review.py: avoided crash when displaying final stats

hooke.conf: 	deactivate hdf5 by default, activate native mfp3d
mfp3d.py: 	adapted driver from Hooke GUI to work in this version
procplots.py:	centerzero only uses last chunk of retract

FMjoin.py:	utility script to put together all files from IgorPro force maps

diff --git a/hooke.conf b/hooke.conf
index a86ca200b3ea8c943ea07930014689cdafe19bbb..672344054938aba5964f0aa9bcd4c54936104e51 100755 (executable)
--- a/hooke.conf
+++ b/hooke.conf
@@ -54,7 +54,8 @@ This section defines which drivers have to be loaded by Hooke.
     <jpk/>\r
     <mfp1dexport/>\r
     <mcs/>
-    <hdf5/>    \r
+    <!-- hdf5/ -->
+    <mfp3d/>                   \r
 </drivers>\r
 \r
 <!--\r

diff --git a/mfp3d.py b/mfp3d.py
new file mode 100644 (file)
index 0000000..9049729
--- /dev/null
+++ b/mfp3d.py
@@ -0,0 +1,295 @@
+#!/usr/bin/env python
+
+'''
+mfp3d.py
+
+Driver for MFP-3D files.
+
+Copyright 2010 by Dr. Rolf Schmidt (Concordia University, Canada)
+This driver is based on the work of R. Naud and A. Seeholzer (see below)
+to read Igor binary waves. Code used with permission.
+
+Modified for usage with Hooke CLI by Alberto Gomez-Casado (University of Twente, The Netherlands)
+
+This program is released under the GNU General Public License version 2.
+'''
+
+# DEFINITION:
+# Reads Igor's (Wavemetric) binary wave format, .ibw, files.
+#
+# ALGORITHM:
+# Parsing proper to version 2, 3, or version 5 (see Technical notes TN003.ifn:
+# http://mirror.optus.net.au/pub/wavemetrics/IgorPro/Technical_Notes/) and data
+# type 2 or 4 (non complex, single or double precision vector, real values).
+#
+# AUTHORS:
+# Matlab version: R. Naud August 2008 (http://lcn.epfl.ch/~naud/Home.html)
+# Python port: A. Seeholzer October 2008
+#
+# VERSION: 0.1
+#
+# COMMENTS:
+# Only tested for version 2 Igor files for now, testing for 3 and 5 remains to be done.
+# More header data could be passed back if wished. For significance of ignored bytes see
+# the technical notes linked above.
+
+import numpy
+import os.path
+import struct
+
+import libhookecurve as lhc
+
+
+__version__='0.0.0.20100310'
+
+
+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 mfp3dDriver(lhc.Driver):
+
+    #Construction and other special methods
+    
+    def __init__(self,filename):
+        '''
+        constructor method
+        '''
+           
+       self.textfile    =file(filename)
+        self.binfile=file(filename,'rb')
+       #unnecesary, but some other part of the program expects these to be open     
+
+        self.forcechunk=0
+        self.distancechunk=1
+       #TODO eliminate the need to set chunk numbers
+        
+        self.filepath=filename
+        self.debug=True
+        
+       self.data = []
+        self.note = []
+        self.retract_velocity = None
+        self.spring_constant = None
+        self.filename = filename
+
+        self.filedata = open(filename,'rU')
+        self.lines = list(self.filedata.readlines())
+        self.filedata.close()
+
+        self.filetype = 'mfp3d'
+        self.experiment = 'smfs'
+             
+     
+    def _get_data_chunk(self,whichchunk):
+
+       data = None
+        f = open(self.filename, 'rb')
+        ####################### ORDERING
+        # machine format for IEEE floating point with big-endian
+        # byte ordering
+        # MacIgor use the Motorola big-endian 'b'
+        # WinIgor use Intel little-endian 'l'
+        # If the first byte in the file is non-zero, then the file is a WinIgor
+        firstbyte = struct.unpack('b', f.read(1))[0]
+        if firstbyte == 0:
+            format = '>'
+        else:
+            format = '<'
+        #######################  CHECK VERSION
+        f.seek(0)
+        version = struct.unpack(format+'h', f.read(2))[0]
+        #######################  READ DATA AND ACCOMPANYING INFO
+        if version == 2 or version == 3:
+            # pre header
+            wfmSize = struct.unpack(format+'i', f.read(4))[0] # The size of the WaveHeader2 data structure plus the wave data plus 16 bytes of padding.
+            noteSize = struct.unpack(format+'i', f.read(4))[0] # The size of the note text.
+            if version==3:
+                formulaSize = struct.unpack(format+'i', f.read(4))[0]
+            pictSize = struct.unpack(format+'i', f.read(4))[0] # Reserved. Write zero. Ignore on read.
+            checksum = struct.unpack(format+'H', f.read(2))[0] # Checksum over this header and the wave header.
+            # wave header
+            dtype = struct.unpack(format+'h', f.read(2))[0]
+            if dtype == 2:
+                dtype = numpy.float32(.0).dtype
+            elif dtype == 4:
+                dtype = numpy.double(.0).dtype
+            else:
+                assert False, "Wave is of type '%i', not supported" % dtype
+            dtype = dtype.newbyteorder(format)
+
+            ignore = f.read(4) # 1 uint32
+            bname = self._flatten(struct.unpack(format+'20c', f.read(20)))
+            ignore = f.read(4) # 2 int16
+            ignore = f.read(4) # 1 uint32
+            dUnits = self._flatten(struct.unpack(format+'4c', f.read(4)))
+            xUnits = self._flatten(struct.unpack(format+'4c', f.read(4)))
+            npnts = struct.unpack(format+'i', f.read(4))[0]
+            amod = struct.unpack(format+'h', f.read(2))[0]
+            dx = struct.unpack(format+'d', f.read(8))[0]
+            x0 = struct.unpack(format+'d', f.read(8))[0]
+            ignore = f.read(4) # 2 int16
+            fsValid = struct.unpack(format+'h', f.read(2))[0]
+            topFullScale = struct.unpack(format+'d', f.read(8))[0]
+            botFullScale = struct.unpack(format+'d', f.read(8))[0]
+            ignore = f.read(16) # 16 int8
+            modDate = struct.unpack(format+'I', f.read(4))[0]
+            ignore = f.read(4) # 1 uint32
+            # Numpy algorithm works a lot faster than struct.unpack
+            data = numpy.fromfile(f, dtype, npnts)
+
+        elif version == 5:
