Index: /fact/tools/pyscripts/pyfact/pynew.py
===================================================================
--- /fact/tools/pyscripts/pyfact/pynew.py	(revision 13250)
+++ /fact/tools/pyscripts/pyfact/pynew.py	(revision 13250)
@@ -0,0 +1,365 @@
+#!/usr/bin/python -tt
+#
+# Werner Lustermann
+# ETH Zurich
+#
+from ctypes import *
+import numpy as np
+from scipy import signal
+
+# get the ROOT stuff + my shared libs
+from ROOT import gSystem
+# fitslib.so is made from fits.h and is used to access the data
+gSystem.Load('~/py/fitslib.so')
+from ROOT import *
+
+class RawDataFeeder( object ):
+    """
+    """
+    
+    def __init__(self, filelist):
+        self.filelist = filelist
+        self._current_RawData = RawData(filelist[0][0], filelist[0][1], return_dict=True)
+        del filelist[0]
+    
+    def __iter__(self):
+        return self
+    
+    def next():
+        try:
+            return self._current_RawData.next()
+        except StopIteration:
+            # current_RawData was completely processed
+            # delete it (I hope this calls the destructor of the fits file and/or closes it)
+            del self._current_RawData
+            # and remake it, if possible
+            if len(self.filelist) > 0:
+                self._current_RawData = RawData(filelist[0][0], filelist[0][1], return_dict=True)
+                del filelist[0]
+            else:
+                raise
+        
+
+class RawData( object ):
+    """ raw data access and calibration
+    
+    - open raw data file and drs calibration file
+    - performs amplitude calibration
+    - performs baseline substraction if wanted
+    - provides all data in an array:
+      row = number of pixel
+      col = length of region of interest
+      
+    """
+
+    def __init__(self, data_file_name, calib_file_name, 
+                user_action_calib=lambda acal_data, data, blm, tom, gm, scells, nroi: None,
+                baseline_file_name='',
+                return_dict = None):
+        """ initialize object
+        
+        open data file and calibration data file
+        get basic information about the data in data_file_name
+        allocate buffers for data access
+
+        data_file_name   : fits or fits.gz file of the data including the path
+        calib_file_name : fits or fits.gz file containing DRS calibration data
+        baseline_file_name : npy file containing the baseline values
+        """
+        # manual implementation of default value, but I need to find out
+        # if the user of this class is aware of the new option
+        if return_dict == None:
+            print 'Warning: Rawdata.__init__() has a new option "return_dict"'
+            print 'the default value of this option is False, so nothing changes for you at the moment.'
+            print
+            print 'you probably want, to get a dictionary out of the next() method anyway'
+            print ' so please change your scripts and set this option to True, for the moment'
+            print 'e.g. like this: run = RawData(data_filename, calib_filename, return_dict = True)'
+            print "after a while, the default value, will turn to True .. so you don't have to give the option anymore"
+            print 'and some time later, the option will not be supported anymore'
+            return_dict = False
+
+        self.return_dict = return_dict
+        
+        self.data_file_name = data_file_name
+        self.calib_file_name = calib_file_name
+        self.baseline_file_name = baseline_file_name
+
+        self.user_action_calib = user_action_calib
+        
+        # baseline correction: True / False
+        if len(baseline_file_name) == 0:
+            self.correct_baseline = False
+        else:
+            self.correct_baseline = True
+        
+        # access data file
+        try:
+            data_file = fits(self.data_file_name)
+        except IOError:
+            print 'problem accessing data file: ', data_file_name
+            raise  # stop ! no data
+        #: data file (fits object)
+        self.data_file = data_file
+        
+        # get basic information about the data file
+        #: region of interest (number of DRS slices read)
+        self.nroi    = data_file.GetUInt('NROI')
+        #: number of pixels (should be 1440)
+        self.npix    = data_file.GetUInt('NPIX')
+        #: number of events in the data run
+        self.nevents = data_file.GetNumRows()
+        
+        # allocate the data memories
+        self.event_id = c_ulong()
+        self.trigger_type = c_ushort()
+        #: 1D array with raw data
+        self.data  = np.zeros( self.npix * self.nroi, np.int16 )
+        #: slice where drs readout started
+        self.start_cells = np.zeros( self.npix, np.int16 )
+        #: time when the FAD was triggered, in some strange units...
