| 1 | #!/usr/bin/python -tt
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| 2 | #
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| 3 | # Werner Lustermann, Dominik Neise
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| 4 | # ETH Zurich, TU Dortmund
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| 5 | #
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| 6 | from ctypes import *
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| 7 | import numpy as np
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| 8 | from scipy import signal
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| 9 |
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| 10 | # get the ROOT stuff + my shared libs
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| 11 | from ROOT import gSystem
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| 12 | # pyfits_h.so is made from pyfits.h and is used to access the data
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| 13 | # make sure the location of pyfits_h.so is in LD_LIBRARY_PATH.
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| 14 | # having it in PYTHONPATH is *not* sufficient
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| 15 | gSystem.Load('pyfits_h.so')
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| 16 | from ROOT import *
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| 17 |
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| 18 | class RawDataFeeder( object ):
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| 19 | """ Wrapper class for RawData class
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| 20 | capable of iterating over multiple RawData Files
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| 21 | """
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| 22 |
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| 23 | def __init__(self, filelist):
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| 24 | """ *filelist* list of files to iterate over
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| 25 | the list should contain tuples, or sublists of two filenames
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| 26 | the first should be a data file (\*.fits.gz)
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| 27 | the second should be an amplitude calibration file(\*.drs.fits.gz)
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| 28 | """
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| 29 | # sanity check for input
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| 30 | if type(filelist) != type(list()):
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| 31 | raise TypeError('filelist should be a list')
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| 32 | for entry in filelist:
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| 33 | if len(entry) != 2:
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| 34 | raise TypeError('the entries of filelist should have length == 2')
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| 35 | for path in entry:
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| 36 | if type(path) != type(str()):
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| 37 | raise TypeError('the entries of filelist should be path, i.e. of type str()')
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| 38 | #todo check if 'path' is a valid path
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| 39 | # else: throw an Exception, or Warning?
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| 40 |
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| 41 | self.filelist = filelist
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| 42 | self._current_RawData = RawData(filelist[0][0], filelist[0][1], return_dict=True)
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| 43 | del filelist[0]
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| 44 |
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| 45 | def __iter__(self):
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| 46 | return self
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| 47 |
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| 48 | def next():
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| 49 | """ Method being called by the iterator.
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| 50 | Since the RawData Objects are simply looped over, the event_id from the
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| 51 | RawData object will not be unique.
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| 52 | Each RawData obejct will start with event_id = 1 as usual.
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| 53 | """
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| 54 | try:
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| 55 | return self._current_RawData.next()
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| 56 | except StopIteration:
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| 57 | # current_RawData was completely processed
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| 58 | # delete it (I hope this calls the destructor of the fits file and/or closes it)
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| 59 | del self._current_RawData
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| 60 | # and remake it, if possible
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| 61 | if len(self.filelist) > 0:
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| 62 | self._current_RawData = RawData(filelist[0][0], filelist[0][1], return_dict=True)
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| 63 | del filelist[0]
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| 64 | else:
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| 65 | raise
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| 66 |
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| 67 |
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| 68 |
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| 69 | class RawData( object ):
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| 70 | """ raw data access and calibration
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| 71 |
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| 72 | - open raw data file and drs calibration file
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| 73 | - performs amplitude calibration
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| 74 | - performs baseline substraction if wanted
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| 75 | - provides all data in an array:
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| 76 | row = number of pixel
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| 77 | col = length of region of interest
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| 78 |
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| 79 | """
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| 80 |
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| 81 |
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| 82 | def __init__(self, data_file_name, calib_file_name,
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| 83 | user_action_calib=lambda acal_data, data, blm, tom, gm, scells, nroi: None,
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| 84 | baseline_file_name='',
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| 85 | return_dict = None,
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| 86 | do_calibration = True):
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| 87 | """ initialize object
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| 88 |
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| 89 | open data file and calibration data file
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| 90 | get basic information about the data in data_file_name
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| 91 | allocate buffers for data access
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| 92 |
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| 93 | data_file_name : fits or fits.gz file of the data including the path
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| 94 | calib_file_name : fits or fits.gz file containing DRS calibration data
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| 95 | baseline_file_name : npy file containing the baseline values
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| 96 | """
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| 97 | self.__module__='pyfact'
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| 98 | # manual implementation of default value, but I need to find out
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| 99 | # if the user of this class is aware of the new option
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| 100 | if return_dict == None:
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| 101 | print 'Warning: Rawdata.__init__() has a new option "return_dict"'
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| 102 | print 'the default value of this option is False, so nothing changes for you at the moment.'