+            # pre header
+            checksum = struct.unpack(format+'H', f.read(2))[0] # Checksum over this header and the wave header.
+            wfmSize = struct.unpack(format+'i', f.read(4))[0] # The size of the WaveHeader2 data structure plus the wave data plus 16 bytes of padding.
+            formulaSize = struct.unpack(format+'i', f.read(4))[0]
+            noteSize = struct.unpack(format+'i', f.read(4))[0] # The size of the note text.
+            dataEUnitsSize = struct.unpack(format+'i', f.read(4))[0]
+            dimEUnitsSize = struct.unpack(format+'4i', f.read(16))
+            dimLabelsSize = struct.unpack(format+'4i', f.read(16))
+            sIndicesSize = struct.unpack(format+'i', f.read(4))[0]
+            optionSize1 = struct.unpack(format+'i', f.read(4))[0]
+            optionSize2 = struct.unpack(format+'i', f.read(4))[0]
+
+            # header
+            ignore = f.read(4)
+            CreationDate =  struct.unpack(format+'I',f.read(4))[0]
+            modData =  struct.unpack(format+'I',f.read(4))[0]
+            npnts =  struct.unpack(format+'i',f.read(4))[0]
+            # wave header
+            dtype = struct.unpack(format+'h',f.read(2))[0]
+            if dtype == 2:
+                dtype = numpy.float32(.0).dtype
+            elif dtype == 4:
+                dtype = numpy.double(.0).dtype
+            else:
+                assert False, "Wave is of type '%i', not supported" % dtype
+            dtype = dtype.newbyteorder(format)
+
+            ignore = f.read(2) # 1 int16
+            ignore = f.read(6) # 6 schar, SCHAR = SIGNED CHAR?         ignore = fread(fid,6,'schar'); #
+            ignore = f.read(2) # 1 int16
+            bname = self._flatten(struct.unpack(format+'32c',f.read(32)))
+            ignore = f.read(4) # 1 int32
+            ignore = f.read(4) # 1 int32
+            ndims = struct.unpack(format+'4i',f.read(16)) # Number of of items in a dimension -- 0 means no data.
+            sfA = struct.unpack(format+'4d',f.read(32))
+            sfB = struct.unpack(format+'4d',f.read(32))
+            dUnits = self._flatten(struct.unpack(format+'4c',f.read(4)))
+            xUnits = self._flatten(struct.unpack(format+'16c',f.read(16)))
+            fsValid = struct.unpack(format+'h',f.read(2))
+            whpad3 = struct.unpack(format+'h',f.read(2))
+            ignore = f.read(16) # 2 double
+            ignore = f.read(40) # 10 int32
+            ignore = f.read(64) # 16 int32
+            ignore = f.read(6) # 3 int16
+            ignore = f.read(2) # 2 char
+            ignore = f.read(4) # 1 int32
+            ignore = f.read(4) # 2 int16
+            ignore = f.read(4) # 1 int32
+            ignore = f.read(8) # 2 int32
+
+            data = numpy.fromfile(f, dtype, npnts)
+            note_str = f.read(noteSize)
+            note_lines = note_str.split('\r')
+            self.note = {}
+            for line in note_lines:
+               if ':' in line:
+                   key, value = line.split(':', 1)
+                    self.note[key] = value
+            self.retract_velocity = float(self.note['RetractVelocity'])
+            self.spring_constant = float(self.note['SpringConstant'])
+        else:
+            assert False, "Fileversion is of type '%i', not supported" % dtype
+            data = []
+
+        f.close()
+        if len(data) > 0:
+            #we have 3 columns: deflection, LVDT, raw
+            #TODO detect which is each one
+           count = npnts / 3
+            lvdt = data[:count] 
+            deflection = data[count:2 * count] 
+            #every column contains data for extension and retraction
+            #we assume the same number of points for each
+            #we could possibly extract this info from the note
+            count = npnts / 6
+
+           forcechunk=deflection*self.spring_constant
+           distancechunk=lvdt
+       
+           if  whichchunk==self.forcechunk:
+               return forcechunk
+           if whichchunk==self.distancechunk:
+               return distancechunk
+        else:
+            return None                          
+        
+    def _force(self):
+       #returns force vector
+        Kspring=self.spring_constant
+        return DataChunk([(meter*Kspring) for meter in self._deflection()])
+
+    def _deflection(self):
+        #for internal use (feeds _force)
+        deflect=self.data_chunks[self.forcechunk]/self.spring_constant              
+        return deflect
+
+    def _flatten(self, tup):
+        out = ''
+        for ch in tup:
+            out += ch
+        return out            
+    
+    def _Z(self):   
+        return DataChunk(self.data_chunks[self.distancechunk])
+        
+    def is_me(self):
+        if len(self.lines) < 34:
+            return False
+
+        name, extension = os.path.splitext(self.filename)
+        if extension == '.ibw':
+            for line in self.lines:
+                if line.startswith('ForceNote:'):
+                   self.data_chunks=[self._get_data_chunk(num) for num in [0,1,2]]
+                    return True
+            else:
+                return False
+        else:
+            return False
+    
+    def close_all(self):
+        '''
+        Explicitly closes all files
+        '''
+        self.textfile.close()
+        self.binfile.close()
+    
+    def default_plots(self):
+        '''
+        creates the default PlotObject
+        '''
+        force=self._force()
+        zdomain=self._Z()
+        main_plot=lhc.PlotObject()
+        main_plot.vectors=[[zdomain.ext(), force.ext()],[zdomain.ret(), force.ret()]]
+        main_plot.normalize_vectors()
+        main_plot.units=['meters','newton']
+        main_plot.destination=0
+        main_plot.title=self.filepath
+        
+        
+        return [main_plot]
+
+    def deflection(self):
+        #interface for correct plotmanip and others
+        deflectionchunk=DataChunk(self._deflection())
+        return deflectionchunk.ext(),deflectionchunk.ret()

