1 | %'sub_field_series': substract the two input field series, then possibly project them on a grid (like merge_proj;m) |
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2 | % GUI_input=sub_field_series(num_i1,num_i2,num_j1,num_j2,Series) |
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3 | % |
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4 | %OUTPUT |
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5 | % GUI_input=list of options in the GUI series.fig needed for the function |
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6 | % |
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7 | %INPUT: |
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8 | %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) |
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9 | %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) |
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10 | %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) |
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11 | %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) |
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12 | %Series: Matlab structure containing information set by the series interface |
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13 | % |
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14 | function GUI_input=sub_field_series(num_i1,num_i2,num_j1,num_j2,Series) |
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15 | |
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16 | %requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) |
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17 | if ~exist('num_i1','var') |
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18 | GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') |
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19 | 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) |
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20 | 'RootFile';'on';... %root input file name ('on' by default) |
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21 | 'FileExt';'on';... %input file extension ('on' by default) |
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22 | 'NomType';'on';...%type of file indexing ('on' by default) |
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23 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
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24 | 'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default) |
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25 | 'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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26 | 'CoordType';'on';...%can use a transform function 'off' by default |
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27 | % 'GetObject';'on';...%can use projection object ,'off' by default |
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28 | %'GetMask';'on'...%can use mask option ,'off' by default |
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29 | %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter |
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30 | ''}; |
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31 | return %exit the function |
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32 | end |
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33 | |
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34 | %------------------------------------------------- |
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35 | hseries=guidata(Series.hseries);%handles of the GUI series |
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36 | WaitbarPos=get(hseries.waitbar_frame,'Position'); %positiopn of waitbar frame |
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37 | %------------------------------------------------- |
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38 | |
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39 | |
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40 | %% numbers of view fields (nbre of inputs in RootPath) |
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41 | testcell=iscell(Series.RootFile); |
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42 | if ~testcell |
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43 | Series.RootPath={Series.RootPath}; |
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44 | Series.RootFile={Series.RootFile}; |
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45 | Series.SubDir={Series.SubDir}; |
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46 | Series.FileExt={Series.FileExt}; |
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47 | Series.NomType={Series.NomType}; |
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48 | num_i1={num_i1}; |
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49 | num_i2={num_i2}; |
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50 | num_j1={num_j1}; |
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51 | num_j2={num_j2}; |
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52 | end |
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53 | nbview=length(Series.RootFile);%number of views (file series to merge) |
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54 | nbfield=size(num_i1{1},1)*size(num_i1{1},2);%number of fields in the time series |
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55 | hhh=which('mmreader'); |
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56 | for iview=1:nbview |
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57 | test_movie(iview)=0; |
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58 | if ~isequal(hhh,'')&& mmreader.isPlatformSupported() |
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59 | if isequal(lower(Series.FileExt{iview}),'.avi') |
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60 | MovieObject{iview}=mmreader(fullfile(Series.RootPath{iview},[Series.RootFile{iview} Series.FileExt{iview}])); |
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61 | test_movie(iview)=1; |
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62 | end |
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63 | end |
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64 | end |
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65 | |
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66 | %% Calibration data and timing: read the ImaDoc files |
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67 | timecell={}; |
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68 | itime=0; |
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69 | NbSlice_calib={}; %test for z index |
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70 | for iview=1:nbview%Loop on views |
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71 | XmlData{iview}=[];%default |
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72 | filebase{iview}=fullfile(Series.RootPath{iview},Series.RootFile{iview}); |
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73 | if exist([filebase{iview} '.xml'],'file') |
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74 | [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); |
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75 | if isfield(XmlData{iview},'Time') |
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76 | itime=itime+1; |
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77 | timecell{itime}=XmlData{iview}.Time; |
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78 | end |
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79 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') |
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80 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1); |
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81 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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82 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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83 | end |
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84 | end |
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85 | elseif exist([filebase{iview} '.civ'],'file') |