+        self.board_times = np.zeros( 40, np.int32 )
+
+        # set the pointers to the data++
+        data_file.SetPtrAddress('EventNum', self.event_id)
+        data_file.SetPtrAddress('TriggerType', self.trigger_type)
+        data_file.SetPtrAddress('StartCellData', self.start_cells) 
+        data_file.SetPtrAddress('Data', self.data) 
+        data_file.SetPtrAddress('BoardTime', self.board_times) 
+                
+        # open the calibration file
+        try:
+            calib_file = fits(self.calib_file_name)
+        except IOError:
+            print 'problem accessing calibration file: ', calib_file_name
+            raise
+        #: drs calibration file
+        self.calib_file = calib_file
+        
+        baseline_mean = calib_file.GetN('BaselineMean')
+        gain_mean = calib_file.GetN('GainMean')
+        trigger_offset_mean = calib_file.GetN('TriggerOffsetMean')
+
+        self.blm = np.zeros(baseline_mean, np.float32)
+        self.gm  = np.zeros(gain_mean, np.float32)
+        self.tom = np.zeros(trigger_offset_mean, np.float32)
+
+        self.Nblm = baseline_mean / self.npix
+        self.Ngm  = gain_mean / self.npix
+        self.Ntom  = trigger_offset_mean / self.npix
+
+        calib_file.SetPtrAddress('BaselineMean', self.blm)
+        calib_file.SetPtrAddress('GainMean', self.gm)
+        calib_file.SetPtrAddress('TriggerOffsetMean', self.tom)
+        calib_file.GetRow(0)
+
+        self.v_bsl = np.zeros(self.npix)  # array of baseline values (all ZERO)
+
+    def __iter__(self):
+        """ iterator """
+        return self
+        
+    def __add__(self, jump_over):
+        self.data_file.GetRow(jump_over)
+        return self
+        
+    def next(self):
+        """ used by __iter__ """
+
+        if self.data_file.GetNextRow() == False:
+            raise StopIteration
+        else:
+            self.calibrate_drs_amplitude()
+
+        #print 'nevents = ', self.nevents, 'event_id = ', self.event_id.value
+        if self.return_dict:
+            return self.__dict__
+        else:
+            return self.acal_data, self.start_cells, self.trigger_type.value
+
+    def next_event(self):
+        """ load the next event from disk and calibrate it
+        
+        """
+
+        self.data_file.GetNextRow()
+        self.calibrate_drs_amplitude()
+
+    def calibrate_drs_amplitude(self):
+        """ perform the drs amplitude calibration of the event data
+        
+        """
+
+        to_mV = 2000./4096.
+        #: 2D array with amplitude calibrated dat in mV
+        acal_data = self.data * to_mV  # convert ADC counts to mV
+
+        # make 2D arrays: row = pixel, col = drs_slice
+        acal_data = np.reshape(acal_data, (self.npix, self.nroi) )
+        blm = np.reshape(self.blm, (self.npix, self.Nblm) )
+        tom = np.reshape(self.tom, (self.npix, self.Ntom) )
+        gm  = np.reshape(self.gm,  (self.npix, self.Ngm) )
+        
+        for pixel in range( self.npix ):
+            # rotate the pixel baseline mean to the Data startCell
+            blm_pixel = np.roll( blm[pixel,:], -self.start_cells[pixel] )
+            # rotate the pixel gain mean to the Data startCell
+            gm_pixel = np.roll( gm[pixel,:], -self.start_cells[pixel] )
+            # the 'trigger offset mean' does not need to be rolled
+            # on the contrary, it seems there is an offset in the DRS data,
+            # which is related to its distance to the startCell, not to its 
+            # distance to the beginning of the physical pipeline in the DRS chip
+            tom_pixel = tom[pixel,:]
+            
+            acal_data[pixel,:] -= blm_pixel[0:self.nroi]
+            acal_data[pixel,:] -= tom_pixel[0:self.nroi]
+            acal_data[pixel,:] /= gm_pixel[0:self.nroi]
+            
+        self.acal_data = acal_data * 1907.35
+        
+        #print 'blm _pyfact', blm[0,0:20] 
+        #t = np.roll( blm[0,:], -self.start_cells[0] )
+        #print 'blm _pyfact', t[0:20]
+        #print 'start_pyfact: ', self.start_cells[0]
+        #print 'acal _pyfact: ', self.acal_data[0,0:10] 
+        #t = np.roll( gm[0,:], -self.start_cells[0] )
+        #print 'gm _pyfact: ', t[0:10] 
+        self.user_action_calib( self.acal_data, 
+            np.reshape(self.data, (self.npix, self.nroi) ), blm, tom, gm, self.start_cells, self.nroi)
