PercentCoverBatch.txt
— 2.1 KB
File contents
## change extension from .txt to .sh and confirm that permissions are set to allow execution to run as a shell script # This shell script will batch process images, and write the results to a text file # find all JPG files in the directory, and run this program # the call to ImageAnalysisPercentLeafCover should include all the appropriate thresholds # and the threshold line should later be copied to the results text file # # ============parameters and defaults used by the image analysis program =============== # -txg,600,Max intensity for green leaves # -tmg,150,Min intensity for green leaves # -trg, 1.0,Max red/green ratio for green leaves # -txp,600,Max intensity for purple leaves # -tmp,200,Min intensity for purple leaves # -tgbp,1.1,Max green/blue ratio for purple leaves # -tri,360,Min intensity for residue # -trr,155,Min red for residue # -tsi,360,Max intensity for soil # -tsr,155,Max red for soil # -bl,2,Percentage range for border-line pixels # -s,false,Show image # -header,true,Include header in textfile # -tf,false,Data to textfile # -v,false,Be verbose # -V,false,Be super verbose # Rename the images, removing any spaces from the names (Cimg doesn't like spaces) rename 's\ \_\g' *.JPG find ./ -name "*.JPG" -exec ~/Data/neipm/Image\ Analysis/ImageAnalysisPercentLeafCover/Debug/ImageAnalysisPercentLeafCover -txg 450 -tmg 100 -trg 0.98 -txp 350 -tmp 100 -tgbp 1.15 -tri 260 -trr 110 -tsi 230 -tsr 100 -tf {} \; ## next lines do this: # copy first line (header) from one file # concatenate the text files together, leaving out any lines that start with Date # add these data together # remove all dat.txt files except results.txt cat *dat.txt | line > firstlinedat.txt cat *dat.txt | grep -v Date > datadat.txt cat firstlinedat.txt datadat.txt > results.txt rm *dat.txt # find syntax: # find wheretolook whattolookfor -exec pathtoexecutable optionspassedtoexecutable {} \; # example of find as used here # find ./ -name "*.JPG" -exec ../ImageAnalysisPercentLeafCover/Debug/ImageAnalysisPercentLeafCover -V -tf {} \;
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Spotlight
Amelia Henry receives humanitarian award
Jagdeep Sidhu receives research award
Roots lab research focus of podcast from West German Public Radio
Newly discovered trait helps plants grow deeper roots in dry, compacted soils | Penn State University
CSA news article on Roots Lab work with bean breeding
Jagdeep Sidhu Receives College Research Funding
Jonathan Lynch recognized as Highly Cited Researcher by Clarivate
Graduate student receives special award for early career contributions to ASPB
LAT root image wins photo competition of Egyptian Academy of Scientific Research
Graduate student awarded Outstanding Agricultural Graduate Student Award from AASIO
News story on bean root architecture reaches 6 million people, worth $240,000
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Field work proceeds with physical distancing, safety precautions