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86 | [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); |
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87 | itime=itime+1; |
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88 | timecell{itime}=time; |
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89 | XmlData{iview}.Time=time; |
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90 | GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; |
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91 | GeometryCalib.Tx=0; |
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92 | GeometryCalib.Ty=0; |
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93 | GeometryCalib.Tz=1; |
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94 | GeometryCalib.dpx=1; |
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95 | GeometryCalib.dpy=1; |
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96 | GeometryCalib.sx=1; |
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97 | GeometryCalib.Cx=0; |
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98 | GeometryCalib.Cy=0; |
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99 | GeometryCalib.f=1; |
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100 | GeometryCalib.kappa1=0; |
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101 | GeometryCalib.CoordUnit='cm'; |
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102 | XmlData{iview}.GeometryCalib=GeometryCalib; |
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103 | if error==1 |
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104 | msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); |
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105 | end |
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106 | end |
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107 | end |
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108 | |
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109 | %% check coincidence in time |
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110 | multitime=0; |
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111 | if isempty(timecell) |
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112 | time=[]; |
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113 | elseif length(timecell)==1 |
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114 | time=timecell{1}; |
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115 | elseif length(timecell)>1 |
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116 | multitime=1; |
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117 | for icell=1:length(timecell) |
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118 | if ~isequal(size(timecell{icell}),size(timecell{1})) |
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119 | msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') |
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120 | time=timecell{1}; |
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121 | multitime=0; |
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122 | break |
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123 | end |
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124 | end |
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125 | end |
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126 | if multitime |
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127 | for icell=1:length(timecell) |
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128 | time(icell,:,:)=timecell{icell}; |
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129 | end |
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130 | diff_time=max(max(diff(time))); |
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131 | if diff_time>0 |
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132 | msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)]) |
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133 | end |
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134 | end |
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135 | if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file' |
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136 | time=[]; |
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137 | end |
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138 | |
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139 | %% coordinate transform or other user defined transform |
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140 | transform_fct=[];%default |
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141 | if isfield(Series,'transform_fct') |
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142 | transform_fct=Series.transform_fct; |
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143 | end |
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144 | |
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145 | %% Field and velocity type (the same for all views) |
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146 | FieldName=''; |
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147 | if strcmp(get(hseries.FieldMenu,'Visible'),'on') |
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148 | Field_str=get(hseries.FieldMenu,'String'); |
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149 | val=get(hseries.FieldMenu,'Value'); |
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150 | FieldName=Field_str(val);%the same set of fields for all views |
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151 | VelType_str=get(hseries.VelTypeMenu,'String'); |
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152 | VelType_val=get(hseries.VelTypeMenu,'Value'); |
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153 | VelType=VelType_str{VelType_val}; %the same for all views |
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154 | if strcmp(FieldName,'') |
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155 | msgbox_uvmat('ERROR','no input field defined in FieldMenu') |
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156 | elseif strcmp(FieldName,'get_field...') |
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157 | hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI |
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158 | SubField=get_field('read_get_field',hObject,eventdata,hget_field); %read the names of the variables to plot in the get_field GUI |
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159 | end |
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160 | end |
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161 | %detect whether all the files are 'images' or 'netcdf' |
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162 | testima=0; |
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163 | testvol=0; |
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164 | testcivx=0; |
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165 | testnc=0; |
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166 | FileExt=get(hseries.FileExt,'String'); |
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167 | for iview=1:nbview |
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168 | ext=FileExt{iview}; |
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169 | form=imformats(ext(2:end)); |
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170 | if isequal(lower(ext),'.vol') |
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171 | testvol=testvol+1; |
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172 | elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab |
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173 | testima=testima+1; |
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174 | elseif isequal(ext,'.nc') |
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175 | testnc=testnc+1; |
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176 | end |
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177 | end |
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178 | if testvol |
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179 | msgbox_uvmat('ERROR','volume images not implemented yet') |
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180 | return |
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181 | end |
