[379] | 1 | |
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[181] | 2 | %'read_field': read input fields in different formats |
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| 3 | %-------------------------------------------------------------------------- |
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[450] | 4 | % function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num) |
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[181] | 5 | % |
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| 6 | % OUTPUT: |
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| 7 | % Field: matlab structure representing the field |
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| 8 | % ParamOut: structure representing parameters: |
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| 9 | % .FieldName; field name |
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| 10 | % .FieldList: menu of possible fields |
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| 11 | % .VelType |
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| 12 | % .CivStage: stage of civx processing (=0, not Civx, =1 (civ1), =2 (fix1).... |
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| 13 | % .Npx,.Npy: for images, nbre of pixels in x and y |
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| 14 | % errormsg: error message, ='' by default |
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| 15 | % |
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| 16 | %INPUT |
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[466] | 17 | % FileName: name of the input file |
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[181] | 18 | % FileType: type of file |
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| 19 | % = netcdf : netcdf file |
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| 20 | % = image : usual image as recognised by Matlab |
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| 21 | % = multimage: image series stored in a single file |
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[441] | 22 | % = mmreader: movie read with mmreader |
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| 23 | % = video: movie read with VideoReader (recent versions of Matlab) |
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[181] | 24 | % = vol: images representing scanned volume (images concatened in the y direction) |
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[450] | 25 | % ParamIn: movie object or Matlab structure of input parameters |
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[445] | 26 | % .FieldName: name (char string) of the input field (for Civx data) |
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| 27 | % .VelType: char string giving the type of velocity data ('civ1', 'filter1', 'civ2'...) |
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[181] | 28 | % .ColorVar: variable used for vector color |
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| 29 | % .Npx, .Npy: nbre of pixels along x and y (used for .vol input files) |
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[466] | 30 | % num: frame number for movies |
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| 31 | |
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[450] | 32 | function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num) |
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[181] | 33 | Field=[]; |
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[354] | 34 | if ~exist('num','var') |
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| 35 | num=1; |
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| 36 | end |
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| 37 | if ~exist('ParamIn','var') |
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| 38 | ParamIn=[]; |
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| 39 | end |
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| 40 | ParamOut=ParamIn;%default |
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[181] | 41 | errormsg=''; |
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[466] | 42 | % if isfield(ParamIn,'VelType') |
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| 43 | % VelType=ParamIn.VelType; |
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| 44 | % end |
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[334] | 45 | A=[]; |
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| 46 | %% distingush different input file types |
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[445] | 47 | try |
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| 48 | switch FileType |
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| 49 | case {'civx','civdata','netcdf'} %read the first nc field |
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| 50 | % ParamOut.FieldName=ParamIn.FieldName; |
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| 51 | GUIName='get_field'; %default name of the GUI get_field |
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| 52 | if isfield(ParamIn,'GUIName') |
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| 53 | GUIName=ParamIn.GUIName; |
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| 54 | end |
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| 55 | CivStage=0; |
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| 56 | if ~strcmp(ParamIn.FieldName,'get_field...')% if get_field is not requested, look for Civx data |
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| 57 | FieldList=calc_field;%list of possible fields for Civx data |
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| 58 | ParamOut.ColorVar='';%default |
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[472] | 59 | if ischar(ParamIn.FieldName) |
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| 60 | FieldName=ParamIn.FieldName; |
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| 61 | else |
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| 62 | FieldName=ParamIn.FieldName{1}; |
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| 63 | end |
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| 64 | field_index=strcmp(FieldName,FieldList);%look for ParamIn.FieldName in the list of possible fields for Civx data |
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[445] | 65 | if isempty(find(field_index,1))% ParamIn.FieldName is not in the list, check whether Civx data exist |
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[450] | 66 | Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ','CivStage'); |
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[445] | 67 | % case of new civdata conventions |
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| 68 | if isequal(Data.Conventions,'uvmat/civdata') |
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| 69 | ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default |
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| 70 | ParamOut.ColorVar='ima_cor'; |
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| 71 | InputField=[{ParamOut.FieldName} {ParamOut.ColorVar}]; |
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[450] | 72 | [Field,ParamOut.VelType,errormsg]=read_civdata(FileName,InputField,ParamIn.VelType,Data.CivStage); |
