Support for HDF5 files created with Igor Pro (see wiki for how to create the HDF5...

diff --git a/hdf5.py b/hdf5.py
new file mode 100644 (file)
index 0000000..8feb89b
--- /dev/null
+++ b/hdf5.py
@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+
+'''
+hdf5.py
+
+Driver for text-exported HDF5 files from Igor pro
+
+Alberto Gomez-Casado (c) 2010
+Massimo Sandal      (c) 2009   
+'''
+
+import libhookecurve as lhc
+import libhooke as lh
+
+class hdf5Driver(lhc.Driver):
+    
+    def __init__(self, filename):
+        
+        self.filename=filename
+        self.filedata=open(filename,'rU')
+        self.lines=list(self.filedata.readlines())
+        self.filedata.close()
+        
+        self.filetype='hdf5'
+        self.experiment='smfs'
+        
+    def close_all(self):
+        self.filedata.close()
+        
+    def is_me(self):
+        self.raw_header=self.lines[0]      
+               
+        if 'IGP-HDF5-Hooke' in self.raw_header:
+            return True
+        else:
+            return False
+        
+    def _read_columns(self):
+        
+        self.raw_columns=self.lines[4:]
+        
+        kline=None
+        for line in self.lines:
+            if line[:7]=='SpringC':
+                kline=line
+                break
+        
+        kline=kline.split(':')
+        
+        self.k=float(kline[1])
+        
+        
+        xext=[]
+        xret=[]
+        yext=[]
+        yret=[]
+        for line in self.raw_columns:
+            spline=line.split()
+            xext.append(float(spline[0]))
+            yext.append(float(spline[1]))
+            xret.append(float(spline[2]))
+            yret.append(float(spline[3]))
+            
+        return [[xext,yext],[xret,yret]]
+        
+    def deflection(self):
+        self.data=self._read_columns()
+        return self.data[0][1],self.data[1][1]
+        
+        
+    def default_plots(self):   
+        main_plot=lhc.PlotObject()
+        defl_ext,defl_ret=self.deflection()
+        yextforce=[i*self.k for i in defl_ext]
+        yretforce=[i*self.k for i in defl_ret]
+        main_plot.add_set(self.data[0][0],yextforce)
+        main_plot.add_set(self.data[1][0],yretforce)
+        main_plot.normalize_vectors()
+        main_plot.units=['Z','force']  #FIXME: if there's an header saying something about the time count, should be used
+        main_plot.destination=0
+        main_plot.title=self.filename
+        #main_plot.colors=['red','blue']
+        return [main_plot]

diff --git a/hooke.conf b/hooke.conf
index 75a31f96a0116909bf8e37e004bb7e34d8574a62..43625b48c465381888d34c411b546862f88caca3 100755 (executable)
--- a/hooke.conf
+++ b/hooke.conf
@@ -50,7 +50,8 @@ This section defines which drivers have to be loaded by Hooke.
     <!-- tutorialdriver/ -->\r
     <jpk/>\r
     <mfp1dexport/>\r
-    <mcs/>\r
+    <mcs/>
+    <hdf5/>    \r
 </drivers>\r
 \r
 <!--\r

diff --git a/mfp_igor_scripts/h5export.py b/mfp_igor_scripts/h5export.py
new file mode 100644 (file)
index 0000000..f49b3a8
--- /dev/null
+++ b/mfp_igor_scripts/h5export.py
@@ -0,0 +1,49 @@
+import h5py
+import numpy
+import os
+import sys
+
+h5file=os.path.realpath(sys.argv[-1])
+h5dir=os.path.dirname(h5file)
+
+f=h5py.File(h5file)
+
+exportdir=os.path.join(h5dir,'exported')
+try:
+       os.mkdir(exportdir)
+except:
+       print 'mkdir error, maybe the export directory already exists?'
+
+def h5exportfunc(name):
+       Deflname=name
+       if Deflname.endswith('Defl'):      #search for _Defl dataset            
+               LVDTname=str.replace(Deflname,'Defl','LVDT')  #and correspondant LVDT dataset
+               Defldata=f[Deflname][:]   #store the data in local var
+               LVDTdata=f[LVDTname][:]
+               #find useful attr (springc)
+               try:
+                       notes=f[Deflname].attrs['IGORWaveNote']
+                       springmatch=notes.index("SpringConstant: ")+len("SpringConstant: ")
+                       springc=notes[springmatch:].split("\r",1)[0]  #probably extracting the leading numbers can be way more elegant than this
+                       print Deflname  
+               except:
+                       print 'Something bad happened with '+Deflname+', ignoring it'
+                       return None
+                       #returning anything but None halts the visit procedure
+               
+               fp=open(os.path.join(exportdir,name.replace('/',''))+'.txt','w')  
+               #uses the full HDF5 path (slashes out) to avoid potential overwriting             
+               #write attr
+               fp.writelines("IGP-HDF5-Hooke\n")
+               fp.writelines('SpringConstant: '+springc+'\n\n')
+               fp.writelines('App x\tApp y\tRet x\tRet y\n')
+               #write LVDT and Defl data
+               half=Defldata.size/2
+               for i in numpy.arange(0,half):
+                       fp.writelines(str(LVDTdata[i])+'\t'+str(Defldata[i])+'\t'+str(LVDTdata[i+half])+'\t'+str(Defldata[i+half])+'\n')        
+               #close the file
+               fp.close()
+               return None
+
+
+f.visit(h5exportfunc)