Put name on everything in prep for v1.0

JonKing93 · Jan 24, 2019 · 740a4ea · 740a4ea
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Showing 78 changed files with 521 additions and 128 deletions.
diff --git a/1. File IO/User Operations/buildMetadata.m b/1. File IO/User Operations/buildMetadata.m
@@ -24,7 +24,7 @@
 % ----- Outputs -----
 %
 % meta: The metadata structure used by dash.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 %

diff --git a/1. File IO/User Operations/deleteGridfile.m b/1. File IO/User Operations/deleteGridfile.m
@@ -24,7 +24,7 @@
 % meta: A metadata structure built for Dash. Metadata at the indices for
 %       deletion are compared to this structure. If the metadata do not 
 %       match, the deletion is aborted.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/1. File IO/User Operations/extendGridfile.m b/1. File IO/User Operations/extendGridfile.m
@@ -30,7 +30,7 @@
 % meta: A vector containing metadata for the new indices along the 
 %       extended dimension. (NOT a metadata structure) If STRIDE > 1, must
 %       include metadata for extended indices at which data is not written.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/1. File IO/User Operations/fillGridfile.m b/1. File IO/User Operations/fillGridfile.m
@@ -24,7 +24,7 @@
 % meta: A metadata structure built for dash. Metadata at the fill
 %       indices are compared to this structure. If the metadata do not 
 %       match, the fill is aborted.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/1. File IO/User Operations/indexGridfile.m b/1. File IO/User Operations/indexGridfile.m
@@ -1,4 +1,3 @@
-%% This adds new data to indices.
 function[] = indexGridfile( file, gridData, gridDims, loc, meta )
 %% Writes data to specified exisiting indices in a gridded .mat file.
 %
@@ -28,7 +27,7 @@
 % meta: A metadata structure built for dash. Metadata at the write indices
 %       are compared to this structure. If the metadata do not match, the
 %       write is aborted.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/1. File IO/User Operations/metaGridfile.m b/1. File IO/User Operations/metaGridfile.m
@@ -14,7 +14,7 @@
 % dimID: The order of the dimensions of the saved gridded data.
 %
 % gridSize: The size of the gridded data.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/1. File IO/User Operations/newGridfile.m b/1. File IO/User Operations/newGridfile.m
@@ -16,7 +16,7 @@
 %
 % meta: A metadata structure for the gridded data. See the buildMetadata.m
 %       function.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/1. File IO/Utilities/compareMetadata.m b/1. File IO/Utilities/compareMetadata.m
@@ -12,6 +12,9 @@
 %
 % ic: A cell of indices specifying metadata indices in m.
 
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
+
 % Get the existing metadata
 oldMeta = m.meta;
 dimID = m.dimID;

diff --git a/1. File IO/Utilities/fileCheck.m b/1. File IO/Utilities/fileCheck.m
@@ -16,6 +16,9 @@
 %
 % m: A matfile object for a gridded .mat file.
 
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
+
 % Check that the file is a .mat file
 if isstring(file)
     file = char(file);

diff --git a/1. File IO/Utilities/fullSize.m b/1. File IO/Utilities/fullSize.m
@@ -14,6 +14,9 @@
 %
 % siz: The size of the array.
 
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
+
 % Get the size
 siz = size(X);
 nDim = numel(siz);

diff --git a/1. File IO/Utilities/getIndexCell.m b/1. File IO/Utilities/getIndexCell.m
@@ -17,6 +17,9 @@
 %
 % nAdd: The number of new indices added in each dimension.
 
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
+
 % Get the size of the existing data
 sData = size( m.gridData );
 nDim = numel(sData);   

diff --git a/1. File IO/Utilities/getPermutation.m b/1. File IO/Utilities/getPermutation.m
@@ -17,6 +17,9 @@
 %
 % permDex: The permutation index.
 
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
+
 % Check that the values are all recognized
 allVals = [X(:);Y(:)];
 for d = 1:numel(allVals)

diff --git a/1. File IO/Utilities/permuteInputs.m b/1. File IO/Utilities/permuteInputs.m
@@ -19,6 +19,9 @@
 %
 % dimLoc: Permuted indexing locations.
 