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| 103 | print
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| 104 | print 'you probably want, to get a dictionary out of the next() method anyway'
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| 105 | print ' so please change your scripts and set this option to True, for the moment'
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| 106 | print 'e.g. like this: run = RawData(data_filename, calib_filename, return_dict = True)'
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| 107 | print "after a while, the default value, will turn to True .. so you don't have to give the option anymore"
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| 108 | print 'and some time later, the option will not be supported anymore'
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| 109 | return_dict = False
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| 110 | self.return_dict = return_dict
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| 111 |
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| 112 | self.do_calibration = do_calibration
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| 113 |
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| 114 | self.data_file_name = data_file_name
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| 115 | self.calib_file_name = calib_file_name
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| 116 | self.baseline_file_name = baseline_file_name
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| 117 |
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| 118 | self.user_action_calib = user_action_calib
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| 119 |
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| 120 | # baseline correction: True / False
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| 121 | if len(baseline_file_name) == 0:
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| 122 | self.correct_baseline = False
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| 123 | else:
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| 124 | self.correct_baseline = True
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| 125 |
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| 126 | # access data file
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| 127 | try:
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| 128 | data_file = fits(self.data_file_name)
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| 129 | except IOError:
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| 130 | print 'problem accessing data file: ', data_file_name
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| 131 | raise # stop ! no data
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| 132 | #: data file (fits object)
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| 133 | self.data_file = data_file
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| 134 |
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| 135 | # get basic information about the data file
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| 136 | #: region of interest (number of DRS slices read)
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| 137 | self.nroi = data_file.GetUInt('NROI')
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| 138 | #: number of pixels (should be 1440)
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| 139 | self.npix = data_file.GetUInt('NPIX')
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| 140 | #: number of events in the data run
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| 141 | self.nevents = data_file.GetNumRows()
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| 142 |
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| 143 | # allocate the data memories
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| 144 | self.event_id = c_ulong()
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| 145 | self.trigger_type = c_ushort()
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| 146 | #: 1D array with raw data
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| 147 | self.data = np.zeros( self.npix * self.nroi, np.int16 )
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| 148 | #: slice where drs readout started
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| 149 | self.start_cells = np.zeros( self.npix, np.int16 )
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| 150 | #: time when the FAD was triggered, in some strange units...
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| 151 | self.board_times = np.zeros( 40, np.int32 )
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| 152 |
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| 153 | # set the pointers to the data++
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| 154 | data_file.SetPtrAddress('EventNum', self.event_id)
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| 155 | data_file.SetPtrAddress('TriggerType', self.trigger_type)
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| 156 | data_file.SetPtrAddress('StartCellData', self.start_cells)
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| 157 | data_file.SetPtrAddress('Data', self.data)
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| 158 | data_file.SetPtrAddress('BoardTime', self.board_times)
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| 159 |
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| 160 | # open the calibration file
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| 161 | try:
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| 162 | calib_file = fits(self.calib_file_name)
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| 163 | except IOError:
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| 164 | print 'problem accessing calibration file: ', calib_file_name
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| 165 | raise
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| 166 | #: drs calibration file
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| 167 | self.calib_file = calib_file
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| 168 |
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| 169 | baseline_mean = calib_file.GetN('BaselineMean')
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| 170 | gain_mean = calib_file.GetN('GainMean')
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| 171 | trigger_offset_mean = calib_file.GetN('TriggerOffsetMean')
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| 172 |
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| 173 | self.blm = np.zeros(baseline_mean, np.float32)
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| 174 | self.gm = np.zeros(gain_mean, np.float32)
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| 175 | self.tom = np.zeros(trigger_offset_mean, np.float32)
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| 176 |
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| 177 | self.Nblm = baseline_mean / self.npix
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| 178 | self.Ngm = gain_mean / self.npix
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| 179 | self.Ntom = trigger_offset_mean / self.npix
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| 180 |
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| 181 | calib_file.SetPtrAddress('BaselineMean', self.blm)
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| 182 | calib_file.SetPtrAddress('GainMean', self.gm)
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| 183 | calib_file.SetPtrAddress('TriggerOffsetMean', self.tom)
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| 184 | calib_file.GetRow(0)
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| 185 |
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| 186 | self.v_bsl = np.zeros(self.npix) # array of baseline values (all ZERO)
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| 187 |
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| 188 | def __iter__(self):
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| 189 | """ iterator """
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| 190 | return self
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| 191 |
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| 192 | def __add__(self, jump_over):
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| 193 | self.data_file.GetRow(jump_over)
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| 194 | return self
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| 195 |
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| 196 | def next(self):
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| 197 | """ used by __iter__ """
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| 198 |
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| 199 | if self.data_file.GetNextRow() == False:
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| 200 | raise StopIteration
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| 201 | else:
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| 202 | if self.do_calibration == True:
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| 203 | self.calibrate_drs_amplitude()
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| 204 |
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| 205 | #print 'nevents = ', self.nevents, 'event_id = ', self.event_id.value
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| 206 | if self.return_dict:
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| 207 | return self.__dict__
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| 208 | else:
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| 209 | return self.acal_data, self.start_cells, self.trigger_type.value
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| 210 |
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| 211 | def next_event(self):
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| 212 | """ load the next event from disk and calibrate it
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| 213 |
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| 214 | """
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| 215 |
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| 216 | self.data_file.GetNextRow()
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| 217 | self.calibrate_drs_amplitude()
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| 218 |
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| 219 | def calibrate_drs_amplitude(self):
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| 220 | """ perform the drs amplitude calibration of the event data
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| 221 |
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| 222 | """
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| 223 |
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| 224 | to_mV = 2000./4096.
