[497] | 1 | %'read_field': read the fields from files in different formats (netcdf files, images, video) |
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[181] | 2 | %-------------------------------------------------------------------------- |
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[450] | 3 | % function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num) |
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[181] | 4 | % |
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| 5 | % OUTPUT: |
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| 6 | % Field: matlab structure representing the field |
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| 7 | % ParamOut: structure representing parameters: |
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| 8 | % .FieldName; field name |
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| 9 | % .VelType |
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| 10 | % .CivStage: stage of civx processing (=0, not Civx, =1 (civ1), =2 (fix1).... |
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| 11 | % .Npx,.Npy: for images, nbre of pixels in x and y |
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| 12 | % errormsg: error message, ='' by default |
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| 13 | % |
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| 14 | %INPUT |
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[466] | 15 | % FileName: name of the input file |
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[497] | 16 | % FileType: type of file, as determined by the function get_file_type.m |
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[450] | 17 | % ParamIn: movie object or Matlab structure of input parameters |
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[445] | 18 | % .FieldName: name (char string) of the input field (for Civx data) |
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| 19 | % .VelType: char string giving the type of velocity data ('civ1', 'filter1', 'civ2'...) |
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[181] | 20 | % .ColorVar: variable used for vector color |
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| 21 | % .Npx, .Npy: nbre of pixels along x and y (used for .vol input files) |
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[466] | 22 | % num: frame number for movies |
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[497] | 23 | % |
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| 24 | % see also read_image.m,read_civxdata.m,read_civdata.m, |
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[466] | 25 | |
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[450] | 26 | function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num) |
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[181] | 27 | Field=[]; |
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[354] | 28 | if ~exist('num','var') |
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| 29 | num=1; |
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| 30 | end |
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| 31 | if ~exist('ParamIn','var') |
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| 32 | ParamIn=[]; |
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| 33 | end |
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| 34 | ParamOut=ParamIn;%default |
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[181] | 35 | errormsg=''; |
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[635] | 36 | if ~exist(FileName,'file') |
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| 37 | erromsg=['input file ' FileName ' does not exist']; |
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| 38 | return |
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| 39 | end |
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[334] | 40 | A=[]; |
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[575] | 41 | InputField={}; |
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| 42 | check_colorvar=0; |
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[526] | 43 | if isstruct(ParamIn) |
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[575] | 44 | if isfield(ParamIn,'FieldName') |
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| 45 | if ischar(ParamIn.FieldName) |
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[576] | 46 | InputField={ParamIn.FieldName}; |
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[575] | 47 | else |
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| 48 | InputField= ParamIn.FieldName; |
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| 49 | end |
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[526] | 50 | end |
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| 51 | if isfield(ParamIn,'ColorVar') |
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| 52 | InputField=[ParamIn.FieldName {ParamIn.ColorVar}]; |
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| 53 | check_colorvar=1; |
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| 54 | end |
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[521] | 55 | end |
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[575] | 56 | |
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[334] | 57 | %% distingush different input file types |
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[527] | 58 | switch FileType |
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| 59 | case 'civdata' |
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| 60 | [Field,ParamOut.VelType,errormsg]=read_civdata(FileName,InputField,ParamIn.VelType); |
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| 61 | if ~isempty(errormsg),errormsg=['read_civdata / ' errormsg];return,end |
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| 62 | ParamOut.CivStage=Field.CivStage; |
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| 63 | case 'civx' |
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| 64 | ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default |
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| 65 | [Field,ParamOut.VelType,errormsg]=read_civxdata(FileName,InputField,ParamIn.VelType); |
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| 66 | if ~isempty(errormsg),errormsg=['read_civxdata / ' errormsg];return,end |
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| 67 | ParamOut.CivStage=Field.CivStage; |
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| 68 | case 'netcdf' |
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| 69 | ListVar={}; |
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| 70 | for ilist=1:numel(InputField) |
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| 71 | r=regexp(InputField{ilist},'(?<Operator>(^vec|^norm))\((?<UName>.+),(?<VName>.+)\)$','names'); |
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| 72 | if isempty(r) |
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| 73 | ListVar=[ListVar InputField(ilist)]; |
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| 74 | Role{numel(ListVar)}='scalar'; |
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| 75 | % FieldRequest{numel(ListVar)}='interp_lin';%scalar field (requires interpolation for plot) |
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[493] | 76 | else |
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[527] | 77 | ListVar=[ListVar {r.UName,r.VName}]; |
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| 78 | Role{numel(ListVar)}='vector_y'; |
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| 79 | Role{numel(ListVar)-1}='vector_x'; |
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| 80 | % TODO; introduce that for unstructured coordinates |
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| 81 | % switch r.Operator TODO; introduce that for unstructured coordinates |
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| 82 | % case 'norm' |
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| 83 | % FieldRequest{numel(ListVar)-1}='interp_lin';%scalar field (requires interpolation for plot) |
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| 84 | % FieldRequest{numel(ListVar)}='interp_lin'; |
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| 85 | % otherwise |
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| 86 | % FieldRequest{numel(ListVar)-1}=''; |
