hdf5: work more broadly

Author: scivision

+stdlib/auto_chunk_size.m

@@ -7,9 +7,9 @@
 % * dims: proposed dataset dimensions (like size())
 
 function csize = auto_chunk_size(dims)
-arguments
-  dims (1,:) {mustBeInteger,mustBePositive}
-end
+% arguments
+%   dims (1,:) {mustBeInteger,mustBePositive}
+% end
 
 CHUNK_BASE = 16000;  % Multiplier by which chunks are adjusted
 CHUNK_MIN = 8000;    % lower limit: 8 kbyte

+stdlib/h5create_group.m

@@ -7,10 +7,10 @@
 % * HDF5 file handle
 
 function fid = h5create_group(file, hpath)
-arguments
-  file (1,1)
-  hpath (1,1) string
-end
+% arguments
+%   file (1,1)
+%   hpath (1,1) string
+% end
 
 % polymorphic fid/filename
 if isa(file, 'H5ML.id')
@@ -25,17 +25,18 @@
 end
 
 % are there any groups
-grps = split(hpath, "/");
+grps = split(hpath, '/');
 if length(grps) < 3
   return
 end
 
 % recursively create groups as needed
 plist = 'H5P_DEFAULT';
-groot = H5G.open(fid, "/");
+groot = H5G.open(fid, '/');
 
 for i = 0:length(grps) - 3
-  n = join(grps(1:i+2), "/");
+  n = join(grps(1:i+2), '/');
+  n = n{1};
 
   if ~H5L.exists(groot, n, plist)
     gid = H5G.create(fid, n, plist, plist, plist);

+stdlib/h5save.m

@@ -18,15 +18,23 @@
 % Likewise, the type of the dataset may be explicitly specified with the "type" argument.
 %  h5save(filename, dataset_name, dataset, type="int32")
 
-function h5save(filename, varname, A, opts)
-arguments
-  filename (1,1) string
-  varname (1,1) string
-  A {mustBeNonempty}
-  opts.size (1,:) double {mustBeInteger,mustBeNonnegative} = []
-  opts.type (1,1) string = ""
-  opts.compressLevel (1,1) double {mustBeInteger,mustBeNonnegative} = 0
-end
+function h5save(filename, varname, A, varargin)
+% arguments
+%   filename (1,1) string
+%   varname (1,1) string
+%   A {mustBeNonempty}
+%   opts.size (1,:) double {mustBeInteger,mustBeNonnegative} = []
+%   opts.type (1,1) string = ""
+%   opts.compressLevel (1,1) double {mustBeInteger,mustBeNonnegative} = 0
+% end
+
+p = inputParser;
+addParameter(p, 'size', []);
+addParameter(p, 'type', '');
+addParameter(p, 'compressLevel', 0, @(x) mustBeInteger(x) && mustBeNonnegative(x));
+parse(p, varargin{:});
+
+opts = p.Results;
 
 if isnumeric(A)
   mustBeReal(A)
@@ -42,7 +50,7 @@ function h5save(filename, varname, A, opts)
   h5save_exist(filename, varname, A, opts.size)
 catch e
   switch e.identifier
-    case {'MATLAB:imagesci:hdf5io:resourceNotFound', 'MATLAB:imagesci:h5info:unableToFind', 'MATLAB:imagesci:h5info:fileOpenErr'}
+    case {'MATLAB:imagesci:hdf5io:resourceNotFound', 'MATLAB:imagesci:h5info:unableToFind', 'MATLAB:imagesci:h5info:fileOpenErr', 'MATLAB:imagesci:h5info:libraryError'}
       h5save_new(filename, varname, A, opts.size, opts.compressLevel)
     otherwise
       rethrow(e)

+stdlib/h5size.m

@@ -8,7 +8,8 @@
 
 function fsize = h5size(file, variable)
 
-dsi = h5info(file, variable).Dataspace;
+finf = h5info(file, variable);
+dsi = finf.Dataspace;
 
 if dsi.Type == "scalar"
   fsize = [];

