initial commit

Author: scivision

.github/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at info@scivision.dev. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

.github/FUNDING.yml

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+# These are supported funding model platforms
+
+github: [scivision]
+ko_fi: scivision

.github/workflows/ci.yml

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+name: ci
+
+on:
+  push:
+    paths:
+    - "**.m"
+    - ".github/workflows/ci.yml"
+
+jobs:
+
+  linux:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - run: |
+        sudo apt -yq update
+        sudo apt install -yq --no-install-recommends octave octave-netcdf
+
+    - run: octave-cli --eval test_netcdf

Readme.md

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+# Matlab HDF5 and NetCDF4 high-level functions
+
+![ci](https://github.com/scivision/matlab-hdf5/workflows/ci/badge.svg)
+
+These functions are sorely needed in Matlab itself.
+The NetCDF4 functions also work with GNU Octave when octave-netcdf is installed.
+
+## hdf5
+
+* Check that a dataset exists in file:
+
+    ```matlab
+    h5exists(filename, dataset_name)
+    ```
+
+* Save a varable to a dataset. If dataset exists, the existing dataset shape must match the variable.
+
+    ```matlab
+    h5save(filename, dataset_name, dataset)
+    ```
+
+* Get the dataset size (shape)
+
+    ```matlab
+    h5size(filename, dataset_name)
+    ```
+
+* Get the names of all datasets in a file
+
+    ```matlab
+    h5variables(filename)
+    ```
+
+### netcdf
+
+* Check that a variable exists in file:
+
+    ```matlab
+    ncexists(filename, variable_name)
+    ```
+
+* Save a varable to a dataset. If dataset exists, the existing dataset shape must match the variable.
+
+    ```matlab
+    ncsave(filename, variable_name, variable)
+    ```
+
+* Get the dataset size (shape)
+
+    ```matlab
+    ncsize(filename, variable_name)
+    ```
+
+* Get the names of all datasets in a file
+
+    ```matlab
+    ncvariables(filename)
+    ```

coerce_ds.m

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+function A = coerce_ds(A, dtype)
+% used by h5save and ncsave
+narginchk(2,2)
+validateattributes(A, {'numeric'}, {'nonempty'},1)
+validateattributes(dtype, {'char'}, {'vector'},2)
+
+switch dtype
+  case {'float64', 'double'}
+    if ~isa(A, 'double')
+      A = double(A);
+    end
+  case {'float32', 'single'}
+    if ~isa(A, 'single')
+      A = single(A);
+    end
+  case {'int32'}
+     if ~isa(A, 'int32')
+       A = int32(A);
+     end
+  case {'int64'}
+     if ~isa(A, 'int64')
+       A = int64(A);
+     end
+  case {'char', 'string'}
+    if ~isstring(A)
+      A = string(A);
+    end
+  otherwise, error('create_ds:type_error', 'unknown data type %s', dtype)
+end
+
+end % function

expanduser.m

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+%!assert(ischar(expanduser('~')))
+function expanded = expanduser(p)
+% expanded = expanduser(path)
+%
+%   expands tilde ~ into user home directory for Matlab and GNU Octave.
+%
+%   Useful for Matlab functions like h5read() and some Computer Vision toolbox functions
+%   that can't handle ~ and Matlab does not consider it a bug per conversations with
+%   Mathworks staff
+%
+%  Benchmark: on laptop and Matlab R2020a
+%
+%   about 200 microseconds
+%   f = @() expanduser('~/foo');
+%   timeit(f)
+%
+%   about 2 microseconds:
+%   f = @() expanduser('foo');
+%   timeit(f)
+%
+%   See also absolute_path
+
+narginchk(1,1)
+
+if isempty(p)
+  expanded = '';
+  return
+end
+
+validateattributes(p, {'char'}, {'vector'})
+%% GNU Octave
+if isoctave
+  expanded = tilde_expand(p);
+  return
+end
+
+%% Matlab
+expanded = p;
+
+if strcmp(expanded(1), '~')
+
+  home = [];
+  if isunix
+    home = getenv('HOME');
+  elseif ispc
+    home = getenv('USERPROFILE');
+  end
+
+  if isempty(home)
+    % this is 100x slower than getenv() on Matlab R2020a
+    home = char(java.lang.System.getProperty("user.home"));
+  end
+
+  expanded = fullfile(home, expanded(2:end));
+end
+
+end %function