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
+
 % Get the permutation ordering
 permDex = getPermutation( gridDims, m.dimID, getKnownIDs );
 

diff --git a/2. Design State Vector/User Operations/addVariable.m b/2. Design State Vector/User Operations/addVariable.m
@@ -20,7 +20,7 @@
 % ----- Outputs -----
 %
 % design: The updated state vector design.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/2. Design State Vector/User Operations/coupleVariables.m b/2. Design State Vector/User Operations/coupleVariables.m
@@ -18,7 +18,7 @@
 % ----- Outputs -----
 %
 % design: The updated state vector design.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/2. Design State Vector/User Operations/deleteVariable.m b/2. Design State Vector/User Operations/deleteVariable.m
@@ -13,7 +13,7 @@
 % ----- Outputs -----
 %
 % design: The updated state vector design.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/2. Design State Vector/User Operations/dispDesign.m b/2. Design State Vector/User Operations/dispDesign.m
@@ -16,6 +16,20 @@
 % dispDesign( d, var, dim, longform )
 % Specifies whether to display all metadata values in the state or ensemble
 % indices of a specific dimension of a variable in a state vector design.
+%
+% ----- Inputs -----
+%
+% d: A state vector design
+%
+% var: The name of a variable in the design
+%
+% dim: The name of a dimension in the variable
+%
+% longform: A scalar logical. If true, displays all dimension metadata at
+%       the state or ensemble indices.
+
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
 
 % Check the design is a design
 if ~isa(d, 'stateDesign')

diff --git a/2. Design State Vector/User Operations/editDesign.m b/2. Design State Vector/User Operations/editDesign.m
@@ -65,6 +65,10 @@
 % overlap: A scalar logical indicating whether to allow non-duplicate,
 %       overlapping sequences in the ensemble.
 %
+% ----- Outputs -----
+%
+% design: The updated state vector design.
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/2. Design State Vector/User Operations/syncVariables.m b/2. Design State Vector/User Operations/syncVariables.m
@@ -24,7 +24,7 @@
 % ----- Outputs -----
 %
 % design: The updated state vector design
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/2. Design State Vector/User Operations/uncoupleVariables.m b/2. Design State Vector/User Operations/uncoupleVariables.m
@@ -17,7 +17,7 @@
 % ----- Outputs -----
 %
 % design: The updated state vector design.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/2. Design State Vector/User Operations/unsyncVariables.m b/2. Design State Vector/User Operations/unsyncVariables.m
@@ -19,7 +19,7 @@
 % ----- Outputs -----
 %
 % design: The updated state vector design.
-%
+
 % ----- Written By -----
 % Jonathan King, University of Arizona, 2019
 

diff --git a/2. Design State Vector/Utilities/Dimension Indices/ensDimension.m b/2. Design State Vector/Utilities/Dimension Indices/ensDimension.m
@@ -1,5 +1,20 @@
 function[design] = ensDimension( design, var, dim, varargin )
 %% Edits an ensemble dimension.
+%
+% See editDesign for use.
+%
+% ----- Inputs -----
+%
+% design: the state vector design
+%
+% var: Variable name
+%
+% dim: Dimension name
+%
+% flags: 'index','seq','mean','nanflag','meta','overlap'
+
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
 
  % Parse inputs
 [index, seq, mean, nanflag, ensMeta, overlap] = parseInputs( varargin, ...

diff --git a/2. Design State Vector/Utilities/Dimension Indices/getMatchingMetaDex.m b/2. Design State Vector/Utilities/Dimension Indices/getMatchingMetaDex.m
@@ -1,6 +1,28 @@
 function[index, ix] = getMatchingMetaDex( var, dim, meta, isState )
 %% This gets indices of a dimensions of a specific variables that match a
 % metadata template.
+%
+% [index, ix] = getMatchingMetaDex( var, dim, meta, isState )
+% Returns indices that match a metadata template.
+%
+% ----- Inputs -----
+%
+% var: A varDesign
+%
+% dim: Dimension name
+%
+% meta: Metadata template for the dimension.
+%
+% isState: Scalar logical. True if for state dimensions, false for ens.
+%
+% ----- Outputs -----
+%
+% index: The indices in the variable that match the metadata
+% 
+% ix: The indices in the template that the variable matches.
+
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
 