+stdlib/h5variables.m

@@ -9,16 +9,11 @@
 % * names: variable names
 
 function names = h5variables(file, group)
-arguments
-  file
-  group (1,1) string = ""
+if nargin < 2
+  group = '/';
 end
 
-if stdlib.strempty(group)
-  finf = h5info(file);
-else
-  finf = h5info(file, group);
-end
+finf = h5info(file, group);
 
 ds = finf.Datasets;
 

+stdlib/private/coerce_ds.m

@@ -1,9 +1,9 @@
 function A = coerce_ds(A, dtype)
 % used by h5save and ncsave
-arguments
-  A
-  dtype (1,1) string
-end
+% arguments
+%   A
+%   dtype (1,1) string
+% end
 
 if ischar(A)
   A = string(A);

+stdlib/private/h5save_exist.m

@@ -2,11 +2,14 @@
 % normally users use h5save() instead of this function
 
 function h5save_exist(filename, varname, A, sizeA)
-arguments
-  filename
-  varname
-  A
-  sizeA (1,:) double {mustBeInteger,mustBeNonnegative} = []
+% arguments
+%   filename
+%   varname
+%   A
+%   sizeA (1,:) double {mustBeInteger,mustBeNonnegative} = []
+% end
+if nargin < 4
+  sizeA = [];
 end
 
 diskshape = stdlib.h5size(filename, varname);

+stdlib/private/h5save_new.m

@@ -2,13 +2,20 @@
 % normally users will use h5save() instead of this function
 
 function h5save_new(filename, varname, A, sizeA, compressLevel)
-arguments
-  filename
-  varname
-  A
-  sizeA (1,:) double {mustBeInteger,mustBeNonnegative} = []
-  compressLevel (1,1) double {mustBeInteger,mustBeNonnegative} = 0
+% arguments
+%   filename
+%   varname
+%   A
+%   sizeA (1,:) double {mustBeInteger,mustBeNonnegative} = []
+%   compressLevel (1,1) double {mustBeInteger,mustBeNonnegative} = 0
+% end
+if nargin < 4
+  sizeA = [];
 end
+if nargin < 5
+  compressLevel = 0;
+end
+
 
 if isempty(sizeA)
   sizeA = defaultSize(A);

+stdlib/private/h5save_scalar.m

@@ -1,12 +1,12 @@
 function h5save_scalar(filename, hpath, A)
 %% write HDF5 scalar as a scalar
 %  h5create doesn't support scalars
-arguments
-  filename (1,1) string
-  hpath (1,1) string
-  A (1,1)
-end
-% filename must be a scalar string--char does not work
+% arguments
+%   filename (1,1) string
+%   hpath (1,1) string
+%   A (1,1)
+% end
+
 
 dcpl = 'H5P_DEFAULT';
 

test/TestHDF5.m

@@ -16,9 +16,9 @@
 
 properties (TestParameter)
 str = {"string", 'char'}
-type = {"single", "double", ...
-            "int8", "int16", "int32", "int64", ...
-            "uint8", "uint16", "uint32", "uint64", "string"}
+type = {'single', 'double', ...
+            'int8', 'int16', 'int32', 'int64', ...
+            'uint8', 'uint16', 'uint32', 'uint64', 'string'}
 end
 
 methods(TestClassSetup)
@@ -34,9 +34,9 @@ function setupData(tc)
 methods(TestMethodSetup)
 
 function setup_file(tc)
-tc.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture())
+tc.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture());
 
-tc.file = fullfile(pwd(), class(tc) + ".h5");
+tc.file = [pwd(), class(tc), '.h5'];
 
 % create test data first, so that parallel tests works
 stdlib.h5save(tc.file, '/A0', tc.A0)
@@ -57,13 +57,12 @@ function setup_file(tc)
 stdlib.h5save(tc.file, '/t/y', 13)
 stdlib.h5save(tc.file, '/j/a/b', 6)
 
-tc.assertThat(tc.file, matlab.unittest.constraints.IsFile)
 end
 
 end
 
 
-methods (Test, TestTags = {'R2019b'})
+methods (Test, TestTags = {'R2017b'})
 
 function test_auto_chunk_size(tc)
 