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[472] | 73 | if ~isempty(errormsg),errormsg=['read_civdata:' errormsg];return,end |
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[445] | 74 | CivStage=Field.CivStage; |
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| 75 | ParamOut.CivStage=Field.CivStage; |
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| 76 | %case of old civx conventions |
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| 77 | elseif ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0) |
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| 78 | ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default |
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| 79 | ParamOut.ColorVar='ima_cor'; |
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| 80 | InputField=[{ParamOut.FieldName} {ParamOut.ColorVar}]; |
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[450] | 81 | [Field,ParamOut.VelType]=read_civxdata(FileName,InputField,ParamIn.VelType); |
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[472] | 82 | if ~isempty(errormsg),errormsg=['read_civxdata:' errormsg];return,end |
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[445] | 83 | CivStage=Field.CivStage; |
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| 84 | ParamOut.CivStage=Field.CivStage; |
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| 85 | % not cvix file, fields will be chosen through the GUI get_field |
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| 86 | else |
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| 87 | ParamOut.FieldName='get_field...'; |
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| 88 | hget_field=findobj(allchild(0),'Name',GUIName);%find the get_field... GUI |
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| 89 | if ~isempty(hget_field) |
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| 90 | delete(hget_field)%delete get_field for reinitialisation |
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| 91 | end |
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| 92 | end |
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[472] | 93 | else |
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| 94 | InputField=ParamOut.FieldName; |
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| 95 | if ischar(InputField) |
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| 96 | InputField={InputField}; |
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| 97 | end |
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[445] | 98 | if isfield(ParamIn,'ColorVar') |
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| 99 | ParamOut.ColorVar=ParamIn.ColorVar; |
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| 100 | InputField=[InputField {ParamOut.ColorVar}]; |
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| 101 | end |
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[450] | 102 | [Field,ParamOut.VelType,errormsg]=read_civxdata(FileName,InputField,ParamIn.VelType); |
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[472] | 103 | if ~isempty(errormsg),errormsg=['read_civxdata:' errormsg];return,end |
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[404] | 104 | CivStage=Field.CivStage; |
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[405] | 105 | ParamOut.CivStage=Field.CivStage; |
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[334] | 106 | end |
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[445] | 107 | ParamOut.FieldList=[{'image'};FieldList;{'get_field...'}]; |
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| 108 | end |
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| 109 | if CivStage==0% read the field names on the interface get_field. |
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| 110 | hget_field=findobj(allchild(0),'Name',GUIName);%find the get_field... GUI |
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| 111 | if isempty(hget_field)% open the GUI get_field if it is not found |
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[450] | 112 | hget_field= get_field(FileName);%open the get_field GUI |
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[445] | 113 | set(hget_field,'Name',GUIName)%update the name of get_field (e.g. get_field_1) |
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[334] | 114 | end |
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[445] | 115 | hhget_field=guidata(hget_field); |
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| 116 | %% update the get_field GUI |
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[450] | 117 | set(hhget_field.inputfile,'String',FileName) |
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[445] | 118 | set(hhget_field.list_fig,'Value',1) |
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| 119 | if exist('num','var')&&~isnan(num) |
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| 120 | set(hhget_field.TimeIndexValue,'String',num2str(num)) |
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[334] | 121 | end |
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[445] | 122 | funct_list=get(hhget_field.ACTION,'UserData'); |
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| 123 | funct_index=get(hhget_field.ACTION,'Value'); |
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| 124 | funct=funct_list{funct_index};%select the current action in get_field, e;g. PLOT |
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| 125 | 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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| 126 | Tabchar={''};%default |
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| 127 | Tabcell=[]; |
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[450] | 128 | set(hhget_field.inputfile,'String',FileName) |
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[445] | 129 | if isfield(Field,'ListGlobalAttribute')&& ~isempty(Field.ListGlobalAttribute) |
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| 130 | for iline=1:length(Field.ListGlobalAttribute) |
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| 131 | Tabcell{iline,1}=Field.ListGlobalAttribute{iline}; |
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| 132 | if isfield(Field, Field.ListGlobalAttribute{iline}) |
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[472] | 133 | val=Field.(Field.ListGlobalAttribute{iline}); |
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[445] | 134 | if ischar(val); |
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| 135 | Tabcell{iline,2}=val; |
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| 136 | else |
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| 137 | Tabcell{iline,2}=num2str(val); |
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| 138 | end |
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[334] | 139 | end |
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[181] | 140 | end |
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[445] | 141 | if ~isempty(Tabcell) |
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| 142 | Tabchar=cell2tab(Tabcell,'='); |
