[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 | % .FieldList: menu of possible fields |
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| 10 | % .VelType |
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| 11 | % .CivStage: stage of civx processing (=0, not Civx, =1 (civ1), =2 (fix1).... |
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| 12 | % .Npx,.Npy: for images, nbre of pixels in x and y |
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| 13 | % errormsg: error message, ='' by default |
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| 14 | % |
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| 15 | %INPUT |
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[466] | 16 | % FileName: name of the input file |
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[497] | 17 | % FileType: type of file, as determined by the function get_file_type.m |
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[450] | 18 | % ParamIn: movie object or Matlab structure of input parameters |
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[445] | 19 | % .FieldName: name (char string) of the input field (for Civx data) |
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| 20 | % .VelType: char string giving the type of velocity data ('civ1', 'filter1', 'civ2'...) |
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[181] | 21 | % .ColorVar: variable used for vector color |
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| 22 | % .Npx, .Npy: nbre of pixels along x and y (used for .vol input files) |
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[466] | 23 | % num: frame number for movies |
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[497] | 24 | % |
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| 25 | % see also read_image.m,read_civxdata.m,read_civdata.m, |
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[466] | 26 | |
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[450] | 27 | function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num) |
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[181] | 28 | Field=[]; |
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[354] | 29 | if ~exist('num','var') |
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| 30 | num=1; |
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| 31 | end |
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| 32 | if ~exist('ParamIn','var') |
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| 33 | ParamIn=[]; |
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| 34 | end |
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| 35 | ParamOut=ParamIn;%default |
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[181] | 36 | errormsg=''; |
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[466] | 37 | % if isfield(ParamIn,'VelType') |
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| 38 | % VelType=ParamIn.VelType; |
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| 39 | % end |
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[334] | 40 | A=[]; |
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[521] | 41 | if ischar(ParamIn.FieldName) |
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| 42 | ParamIn.FieldName={ParamIn.FieldName}; |
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| 43 | end |
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| 44 | if isfield(ParamIn,'ColorVar') |
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| 45 | InputField=[ParamIn.FieldName {ParamIn.ColorVar}]; |
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| 46 | check_colorvar=1; |
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| 47 | else |
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| 48 | InputField= ParamIn.FieldName; |
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| 49 | check_colorvar=0; |
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| 50 | end |
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[334] | 51 | %% distingush different input file types |
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[445] | 52 | try |
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| 53 | switch FileType |
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[517] | 54 | case 'civdata' |
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[521] | 55 | [Field,ParamOut.VelType,errormsg]=read_civdata(FileName,InputField,ParamIn.VelType); |
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| 56 | if ~isempty(errormsg),errormsg=['read_civdata:' errormsg];return,end |
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| 57 | ParamOut.CivStage=Field.CivStage; |
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| 58 | case 'civx' |
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[517] | 59 | ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default |
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[521] | 60 | [Field,ParamOut.VelType]=read_civxdata(FileName,InputField,ParamIn.VelType); |
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| 61 | if ~isempty(errormsg),errormsg=['read_civxdata:' errormsg];return,end |
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| 62 | ParamOut.CivStage=Field.CivStage; |
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[517] | 63 | case 'netcdf' |
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[521] | 64 | ListVar={}; |
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| 65 | for ilist=1:numel(InputField) |
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| 66 | r=regexp(InputField{ilist},'(?<Operator>(^vec|^norm))\((?<UName>.+),(?<VName>.+)\)$','names'); |
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[517] | 67 | if isempty(r) |
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[521] | 68 | ListVar=[ListVar InputField(ilist)]; |
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| 69 | Role{numel(ListVar)}='scalar'; |
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| 70 | % FieldRequest{numel(ListVar)}='interp_lin';%scalar field (requires interpolation for plot) |
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[517] | 71 | else |
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| 72 | ListVar=[ListVar {r.UName,r.VName}]; |
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[521] | 73 | Role{numel(ListVar)}='vector_y'; |
