1 | |
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2 | %'read_field': read input fields in different formats |
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3 | %-------------------------------------------------------------------------- |
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4 | % function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num) |
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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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17 | % FileName: name of the input file |
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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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22 | % = mmreader: movie read with mmreader |
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23 | % = video: movie read with VideoReader (recent versions of Matlab) |
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24 | % = vol: images representing scanned volume (images concatened in the y direction) |
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25 | % ParamIn: movie object or Matlab structure of input parameters |
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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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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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30 | % num: frame number for movies |
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31 | |
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32 | function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num) |
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33 | Field=[]; |
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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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41 | errormsg=''; |
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42 | % if isfield(ParamIn,'VelType') |
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43 | % VelType=ParamIn.VelType; |
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44 | % end |
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45 | A=[]; |
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46 | %% distingush different input file types |
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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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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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65 | if isempty(find(field_index,1))% ParamIn.FieldName is not in the list, check whether Civx data exist |
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66 | Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ','CivStage'); |
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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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72 | [Field,ParamOut.VelType,errormsg]=read_civdata(FileName,InputField,ParamIn.VelType,Data.CivStage); |
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73 | if ~isempty(errormsg),errormsg=['read_civdata:' errormsg];return,end |
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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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81 | [Field,ParamOut.VelType]=read_civxdata(FileName,InputField,ParamIn.VelType); |
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82 | if ~isempty(errormsg),errormsg=['read_civxdata:' errormsg];return,end |
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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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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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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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102 | [Field,ParamOut.VelType,errormsg]=read_civxdata(FileName,InputField,ParamIn.VelType); |
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103 | if ~isempty(errormsg),errormsg=['read_civxdata:' errormsg];return,end |
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104 | CivStage=Field.CivStage; |
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105 | ParamOut.CivStage=Field.CivStage; |
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106 | end |
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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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112 | hget_field= get_field(FileName);%open the get_field GUI |
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113 | set(hget_field,'Name',GUIName)%update the name of get_field (e.g. get_field_1) |
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114 | end |
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115 | hhget_field=guidata(hget_field); |
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116 | %% update the get_field GUI |
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117 | set(hhget_field.inputfile,'String',FileName) |
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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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121 | end |
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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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128 | set(hhget_field.inputfile,'String',FileName) |
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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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133 | val=Field.(Field.ListGlobalAttribute{iline}); |
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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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139 | end |
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140 | end |
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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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145 | end |
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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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150 | end |
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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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155 | end |
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156 | case 'video' |
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157 | if strcmp(class(ParamIn),'VideoReader') |
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158 | A=read(ParamIn,num); |
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159 | else |
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160 | ParamOut=VideoReader(FileName); |
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161 | A=read(ParamOut,num); |
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162 | end |
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163 | case 'mmreader' |
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164 | if strcmp(class(ParamIn),'mmreader') |
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165 | A=read(ParamIn,num); |
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166 | else |
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167 | ParamOut=mmreader(FileName); |
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168 | A=read(ParamOut,num); |
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169 | end |
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170 | case 'vol' |
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171 | A=imread(FileName); |
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172 | Npz=size(A,1)/ParamIn.Npy; |
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173 | A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz); |
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174 | A=permute(A,[3 2 1]); |
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175 | case 'multimage' |
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176 | warning 'off' |
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177 | A=imread(FileName,num); |
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178 | case 'image' |
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179 | A=imread(FileName); |
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180 | end |
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181 | catch ME |
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182 | errormsg=[FileType ' input: ' ME.message]; |
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183 | return |
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184 | end |
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185 | |
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186 | %% case of image |
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187 | if ~isempty(A) |
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188 | if isstruct(ParamOut) |
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189 | ParamOut.FieldName='image'; |
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190 | ParamOut.FieldList={'image'}; |
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191 | end |
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192 | Npz=1;%default |
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193 | npxy=size(A); |
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194 | % Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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195 | % Rangy=[npxy(1)-0.5 0.5]; % |
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196 | Field.NbDim=2;%default |
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197 | Field.AName='image'; |
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198 | Field.ListVarName={'AY','AX','A'}; % |
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199 | if ndims(A)==3 |
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200 | if Npz==1;%color |
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201 | Field.VarDimName={'AY','AX',{'AY','AX','rgb'}}; % |
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202 | Field.AY=[npxy(1)-0.5 0.5]; |
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203 | Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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204 | if isstruct(ParamOut) |
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205 | ParamOut.Npx=npxy(2);% display image size on the interface |
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206 | ParamOut.Npy=npxy(1); |
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207 | end |
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208 | Field.VarAttribute{3}.Mesh=1; |
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209 | else |
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210 | Field.NbDim=3; |
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211 | Field.ListVarName=['AZ' Field.ListVarName]; |
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212 | Field.VarDimName={'AZ','AY','AX',{'AZ','AY','AX'}}; |
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213 | Field.AZ=[npxy(1)-0.5 0.5]; |
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214 | Field.AY=[npxy(2)-0.5 0.5]; |
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215 | Field.AX=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers |
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216 | if isstruct(ParamOut) |
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217 | ParamOut.Npx=npxy(3);% display image size on the interface |
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218 | ParamOut.Npy=npxy(2); |
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219 | end |
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220 | Field.VarAttribute{4}.Mesh=1; |
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221 | end |
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222 | else |
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223 | Field.VarDimName={'AY','AX',{'AY','AX'}}; % |
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224 | Field.AY=[npxy(1)-0.5 0.5]; |
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225 | Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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226 | ParamOut.Npx=npxy(2);% display image size on the interface |
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227 | ParamOut.Npy=npxy(1); |
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228 | Field.VarAttribute{3}.Mesh=1; |
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229 | end |
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230 | Field.A=A; |
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231 | Field.CoordUnit='pixel'; %used for mouse_motion |
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232 | end |
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233 | |
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234 | |
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235 | |
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