 % Get the metadata for the variable in the dimension
 dimMeta = var.meta.(dim);

diff --git a/2. Design State Vector/Utilities/Dimension Indices/stateDimension.m b/2. Design State Vector/Utilities/Dimension Indices/stateDimension.m
@@ -1,5 +1,19 @@
 function[design] = stateDimension( design, var, dim, varargin )
 %% Edits a state dimension.
+%
+% See editDesign for use.
+%
+% ----- Inputs ----- 
+% design: state vector design
+%
+% var: Variable name
+%
+% dim: Dimension name
+%
+% flags: 'index','mean','nanflag'
+
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
 
 % Parse the inputs
 [index, takeMean, nanflag] = parseInputs( varargin, {'index','mean','nanflag'}, {[],[],[]}, {[],[],{'omitnan','includenan'}} );

diff --git a/2. Design State Vector/Utilities/Display/dispDimension.m b/2. Design State Vector/Utilities/Display/dispDimension.m
@@ -1,4 +1,19 @@
 function[] = dispDimension(var, d, long)
+%% Displays the design of a dimension in a variable in a state vector design.
+%
+% dispDimension( var, d, long )
+%
+% ----- Inputs -----
+%
+% var: A varDesign
+%
+% d: The index of the dimension in the varDesign
+%
+% long: Logical scalar indicating whether to display indexed metadata. True
+%   to display, false (default) to not display.
+
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
 
 % Dimension name
 fprintf('\t\t\t%s\n', var.dimID{d});

diff --git a/2. Design State Vector/Utilities/Display/dispVariable.m b/2. Design State Vector/Utilities/Display/dispVariable.m
@@ -1,32 +1,49 @@
-function[] = dispVariable( d, v, dim, longform )
+function[] = dispVariable( design, v, dim, longform )
+%% Displays a variable in a state vector design.
+%
+% dispVariable( design, v, dim, longform )
+%
+% ----- Inputs -----
+%
+% design: A state vector design
+%
+% v: The index of a variable in the design.
+%
+% dim: The name of a dimension to display or 'all' to display all
+%   dimensions.
+%
+% long: Logical scalar for whether to display indexed dimensional metadata.
+
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
 
 % Get the variables
 if strcmp(dim,'all')
-    dim = 1:numel(d.var(v).dimID);
+    dim = 1:numel(design.var(v).dimID);
 end
 
 % Variable name 
-fprintf('\t%s\n', d.var(v).name  );
+fprintf('\t%s\n', design.var(v).name  );
 
 % Reference file
-fprintf( '\t\tGridfile: %s\n', d.var(v).file );
+fprintf( '\t\tGridfile: %s\n', design.var(v).file );
 
 % Coupled Varialbes
-if any( d.isCoupled(v,:) )
+if any( design.isCoupled(v,:) )
     fprintf( '\t\tCoupled Variables: ' );
-    disp( d.varName( d.isCoupled(v,:) ) );
+    disp( design.varName( design.isCoupled(v,:) ) );
     fprintf('\b');
 end
 
 % Synced Variables
-if any(d.isSynced(v,:))
+if any(design.isSynced(v,:))
     fprintf('\t\tSynced Variables:\n');
-    disp( d.varName( d.isSynced(v,:) ) );
+    disp( design.varName( design.isSynced(v,:) ) );
     fprintf('\b');
 end
 
 % Overlap
-if d.var(v).overlap
+if design.var(v).overlap
     overStr = 'Allowed';
 else
     overStr = 'Forbidden';
@@ -38,7 +55,7 @@
 
 % Display the dimensions
 for k = 1:numel(dim)
-    dispDimension( d.var(v), dim(k), longform );
+    dispDimension( design.var(v), dim(k), longform );
 end
 
 end
diff --git a/2. Design State Vector/Utilities/General/checkDesignVar.m b/2. Design State Vector/Utilities/General/checkDesignVar.m
@@ -1,7 +1,10 @@
 function[varDex] = checkDesignVar( design, var )
 %% Ensures a design contains the vars
 %
-% varDex: The variable indices
+% var: Variable name
+%
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
 
 % Check there is a variable design
 if ~isa( design, 'stateDesign') || ~isscalar(design)

diff --git a/2. Design State Vector/Utilities/General/checkIndices.m b/2. Design State Vector/Utilities/General/checkIndices.m
@@ -1,5 +1,12 @@
 function[] = checkIndices(var, d, index)
 %% Low level error checking for indices for a dimension.
+%
+% var: varDesign
+%
+% d: Dimension index
+%
+% ----- Written By -----
+% Jonathan King, University of Arizona, 2019
 
 % Get the size of the data
 dimSize = var.dimSize(d);