diff --git a/mfp_igor_scripts/FMjoin.py b/mfp_igor_scripts/FMjoin.py
new file mode 100644 (file)
index 0000000..311892b
--- /dev/null
+++ b/mfp_igor_scripts/FMjoin.py
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+'''
+FMjoin.py
+Copies all .ibw files contained in a folder and its subfolders into a single folder. Useful for force maps.
+
+Usage: 
+python FMjoin.py origindir destdir
+
+
+Alberto Gomez-Casado (c) 2010, University of Twente (The Netherlands)
+This program is released under the GNU General Public License version 2.
+'''
+
+import os
+import shutil
+import sys
+
+def main(*args):
+       if len(sys.argv) < 2:
+               print 'You must at least specify origin and destination folders.'
+               return 0
+       origin=sys.argv[1]
+       dest=sys.argv[2]
+   
+       if os.path.exists(origin):
+               if os.path.exists(dest):
+                       if os.listdir(dest)!=[]:
+                               print 'Destination folder is not empty! Use another folder.'
+                               return 0
+               else:
+                       print 'Destination folder does not exist, will create it'
+                       os.mkdir(dest)
+       else:
+               print 'You provided a wrong origin folder name, try again.'
+       
+       origin=os.path.abspath(origin)
+       dest=os.path.abspath(dest)
+       
+       for root, dirs, files in os.walk(origin):
+               for filename in files:
+                       if filename.split('.')[1]!="ibw":
+                               continue
+                       filepath=os.path.join(root,filename)
+                       #to avoid overwriting, we collapse unique paths into filenames
+                       rawdest=filepath.split(os.path.commonprefix([origin, filepath]))[1]
+                       rawdest=rawdest.replace('/','') #for linux
+                       rawdest=rawdest.replace('\\','') #for windows
+                       destfile=os.path.join(dest,rawdest)
+                       print 'Copying '+rawdest
+                       shutil.copy(filepath,destfile)
+    
+        return 0
+ 
+if __name__ == '__main__':
+    sys.exit(main(*sys.argv))
+
+