@@ -89,19 +88,19 @@ function test_get_variables(tc)
 tc.verifyEqual(sort(v), k)
 
 % 1-level group
-v = stdlib.h5variables(tc.file, "/t");
+v = stdlib.h5variables(tc.file, '/t');
 tc.verifyEqual(sort(v), ["x", "y"])
 
 % traversal
-tc.verifyEmpty(stdlib.h5variables(tc.file, "/j") )
+tc.verifyEmpty(stdlib.h5variables(tc.file, '/j') )
 
-tc.verifyEqual(stdlib.h5variables(tc.file, "/j/a") , "b")
+tc.verifyEqual(stdlib.h5variables(tc.file, '/j/a') , "b")
 
 end
 
 
 function test_exists(tc)
-e = stdlib.h5exists(tc.file, "/A0");
+e = stdlib.h5exists(tc.file, '/A0');
 
 tc.verifyThat(e, matlab.unittest.constraints.IsScalar)
 tc.verifyTrue(e);
@@ -178,11 +177,11 @@ function test_read(tc)
 
 function test_shape(tc)
 
-stdlib.h5save(tc.file, "/vector1", 34, "size", 1)
+stdlib.h5save(tc.file, '/vector1', 34, "size", 1)
 s = stdlib.h5size(tc.file, '/vector1');
 tc.verifyEqual(s, 1);
 
-stdlib.h5save(tc.file, "/scalar", 34, "size", 0)
+stdlib.h5save(tc.file, '/scalar', 34, "size", 0)
 s = stdlib.h5size(tc.file, '/scalar');
 tc.verifyEmpty(s);
 
@@ -195,14 +194,14 @@ function test_coerce(tc, type)
   tc.assumeFalse(stdlib.matlabOlderThan("R2020b"))
 end
 
-stdlib.h5save(tc.file, "/" + type, 0, "type", type)
+stdlib.h5save(tc.file, ['/', type], 0, "type", type)
 
 switch type
 case "string", vt = 'char';
 otherwise, vt = type;
 end
 
-tc.verifyClass(h5read(tc.file, "/"+type), vt)
+tc.verifyClass(h5read(tc.file, ['/', type]), vt)
 
 end
 
@@ -216,33 +215,33 @@ function test_rewrite(tc)
 
 function test_int8(tc)
 
-stdlib.h5save(tc.file, "/i1", int8(127))
+stdlib.h5save(tc.file, '/i1', int8(127))
 
-a = h5read(tc.file, "/i1");
+a = h5read(tc.file, '/i1');
 tc.verifyEqual(a, int8(127))
 
 % test rewrite
-stdlib.h5save(tc.file, "/i1", int8(-128))
+stdlib.h5save(tc.file, '/i1', int8(-128))
 
-a = h5read(tc.file, "/i1");
+a = h5read(tc.file, '/i1');
 tc.verifyEqual(a, int8(-128))
 
 % test int8 array
-stdlib.h5save(tc.file, "/Ai1", int8([1, 2]))
-a = h5read(tc.file, "/Ai1");
+stdlib.h5save(tc.file, '/Ai1', int8([1, 2]))
+a = h5read(tc.file, '/Ai1');
 tc.verifyEqual(a, int8([1;2]))
 end
 
 function test_real_only(tc)
 
-tc.verifyError(@() stdlib.h5save(tc.file, "/bad_imag", 1j), 'MATLAB:validators:mustBeReal')
+tc.verifyError(@() stdlib.h5save(tc.file, '/bad_imag', 1j), 'MATLAB:validators:mustBeReal')
 tc.verifyError(@() stdlib.h5variables(tc.file, '/nothere'), 'MATLAB:imagesci:h5info:unableToFind')
 end
 
 end
 
 
-methods (Test, TestTags=["R2020b", "hdf5"])
+methods (Test, TestTags={'R2020b'})
 
 function test_string(tc, str)
 tc.assumeFalse(stdlib.matlabOlderThan("R2020b"))