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| 74 | Role{numel(ListVar)-1}='vector_x'; |
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| 75 | % switch r.Operator |
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| 76 | % case 'norm' |
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| 77 | % FieldRequest{numel(ListVar)-1}='interp_lin';%scalar field (requires interpolation for plot) |
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| 78 | % FieldRequest{numel(ListVar)}='interp_lin'; |
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| 79 | % otherwise |
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| 80 | % FieldRequest{numel(ListVar)-1}=''; |
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| 81 | % end |
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[334] | 82 | end |
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[445] | 83 | end |
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[521] | 84 | if check_colorvar |
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| 85 | Role{numel(ListVar)}='ancillary';% scalar used for color vector (not projected) |
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| 86 | end |
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| 87 | [Field,var_detect,ichoice]=nc2struct(FileName,[ParamIn.CoordName ListVar]); |
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| 88 | for ivar=1:numel(ListVar) |
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| 89 | Field.VarAttribute{ivar+2}.Role=Role{ivar}; |
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| 90 | % Field.VarAttribute{ivar+2}.FieldRequest=FieldRequest{ivar}; |
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| 91 | end |
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| 92 | % GUIName='get_field'; %default name of the GUI get_field |
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| 93 | % if isfield(ParamIn,'GUIName') |
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| 94 | % GUIName=ParamIn.GUIName; |
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| 95 | % end |
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| 96 | % CivStage=0; |
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| 97 | % % if ~strcmp(ParamIn.FieldName,'get_field...')% if get_field is not requested, look for Civx data |
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| 98 | % FieldList=calc_field;%list of possible fields for Civx data |
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| 99 | % ParamOut.ColorVar='';%default |
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| 100 | % if ischar(ParamIn.FieldName) |
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| 101 | % FieldName=ParamIn.FieldName; |
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| 102 | % else |
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| 103 | % FieldName=ParamIn.FieldName{1}; |
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| 104 | % end |
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| 105 | % field_index=strcmp(FieldName,FieldList);%look for ParamIn.FieldName in the list of possible fields for Civx data |
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| 106 | % if isempty(find(field_index,1))% ParamIn.FieldName is not in the list, check whether Civx data exist |
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| 107 | % Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ','CivStage'); |
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| 108 | % % case of new civdata conventions |
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| 109 | % if isequal(Data.Conventions,'uvmat/civdata') |
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| 110 | % |
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| 111 | % %case of old civx conventions |
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| 112 | % elseif ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0) |
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| 113 | % ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default |
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| 114 | % ParamOut.ColorVar='ima_cor'; |
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| 115 | % InputField=[{ParamOut.FieldName} {ParamOut.ColorVar}]; |
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| 116 | % [Field,ParamOut.VelType]=read_civxdata(FileName,InputField,ParamIn.VelType); |
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| 117 | % if ~isempty(errormsg),errormsg=['read_civxdata:' errormsg];return,end |
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| 118 | % CivStage=Field.CivStage; |
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| 119 | % ParamOut.CivStage=Field.CivStage; |
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| 120 | % % not cvix file, fields will be chosen through the GUI get_field |
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| 121 | % else |
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| 122 | % ParamOut.FieldName='get_field...'; |
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| 123 | % hget_field=findobj(allchild(0),'Name',GUIName);%find the get_field... GUI |
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| 124 | % if ~isempty(hget_field) |
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| 125 | % delete(hget_field)%delete get_field for reinitialisation |
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| 126 | % end |
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| 127 | % end |
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| 128 | % else |
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| 129 | % InputField=ParamOut.FieldName; |
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| 130 | % if ischar(InputField) |
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| 131 | % InputField={InputField}; |
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| 132 | % end |
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| 133 | % if isfield(ParamIn,'ColorVar') |
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| 134 | % ParamOut.ColorVar=ParamIn.ColorVar; |
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| 135 | % InputField=[InputField {ParamOut.ColorVar}]; |
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| 136 | % end |
