1 | %'read_field': read input fields in different formats |
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2 | %-------------------------------------------------------------------------- |
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3 | % function [Field,ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn) |
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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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16 | % ObjectName: name of the input file, or movie object when the Matlab function mmreader is used |
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17 | % FileType: type of file |
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18 | % = netcdf : netcdf file |
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19 | % = image : usual image as recognised by Matlab |
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20 | % = multimage: image series stored in a single file |
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21 | % = movie: movie read with mmreader |
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22 | % = avi: avi movie read with aviread (OBSOLETE, used only when mmreader is not available, old versions of Matlab) |
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23 | % = vol: images representing scanned volume (images concatened in the y direction) |
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24 | % ParamIn: Matlab structure of input parameters |
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25 | % .FieldName: name of the input field (for Civx data) |
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26 | % .VelType: type of velocity data ('civ1', 'filter1', 'civ2'...) |
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27 | % .ColorVar: variable used for vector color |
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28 | % .Npx, .Npy: nbre of pixels along x and y (used for .vol input files) |
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29 | function [Field,ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num) |
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30 | Field=[]; |
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31 | ParamOut=[]; |
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32 | errormsg=''; |
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33 | if isfield(ParamIn,'VelType') |
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34 | VelType=ParamIn.VelType; |
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35 | end |
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36 | A=[]; |
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37 | %% distingush different input file types |
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38 | switch FileType |
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39 | case {'civx','civdata','netcdf'} %read the first nc field |
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40 | ParamOut.FieldName=ParamIn.FieldName; |
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41 | GUIName='get_field'; %default name of the GUI get_field |
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42 | if isfield(ParamIn,'GUIName') |
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43 | GUIName=ParamIn.GUIName; |
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44 | end |
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45 | test_civx=0; |
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46 | if ~strcmp(ParamIn.FieldName,'get_field...')% if get_field is not requested, look for Civx data |
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47 | FieldList=calc_field;%list of possible fields for Civx data |
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48 | ParamOut.ColorVar='';%default |
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49 | field_index=strcmp(ParamIn.FieldName,FieldList);%look for ParamIn.FieldName in the list of possible fields for Civx data |
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50 | if isempty(find(field_index,1))% ParamIn.FieldName is not in the list, check whether Civx data exist |
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51 | Data=nc2struct(ObjectName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ'); |
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52 | % case of new civdata conventions |
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53 | if isequal(Data.Conventions,'uvmat/civdata') |
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54 | ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default |
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55 | ParamOut.ColorVar='ima_cor'; |
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56 | InputField=[{ParamOut.FieldName} {ParamOut.ColorVar}]; |
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57 | [Field,ParamOut.VelType]=read_civdata(ObjectName,InputField,ParamIn.VelType); |
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58 | test_civx=Field.CivStage; |
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59 | %case of old civx conventions |
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60 | elseif ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0) |
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61 | ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default |
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62 | ParamOut.ColorVar='ima_cor'; |
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63 | InputField=[{ParamOut.FieldName} {ParamOut.ColorVar}]; |
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64 | [Field,ParamOut.VelType]=read_civxdata(ObjectName,InputField,ParamIn.VelType); |
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65 | test_civx=Field.CivStage; |
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66 | ParamOut.CivStage=Field.CivStage; |
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67 | % not cvix file, fields will be chosen through the GUI get_field |
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68 | else |
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69 | ParamOut.FieldName='get_field...'; |
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70 | hget_field=findobj(allchild(0),'Name',GUIName);%find the get_field... GUI |
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71 | if ~isempty(hget_field) |
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72 | delete(hget_field)%delete get_field for reinitialisation |
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73 | end |
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74 | end |
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75 | else |
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76 | InputField={ParamOut.FieldName}; |
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77 | if isfield(ParamIn,'ColorVar') |
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78 | ParamOut.ColorVar=ParamIn.ColorVar; |
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79 | InputField=[InputField {ParamOut.ColorVar}]; |
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80 | end |
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81 | [Field,ParamOut.VelType,errormsg]=read_civxdata(ObjectName,InputField,ParamIn.VelType); |
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82 | if ~isempty(errormsg) |
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83 | return |
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84 | end |
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85 | test_civx=Field.CivStage; |
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86 | ParamOut.CivStage=Field.CivStage; |
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87 | end |
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88 | end |
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89 | if ~test_civx% read the field names on the interface get_field. |
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90 | hget_field=findobj(allchild(0),'Name',GUIName);%find the get_field... GUI |
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91 | if isempty(hget_field)% open the GUI get_field if it is not found |
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92 | hget_field= get_field(ObjectName);%open the get_field GUI |
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93 | set(hget_field,'Name',GUIName)%update the name of get_field (e.g. get_field_1) |
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94 | end |
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95 | hhget_field=guidata(hget_field); |
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96 | %% update the get_field GUI |
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97 | set(hhget_field.inputfile,'String',ObjectName) |
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98 | set(hhget_field.list_fig,'Value',1) |
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99 | if exist('num','var')&&~isnan(num) |
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100 | set(hhget_field.TimeIndexValue,'String',num2str(num)) |
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101 | end |
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102 | funct_list=get(hhget_field.ACTION,'UserData'); |
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103 | funct_index=get(hhget_field.ACTION,'Value'); |
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104 | funct=funct_list{funct_index};%select the current action in get_field, e;g. PLOT |