+
+        
+    def baseline_read_values(self, file, bsl_hist='bsl_sum/hplt_mean'):
+        """
+        
+        open ROOT file with baseline histogram and read baseline values
+        file       name of the root file
+        bsl_hist   path to the histogram containing the basline values
+
+        """
+
+        try:
+            f = TFile(file)
+        except:
+            print 'Baseline data file could not be read: ', file
+            return
+        
+        h = f.Get(bsl_hist)
+
+        for i in range(self.npix):
+            self.v_bsl[i] = h.GetBinContent(i+1)
+
+        f.Close()
+        
+    def baseline_correct(self):
+        """ subtract baseline from the data
+
+        """
+        
+        for pixel in range(self.npix):
+            self.acal_data[pixel,:] -= self.v_bsl[pixel]
+                    
+    def info(self):
+        """ print run information
+        
+        """
+        
+        print 'data file:  ', data_file_name
+        print 'calib file: ', calib_file_name
+        print 'calibration file'
+        print 'N baseline_mean: ', self.Nblm
+        print 'N gain mean: ', self.Ngm
+        print 'N TriggeroffsetMean: ', self.Ntom
+        
+# -----------------------------------------------------------------------------
+class fnames( object ):
+    """ organize file names of a FACT data run
+
+    """
+    
+    def __init__(self, specifier = ['012', '023', '2011', '11', '24'],
+                 rpath = '/scratch_nfs/res/bsl/',
+                 zipped = True):
+        """
+        specifier : list of strings defined as:
+            [ 'DRS calibration file', 'Data file', 'YYYY', 'MM', 'DD']
+            
+        rpath     : directory path for the results; YYYYMMDD will be appended to rpath
+        zipped    : use zipped (True) or unzipped (Data) 
+
+        """
+        
+        self.specifier = specifier
+        self.rpath     = rpath
+        self.zipped    = zipped
+        
+        self.make( self.specifier, self.rpath, self.zipped )
+
+
+    def make( self, specifier, rpath, zipped ):
+        """ create (make) the filenames
+
+        names   : dictionary of filenames, tags { 'data', 'drscal', 'results' }
+        data    : name of the data file
+        drscal  : name of the drs calibration file
+        results : radikal of file name(s) for results (to be completed  by suffixes)
+        """
+
+        self.specifier = specifier
+        
+        if zipped:
+            dpath = '/data00/fact-construction/raw/'
+            ext   = '.fits.gz'
+        else:
+            dpath = '/data03/fact-construction/raw/'
+            ext   = '.fits'
+    
+        year  = specifier[2]
+        month = specifier[3]
+        day   = specifier[4]
+        
+        yyyymmdd = year + month + day
+        dfile = specifier[1]
+        cfile = specifier[0]
+
+        rpath = rpath + yyyymmdd + '/'
+        self.rpath = rpath 
+        self.names = {}
+
+        tmp = dpath + year + '/' + month + '/' + day + '/' + yyyymmdd + '_'
+        self.names['data']  =  tmp + dfile + ext
+        self.names['drscal'] = tmp + cfile + '.drs' + ext
+        self.names['results'] =  rpath + yyyymmdd + '_' + dfile + '_' + cfile 
+
+        self.data    = self.names['data']
+        self.drscal  = self.names['drscal']
+        self.results = self.names['results']
+
+    def info( self ):
+        """ print complete filenames
+
+        """
+        
+        print 'file names:'
+        print 'data:    ', self.names['data']
+        print 'drs-cal: ', self.names['drscal']
+        print 'results: ', self.names['results']
+
+# end of class definition: fnames( object )
+
+def _test_iter():
+    """ test for function __iter__ """
+
+#    data_file_name = '/data00/fact-construction/raw/2011/11/24/20111124_111.fits.gz'
+#    calib_file_name =     data_file_name = 
+    data_file_name =  '/home/luster/win7/FACT/data/raw/20120114/20120114_028.fits.gz'
+    calib_file_name = '/home/luster/win7/FACT/data/raw/20120114/20120114_022.drs.fits.gz'
+    run = RawData( data_file_name, calib_file_name )
+
+    for data, scell, tt in run:
+        print 'data[0,0] = ', data[0,0], "start_cell[0] =", scell[0], "trigger type = ", tt
+
+
+if __name__ == '__main__':
+    """ tests  """
+
+    _test_iter()