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| 225 | #: 2D array with amplitude calibrated dat in mV
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| 226 | acal_data = self.data * to_mV # convert ADC counts to mV
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| 227 |
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| 228 | # make 2D arrays: row = pixel, col = drs_slice
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| 229 | acal_data = np.reshape(acal_data, (self.npix, self.nroi) )
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| 230 | blm = np.reshape(self.blm, (self.npix, self.Nblm) )
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| 231 | tom = np.reshape(self.tom, (self.npix, self.Ntom) )
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| 232 | gm = np.reshape(self.gm, (self.npix, self.Ngm) )
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| 233 |
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| 234 | # double the calibration constants
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| 235 | blm = np.hstack((blm,blm))
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| 236 | gm = np.hstack((gm,gm))
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| 237 |
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| 238 | for pixel in range( self.npix ):
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| 239 | # rotate the pixel baseline mean to the Data startCell
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| 240 | #blm_pixel = np.roll( blm[pixel,:], -self.start_cells[pixel] )
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| 241 | blm_pixel = blm[pixel, self.start_cells[pixel]:self.start_cells[pixel]+self.nroi]
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| 242 | # rotate the pixel gain mean to the Data startCell
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| 243 | #gm_pixel = np.roll( gm[pixel,:], -self.start_cells[pixel] )
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| 244 | gm_pixel = gm[pixel, self.start_cells[pixel]:self.start_cells[pixel]+self.nroi]
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| 245 | # the 'trigger offset mean' does not need to be rolled
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| 246 | # on the contrary, it seems there is an offset in the DRS data,
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| 247 | # which is related to its distance to the startCell, not to its
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| 248 | # distance to the beginning of the physical pipeline in the DRS chip
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| 249 | tom_pixel = tom[pixel,0:self.nroi ]
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| 250 |
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| 251 | acal_data[pixel,:] -= blm_pixel
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| 252 | acal_data[pixel,:] -= tom_pixel
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| 253 | acal_data[pixel,:] /= gm_pixel
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| 254 |
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| 255 | self.acal_data = acal_data * 1907.35
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| 256 |
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| 257 | #print 'blm _pyfact', blm[0,0:20]
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| 258 | #t = np.roll( blm[0,:], -self.start_cells[0] )
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| 259 | #print 'blm _pyfact', t[0:20]
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| 260 | #print 'start_pyfact: ', self.start_cells[0]
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| 261 | #print 'acal _pyfact: ', self.acal_data[0,0:10]
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| 262 | #t = np.roll( gm[0,:], -self.start_cells[0] )
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| 263 | #print 'gm _pyfact: ', t[0:10]
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| 264 | self.user_action_calib( self.acal_data,
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| 265 | np.reshape(self.data, (self.npix, self.nroi) ), blm, tom, gm, self.start_cells, self.nroi)
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| 266 |
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| 267 |
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| 268 | def baseline_read_values(self, file, bsl_hist='bsl_sum/hplt_mean'):
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| 269 | """
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| 270 |
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| 271 | open ROOT file with baseline histogram and read baseline values
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| 272 | file name of the root file
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| 273 | bsl_hist path to the histogram containing the basline values
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| 274 |
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| 275 | """
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| 276 |
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| 277 | try:
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| 278 | f = TFile(file)
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| 279 | except:
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| 280 | print 'Baseline data file could not be read: ', file
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| 281 | return
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| 282 |
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| 283 | h = f.Get(bsl_hist)
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| 284 |
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| 285 | for i in range(self.npix):
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| 286 | self.v_bsl[i] = h.GetBinContent(i+1)
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| 287 |
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| 288 | f.Close()
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| 289 |
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| 290 | def baseline_correct(self):
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| 291 | """ subtract baseline from the data
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| 292 |
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| 293 | """
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| 294 |
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| 295 | for pixel in range(self.npix):
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| 296 | self.acal_data[pixel,:] -= self.v_bsl[pixel]
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| 297 |
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| 298 | def info(self):
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| 299 | """ print run information
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| 300 |
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| 301 | """
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| 302 |
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| 303 | print 'data file: ', data_file_name
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| 304 | print 'calib file: ', calib_file_name
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| 305 | print 'calibration file'
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| 306 | print 'N baseline_mean: ', self.Nblm
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| 307 | print 'N gain mean: ', self.Ngm
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| 308 | print 'N TriggeroffsetMean: ', self.Ntom
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| 309 |
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| 310 | # -----------------------------------------------------------------------------
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| 311 | class fnames( object ):
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| 312 | """ organize file names of a FACT data run