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| 137 | % [Field,ParamOut.VelType,errormsg]=read_civxdata(FileName,InputField,ParamIn.VelType); |
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| 138 | % if ~isempty(errormsg),errormsg=['read_civxdata:' errormsg];return,end |
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| 139 | % CivStage=Field.CivStage; |
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| 140 | % ParamOut.CivStage=Field.CivStage; |
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| 141 | % end |
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| 142 | % ParamOut.FieldList=[{'image'};FieldList;{'get_field...'}]; |
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| 143 | % end |
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| 144 | % if CivStage==0% read the field names on the interface get_field. |
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| 145 | % hget_field=findobj(allchild(0),'Name',GUIName);%find the get_field... GUI |
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| 146 | % if isempty(hget_field)% open the GUI get_field if it is not found |
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| 147 | % hget_field= get_field(FileName);%open the get_field GUI |
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| 148 | % set(hget_field,'Name',GUIName)%update the name of get_field (e.g. get_field_1) |
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| 149 | % end |
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| 150 | % hhget_field=guidata(hget_field); |
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| 151 | % %% update the get_field GUI |
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| 152 | % set(hhget_field.inputfile,'String',FileName) |
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| 153 | % set(hhget_field.list_fig,'Value',1) |
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| 154 | % if exist('num','var')&&~isnan(num) |
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| 155 | % set(hhget_field.TimeIndexValue,'String',num2str(num)) |
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| 156 | % end |
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| 157 | % % funct_list=get(hhget_field.ACTION,'UserData'); |
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| 158 | % % funct_index=get(hhget_field.ACTION,'Value'); |
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| 159 | % % funct=funct_list{funct_index};%select the current action in get_field, e;g. PLOT |
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| 160 | % % Field=funct(hget_field); %%activate the current action selected in get_field, e;g.read the names of the variables to plot |
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| 161 | % [Field,errormsg]=read_get_field(hget_field); |
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| 162 | % Tabchar={''};%default |
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| 163 | % Tabcell=[]; |
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| 164 | % set(hhget_field.inputfile,'String',FileName) |
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| 165 | % if isfield(Field,'ListGlobalAttribute')&& ~isempty(Field.ListGlobalAttribute) |
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| 166 | % for iline=1:length(Field.ListGlobalAttribute) |
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| 167 | % Tabcell{iline,1}=Field.ListGlobalAttribute{iline}; |
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| 168 | % if isfield(Field, Field.ListGlobalAttribute{iline}) |
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| 169 | % val=Field.(Field.ListGlobalAttribute{iline}); |
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| 170 | % if ischar(val); |
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| 171 | % Tabcell{iline,2}=val; |
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| 172 | % else |
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| 173 | % Tabcell{iline,2}=num2str(val); |
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| 174 | % end |
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| 175 | % end |
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| 176 | % end |
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| 177 | % if ~isempty(Tabcell) |
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| 178 | % Tabchar=cell2tab(Tabcell,'='); |
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| 179 | % Tabchar=[{''};Tabchar]; |
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| 180 | % end |
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| 181 | % end |
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| 182 | % ParamOut.CivStage=0; |
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| 183 | % ParamOut.VelType=[]; |
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| 184 | % if isfield(Field,'TimeIndex') |
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| 185 | % ParamOut.TimeIndex=Field.TimeIndex; |
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| 186 | % end |
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| 187 | % if isfield(Field,'TimeValue') |
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| 188 | % ParamOut.TimeValue=Field.TimeValue; |
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| 189 | % end |
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| 190 | % ParamOut.FieldList={'get_field...'}; |
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| 191 | |
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[493] | 192 | case 'video' |
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| 193 | if strcmp(class(ParamIn),'VideoReader') |
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| 194 | A=read(ParamIn,num); |
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| 195 | else |
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| 196 | ParamOut=VideoReader(FileName); |
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| 197 | A=read(ParamOut,num); |
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| 198 | end |
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| 199 | case 'mmreader' |
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| 200 | if strcmp(class(ParamIn),'mmreader') |
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| 201 | A=read(ParamIn,num); |
