Fixed cantilever-data figure Makefile dependencies (again :p)

diff --git a/tex/src/figures/cantilever-data/Makefile b/tex/src/figures/cantilever-data/Makefile
index f08f706b0fde4e75386449bfacfcca785200f686..fa4881d80ffebcd982a69f690ce1c4da36bd93ee 100644 (file)
--- a/tex/src/figures/cantilever-data/Makefile
+++ b/tex/src/figures/cantilever-data/Makefile
@@ -8,11 +8,15 @@ V_DEP_DATA = v-dep.d/v_dep_131.98.dat \
        v-dep.d/v_dep_131.98.fit \
        v-dep.d/v_dep_24.33.dat \
        v-dep.d/v_dep_24.33.fit
-LOADING_RATE_DATA = loading-rate.d/loading_rate_131.98 \
-       loading-rate.d/loading_rate_24.33
+LOADING_RATE_DATA = loading-rate.d/loading_rate_131.98.dat \
+       loading-rate.d/loading_rate_24.33.dat
 DATA = $(V_DEP_DATA) $(LOADING_RATE_DATA)
 DATA_DIRS = data v-dep.d loading-rate.d
 
+# Never delete intermediates.  (`info make` 10.4 Chains of Implicit Rules)
+.SECONDARY :
+
+
 all : $(FIGS:%=%_.tex)
 
 clean :
@@ -25,17 +29,25 @@ clean :
 $(DATA_DIRS) :
        mkdir $@
 
-data/raw : extract_f_v_k_data.sh $(DATA_DIRS)
+data/raw : extract_f_v_k_data.sh | data
        touch data/raw
 #      ./$< > $@
 
-data/spring-constants data/averaged-data : avg_data.py data/raw
+data/avg : avg_data.py data/raw
+       touch $@ # "avg" marks the time of last avg_data.py run
        python $<
 
-v-dep.d/v_dep_%.dat : \
-               get_v_dep.sh data/spring-constants data/averaged-data
+data/spring-constants data/averaged-data : data/avg
+       @echo "$@ already build for target data/avg"
+
+v-dep.d/dat : get_v_dep.sh data/spring-constants data/averaged-data \
+               | v-dep.d
+       touch $@ # "dat" marks the time of last *.dat file generation
        ./$<
 
+v-dep.d/v_dep_%.dat : v-dep.d/dat
+       @echo "$@ already build for target v-dep.d/dat"
+
 v-dep.d/v_dep_%.fit : fit_data.py v-dep.d/v_dep_%.dat
        python $^ > $@
 
@@ -51,5 +63,10 @@ v-dep.eps : v-dep.pdf
 v-dep-rotated.pdf : v-dep.pdf
        pdftk $< cat 1E output $@
 
-loading-rate.d/loading_rate_% : get_loading_rates.py avg_data.py data/raw
+loading-rate.d/dat : get_loading_rates.py avg_data.py data/raw \
+               | loading-rate.d
+       touch $@ # "dat" marks the time of last *.dat file generation
        python $<
+
+loading-rate.d/loading_rate_%.dat : loading-rate.d/dat
+       @echo "$@ already build for target loading-rate.d/dat"

diff --git a/tex/src/figures/cantilever-data/avg_data.py b/tex/src/figures/cantilever-data/avg_data.py
index b422291d453fc473644c188c319ef1602a613029..73bab0d5f6ffa2cf177daefc960003ac3d8b8aef 100755 (executable)
--- a/tex/src/figures/cantilever-data/avg_data.py
+++ b/tex/src/figures/cantilever-data/avg_data.py
@@ -8,59 +8,69 @@ AVGFILE='./data/averaged-data'
 
 KCUTS=[45, 90]
 
-FofV = {}
-Ks = []
-for i in range(len(KCUTS)+1):
-    Ks.append([])
+def read_raw(Kcuts=KCUTS, datafile=DATAFILE):
+    FofV = {}
+    Ks = []
+    for i in range(len(Kcuts)+1):
+        Ks.append([])
+    for line in file(datafile, 'r'):
+        if line[0] == '#':
+            continue # ignore comments
+        fields = line.strip().split('\t')
+        force = float(fields[0])
+        rate = float(fields[1])
+        spring = float(fields[2])
 
-for line in file(DATAFILE, 'r'):
-    if line[0] == '#':
-        continue # ignore comments
-    fields = line.strip().split('\t')
-    force = float(fields[0])
-    rate = float(fields[1])
-    spring = float(fields[2])
-    
-    ispring = 0
-    while ispring < len(KCUTS) and spring > KCUTS[ispring]:
-        ispring += 1
-    Ks[ispring].append(spring)
-    if rate not in FofV.keys():
-        FofV[rate]=[]
-        for i in range(len(Ks)):
-            FofV[rate].append([])
-    FofV[rate][ispring].append(force)
+        ispring = 0
+        while ispring < len(Kcuts) and spring > Kcuts[ispring]:
+            ispring += 1
+        Ks[ispring].append(spring)
+        if rate not in FofV.keys():
+            FofV[rate]=[]
+            for i in range(len(Ks)):
+                FofV[rate].append([])
+        FofV[rate][ispring].append(force)
+    return (Ks, FofV)
 
-avgK = [0]*len(Ks)
-stdK = [0]*len(Ks)
-numK = [0]*len(Ks)
-kf = file(KFILE, 'w')
-for i in range(len(Ks)):
-    K = numpy.array(Ks[i])
-    avgK[i] = K.mean()
-    stdK[i] = K.std()
-    numK[i] = len(K)
-    
-    if i == 1:
-        continue # poor calibration bumps for the older cantilevers
-    print >> kf, "K(%d) = %g +/- %g, (# %d)" % (i, avgK[i], stdK[i], numK[i])
-kf.close()
+def write_k_file(Ks, kfile=KFILE):
+    avgK = [0]*len(Ks)
+    stdK = [0]*len(Ks)
+    numK = [0]*len(Ks)
+    kf = file(kfile, 'w')
+    for i in range(len(Ks)):
+        K = numpy.array(Ks[i])
+        avgK[i] = K.mean()
+        stdK[i] = K.std()
+        numK[i] = len(K)
 
-
-Vs = FofV.keys()
-Vs.sort()
-af = file(AVGFILE, 'w')
-print >> af, '#'+'\t'.join(['Pulling speed (nm/s)','Spring constant (pN/nm)',
-                            'Mean force (pN)','Std. force (pN)','Events (#)'])
-for V in Vs:
-    for i,k in enumerate(avgK):
         if i == 1:
             continue # poor calibration bumps for the older cantilevers
-        F = numpy.array(FofV[V][i])
-        if len(F) == 0:
-            continue
-        outs= [V, k, F.mean(), F.std(), len(F)]
-        souts = ["%.2f" % (x) for x in outs]
-        souts[-1] = "%d" % outs[-1] # special treatment for the integer
-        print >> af, '\t'.join(souts)
-af.close()
+        print >> kf, "K(%d) = %g +/- %g, (# %d)" \
+            % (i, avgK[i], stdK[i], numK[i])
+    kf.close()
+    return (avgK, stdK, numK)
+
+def write_average_file(FofV, avgK, avgfile=AVGFILE):
+    Vs = FofV.keys()
+    Vs.sort()
+    af = file(AVGFILE, 'w')
+    print >> af, '#'+'\t'.join(\
+        ['Pulling speed (nm/s)','Spring constant (pN/nm)',
+         'Mean force (pN)','Std. force (pN)','Events (#)'])
+    for V in Vs:
+        for i,k in enumerate(avgK):
+            if i == 1:
+                continue # poor calibration bumps for the older cantilevers
+            F = numpy.array(FofV[V][i])
+            if len(F) == 0:
+                continue
+            outs= [V, k, F.mean(), F.std(), len(F)]
+            souts = ["%.2f" % (x) for x in outs]
+            souts[-1] = "%d" % outs[-1] # special treatment for the integer
+            print >> af, '\t'.join(souts)
+    af.close()
+
+if __name__ == '__main__':
+    Ks,FofV = read_raw()
+    avgK,stdK,numK = write_k_file(Ks)
+    write_average_file(FofV, avgK)

diff --git a/tex/src/figures/cantilever-data/get_loading_rates.py b/tex/src/figures/cantilever-data/get_loading_rates.py
index bf3c569a8a2f9c8df427a6ccd89e21e0650e4488..efb310cbe34592b8957264459e0728e09d8c01ab 100755 (executable)
--- a/tex/src/figures/cantilever-data/get_loading_rates.py
+++ b/tex/src/figures/cantilever-data/get_loading_rates.py
@@ -14,7 +14,7 @@ OFILEs = [None, None, None]
 for i,K in enumerate(Ks):
     if K == None:
         continue
-    OFILEs[i] = file('loading-rate.d/loading_rate_%.2f' % K, 'w')
+    OFILEs[i] = file('loading-rate.d/loading_rate_%.2f.dat' % K, 'w')
 
 for line in file(DATA, 'r'):
     if line[0] == '#':

diff --git a/tex/src/figures/cantilever-data/loading-rate.asy b/tex/src/figures/cantilever-data/loading-rate.asy
index 114c548b3023a0559be6a657aed496c5c9685d6d..ce6ef9ede3c4bf43dd153e4819e33668f3a4704d 100644 (file)
--- a/tex/src/figures/cantilever-data/loading-rate.asy
+++ b/tex/src/figures/cantilever-data/loading-rate.asy
@@ -6,9 +6,9 @@ scale(Log, Linear);
 real xscale=1;
 real yscale=1;
 
-graphFile("loading-rate.d/loading_rate_131.98", xscale, yscale, phard, m8,
+graphFile("loading-rate.d/loading_rate_131.98.dat", xscale, yscale, phard, m8,
          t=units("131.98","pN/nm"), dots=true);
-graphFile("loading-rate.d/loading_rate_24.33", xscale, yscale, red, m8,
+graphFile("loading-rate.d/loading_rate_24.33.dat", xscale, yscale, red, m8,
          t=units("24.33","pN/nm"), dots=true);
 
 xlimits(1,3e3);