codebase / stimlib

Commit e37ce7bf1167070f130fa7368032073a597d9d62

Authored by David Mayerich
1 parent 3a880d1c

added the ability to build masks from other masks

Showing 5 changed files with 45 additions and 32 deletions   Show diff stats
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stim/envi/bil.h
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... ... @@ -828,16 +828,19 @@ public:
828 828 /// @param mask_band is the band used to specify the mask
829 829 /// @param threshold is the threshold used to determine if the mask value is true or false
830 830 /// @param p is a pointer to a pre-allocated array at least X * Y in size
831   - bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
  831 + bool build_mask(unsigned char* out_mask, double mask_band, double lower, double upper, unsigned char* mask = NULL, bool PROGRESS = false){
832 832  
833 833 T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
834 834 band(temp, mask_band, PROGRESS);
835 835  
836 836 for (unsigned long long i = 0; i < X() * Y(); i++) {
837   - if (temp[i] < threshold)
838   - mask[i] = 0;
839   - else
840   - mask[i] = 255;
  837 + if(mask == NULL || mask[i] != 0){
  838 + if(temp[i] > lower && temp[i] < upper){
  839 + out_mask[i] = 255;
  840 + }
  841 + else
  842 + out_mask[i] = 0;
  843 + }
841 844 }
842 845  
843 846 free(temp);
... ...
stim/envi/bip.h
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... ... @@ -762,16 +762,19 @@ public:
762 762 /// @param mask_band is the band used to specify the mask
763 763 /// @param threshold is the threshold used to determine if the mask value is true or false
764 764 /// @param p is a pointer to a pre-allocated array at least X * Y in size
765   - bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
  765 + bool build_mask(unsigned char* out_mask, double mask_band, double lower, double upper, unsigned char* mask = NULL, bool PROGRESS = false){
766 766  
767 767 T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
768 768 band(temp, mask_band, PROGRESS);
769 769  
770 770 for (unsigned long long i = 0; i < X() * Y();i++) {
771   - if (temp[i] < threshold)
772   - mask[i] = 0;
773   - else
774   - mask[i] = 255;
  771 + if(mask == NULL || mask[i] != 0){
  772 + if(temp[i] > lower && temp[i] < upper){
  773 + out_mask[i] = 255;
  774 + }
  775 + else
  776 + out_mask[i] = 0;
  777 + }
775 778 }
776 779  
777 780 free(temp);
... ...
stim/envi/bsq.h
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... ... @@ -914,16 +914,20 @@ public:
914 914 /// @param mask_band is the band used to specify the mask
915 915 /// @param threshold is the threshold used to determine if the mask value is true or false
916 916 /// @param p is a pointer to a pre-allocated array at least X * Y in size
917   - bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
  917 + bool build_mask(unsigned char* out_mask, double mask_band, double lower, double upper, unsigned char* mask = NULL, bool PROGRESS = false){
  918 + memset(out_mask, 0, X() * Y()); //initialize the mask to zero
918 919  
919 920 T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
920 921 band(temp, mask_band);
921 922  
922 923 for (unsigned long long i = 0; i < X() * Y(); i++) {
923   - if (temp[i] < threshold)
924   - mask[i] = 0;
925   - else
926   - mask[i] = 255;
  924 + if(mask == NULL || mask[i] != 0){
  925 + if(temp[i] > lower && temp[i] < upper){
  926 + out_mask[i] = 255;
  927 + }
  928 + else
  929 + out_mask[i] = 0;
  930 + }
927 931  
928 932 if(PROGRESS) progress = (double) (i+1) / (X() * Y()) * 100;
929 933 }
... ...
stim/envi/envi.h
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... ... @@ -718,31 +718,31 @@ public:
718 718 /// @param mask_band is the label for the band that will be used to build the mask
719 719 /// @param threshold is a value selected such that all band values greater than threshold will have a mask value of 'true'
720 720 /// @param p is memory of size X*Y that will store the resulting mask
721   - bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false) {
  721 + bool build_mask(unsigned char* out_mask, double mask_band, double lower, double upper, unsigned char* mask = NULL, bool PROGRESS = false) {
722 722  
723 723 if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
724 724 if(header.data_type ==envi_header::float32)
725   - return ((bsq<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
  725 + return ((bsq<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
726 726 else if(header.data_type == envi_header::float64)
727   - return ((bsq<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
