From 7c0e9702f66c5ac1f5fb8d80de902341b34bae94 Mon Sep 17 00:00:00 2001
From: albertogomcas <devnull@localhost>
Date: Fri, 22 Jan 2010 07:14:22 +0000
Subject: [PATCH] Support for HDF5 files created with Igor Pro (see wiki for
 how to create the HDF5 file)

---
 hdf5.py                      | 83 ++++++++++++++++++++++++++++++++++++
 hooke.conf                   |  3 +-
 mfp_igor_scripts/h5export.py | 49 +++++++++++++++++++++
 3 files changed, 134 insertions(+), 1 deletion(-)
 create mode 100644 hdf5.py
 create mode 100644 mfp_igor_scripts/h5export.py

diff --git a/hdf5.py b/hdf5.py
new file mode 100644
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 75a31f9..43625b4 100755
--- a/hooke.conf
+++ b/hooke.conf
@@ -50,7 +50,8 @@ This section defines which drivers have to be loaded by Hooke.
     <!-- tutorialdriver/ -->
     <jpk/>
     <mfp1dexport/>
-    <mcs/>
+    <mcs/>
+    <hdf5/>	
 </drivers>
 
 <!--
diff --git a/mfp_igor_scripts/h5export.py b/mfp_igor_scripts/h5export.py
new file mode 100644
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)
-- 
2.26.2