Added first draft of jpk.py driver for JPK instruments -still not full,nor consistent.

diff --git a/hemingclamp.py b/hemingclamp.py
index 881a789d244d62065b0e7c54ffb0d58f0bf124f3..e2f2e1c2ebaee147cf0500b020c3750be382a920 100755 (executable)
--- a/hemingclamp.py
+++ b/hemingclamp.py
@@ -18,17 +18,6 @@ __changelog__='''
 import string
 import libhookecurve as lhc 
 
-def hemingclamp_magic(filepath):
-    '''
-    we define our magic heuristic for HemingClamp files
-    '''
-    myfile=file(filepath)
-    headerlines=myfile.readlines()[0:3]
-    if headerlines[0][0:10]=='#Hemingway' and headerlines[1][0:19]=='#Experiment: FClamp':
-        return True
-    else:
-        return False
-
 class DataChunk(list):
     '''Dummy class to provide ext and ret methods to the data list.
     In this case ext and self can be equal.

diff --git a/hooke.conf b/hooke.conf
index e07dec9e9231f2b9cebd2015bd20c8093e627678..b590ac9563eef91367267f9f4c9b5cf947a08838 100755 (executable)
--- a/hooke.conf
+++ b/hooke.conf
@@ -35,6 +35,7 @@ This section defines which drivers have to be loaded by Hooke.
     <!-- hemingclamp/ -->
     <csvdriver/>
     <!-- tutorialdriver/ -->
+    <jpk/>
 </drivers>
 
 <!--

diff --git a/jpk.py b/jpk.py
new file mode 100644 (file)
index 0000000..2249d85
--- /dev/null
+++ b/jpk.py
@@ -0,0 +1,128 @@
+#!/usr/bin/env python
+
+import string
+import libhookecurve as lhc 
+
+class DataChunk(list):
+    #Dummy class to provide ext and ret methods to the data list.
+    
+    def ext(self):
+        halflen=(len(self)/2)
+        return self[0:halflen]
+        
+    def ret(self):
+        halflen=(len(self)/2)
+        return self[halflen:]
+
+class jpkDriver(lhc.Driver):
+
+    def __init__(self, filename):
+        self.filename=filename #self.filename can always be useful, and should be defined
+        self.filedata = open(filename,'r') #We open the file
+        self.filelines=self.filedata.readlines()
+        self.filedata.close()        
+        '''These are two strings that can be used by Hooke commands/plugins to understand what they are looking at. They have no other
+        meaning. They have to be somehow defined however - commands often look for those variables.
+        
+        self.filetype should contain the name of the exact filetype defined by the driver (so that filetype-specific commands can know
+                      if they're dealing with the correct filetype)
+        self.experiment should contain instead the type of data involved (for example, various drivers can be used for force-clamp experiments,
+                      but hooke commands could like to know if we're looking at force clamp data, regardless of their origin, and not other 
+                      kinds of data)
+        
+        Of course, all other variables you like can be defined in the class.
+        '''
+        self.filetype = 'jpk'
+        self.experiment = 'smfsz'
+                  
+        
+
+    def __del__(self):
+        self.filedata.close()   
+    
+    def is_me(self):
+        '''
+        we define our magic heuristic for HemingClamp files
+        '''
+        myfile=file(self.filename)
+        headerlines=myfile.readlines()[0:3]
+        myfile.close()
+        if headerlines[0][0:11]=='# xPosition' and headerlines[1][0:11]=='# yPosition':
+            return True
+        else:
+            return False
+        
+    def close_all(self):
+        self.filedata.close()
+        
+    def _read_data_segment(self):
+        #routine that actually reads the data
+        
+        height_ms=[]
+        height_m=[]
+        height=[]
+        v_deflection=[]
+        h_deflection=[]
+        
+        self.springconstant=0 #if we don't meet any spring constant, use deflection...
+        
+        for line in self.filelines:
+            #we meet the segment defining the order of data columns
+            
+            if line[0:9]=='# columns':
+                splitline=line.split()[2:]
+                height_ms_index=splitline.index('smoothedStrainGaugeHeight')
+                height_m_index=splitline.index('strainGaugeHeight')
+                height_index=splitline.index('height')
+                v_deflection_index=splitline.index('vDeflection')
+                #h_deflection=splitline.index('hDeflection')
+            
+            if line[0:16]=='# springConstant':
+                self.springconstant=float(line.split()[2])
+    
+            if line[0] != '#' and len(line.split())>1:
+                dataline=line.split()
+                height_ms.append(float(dataline[height_ms_index]))
+                height_m.append(float(dataline[height_m_index]))
+                height.append(float(dataline[height_index]))
+                v_deflection.append(float(dataline[v_deflection_index]))
+                #h_deflection.append(float(dataline[h_deflection_index]))
+        
+        if self.springconstant != 0:
+            force=[item*self.springconstant for item in v_deflection]
+        else: #we have measured no spring constant :(
+            force=v_deflection
+            
+        height_ms=[item*-1 for item in height_ms]
+        height_m=[item*-1 for item in height_m]
+        height=[item*-1 for item in height]
+        
+        return DataChunk(height_ms),DataChunk(height_m),DataChunk(height),DataChunk(v_deflection),DataChunk(force)
+        
+    def default_plots(self):
+        
+        height_ms,height_m,height,v_deflection,force=self._read_data_segment()
+        
+        height_ms_ext=height_ms.ext()
+        height_ms_ret=height_ms.ret()
+        force_ext=force.ext()
+        force_ret=force.ret()
+        #reverse the return data, to make it coherent with hooke standard
+        height_ms_ret.reverse
+        force_ret.reverse
+        
+        main_plot=lhc.PlotObject()  
+        main_plot.add_set(height_ms_ext,force_ext)
+        main_plot.add_set(height_ms_ret,force_ret)
+        
+        if self.springconstant != 0:
+            main_plot.units=['meters','force']
+        else:
+            main_plot.units=['meters','meters']
+        
+        main_plot.normalize_vectors()
+        
+        main_plot.destination=0
+        main_plot.title=self.filename
+        
+        return [main_plot]
\ No newline at end of file