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182 | if testnc~=nbview && testima~=nbview && testvol~=nbview |
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183 | msgbox_uvmat('ERROR','need a set of images or a set of netcdf files with the same fields as input') |
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184 | return |
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185 | end |
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186 | if ~isequal(FieldName,'get_field...') |
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187 | testcivx=testnc; |
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188 | end |
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189 | |
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190 | %% name of output files and directory: |
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191 | ProjectDir=fileparts(fileparts(Series.RootPath{1}));% preoject directory (GERK) |
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192 | prompt={['result directory (in' ProjectDir ')']}; |
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193 | RootPath=get(hseries.RootPath,'String'); |
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194 | SubDir=get(hseries.SubDir,'String'); |
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195 | if isequal(length(RootPath),1) |
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196 | fulldir=RootPath{1}; |
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197 | subdir='merge_proj'; |
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198 | res_subdir=fullfile(fulldir,subdir); |
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199 | else |
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200 | def={fullfile(ProjectDir,'0_RESULTS')}; |
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201 | dlgTitle='result directory'; |
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202 | lineNo=1; |
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203 | answer=msgbox_uvmat('INPUT_TXT',dlgTitle,def); |
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204 | fulldir=answer{1}; |
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205 | subdir=[]; |
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206 | dirlist=sort(Series.RootFile); |
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207 | for iview=1:nbview |
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208 | if ~isempty(subdir) |
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209 | subdir=[subdir '-']; |
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210 | end |
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211 | subdir=[subdir dirlist{iview}]; |
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212 | end |
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213 | res_subdir=fullfile(fulldir,subdir); |
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214 | end |
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215 | ext=FileExt{1}; |
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216 | if ~exist(fulldir,'dir') |
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217 | msgbox_uvmat('ERROR',['directory ' fulldir ' needs to be created']) |
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218 | return |
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219 | end |
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220 | if ~exist(res_subdir,'dir') |
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221 | dircur=pwd; |
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222 | cd(fulldir); |
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223 | succeed=mkdir(subdir); |
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224 | if succeed |
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225 | [xx,msg2] = fileattrib(res_subdir,'+w','g'); %yield writing access (+w) to user group (g) |
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226 | if ~strcmp(msg2,'') |
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227 | msgbox_uvmat('ERROR',['pb of permission for ' res_subdir ': ' msg2])%error message for directory creation |
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228 | cd(dircur) |
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229 | return |
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230 | end |
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231 | cd(dircur); |
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232 | else |
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233 | msgbox_uvmat('ERROR',['Cannot create directory ' fulldir]) |
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234 | return |
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235 | end |
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236 | end |
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237 | filebasesub=fullfile(res_subdir,Series.RootFile{1}); |
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238 | filebase_merge=fullfile(res_subdir,'merged');%root name for the merged files |
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239 | |
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240 | %% MAIN LOOP |
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241 | for ifile=1:nbfield |
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242 | stopstate=get(hseries.RUN,'BusyAction'); |
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243 | if isequal(stopstate,'queue')% enable STOP command from the 'series' interface |
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244 | update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield) |
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245 | |
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246 | %% ----------LOOP ON VIEWS---------------------- |
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247 | nbtime=0; |
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248 | for iview=1:nbview |
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249 | %name of the current file |
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250 | filename=name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview}); |
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251 | if ~exist(filename,'file') |
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252 | msgbox_uvmat('ERROR',['missing input file' filename]) |
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253 | break |
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254 | end |
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255 | %reading the current file |
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256 | if testima |
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257 | if test_movie(iview) |
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258 | Field{iview}.A=read(MovieObject{iview},num_i1{iview}(ifile)); |
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259 | else |
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260 | Field{iview}.A=imread(filename); |
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261 | end % TODO: introduce ListVarName |
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262 | npxy=size(Field{iview}.A); |
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263 | Field{iview}.ListVarName={'AX','AY','A'}; |
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264 | Field{iview}.VarDimName={'AX','AY',{'AY','AX'}}; |
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265 | Field{iview}.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
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266 | Field{iview}.AY=[npxy(1)-0.5 0.5]; |
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267 | Field{iview}.CoordUnit='pixel'; |
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268 | Field{iview}.AName='image'; |
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269 | timeread(iview)=0; |
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270 | else |
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271 | if testcivx |
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272 | [Field{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); |
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273 | else |