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| 313 |
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| 314 | """
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| 315 |
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| 316 | def __init__(self, specifier = ['012', '023', '2011', '11', '24'],
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| 317 | rpath = '/scratch_nfs/res/bsl/',
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| 318 | zipped = True):
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| 319 | """
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| 320 | specifier : list of strings defined as:
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| 321 | [ 'DRS calibration file', 'Data file', 'YYYY', 'MM', 'DD']
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| 322 |
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| 323 | rpath : directory path for the results; YYYYMMDD will be appended to rpath
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| 324 | zipped : use zipped (True) or unzipped (Data)
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| 325 |
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| 326 | """
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| 327 |
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| 328 | self.specifier = specifier
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| 329 | self.rpath = rpath
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| 330 | self.zipped = zipped
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| 331 |
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| 332 | self.make( self.specifier, self.rpath, self.zipped )
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| 333 |
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| 334 |
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| 335 | def make( self, specifier, rpath, zipped ):
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| 336 | """ create (make) the filenames
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| 337 |
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| 338 | names : dictionary of filenames, tags { 'data', 'drscal', 'results' }
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| 339 | data : name of the data file
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| 340 | drscal : name of the drs calibration file
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| 341 | results : radikal of file name(s) for results (to be completed by suffixes)
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| 342 | """
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| 343 |
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| 344 | self.specifier = specifier
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| 345 |
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| 346 | if zipped:
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| 347 | dpath = '/data00/fact-construction/raw/'
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| 348 | ext = '.fits.gz'
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| 349 | else:
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| 350 | dpath = '/data03/fact-construction/raw/'
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| 351 | ext = '.fits'
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| 352 |
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| 353 | year = specifier[2]
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| 354 | month = specifier[3]
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| 355 | day = specifier[4]
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| 356 |
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| 357 | yyyymmdd = year + month + day
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| 358 | dfile = specifier[1]
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| 359 | cfile = specifier[0]
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| 360 |
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| 361 | rpath = rpath + yyyymmdd + '/'
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| 362 | self.rpath = rpath
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| 363 | self.names = {}
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| 364 |
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| 365 | tmp = dpath + year + '/' + month + '/' + day + '/' + yyyymmdd + '_'
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| 366 | self.names['data'] = tmp + dfile + ext
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| 367 | self.names['drscal'] = tmp + cfile + '.drs' + ext
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| 368 | self.names['results'] = rpath + yyyymmdd + '_' + dfile + '_' + cfile
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| 369 |
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| 370 | self.data = self.names['data']
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| 371 | self.drscal = self.names['drscal']
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| 372 | self.results = self.names['results']
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| 373 |
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| 374 | def info( self ):
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| 375 | """ print complete filenames
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| 376 |
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| 377 | """
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| 378 |
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| 379 | print 'file names:'
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| 380 | print 'data: ', self.names['data']
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| 381 | print 'drs-cal: ', self.names['drscal']
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| 382 | print 'results: ', self.names['results']
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| 383 |
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| 384 | # end of class definition: fnames( object )
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| 385 |
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| 386 | def _test_iter( nevents ):
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| 387 | """ test for function __iter__ """
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| 388 |
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| 389 | data_file_name = '/data00/fact-construction/raw/2011/11/24/20111124_117.fits.gz'
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| 390 | calib_file_name = '/data00/fact-construction/raw/2011/11/24/20111124_114.drs.fits.gz'
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| 391 | # data_file_name = '/home/luster/win7/FACT/data/raw/20120114/20120114_028.fits.gz'
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| 392 | # calib_file_name = '/home/luster/win7/FACT/data/raw/20120114/20120114_022.drs.fits.gz'
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| 393 | run = RawData( data_file_name, calib_file_name , return_dict=True)
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| 394 |
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| 395 | for event in run:
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| 396 | print 'ev ', event['event_id'].value, 'data[0,0] = ', event['acal_data'][0,0], 'start_cell[0] = ', event['start_cells'][0], 'trigger type = ', event['trigger_type']
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| 397 | if run.event_id.value == nevents:
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| 398 | break
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| 399 |
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| 400 | if __name__ == '__main__':
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| 401 | """ tests """
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| 402 |
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| 403 | _test_iter(10)
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