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| 87 | % end |
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[493] | 88 | end |
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[527] | 89 | end |
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| 90 | if check_colorvar |
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| 91 | Role{numel(ListVar)}='ancillary';% scalar used for color vector (not projected) |
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| 92 | end |
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[595] | 93 | [Field,var_detect,ichoice]=nc2struct(FileName,[ParamIn.Coord_x (ParamIn.Coord_y) ListVar]); |
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[534] | 94 | if isfield(Field,'Txt') |
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| 95 | errormsg=Field.Txt; |
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| 96 | return |
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| 97 | end |
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[527] | 98 | for ivar=1:numel(ListVar) |
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| 99 | Field.VarAttribute{ivar+2}.Role=Role{ivar}; |
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| 100 | % Field.VarAttribute{ivar+2}.FieldRequest=FieldRequest{ivar}; |
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| 101 | end |
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| 102 | |
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| 103 | case 'video' |
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| 104 | if strcmp(class(ParamIn),'VideoReader') |
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| 105 | A=read(ParamIn,num); |
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| 106 | else |
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| 107 | ParamOut=VideoReader(FileName); |
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| 108 | A=read(ParamOut,num); |
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| 109 | end |
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| 110 | case 'mmreader' |
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| 111 | if strcmp(class(ParamIn),'mmreader') |
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| 112 | A=read(ParamIn,num); |
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| 113 | else |
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| 114 | ParamOut=mmreader(FileName); |
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| 115 | A=read(ParamOut,num); |
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| 116 | end |
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| 117 | case 'vol' |
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| 118 | A=imread(FileName); |
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| 119 | Npz=size(A,1)/ParamIn.Npy; |
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| 120 | A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz); |
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| 121 | A=permute(A,[3 2 1]); |
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| 122 | case 'multimage' |
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| 123 | warning 'off' |
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| 124 | A=imread(FileName,num); |
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| 125 | case 'image' |
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| 126 | A=imread(FileName); |
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| 127 | end |
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| 128 | if ~isempty(errormsg) |
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| 129 | errormsg=[FileType ' input: ' errormsg]; |
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[445] | 130 | return |
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[334] | 131 | end |
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[445] | 132 | |
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[334] | 133 | %% case of image |
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| 134 | if ~isempty(A) |
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[452] | 135 | if isstruct(ParamOut) |
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[580] | 136 | ParamOut.FieldName='image'; |
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[452] | 137 | end |
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[182] | 138 | Npz=1;%default |
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[181] | 139 | npxy=size(A); |
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[580] | 140 | % Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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| 141 | % Rangy=[npxy(1)-0.5 0.5]; % |
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[181] | 142 | Field.NbDim=2;%default |
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| 143 | Field.AName='image'; |
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| 144 | Field.ListVarName={'AY','AX','A'}; % |
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| 145 | if ndims(A)==3 |
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| 146 | if Npz==1;%color |
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| 147 | Field.VarDimName={'AY','AX',{'AY','AX','rgb'}}; % |
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| 148 | Field.AY=[npxy(1)-0.5 0.5]; |
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| 149 | Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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[452] | 150 | if isstruct(ParamOut) |
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[580] | 151 | ParamOut.Npx=npxy(2);% display image size on the interface |
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| 152 | ParamOut.Npy=npxy(1); |
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[452] | 153 | end |
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[186] | 154 | Field.VarAttribute{3}.Mesh=1; |
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[181] | 155 | else |
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| 156 | Field.NbDim=3; |
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| 157 | Field.ListVarName=['AZ' Field.ListVarName]; |
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| 158 | Field.VarDimName={'AZ','AY','AX',{'AZ','AY','AX'}}; |
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| 159 | Field.AZ=[npxy(1)-0.5 0.5]; |
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| 160 | Field.AY=[npxy(2)-0.5 0.5]; |
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| 161 | Field.AX=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers |
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[452] | 162 | if isstruct(ParamOut) |
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[580] | 163 | ParamOut.Npx=npxy(3);% display image size on the interface |
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| 164 | ParamOut.Npy=npxy(2); |
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| 165 | end |
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[186] | 166 | Field.VarAttribute{4}.Mesh=1; |
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[181] | 167 | end |
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| 168 | else |
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| 169 | Field.VarDimName={'AY','AX',{'AY','AX'}}; % |
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| 170 | Field.AY=[npxy(1)-0.5 0.5]; |
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| 171 | Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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[182] | 172 | ParamOut.Npx=npxy(2);% display image size on the interface |
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| 173 | ParamOut.Npy=npxy(1); |
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[186] | 174 | Field.VarAttribute{3}.Mesh=1; |
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[181] | 175 | end |
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| 176 | Field.A=A; |
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| 177 | Field.CoordUnit='pixel'; %used for mouse_motion |
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| 178 | end |
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| 179 | |
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| 180 | |
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[334] | 181 | |
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