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105 | 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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106 | Tabchar={''};%default |
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107 | Tabcell=[]; |
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108 | set(hhget_field.inputfile,'String',ObjectName) |
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109 | if isfield(Field,'ListGlobalAttribute')&& ~isempty(Field.ListGlobalAttribute) |
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110 | for iline=1:length(Field.ListGlobalAttribute) |
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111 | Tabcell{iline,1}=Field.ListGlobalAttribute{iline}; |
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112 | if isfield(Field, Field.ListGlobalAttribute{iline}) |
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113 | eval(['val=Field.' Field.ListGlobalAttribute{iline} ';']) |
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114 | if ischar(val); |
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115 | Tabcell{iline,2}=val; |
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116 | else |
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117 | Tabcell{iline,2}=num2str(val); |
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118 | end |
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119 | end |
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120 | end |
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121 | if ~isempty(Tabcell) |
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122 | Tabchar=cell2tab(Tabcell,'='); |
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123 | Tabchar=[{''};Tabchar]; |
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124 | end |
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125 | end |
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126 | %set(hhget_field.attributes,'String',Tabchar);%update list of global attributes in get_field |
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127 | ParamOut.CivStage=0; |
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128 | ParamOut.VelType=[]; |
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129 | if isfield(Field,'TimeIndex') |
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130 | ParamOut.TimeIndex=Field.TimeIndex; |
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131 | end |
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132 | if isfield(Field,'TimeValue') |
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133 | ParamOut.TimeValue=Field.TimeValue; |
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134 | end |
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135 | end |
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136 | if test_civx |
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137 | ParamOut.FieldList=[{'image'};FieldList;{'get_field...'}]; |
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138 | else |
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139 | ParamOut.FieldList={'get_field...'}; |
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140 | end |
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141 | |
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142 | case 'movie' |
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143 | try |
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144 | A=read(ObjectName,num); |
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145 | FieldName='image'; |
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146 | catch ME |
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147 | errormsg=ME.message; |
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148 | return |
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149 | end |
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150 | case 'avi' |
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151 | try |
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152 | mov=aviread(ObjectName,num); |
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153 | catch ME |
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154 | errormsg=ME.message; |
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155 | return |
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156 | end |
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157 | A=frame2im(mov(1)); |
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158 | FieldName='image'; |
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159 | case 'vol' |
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160 | A=imread(ObjectName); |
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161 | Npz=size(A,1)/ParamIn.Npy; |
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162 | A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz); |
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163 | A=permute(A,[3 2 1]); |
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164 | FieldName='image'; |
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165 | case 'multimage' |
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166 | A=imread(ObjectName,num); |
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167 | FieldName='image'; |
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168 | case 'image' |
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169 | A=imread(ObjectName); |
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170 | FieldName='image'; |
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171 | end |
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172 | %% case of image |
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173 | if ~isempty(A) |
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174 | ParamOut.FieldName='image'; |
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175 | ParamOut.FieldList={'image'}; |
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176 | Npz=1;%default |
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177 | npxy=size(A); |
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178 | Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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179 | Rangy=[npxy(1)-0.5 0.5]; % |
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180 | Field.NbDim=2;%default |
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181 | Field.AName='image'; |
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182 | Field.ListVarName={'AY','AX','A'}; % |
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183 | if ndims(A)==3 |
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184 | if Npz==1;%color |
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185 | Field.VarDimName={'AY','AX',{'AY','AX','rgb'}}; % |
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186 | Field.AY=[npxy(1)-0.5 0.5]; |
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187 | Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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188 | ParamOut.Npx=npxy(2);% display image size on the interface |
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189 | ParamOut.Npy=npxy(1); |
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190 | Field.VarAttribute{3}.Mesh=1; |
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191 | else |
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192 | Field.NbDim=3; |
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193 | Field.ListVarName=['AZ' Field.ListVarName]; |
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194 | Field.VarDimName={'AZ','AY','AX',{'AZ','AY','AX'}}; |
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195 | Field.AZ=[npxy(1)-0.5 0.5]; |
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196 | Field.AY=[npxy(2)-0.5 0.5]; |
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197 | Field.AX=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers |
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198 | ParamOut.Npx=npxy(3);% display image size on the interface |
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199 | ParamOut.Npy=npxy(2); |
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200 | Field.VarAttribute{4}.Mesh=1; |
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201 | end |
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202 | else |
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203 | Field.VarDimName={'AY','AX',{'AY','AX'}}; % |
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204 | Field.AY=[npxy(1)-0.5 0.5]; |
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205 | Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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206 | ParamOut.Npx=npxy(2);% display image size on the interface |
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207 | ParamOut.Npy=npxy(1); |
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208 | Field.VarAttribute{3}.Mesh=1; |
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209 | end |
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210 | Field.A=A; |
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211 | Field.CoordUnit='pixel'; %used for mouse_motion |
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212 | end |
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213 | |
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214 | |
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215 | |
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