<<<<<<< .mine
all: dtiproc.class PARREC.class DTITensor.class GradientsSlicesRemove.class
=======
all: dtiproc.class PARREC.class DTITensor.class Gradients.class DataGrad.class
>>>>>>> .r13

%.class: %.java
	javac -classpath /Users/craig/Documents/Work/src/java:. -O $<

test:
#	java dtiproc ripple_040706_7_1.REC dti.dpf
#	java dtiproc /home/craig/data/20050125dtisp/20050125dtisp_3_1.REC /home/craig/data/20050125dtisp/dti_ser3.dpf 
#	java dtiproc -o . --cmap --fa /kki/g2/jfarrell/data/DTI_studies/20050125_cj/20050125_cj_7_1.REC  craig.dpf
#	java dtiproc -o . --cmap --fa twodti/20050302_5.rec  craig.dpf
#	java dtiproc -p -o . --cmap --fa twodti/20050302_5.rec twodti/ser5.dpf twodti/20050302_6.rec twodti/ser6.dpf
#	java dtiproc -p -o . -s 0.5 --vec --cmap --fa twodti/20050302_6_reg.rec twodti/ser6_reg.dpf
#	java dtiproc -v -v -v --threshold 20 -o . --cmap --adc --fa 20050614mc_5_1.REC gradients.txt
#	java dtiproc --start-slice 20 -p -v -v -v --threshold 20 -o . --cmap --adc --fa 20050614mc_5_1.REC gradients.txt 20050614mc_5_1.REC gradients.txt
#	java dtiproc -v -v -v --threshold 20 -o . --cmap --fa data//New_15_data/20050616_cj_3_1.rec data//New_15_data/20050616_cj_3_1.grad
#	java dtiproc -v -v -v --percentile-threshold 60 -o . --cmap --fa data//Old_15_data/20050317_am_3.rec data//Old_15_data/20050317_am_3.grad
<<<<<<< .mine
	java dtiproc -p --no-scaling -v -v -v --percentile-threshold 60 -o tog/ --cmap --fa data/Registered_Old_15_data_NO_SCALING/TPT_FLT_20050317_am_3_sc.rec data/Registered_Old_15_data_NO_SCALING/TPT_FLT_20050317_am_3.grad
#	java dtiproc -p --no-scaling -v -v -v --percentile-threshold 60 -o tog/ --cmap --fa data/Registered_Old_15_data_NO_SCALING/TPT_FLT_20050317_am_3_sc.rec data/Registered_Old_15_data_NO_SCALING/TPT_FLT_20050317_am_3.grad data/Registered_Old_15_data_NO_SCALING/TPT_FLT_20050317_am_4_sc.rec data/Registered_Old_15_data_NO_SCALING/TPT_FLT_20050317_am_4.grad data/Registered_Old_15_data_NO_SCALING/TPT_FLT_20050317_am_5_sc.rec data/Registered_Old_15_data_NO_SCALING/TPT_FLT_20050317_am_5.grad
#	java dtiproc -p -v -v -v --percentile-threshold 60 -o lkj/ --cmap --fa data/Old_15_data/20050317_am_3.rec data/Old_15_data/20050317_am_3.grad data/Old_15_data/20050317_am_4.rec data/Old_15_data/20050317_am_4.grad data/Old_15_data/20050317_am_5.rec data/Old_15_data/20050317_am_5.grad
=======
#	java -classpath /Users/craig/Documents/Work/src/java:. dtiproc -p --no-scaling -v -v -v --percentile-threshold 60 -o data/ --cmap --fa data/20040413ms_3_1.REC data/bob.dpf
#	java -classpath /Users/craig/Documents/Work/src/java:. dtiproc --include-gradient-directions 0-10,20-32 -p --no-scaling -v -v -v --percentile-threshold 60 -o data/ --cmap --fa data/20050902_3_1.rec data/gradients.txt
#	java -classpath /Users/craig/Documents/Work/src/java:. dtiproc -p --no-scaling -v -v -v --percentile-threshold 60 -o data/ --cmap --fa data/20050902_3_1.rec data/gradients.txt
#	java -classpath /Users/craig/Documents/Work/src/java:. dtiproc --remove-gradient-directions 1,3,5,7,9,11,13,15,17,19,21,23,25,27,29 -p --no-scaling -v -v -v --percentile-threshold 60 -o data/ --fa data/TPT_FLT_20050804_jf_3_1_sc1.rec data/20050804_jf_3_1.grad  # odd
#	java -classpath /Users/craig/Documents/Work/src/java:. dtiproc --remove-gradient-directions 0,2,4,6,8,10,12,14,16,18,20,22,24,26,28 -p --no-scaling -v -v -v --percentile-threshold 60 -o data/ --fa data/TPT_FLT_20050804_jf_3_1_sc1.rec data/20050804_jf_3_1.grad  # even
#	java -classpath /Users/craig/Documents/Work/src/java:. dtiproc --no-scaling -v -v -v --percentile-threshold 60 -o data/ --fa data/TPT_FLT_20050804_jf_3_1_sc1.rec data/20050804_jf_3_1.grad 
	java -classpath /Users/craig/Documents/Work/src/java:. dtiproc --no-scaling -v -v -v --percentile-threshold 60 -o data/ --fa data/TPT_FLT_20050804_jf_3_1_sc1.rec data/20050804_jf_3_1.grad 2,3
#	java -classpath /Users/craig/Documents/Work/src/java:. dtiproc --help
>>>>>>> .r13

jar:
	jar cvf dtiproc.jar *.class  help*.txt
	(cd /Users/craig/Documents/Work/src/java/ && jar uvf /Users/craig/Documents/Work/src/dtiproc/dtiproc.jar cj/math/jama/*.class  )
	(cd /Users/craig/Documents/Work/src/java/ && jar uvf /Users/craig/Documents/Work/src/dtiproc/dtiproc.jar cj/math/jama/util/*.class  )
	(cd /Users/craig/Documents/Work/src/java/ && jar uvf /Users/craig/Documents/Work/src/dtiproc/dtiproc.jar gnu/getopt/*.class  )
	(cd /Users/craig/Documents/Work/src/java/ && jar uvf /Users/craig/Documents/Work/src/dtiproc/dtiproc.jar gnu/getopt/Message*  )
	(cd /Users/craig/Documents/Work/src/java/ && jar uvf /Users/craig/Documents/Work/src/dtiproc/dtiproc.jar cj/appkit/*.class )

clean:
	-rm *.class