h5exists.m

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+function exists = h5exists(filename, varname)
+% check if variable exists in HDF5 file
+%
+% filename: HDF5 filename
+% varname: name of variable inside HDF5 file
+%
+% exists: boolean
+
+narginchk(2,2)
+validateattributes(varname, {'char'}, {'vector'}, 2)
+
+filename = expanduser(filename);
+
+vars = {};
+if is_file(filename)
+  vars = h5variables(filename);
+end
+
+exists = any(strcmp(vars, varname(2:end)));
+
+end % function

h5save.m

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+function h5save(filename, varname, A, sizeA, dtype)
+
+narginchk(3, 5)
+
+if nargin < 4 || isempty(sizeA)
+  if isvector(A)
+    sizeA = length(A);
+  else
+    sizeA = size(A);
+  end
+end
+
+if nargin >= 5 && ~isempty(dtype)
+  A = coerce_ds(A, dtype);
+end
+if ischar(A)
+  A = string(A);
+  sizeA = size(A);
+end
+
+
+
+if h5exists(filename, varname)
+  exist_file(filename, varname, A, sizeA)
+else
+  new_file(filename, varname, A, sizeA)
+end % if
+
+end % function
+
+
+function exist_file(filename, varname, A, sizeA)
+
+diskshape = h5size(filename, varname);
+if length(diskshape) >= 2
+  % start is always a row vector, regardless of shape of array
+  start = ones(1,ndims(A));
+elseif ~isempty(diskshape)
+  start = 1;
+end
+
+if isscalar(A)
+  h5write(filename, varname, A)
+elseif all(diskshape == sizeA)
+  h5write(filename, varname, A, start, sizeA)
+elseif all(diskshape == fliplr(sizeA))
+  h5write(filename, varname, A.', start, fliplr(sizeA))
+else
+  error('h5save:value_error', ['shape of ',varname,': ', int2str(sizeA), ' does not match existing HDF5 shape ', int2str(diskshape)])
+end
+
+end % function
+
+
+function new_file(filename, varname, A, sizeA)
+
+if ~ismatrix(A)
+  % enable Gzip compression--remember Matlab's dim order is flipped from
+  % C / Python
+  switch length(sizeA)
+    case 4, chunksize = [sizeA(1), sizeA(2), 1, sizeA(4)];
+    case 3, chunksize = [sizeA(1), sizeA(2), 1];
+    otherwise, error('h5save:fixme', '%s is bigger than 4 dims', varname)
+  end
+  h5create(filename, varname, sizeA, 'DataType', class(A), ...
+    'Deflate', 1, 'Fletcher32', true, 'Shuffle', true, 'ChunkSize', chunksize)
+else
+  h5create(filename, varname, sizeA, 'DataType', class(A))
+end % if
+
+h5write(filename, varname, A)
+
+end % function
+
+
+
+% Copyright 2020 Michael Hirsch, Ph.D.
+
+% Licensed under the Apache License, Version 2.0 (the "License");
+% you may not use this file except in compliance with the License.
+% You may obtain a copy of the License at
+
+%     http://www.apache.org/licenses/LICENSE-2.0
+
+% Unless required by applicable law or agreed to in writing, software
+% distributed under the License is distributed on an "AS IS" BASIS,
+% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+% See the License for the specific language governing permissions and
+% limitations under the License.

h5size.m

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+function fsize = h5size(filename, variable)
+% get size (shape) of an HDF5 dataset
+%
+% filename: HDF5 filename
+% variable: name of variable inside HDF5 file
+%
+% fsize: vector of variable size per dimension
+
+narginchk(2,2)
+validateattributes(variable, {'char'}, {'vector'}, 2)
+
+finf = h5info(expanduser(filename), variable);
+fsize = finf.Dataspace.Size;
+
+end % function

h5variables.m

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+function [names, groups] = h5variables(filename)
+% get dataset names and groups in an HDF5 file
+narginchk(1,1)
+
+% use temporary variable to be R2017b OK
+finf = h5info(filename);
+ds = finf.Datasets;
+
+names = {ds(:).Name};
+
+if nargout > 1
+  groups = {finf.Groups};
+end
+
+end % function