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274 | [Field{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data |
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275 | Field{iview}.VarAttribute=SubField.VarAttribute; |
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276 | end |
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277 | if isfield(Field{iview},'Txt') |
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278 | msgbox_uvmat('ERROR',Field{iview}.Txt) |
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279 | return |
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280 | end |
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281 | if isfield(Field{iview},'Time') |
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282 | timeread(iview)=Field{iview}.Time; |
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283 | nbtime=nbtime+1; |
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284 | end |
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285 | end |
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286 | if ~isempty(NbSlice_calib) |
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287 | Field{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1; |
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288 | end |
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289 | %transform the input field (e.g; phys) if requested |
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290 | if ~isempty(transform_fct) |
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291 | Field{iview}=transform_fct(Field{iview},XmlData{iview}); %transform to phys if requested |
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292 | end |
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293 | if testcivx |
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294 | Field{iview}=calc_field(FieldName,Field{iview}); |
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295 | end |
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296 | %projection on object (gridded plane) |
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297 | % if test_object |
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298 | % Field{iview}=proj_field(Field{iview},ProjObject); |
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299 | % end |
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300 | end |
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301 | %----------END LOOP ON VIEWS---------------------- |
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302 | |
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303 | %% merge the nbview=2 fields |
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304 | MergeData=sub_field(Field{1},Field{2}) |
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305 | if isfield(MergeData,'Txt') |
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306 | msgbox_uvmat('ERROR',MergeData.Txt) |
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307 | return |
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308 | end |
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309 | |
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310 | % time of the merged field: |
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311 | time_i=0;%default |
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312 | if isempty(time)% time from ImaDoc prevails |
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313 | time_i=sum(timeread)/nbtime; |
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314 | else |
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315 | time_i=(time(iview,num_i1{iview}(ifile),num_j1{iview}(ifile))+time(iview,num_i2{iview}(ifile),num_j2{iview}(ifile)))/2; |
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316 | end |
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317 | |
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318 | % recording the merged field |
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319 | if testima %in case of input images an image is produced |
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320 | % generating the name of the merged field |
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321 | mergename=name_generator(filebase_merge,num_i1{1}(ifile),num_j1{1}(ifile),'.png',Series.NomType{1},1,num_i2{1}(ifile),num_j2{1}(ifile)); |
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322 | if isa(Field{1}.A,'uint8') |
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323 | imwrite(uint8(MergeData.A),mergename,'BitDepth',8); |
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324 | elseif isa(Field{1}.A,'uint16') |
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325 | imwrite(uint16(MergeData.A),mergename,'BitDepth',16); |
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326 | end |
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327 | % imwrite(MergeData.A,mergename,'BitDepth',bitdepth); |
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328 | %write xml calibration file |
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329 | siz=size(MergeData.A); |
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330 | npy=siz(1); |
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331 | npx=siz(2); |
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332 | if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1') |
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333 | Rangx=MergeData.VarAttribute{1}.Coord_2; |
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334 | Rangy=MergeData.VarAttribute{1}.Coord_1; |
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335 | elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') |
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336 | Rangx=[MergeData.AX(1) MergeData.AX(end)]; |
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337 | Rangy=[MergeData.AY(1) MergeData.AY(end)]; |
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338 | else |
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339 | Rangx=[0.5 npx-0.5]; |
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340 | Rangy=[npy-0.5 0.5];%default |
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341 | end |
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342 | pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); |
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343 | pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); |
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344 | T_x=-pxcmx*Rangx(1)+0.5; |
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345 | T_y=-pxcmy*Rangy(2)+0.5; |
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346 | GeometryCal.focal=1; |
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347 | GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; |
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348 | GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; |
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349 | ImaDoc.GeometryCalib=GeometryCal; |
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350 | t=struct2xml(ImaDoc); |
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351 | t=set(t,1,'name','ImaDoc'); |
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352 | save(t,[filebase_merge '.xml']) |
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353 | display([filebase_merge '.xml saved']) |
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354 | else |
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355 | mergename=name_generator(filebase_merge,num_i1{1}(ifile),num_j1{1}(ifile),'.nc',Series.NomType{1},1,num_i2{1}(ifile),num_j2{1}(ifile)); |
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356 | MergeData.ListGlobalAttribute={'Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; |
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357 | MergeData.nb_coord=2; |
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358 | MergeData.nb_dim=2; |
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359 | dt=[]; |
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360 | if isfield(Field{1},'dt')&& isnumeric(Field{1}.dt) |
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361 | dt=Field{1}.dt; |
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362 | end |