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| 202 | else |
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| 203 | ParamOut=mmreader(FileName); |
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| 204 | A=read(ParamOut,num); |
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| 205 | end |
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[445] | 206 | case 'vol' |
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[450] | 207 | A=imread(FileName); |
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[445] | 208 | Npz=size(A,1)/ParamIn.Npy; |
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| 209 | A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz); |
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| 210 | A=permute(A,[3 2 1]); |
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| 211 | case 'multimage' |
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| 212 | warning 'off' |
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[450] | 213 | A=imread(FileName,num); |
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[445] | 214 | case 'image' |
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[450] | 215 | A=imread(FileName); |
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[445] | 216 | end |
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| 217 | catch ME |
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[472] | 218 | errormsg=[FileType ' input: ' ME.message]; |
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[445] | 219 | return |
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[334] | 220 | end |
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[445] | 221 | |
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[334] | 222 | %% case of image |
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| 223 | if ~isempty(A) |
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[452] | 224 | if isstruct(ParamOut) |
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[181] | 225 | ParamOut.FieldName='image'; |
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| 226 | ParamOut.FieldList={'image'}; |
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[452] | 227 | end |
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[182] | 228 | Npz=1;%default |
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[181] | 229 | npxy=size(A); |
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[397] | 230 | % Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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| 231 | % Rangy=[npxy(1)-0.5 0.5]; % |
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[181] | 232 | Field.NbDim=2;%default |
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| 233 | Field.AName='image'; |
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| 234 | Field.ListVarName={'AY','AX','A'}; % |
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| 235 | if ndims(A)==3 |
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| 236 | if Npz==1;%color |
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| 237 | Field.VarDimName={'AY','AX',{'AY','AX','rgb'}}; % |
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| 238 | Field.AY=[npxy(1)-0.5 0.5]; |
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| 239 | Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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[452] | 240 | if isstruct(ParamOut) |
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[182] | 241 | ParamOut.Npx=npxy(2);% display image size on the interface |
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| 242 | ParamOut.Npy=npxy(1); |
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[452] | 243 | end |
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[186] | 244 | Field.VarAttribute{3}.Mesh=1; |
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[181] | 245 | else |
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| 246 | Field.NbDim=3; |
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| 247 | Field.ListVarName=['AZ' Field.ListVarName]; |
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| 248 | Field.VarDimName={'AZ','AY','AX',{'AZ','AY','AX'}}; |
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| 249 | Field.AZ=[npxy(1)-0.5 0.5]; |
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| 250 | Field.AY=[npxy(2)-0.5 0.5]; |
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| 251 | Field.AX=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers |
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[452] | 252 | if isstruct(ParamOut) |
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[182] | 253 | ParamOut.Npx=npxy(3);% display image size on the interface |
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| 254 | ParamOut.Npy=npxy(2); |
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[452] | 255 | end |
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[186] | 256 | Field.VarAttribute{4}.Mesh=1; |
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[181] | 257 | end |
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| 258 | else |
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| 259 | Field.VarDimName={'AY','AX',{'AY','AX'}}; % |
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| 260 | Field.AY=[npxy(1)-0.5 0.5]; |
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| 261 | Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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[182] | 262 | ParamOut.Npx=npxy(2);% display image size on the interface |
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| 263 | ParamOut.Npy=npxy(1); |
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[186] | 264 | Field.VarAttribute{3}.Mesh=1; |
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[181] | 265 | end |
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| 266 | Field.A=A; |
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| 267 | Field.CoordUnit='pixel'; %used for mouse_motion |
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| 268 | end |
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| 269 | |
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| 270 | |
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[334] | 271 | |
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