Merge branch 'commented' of ssh://forge.bexus.org:22/verena/sw-k-means into commented

loadData_1h.py

@@ -30,9 +30,10 @@ class simpledata(object):
             datadict = self.rebin(datadict,keys, safe)
             safe=(~np.isnan(datadict["dsw"]))&(~np.isnan(datadict["vsw"]))&(~np.isnan(datadict["tsw"]))&(~np.isnan(datadict["B"]))&(~np.isnan(datadict["dO7_6"]))&(~np.isnan(datadict["colage"]))&(~np.isnan(datadict["mcsFe"]))&(~np.isinf(datadict["dsw"]))&(~np.isinf(datadict["vsw"]))&(~np.isinf(datadict["tsw"]))&(~np.isinf(datadict["B"]))&(~np.isinf(datadict["dO7_6"]))&(~np.isinf(datadict["colage"]))&(~np.isinf(datadict["mcsFe"]))&(datadict["colage"]>0)&(datadict["mcsFe"]>0)&(datadict["dO7_6"]>0)&(datadict["totalCountsFe"]>10)
         if off_data:
-            keys=["yeartime", "vsw", "dsw", "tsw", "B", "colage", "dO7_6", "ldO7_6",  "elO7_6", "O_error", "mcsFe", "emcsFe","cor_hole", "sec_rev", "stream_belt", "ICME", "totalCountsFe"]
+            safe=(~np.isnan(datadict["dsw"]))&(~np.isnan(datadict["vsw"]))&(~np.isnan(datadict["tsw"]))&(~np.isnan(datadict["B"]))&(~np.isnan(datadict["colage"]))&(~np.isinf(datadict["dsw"]))&(~np.isinf(datadict["vsw"]))&(~np.isinf(datadict["tsw"]))&(~np.isinf(datadict["B"]))&(~np.isinf(datadict["colage"]))&(datadict["colage"]>0)
+            keys=["yeartime", "vsw", "dsw", "tsw", "B", "colage", "cor_hole", "sec_rev", "stream_belt", "ICME"  ]
             datadict = get_off_data( datadict, safe, keys)
-            safe=(~np.isnan(datadict["dsw"]))&(~np.isnan(datadict["vsw"]))&(~np.isnan(datadict["tsw"]))&(~np.isnan(datadict["B"]))&(~np.isnan(datadict["dO7_6"]))&(~np.isnan(datadict["colage"]))&(~np.isnan(datadict["mcsFe"]))&(~np.isinf(datadict["dsw"]))&(~np.isinf(datadict["vsw"]))&(~np.isinf(datadict["tsw"]))&(~np.isinf(datadict["B"]))&(~np.isinf(datadict["dO7_6"]))&(~np.isinf(datadict["colage"]))&(~np.isinf(datadict["mcsFe"]))&(datadict["colage"]>0)&(datadict["mcsFe"]>0)&(datadict["dO7_6"]>0)&(datadict["totalCountsFe"]>10)
+            safe=(~np.isnan(datadict["dsw"]))&(~np.isnan(datadict["vsw"]))&(~np.isnan(datadict["tsw"]))&(~np.isnan(datadict["B"]))&(~np.isnan(datadict["dO7_6"]))&(~np.isnan(datadict["colage"]))&(~np.isnan(datadict["mcsFe"]))&(~np.isinf(datadict["dsw"]))&(~np.isinf(datadict["vsw"]))&(~np.isinf(datadict["tsw"]))&(~np.isinf(datadict["B"]))&(~np.isinf(datadict["dO7_6"]))&(~np.isinf(datadict["colage"]))&(~np.isinf(datadict["mcsFe"]))&(datadict["colage"]>0)&(datadict["mcsFe"]>0)&(datadict["dO7_6"]>0)
 
 
         self.X=np.zeros((datadict["vsw"][safe].shape[0], xlength))
@@ -42,9 +43,13 @@ class simpledata(object):
         self.X[:,4]=datadict["vsw"][safe]
         self.X[:,5]=datadict["colage"][safe]
         self.X[:,6]=datadict["mcsFe"][safe]
-        if logO:
+        if logO :
-            self.X[:,3]=datadict["ldO7_6"][safe]
+            if off_data:
-            self.O_error = datadict["elO7_6"][safe]
+                self.X[:,3]=np.log10(datadict["dO7_6"][safe])
+                self.O_error = datadict["eO7_6"][safe] # does not work this way ...
+            else:
+                self.X[:,3]=datadict["ldO7_6"][safe]
+                self.O_error = datadict["elO7_6"][safe]
         else:
             self.X[:,3]=datadict["dO7_6"][safe]
             self.O_error = datadict["eO7_6"][safe]
@@ -106,7 +111,7 @@ class simpledata(object):
 
 
 
-def loadData(timeframe=[1,366], years=np.arange(2001,2011,1), relevantkeys=["yeartime", "time", "year", "dsw", "vsw", "tsw", "B", "dO7_6", "elO7_6","ldO7_6", "colage", "mcsFe","emcsFe", "ICME", "cor_hole", "sec_rev", "stream_belt", "totalCountsFe"], prepath="", path= "datadir/",  label="2001-2010", rebin= True, off_data= False ):
+def loadData(timeframe=[1,366], years=np.arange(2001,2011,1), relevantkeys=["yeartime", "time", "year", "dsw", "vsw", "tsw", "B", "dO7_6", "elO7_6","ldO7_6", "colage", "mcsFe","emcsFe", "ICME", "cor_hole", "sec_rev", "stream_belt", "totalCountsFe"], prepath="", path= "datadir/",  label="2001-2010", rebin= False, off_data= False ):
     """
     load data from ASCII file
     The time period is specified as timeframe (start day of year, end day of year) und year. 2001-2010
@@ -182,7 +187,7 @@ def getBinned(data, keys,  timekey="doy",  mask=[None], timebins=[None], delta=1
     #print ("counter", counter)
     result[timekey]=shorttime[:-1]#-0.5*delta
     result["shorttime"]=shorttime[:-1]
-    print(len(timebins))
+    #print(len(timebins))
     for key in keys:
             #safe=np.ones(time.shape, dtype=bool)
             #safe*=(np.array(data[key]>minV))*(np.array(data[key]<maxV))*mask
@@ -193,17 +198,21 @@ def getBinned(data, keys,  timekey="doy",  mask=[None], timebins=[None], delta=1
             result[timekey + key]=shorttime[:-1]#-0.5*delta
             y, hx = np.histogram(time[mask], bins=timebins, weights=data[key][mask])
             #print(y)
-            print(np.sum(counts > 6))
+            #print(np.sum(counts > 6))
             result[key]= np.divide(y, counts, out=np.zeros_like(y), where=counts!=0) # y/counts
-            print(len(result[key]))
+            #print(len(result[key]))
 
             result[key][counter==0]=np.nan
             #print(result)
 
     return result
+
+
 def get_off_data(data, mask_safe, keys):
-    start_year = int(data["yeartime"][0])
+
-    end_year = int(data["yeartime"][-1])
+    start_year = int(data["yeartime"][np.isfinite(data["yeartime"])][0])
+    end_year = int(data["yeartime"][np.isfinite(data["yeartime"])][-1])
+    #print(data["yeartime"][np.isfinite(data["yeartime"])])
     previoustime = data["yeartime"]
     swicsdata = np.empty([])
     for year in np.arange(start_year, end_year+2):
@@ -215,21 +224,40 @@ def get_off_data(data, mask_safe, keys):
 
             swicsdata = np.concatenate((swicsdata, data_temp), axis=0)
 
-    swicstime = swicsdata[:,4]
+    swicstime = swicsdata[:,5]
-    hourmask = np.diff(swicstime) < (1/365/23)
+    swicstime = np.append(swicstime, swicstime[-1] +1/365/24 )
-    print(data)
+    # hourmask = np.diff(swicstime) < (1/365/23)
-    delta = np.median(np.diff(swicstime))
-    print(delta)
     time = data["yeartime"]
-    result= getBinned(data, keys,  timekey="yeartime", mask=mask_safe&hourmask, timebins=swicstime)
+
+    delta = np.median(np.diff(swicstime))
+
+    #timebins=np.arange(min(swicstime), max(swicstime), delta)
+
+    hourmask = np.diff(swicstime) < (1/365/23)
+
+    #delta = np.median(np.diff(swicstime))
+
+    counts,shorttime = np.histogram(time,bins=swicstime)
+    # result= getBinned(data, keys,  timekey="yeartime", mask=hourmask, timebins=swicstime)
+    result= {}
+    keepdata = {}
+    for key in keys:
+        #print(key)
+        result[key]=shorttime[:-1]
+        y, hx = np.histogram(time[mask_safe], bins=swicstime, weights=data[key][mask_safe])
+        result[key]=y/counts
+        #print(result[key])
+        keepdata[key] = result[key][hourmask]
+        print(key, data[key].shape)
 
 
-    result["dO7_6"] = swicsdata[:,6][hourmask]
+    keepdata["dO7_6"] = swicsdata[:,7][hourmask]
-    result["eO7_6"] = swicsdata[:,7][hourmask]
+    keepdata["eO7_6"] = swicsdata[:,8][hourmask]
-    result["mcsFe"]= swicsdata[:,10][hourmask]
+    keepdata["mcsFe"]= swicsdata[:,10][hourmask]
-    result["yeartime"] = swicstime[hourmask]
+    keepdata["emcsFe"]= swicsdata[:,11][hourmask]
-    print(len(swicstime))
+
-    print(len(result["dsw"]))
+    keepdata["time"]= swicsdata[:,4][hourmask]
-    print(len(result["mcsFe"]))
+    keepdata["yeartime"] = swicstime[:-1][hourmask]
+
     #print("from "+str(previoustime.shape)+" to " + str(keepdata["yeartime"].shape))
-    return result
+    return keepdata

reduced_kmeans.py

@@ -23,7 +23,7 @@ from bic import compute_bic
 import time
 NoneType = type(None)
 
-from loadData import loadData, loadDataRed
+from loadData_1h import loadData, loadDataRed
 
 # update the matplotlib standard parameters
 backend_bases.register_backend('pdf', FigureCanvasPgf)
@@ -1642,8 +1642,8 @@ def calc_inner_cluster_distances(n_clusters= (2,3,4,5,6,7,8,9,10,11,12), plot =
                     X=data.X[positions]
                     bictmp.append(metrics.silhouette_score(X, cluster_object[t].predict(X)))
                 silhouettelists.append([np.median(siltmp), np.percentile(siltmp, 15.865), np.percentile(siltmp, 84.135)])
-                
+
-            
+
         if save:
             if bic:
                 if silhouette:
@@ -2470,7 +2470,7 @@ def elbow_plot(clusters = (3,7), size = 22,  parameters = ("dsw","tsw","B","dO7_
                 if silhouette:
                     rows+=1
                 fig, axs = plt.subplots(rows,1,sharex= True,figsize =(12,10))
-                        
+
             else:
                 rows=4
                 if bic:
@@ -2663,7 +2663,7 @@ if __name__=="__main__":
         add_label = '_d'
     else:
         ntrials = 100
-        add_label = ''
+        add_label = '_1h_off_SWICS'
 
     if  int(option) ==0:
         #This option creates all needed directories
@@ -2682,7 +2682,7 @@ if __name__=="__main__":
         """
         if option - int(option) == 0:
             option = int(option)
-            data = loadData()
+            data = loadData(off_data = True)
             bigExp_general(data, option,8, ntrials = ntrials)
 
         else:
@@ -2721,7 +2721,7 @@ if __name__=="__main__":
     elif int(option) == 33:
         if  option - int(option) == 0:
             data = loadData()
-            add_label = '_new'
+            #add_label = '_new'
         else:
             data = loadData()
             data.downsample(samples = samples)
@@ -2791,7 +2791,7 @@ if __name__=="__main__":
         compare_combinations_to_full_combi(nclusters = n_clus,clabel = '_'+str(n_clus)+add_label, savelabel = '', ntrials = ntrials)
         data = loadData()
         big_plot(data,savelabel = "_"+str(n_clus)+"_"+add_label, nclusters=n_clus,clabel ='_'+str(n_clus)+ add_label,xu_scores = False,mc_error = None, ntrials = ntrials)
-           
+
     elif int(option) == 70:
         if option - int(option) == 0:
             data = loadData()