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| 143 | Tabchar=[{''};Tabchar]; |
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| 144 | end |
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[181] | 145 | end |
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[445] | 146 | ParamOut.CivStage=0; |
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| 147 | ParamOut.VelType=[]; |
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| 148 | if isfield(Field,'TimeIndex') |
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| 149 | ParamOut.TimeIndex=Field.TimeIndex; |
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[334] | 150 | end |
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[445] | 151 | if isfield(Field,'TimeValue') |
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| 152 | ParamOut.TimeValue=Field.TimeValue; |
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| 153 | end |
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| 154 | ParamOut.FieldList={'get_field...'}; |
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[181] | 155 | end |
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[445] | 156 | case {'video','mmreader'} |
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[450] | 157 | A=read(ParamIn,num); |
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[445] | 158 | case 'vol' |
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[450] | 159 | A=imread(FileName); |
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[445] | 160 | Npz=size(A,1)/ParamIn.Npy; |
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| 161 | A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz); |
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| 162 | A=permute(A,[3 2 1]); |
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| 163 | case 'multimage' |
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| 164 | warning 'off' |
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[450] | 165 | A=imread(FileName,num); |
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[445] | 166 | case 'image' |
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[450] | 167 | A=imread(FileName); |
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[445] | 168 | end |
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| 169 | catch ME |
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[472] | 170 | errormsg=[FileType ' input: ' ME.message]; |
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[445] | 171 | return |
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[334] | 172 | end |
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[445] | 173 | |
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[334] | 174 | %% case of image |
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| 175 | if ~isempty(A) |
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[452] | 176 | if isstruct(ParamOut) |
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[181] | 177 | ParamOut.FieldName='image'; |
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| 178 | ParamOut.FieldList={'image'}; |
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[452] | 179 | end |
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[182] | 180 | Npz=1;%default |
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[181] | 181 | npxy=size(A); |
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[397] | 182 | % Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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| 183 | % Rangy=[npxy(1)-0.5 0.5]; % |
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[181] | 184 | Field.NbDim=2;%default |
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| 185 | Field.AName='image'; |
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| 186 | Field.ListVarName={'AY','AX','A'}; % |
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| 187 | if ndims(A)==3 |
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| 188 | if Npz==1;%color |
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| 189 | Field.VarDimName={'AY','AX',{'AY','AX','rgb'}}; % |
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| 190 | Field.AY=[npxy(1)-0.5 0.5]; |
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| 191 | Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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[452] | 192 | if isstruct(ParamOut) |
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[182] | 193 | ParamOut.Npx=npxy(2);% display image size on the interface |
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| 194 | ParamOut.Npy=npxy(1); |
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[452] | 195 | end |
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[186] | 196 | Field.VarAttribute{3}.Mesh=1; |
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[181] | 197 | else |
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| 198 | Field.NbDim=3; |
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| 199 | Field.ListVarName=['AZ' Field.ListVarName]; |
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| 200 | Field.VarDimName={'AZ','AY','AX',{'AZ','AY','AX'}}; |
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| 201 | Field.AZ=[npxy(1)-0.5 0.5]; |
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| 202 | Field.AY=[npxy(2)-0.5 0.5]; |
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| 203 | Field.AX=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers |
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[452] | 204 | if isstruct(ParamOut) |
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[182] | 205 | ParamOut.Npx=npxy(3);% display image size on the interface |
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| 206 | ParamOut.Npy=npxy(2); |
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[452] | 207 | end |
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[186] | 208 | Field.VarAttribute{4}.Mesh=1; |
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[181] | 209 | end |
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| 210 | else |
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| 211 | Field.VarDimName={'AY','AX',{'AY','AX'}}; % |
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| 212 | Field.AY=[npxy(1)-0.5 0.5]; |
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| 213 | Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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[182] | 214 | ParamOut.Npx=npxy(2);% display image size on the interface |
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| 215 | ParamOut.Npy=npxy(1); |
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[186] | 216 | Field.VarAttribute{3}.Mesh=1; |
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[181] | 217 | end |
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| 218 | Field.A=A; |
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| 219 | Field.CoordUnit='pixel'; %used for mouse_motion |
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| 220 | end |
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| 221 | |
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| 222 | |
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[334] | 223 | |
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