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363 | for iview =2:numel(Field) |
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364 | if ~(isfield(Field{iview},'dt')&& isequal(Field{iview}.dt,dt)) |
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365 | dt=[];%dt not the same for all fields |
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366 | end |
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367 | end |
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368 | if isempty(dt) |
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369 | MergeData.ListGlobalAttribute(6)=[]; |
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370 | else |
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371 | MergeData.dt=dt; |
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372 | end |
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373 | MergeData.Time=time_i; |
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374 | error=struct2nc(mergename,MergeData);%save result file |
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375 | if isempty(error) |
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376 | display(['output file ' mergename ' written']) |
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377 | else |
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378 | display(error) |
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379 | end |
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380 | end |
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381 | end |
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382 | end |
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383 | |
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384 | %'merge_field': concatene fields |
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385 | %------------------------------------------------------------------------ |
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386 | function MergeData=merge_field(Data) |
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387 | %% default output |
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388 | if isempty(Data)||~iscell(Data) |
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389 | MergeData=[]; |
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390 | return |
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391 | end |
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392 | MergeData=Data{1};%default |
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393 | error=0; |
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394 | nbview=length(Data); |
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395 | if nbview==1 |
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396 | return |
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397 | end |
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398 | |
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399 | %% group the variables (fields of 'FieldData') in cells of variables with the same dimensions |
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400 | [CellVarIndex,NbDim,VarTypeCell]=find_field_indices(Data{1}); |
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401 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
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402 | % CellVarIndex=cells of variable index arrays |
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403 | ivar_new=0; % index of the current variable in the projected field |
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404 | for icell=1:length(CellVarIndex) |
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405 | if NbDim(icell)==1 |
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406 | continue |
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407 | end |
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408 | VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName |
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409 | VarType=VarTypeCell{icell}; |
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410 | ivar_X=VarType.coord_x; |
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411 | ivar_Y=VarType.coord_y; |
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412 | ivar_FF=VarType.errorflag; |
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413 | if isempty(ivar_X) |
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414 | test_grid=1;%test for input data on regular grid (e.g. image)coordinates |
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415 | else |
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416 | if length(ivar_Y)~=1 |
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417 | msgbox_uvmat('ERROR','y coordinate missing in proj_field.m') |
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418 | return |
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419 | end |
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420 | test_grid=0; |
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421 | end |
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422 | %case of input fields with unstructured coordinates |
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423 | if ~test_grid |
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424 | for ivar=VarIndex |
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425 | VarName=MergeData.ListVarName{ivar}; |
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426 | for iview=1:nbview |
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427 | eval(['MergeData.' VarName '=[MergeData.' VarName '; Data{iview}.' VarName '];']) |
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428 | end |
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429 | end |
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430 | %case of fields defined on a structured grid |
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431 | else |
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432 | testFF=0; |
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433 | for iview=2:nbview |
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434 | for ivar=VarIndex |
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435 | VarName=MergeData.ListVarName{ivar}; |
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436 | if isfield(MergeData,'VarAttribute') |
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437 | if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag') |
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438 | testFF=1; |
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439 | end |
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440 | end |
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441 | eval(['MergeData.' VarName '=MergeData.' VarName '+ Data{iview}.' VarName ';']) |
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442 | end |
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443 | end |
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444 | if testFF |
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445 | nbaver=nbview-MergeData.FF; |
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446 | indgood=find(nbaver>0); |
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447 | for ivar=VarIndex |
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448 | VarName=MergeData.ListVarName{ivar}; |
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449 | eval(['MergeData.' VarName '(indgood)=double(MergeData.' VarName '(indgood))./nbaver(indgood);']) |
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450 | end |
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451 | else |
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452 | for ivar=VarIndex |
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453 | VarName=MergeData.ListVarName{ivar}; |
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454 | eval(['MergeData.' VarName '=double(MergeData.' VarName ')./nbview;']) |
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455 | end |
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456 | end |
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457 | end |
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458 | end |
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