
-    attach_function 'asprintf', %i[
-      pointer
-      string
-    ], :int
-
-    attach_function 'vdprintf', %i[
-      int
-      string
-      __gnuc_va_list
-    ], :int
-
-    attach_function 'dprintf', %i[
-      int
-      string
-    ], :int
-
-    attach_function 'fscanf', [
-      FILE.ptr,
-      :string
-    ], :int
-
-    attach_function 'scanf', [
-      :string
-    ], :int
-
-    attach_function 'sscanf', %i[
-      string
-      string
-    ], :int
-
     typedef :float, :_Float32
 
     typedef :double, :_Float64
@@ -3147,283 +2908,6 @@ module HDF5
 
     typedef :long_double, :_Float64x
 
-    attach_function 'fscanf', [
-      FILE.ptr,
-      :string
-    ], :int
-
-    attach_function 'scanf', [
-      :string
-    ], :int
-
-    attach_function 'sscanf', %i[
-      string
-      string
-    ], :int
-
-    attach_function 'vfscanf', [
-      FILE.ptr,
-      :string,
-      :__gnuc_va_list
-    ], :int
-
-    attach_function 'vscanf', %i[
-      string
-      __gnuc_va_list
-    ], :int
-
-    attach_function 'vsscanf', %i[
-      string
-      string
-      __gnuc_va_list
-    ], :int
-
-    attach_function 'vfscanf', [
-      FILE.ptr,
-      :string,
-      :__gnuc_va_list
-    ], :int
-
-    attach_function 'vscanf', %i[
-      string
-      __gnuc_va_list
-    ], :int
-
-    attach_function 'vsscanf', %i[
-      string
-      string
-      __gnuc_va_list
-    ], :int
-
-    attach_function 'fgetc', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'getc', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'getchar', [], :int
-
-    attach_function 'getc_unlocked', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'getchar_unlocked', [], :int
-
-    attach_function 'fgetc_unlocked', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'fputc', [
-      :int,
-      FILE.ptr
-    ], :int
-
-    attach_function 'putc', [
-      :int,
-      FILE.ptr
-    ], :int
-
-    attach_function 'putchar', [
-      :int
-    ], :int
-
-    attach_function 'fputc_unlocked', [
-      :int,
-      FILE.ptr
-    ], :int
-
-    attach_function 'putc_unlocked', [
-      :int,
-      FILE.ptr
-    ], :int
-
-    attach_function 'putchar_unlocked', [
-      :int
-    ], :int
-
-    attach_function 'getw', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'putw', [
-      :int,
-      FILE.ptr
-    ], :int
-
-    attach_function 'fgets', [
-      :string,
-      :int,
-      FILE.ptr
-    ], :string
-
-    attach_function '__getdelim', [
-      :pointer,
-      :pointer,
-      :int,
-      FILE.ptr
-    ], :__ssize_t
-
-    attach_function 'getdelim', [
-      :pointer,
-      :pointer,
-      :int,
-      FILE.ptr
-    ], :__ssize_t
-
-    attach_function 'getline', [
-      :pointer,
-      :pointer,
-      FILE.ptr
-    ], :__ssize_t
-
-    attach_function 'fputs', [
-      :string,
-      FILE.ptr
-    ], :int
-
-    attach_function 'puts', [
-      :string
-    ], :int
-
-    attach_function 'ungetc', [
-      :int,
-      FILE.ptr
-    ], :int
-
-    attach_function 'fread', [
-      :pointer,
-      :size_t,
-      :size_t,
-      FILE.ptr
-    ], :ulong
-
-    attach_function 'fwrite', [
-      :pointer,
-      :size_t,
-      :size_t,
-      FILE.ptr
-    ], :ulong
-
-    attach_function 'fread_unlocked', [
-      :pointer,
-      :size_t,
-      :size_t,
-      FILE.ptr
-    ], :size_t
-
-    attach_function 'fwrite_unlocked', [
-      :pointer,
-      :size_t,
-      :size_t,
-      FILE.ptr
-    ], :size_t
-
-    attach_function 'fseek', [
-      FILE.ptr,
-      :long,
-      :int
-    ], :int
-
-    attach_function 'ftell', [
-      FILE.ptr
-    ], :long
-
-    attach_function 'rewind', [
-      FILE.ptr
-    ], :void
-
-    attach_function 'fseeko', [
-      FILE.ptr,
-      :__off_t,
-      :int
-    ], :int
-
-    attach_function 'ftello', [
-      FILE.ptr
-    ], :__off_t
-
-    attach_function 'fgetpos', [
-      FILE.ptr,
-      FposT.ptr
-    ], :int
-
-    attach_function 'fsetpos', [
-      FILE.ptr,
-      FposT.ptr
-    ], :int
-
-    attach_function 'clearerr', [
-      FILE.ptr
-    ], :void
-
-    attach_function 'feof', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'ferror', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'clearerr_unlocked', [
-      FILE.ptr
-    ], :void
-
-    attach_function 'feof_unlocked', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'ferror_unlocked', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'perror', [
-      :string
-    ], :void
-
-    attach_function 'fileno', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'fileno_unlocked', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'pclose', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'popen', %i[
-      string
-      string
-    ], FILE.ptr
-
-    attach_function 'ctermid', [
-      :string
-    ], :string
-
-    attach_function 'flockfile', [
-      FILE.ptr
-    ], :void
-
-    attach_function 'ftrylockfile', [
-      FILE.ptr
-    ], :int
-
-    attach_function 'funlockfile', [
-      FILE.ptr
-    ], :void
-
-    attach_function '__uflow', [
-      FILE.ptr
-    ], :int
-
-    attach_function '__overflow', [
-      FILE.ptr,
-      :int
-    ], :int
-
     enum :H5E_type_t, [
       :H5E_MAJOR, 0,
       :H5E_MINOR, 1