diff --git a/procplots.py b/procplots.py
index 0b2b9bd964c21003d2619b08662558f1b2ff5834..8c58f70d764ee7f002c9e30f08a6c290639bffdc 100755 (executable)
--- a/procplots.py
+++ b/procplots.py
@@ -180,10 +180,10 @@ class procplotsCommands:
      
         
        
-       levelapp=float(np.median(plot.vectors[0][1]))
-       levelret=float(np.median(plot.vectors[1][1]))
+       #levelapp=float(np.median(plot.vectors[0][1]))
+       levelret=float(np.median(plot.vectors[1][1][-300:-1]))
 
-       level=(levelapp+levelret)/2     
+       level=levelret  
 
        approach=[i-level for i in plot.vectors[0][1]]
        retract=[i-level for i in plot.vectors[1][1]]

diff --git a/review.py b/review.py
index 636eb36e2dbdc105369a92521db6958b89e53ba0..0610f6fe2861c2d68704d4ad2f9f4b04ef31d4c6 100644 (file)
--- a/review.py
+++ b/review.py
@@ -127,7 +127,13 @@ class reviewCommands:
                                        
            c+=10
 
-       print 'Kept '+str(len(keep_list))+' curves from '+str(min(c+i+1,len(self.current_list)))
+       #FIXME I don't know why the print below gives errors sometimes
+       try:
+               print 'Kept '+str(len(keep_list))+' curves from '+str(min(c+i+1,len(self.current_list)))
+       except:
+               print 'Display error, never mind, we continue. Below the amount of kept and total curves:'
+               print str(len(keep_list))
+               print str(len(self.current_list))
 
        allok=0  #flag to keep from losing all the work in a slight mistake
        while allok==0: