refact(PP): export find_beam_vars as function

This commit exports the `find_beam_vars` as `IMOS.adcp.beam_vars`, with some improvements to handle cases outside the `binMappingPP` functionality.
aodn · Jun 10, 2021 · b13b8dc · b13b8dc
1 parent 26ca6e5
commit b13b8dc
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Showing 2 changed files with 108 additions and 59 deletions.
diff --git a/Preprocessing/adcpBinMappingPP.m b/Preprocessing/adcpBinMappingPP.m
@@ -91,7 +91,7 @@
     roll = sample_data{k}.variables{rollIdx}.data * pi / 180;
     beamAngle = sample_data{k}.meta.beam_angle * pi / 180;
 
-    %TODO: the adjusted distances should be exported 
+    %TODO: the adjusted distances should be exported
     % as variables to enable further diagnostic plots and debugging.
     %TODO: the adjusted distances should be a Nx4 array or Nx3 array.
     if isRDI% RDI 4 beams
@@ -131,7 +131,7 @@
     % interpolation conditions. This would allow a progress bar here.
 
     for n = 1:number_of_beams
-        beam_vars = get_beam_vars(sample_data{k}, n);
+        beam_vars = IMOS.adcp.beam_vars(sample_data{k}, n);
         [all_beam_vars] = IMOS.concatenate_variables(sample_data{k}.variables, beam_vars);
 
         switch n
@@ -238,60 +238,3 @@
 end
 
 end
-
-function [ibvars] = get_beam_vars(sample_data, n)
-%function [ibvars] = get_beam_vars(sample_data,n)
-%
-% Get the available beam variable names
-% based on the beam number.
-%
-% Inputs:
-%
-% sample_data [struct] - the toolbox struct.
-% n [double] - the beam number [1-4]
-%
-% Outputs:
-%
-% ibvars [cell{str}] - the variable names associated
-%                      with the beam number.
-%
-%
-% author: hugo.oliveira@utas.edu.au
-%
-%
-
-narginchk(2, 2)
-
-if ~isstruct(sample_data)
-    error('Frist argument not a toolbox struct')
-end
-
-switch n
-    case 1
-        beam_vars = {'ABSI1', 'ABSIC1', 'CMAG1', 'SNR1', 'VEL1'};
-    case 2
-        beam_vars = {'ABSI2', 'ABSIC2', 'CMAG2', 'SNR2', 'VEL2'};
-    case 3
-        beam_vars = {'ABSI3', 'ABSIC3', 'CMAG3', 'SNR3', 'VEL3'};
-    case 4
-        beam_vars = {'ABSI4', 'ABSIC4', 'CMAG4', 'VEL4'};
-    otherwise
-        errormsg('Second argument not a valid beam number')
-end
-
-ibvars = cell(1, length(beam_vars));
-is_a_beam_var = @(sample_data, varname)(IMOS.var_contains_dim(sample_data, varname, 'DIST_ALONG_BEAMS'));
-
-c = 0;
-
-for k = 1:length(beam_vars)
-
-    if is_a_beam_var(sample_data, beam_vars{k})
-        c = c + 1;
-        ibvars{c} = beam_vars{k};
-    end
-
-end
-
-ibvars = ibvars(1:c);
-end
diff --git a/Util/+IMOS/+adcp/beam_vars.m b/Util/+IMOS/+adcp/beam_vars.m
@@ -0,0 +1,106 @@
+function [ibvars] = beam_vars(sample_data, n)
+%function [ibvars] = beam_vars(sample_data,n)
+%
+% Get the available beam variable names
+% based on the beam number.
+% If beam number is not provided, all variables
+% names that are along beams are returned.
+%
+% Inputs:
+%
+% sample_data [struct] - the toolbox struct.
+% n [double] - the beam number [1-4]
+%
+% Outputs:
+%
+% ibvars [cell{str}] - the variable names associated
+%                      with the beam number.
+%
+% Example:
+%
+% time = (1:100)';
+% dab = (1:10)';
+% dummy = zeros(100,10);
+% type = @double;
+% dims = IMOS.gen_dimensions('adcp',2,{'TIME','DIST_ALONG_BEAMS'},{type,type},{time,dab});
+% vars = IMOS.gen_variables(dims,{'VEL1','ABSIC1','VEL3','ABSIC3'},{type,type,type,type},{dummy,dummy,dummy,dummy});
+% sample_data.dimensions = dims;
+% sample_data.variables = vars;
+% beam_vars_1 = IMOS.adcp.beam_vars(sample_data,1);
+% assert(numel(whereincell(beam_vars_1,{'ABSIC1','VEL1'}))==2)
+% assert(numel(whereincell(beam_vars_1,{'VEL3','ABSIC3'}))==0)
+%
+% %beam 3
+% beam_vars_3 = IMOS.adcp.beam_vars(sample_data,3);
+% assert(numel(whereincell(beam_vars_3,{'ABSIC1','VEL1'}))==0)
+% assert(numel(whereincell(beam_vars_3,{'VEL3','ABSIC3'}))==2)
+%
+% %all beams available
+% all_beams = IMOS.adcp.beam_vars(sample_data);
+% assert(numel(whereincell(all_beams,{'VEL1','ABSIC1','ABSIC3','VEL3'}))==4)
+%
+% %got a beam_variable name but dimensions are not aligned with DIST_ALONG_BEAMS
+% dummy = zeros(100,100);
+% vars = IMOS.gen_variables(dims,{'VEL1'},{type},{dummy});
+% sample_data.dimensions = dims;
+% sample_data.variables = vars;
+% beam_vars_1 = IMOS.adcp.beam_vars(sample_data,1);
+% assert(isempty(beam_vars_1))
+%
+%
+% author: hugo.oliveira@utas.edu.au
+%
+%
+narginchk(1, 2)
+
+if nargin<2
+	get_all_beam_vars = true;
+	n=inf;
+else
+	get_all_beam_vars = false;
+end
+
+
+if ~isstruct(sample_data)
+    error('Frist argument not a toolbox struct')
+end
+
+beam_vars_1 = {'ABSI1', 'ABSIC1', 'CMAG1', 'SNR1', 'VEL1'};
+beam_vars_2 = {'ABSI2', 'ABSIC2', 'CMAG2', 'SNR2', 'VEL2'};
+beam_vars_3 = {'ABSI3', 'ABSIC3', 'CMAG3', 'SNR3', 'VEL3'};
+beam_vars_4 = {'ABSI4', 'ABSIC4', 'CMAG4', 'VEL4'};
+
+switch n
+    case 1
+        beam_vars = beam_vars_1;
+    case 2
+        beam_vars = beam_vars_2;
+    case 3
+        beam_vars = beam_vars_3;
+    case 4
+        beam_vars = beam_vars_4;
+    otherwise
+		if get_all_beam_vars
+			beam_vars = [beam_vars_1, beam_vars_2, beam_vars_3, beam_vars_4];
+		else
+   	        errormsg('Second argument not a valid beam number')
+		end
+end
+
+%double check if dimensions are
+ibvars = cell(1, length(beam_vars));
+is_a_beam_var = @(sample_data, varname)(IMOS.var_contains_dim(sample_data, varname, 'DIST_ALONG_BEAMS'));
+
+c = 0;
+
+for k = 1:length(beam_vars)
+
+    if is_a_beam_var(sample_data, beam_vars{k})
+        c = c + 1;
+        ibvars{c} = beam_vars{k};
+    end
+
+end
+
+ibvars = ibvars(1:c);
+end