data/lib/hdf5/file.rb

@@ -88,13 +88,31 @@ module HDF5
     end
 
     def create_group(name, &block)
-      ensure_open!
-      Group.create(@file_id, name, @context, &block)
+      group = @context.synchronize do
+        ensure_open!
+        Group.create(@file_id, name, @context)
+      end
+      return group unless block
+
+      begin
+        block.call(group)
+      ensure
+        group.close
+      end
     end
 
     def create_dataset(name, data = nil, **options, &block)
-      ensure_open!
-      Dataset.create(@file_id, name, data, context: @context, **options, &block)
+      dataset = @context.synchronize do
+        ensure_open!
+        Dataset.create(@file_id, name, data, context: @context, **options)
+      end
+      return dataset unless block
+
+      begin
+        block.call(dataset)
+      ensure
+        dataset.close
+      end
     end
 
     def list_entries
@@ -179,6 +197,6 @@ module HDF5
       info[:type] == :H5O_TYPE_DATASET
     end
 
-    prepend FileContext.guard(:flush, :create_group, :create_dataset, :list_entries, :[], :attrs)
+    prepend FileContext.guard(:flush, :list_entries, :[], :attrs, :close, :closed?)
   end
 end

data/lib/hdf5/group.rb

@@ -53,13 +53,31 @@ module HDF5
     end
 
     def create_group(name, &block)
-      ensure_open!
-      self.class.create(@group_id, name, @context, &block)
+      group = HDF5::FFI::CALL_LOCK.synchronize do
+        ensure_open!
+        self.class.create(@group_id, name, @context)
+      end
+      return group unless block
+
+      begin
+        block.call(group)
+      ensure
+        group.close
+      end
     end
 
     def create_dataset(name, data = nil, **options, &block)
-      ensure_open!
-      Dataset.create(@group_id, name, data, context: @context, **options, &block)
+      dataset = HDF5::FFI::CALL_LOCK.synchronize do
+        ensure_open!
+        Dataset.create(@group_id, name, data, context: @context, **options)
+      end
+      return dataset unless block
+
+      begin
+        block.call(dataset)
+      ensure
+        dataset.close
+      end
     end
 
     def list_entries
@@ -148,6 +166,6 @@ module HDF5
       info[:type] == :H5O_TYPE_DATASET
     end
 
-    prepend FileContext.guard(:create_group, :create_dataset, :list_entries, :list_datasets, :[], :attrs)
+    prepend FileContext.guard(:list_entries, :list_datasets, :[], :attrs, :close, :closed?)
   end
 end

data/lib/hdf5/hierarchy.rb

@@ -102,6 +102,6 @@ module HDF5
       self
     end
 
-    prepend FileContext.guard(*instance_methods(false))
+    prepend FileContext.guard(*(instance_methods(false) - %i[each_key open_dataset]))
   end
 end

data/lib/hdf5/selection.rb

@@ -17,8 +17,10 @@ module HDF5
       @stride = []
       @count = []
       @result_shape = []
+      @result_axes = []
 
-      selectors.zip(shape).each do |selector, dimension|
+      selectors.zip(shape).each_with_index do |(selector, dimension), axis|
+        @result_axes << axis unless selector.is_a?(Integer)
         normalize_axis(selector, dimension)
       end
     end
@@ -31,6 +33,20 @@ module HDF5
       count.inject(1, :*)
     end
 
+    def block(ranges)
+      result = dup
+      starts = start.dup
+      counts = count.dup
+      @result_axes.zip(ranges).each do |axis, range|
+        starts[axis] += range.begin * stride[axis]
+        counts[axis] = range.end - range.begin
+      end
+      result.instance_variable_set(:@start, starts)
+      result.instance_variable_set(:@count, counts)
+      result.instance_variable_set(:@result_shape, ranges.map { |range| range.end - range.begin })
+      result
+    end
+
     private
 
     def normalize_axis(selector, dimension)