  727 + return ((bsq<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
728 728 else
729 729 std::cout<<"ERROR: unidentified data type"<<std::endl;
730 730 }
731 731  
732 732 else if(header.interleave == envi_header::BIL){ //if the infile is bil file
733 733 if(header.data_type ==envi_header::float32)
734   - return ((bil<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
  734 + return ((bil<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
735 735 else if(header.data_type == envi_header::float64)
736   - return ((bil<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
  736 + return ((bil<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
737 737 else
738 738 std::cout<<"ERROR: unidentified data type"<<std::endl;
739 739 }
740 740  
741 741 else if(header.interleave == envi_header::BIP){ //if the infile is bip file
742 742 if(header.data_type ==envi_header::float32)
743   - return ((bip<float>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
  743 + return ((bip<float>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
744 744 else if(header.data_type == envi_header::float64)
745   - return ((bip<double>*)file)->build_mask(mask, mask_band, threshold, PROGRESS);
  745 + return ((bip<double>*)file)->build_mask(out_mask, mask_band, lower, upper, mask, PROGRESS);
746 746 else
747 747 std::cout<<"ERROR: unidentified data type"<<std::endl;
748 748 }
... ... @@ -751,30 +751,30 @@ public:
751 751 }
752 752  
753 753 /// Creates a mask with a true value for all pixels that contain finite values
754   - void mask_finite(unsigned char* mask, bool PROGRESS = false){
  754 + void mask_finite(unsigned char* out_mask, unsigned char* mask = NULL, bool PROGRESS = false){
755 755 if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
756 756 if(header.data_type ==envi_header::float32)
757   - ((bsq<float>*)file)->mask_finite(mask, PROGRESS);
  757 + ((bsq<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
758 758 else if(header.data_type == envi_header::float64)
759   - ((bsq<double>*)file)->mask_finite(mask, PROGRESS);
  759 + ((bsq<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
760 760 else
761 761 std::cout<<"ERROR: unidentified data type"<<std::endl;
762 762 }
763 763  
764 764 else if(header.interleave == envi_header::BIL){ //if the infile is bil file
765 765 if(header.data_type ==envi_header::float32)
766   - ((bil<float>*)file)->mask_finite(mask, PROGRESS);
  766 + ((bil<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
767 767 else if(header.data_type == envi_header::float64)
768   - ((bil<double>*)file)->mask_finite(mask, PROGRESS);
  768 + ((bil<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
769 769 else
770 770 std::cout<<"ERROR: unidentified data type"<<std::endl;
771 771 }
772 772  
773 773 else if(header.interleave == envi_header::BIP){ //if the infile is bip file
774 774 if(header.data_type ==envi_header::float32)
775   - ((bip<float>*)file)->mask_finite(mask, PROGRESS);
  775 + ((bip<float>*)file)->mask_finite(out_mask, mask, PROGRESS);
776 776 else if(header.data_type == envi_header::float64)
777   - ((bip<double>*)file)->mask_finite(mask, PROGRESS);
  777 + ((bip<double>*)file)->mask_finite(out_mask, mask, PROGRESS);
778 778 else
779 779 std::cout<<"ERROR: unidentified data type"<<std::endl;
780 780 }
... ...
stim/envi/hsi.h
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... ... @@ -139,9 +139,12 @@ protected:
139 139  
140 140 public:
141 141 /// Get a mask that has all pixels with inf or NaN values masked out (false)
142   - void mask_finite(unsigned char* mask, bool PROGRESS = false){
  142 + void mask_finite(unsigned char* out_mask, unsigned char* mask, bool PROGRESS = false){
143 143 size_t XY = X() * Y();
144   - memset(mask, 255, XY * sizeof(unsigned char)); //initialize the mask to zero (0)
  144 + if(mask == NULL) //if no mask is provided
  145 + memset(mask, 255, XY * sizeof(unsigned char)); //initialize the mask to 255
  146 + else //if a mask is provided
  147 + memcpy(out_mask, mask, XY * sizeof(unsigned char)); //initialize the current mask to that one
145 148 T* page = (T*)malloc(R[0] * R[1] * sizeof(T)); //allocate space for a page of data
146 149  
147 150 for(size_t p = 0; p < R[2]; p++){ //for each page
... ... @@ -155,7 +158,7 @@ public:
155 158 #endif
156 159 size_t x, y, b;
157 160 xyb(p * R[0] * R[1] + i, x, y, b); //find the 3D coordinates of the value
158   - mask[ y * X() + x ] = 0; //remove the pixel (it's bad)
  161 + out_mask[ y * X() + x ] = 0; //remove the pixel (it's bad)
159 162 }
160 163 }
161 164 if(PROGRESS) progress = (double)(p + 1) / (double)R[2] * 100;
... ...