Index: fact/tools/pyscripts/new_pyfact/pyfact.py =================================================================== --- fact/tools/pyscripts/new_pyfact/pyfact.py (revision 17978) +++ fact/tools/pyscripts/new_pyfact/pyfact.py (revision 17979) @@ -10,9 +10,9 @@ ROOT.gROOT.SetBatch(True) -########## BUILDING OF THE SHARED OBJECT FILES ############################### +#--------- BUILDING OF THE SHARED OBJECT FILES ------------------------------- if __name__ == '__main__' and len(sys.argv) > 1 and 'build' in sys.argv[1]: ROOT.gSystem.AddLinkedLibs("-lz") root_make_string = ROOT.gSystem.GetMakeSharedLib() - if not "-std=c++0x" in root_make_string: + if "-std=c++0x" not in root_make_string: make_string = root_make_string.replace('$Opt', '$Opt -std=c++0x -D HAVE_ZLIB') ROOT.gSystem.SetMakeSharedLib(make_string) @@ -21,17 +21,33 @@ ROOT.gROOT.ProcessLine(".L extern_Mars_mcore/zfits.h+O") ROOT.gROOT.ProcessLine(".L extern_Mars_mcore/factfits.h+O") - if not "-std=c++0x" in root_make_string: - make_string = root_make_string.replace('$Opt', "$Opt -std=c++0x -D HAVE_ZLIB -D'PACKAGE_NAME=\"PACKAGE_NAME\"' " - "-D'PACKAGE_VERSION=\"PACKAGE_VERSION\"' -D'REVISION=\"REVISION\"' ") + if "-std=c++0x" not in root_make_string: + make_string = root_make_string.replace( + '$Opt', + "$Opt -std=c++0x " + "-D HAVE_ZLIB " + "-D'PACKAGE_NAME=\"PACKAGE_NAME\"' " + "-D'PACKAGE_VERSION=\"PACKAGE_VERSION\"' " + "-D'REVISION=\"REVISION\"' " + ) ROOT.gSystem.SetMakeSharedLib(make_string) ROOT.gROOT.ProcessLine(".L extern_Mars_mcore/DrsCalib.h+O") - ROOT.gInterpreter.GenerateDictionary("map","map;string;extern_Mars_mcore/fits.h") - ROOT.gInterpreter.GenerateDictionary("pair","map;string;extern_Mars_mcore/fits.h") - ROOT.gInterpreter.GenerateDictionary("map","map;string;extern_Mars_mcore/fits.h") - ROOT.gInterpreter.GenerateDictionary("pair","map;string;extern_Mars_mcore/fits.h") - ROOT.gInterpreter.GenerateDictionary("vector","vector;extern_Mars_mcore/DrsCalib.h") - -########## USAGE ############################################################# + ROOT.gInterpreter.GenerateDictionary( + "map", + "map;string;extern_Mars_mcore/fits.h") + ROOT.gInterpreter.GenerateDictionary( + "pair", + "map;string;extern_Mars_mcore/fits.h") + ROOT.gInterpreter.GenerateDictionary( + "map", + "map;string;extern_Mars_mcore/fits.h") + ROOT.gInterpreter.GenerateDictionary( + "pair", + "map;string;extern_Mars_mcore/fits.h") + ROOT.gInterpreter.GenerateDictionary( + "vector", + "vector;extern_Mars_mcore/DrsCalib.h") + +#-------- USAGE ------------------------------------------------------------- if __name__ == '__main__' and len(sys.argv) < 3: print """ Usage: @@ -52,5 +68,5 @@ sys.exit(1) -######### START OF PYFACT MODULE ############################################ +#-------- START OF PYFACT MODULE -------------------------------------------- path = os.path.dirname(os.path.realpath(__file__)) ROOT.gSystem.Load(path+'/AutoDict_map_string_fits__Entry__cxx.so') @@ -66,27 +82,33 @@ del path -raw_base = '/fact/raw' -aux_base = '/fact/aux' +env_name = 'FACT_DATA_BASE_DIR' +if env_name in os.environ: + base_path = os.environ[env_name] + raw_base = os.path.join(base_path, 'raw') + aux_base = os.path.join(base_path, 'aux') +else: + raw_base = os.path.join('fact', 'raw') + aux_base = os.path.join('fact', 'aux') def stub_to_auxfile(s, s2=None, basep=aux_base, basen="*"): - """ FIXME :-) + """ FIXME :-) It's not yet clear how to generate aux file names from stubs, or iterables """ if s2 is not None: - s = "{0}_{1:03d}".format(s,s2) + s = "{0}_{1:03d}".format(s, s2) y = s[0:4] m = s[4:6] d = s[6:8] date = s[0:8] - r = s[9:12] - return os.path.join(basep,y,m,d,date+'.'+basen+'.fits') + #r = s[9:12] + return os.path.join(basep, y, m, d, date + '.' + basen + '.fits') def make_path(s): """ make path to fits file - + s : string or iterable - + Fits files in pyfact do not need to be specified by full paths A so called stub path is sufficient. A valid stub path looks like: @@ -96,5 +118,5 @@ In addition a file can be specified by a 2-element integer iterable, - e.g. a list or a tuple, whose first element is the integer denoting the + e.g. a list or a tuple, whose first element is the integer denoting the 'night' : yyyymmdd the 2nd integer is the 'run' : rrr @@ -103,6 +125,6 @@ the pyfact.Fits class can handle .fits, .fits.gz, and .fits.fz files. - stubs dont's specify which one should be used, so we need to check - which one exists, if more than one file exists fitting to the stub, + stubs dont's specify which one should be used, so we need to check + which one exists, if more than one file exists fitting to the stub, the order of precendence is: * .fits -- since access should be pretty fast @@ -116,5 +138,5 @@ night = int(s[0]) run = int(s[1]) - _s = "{0:08d}_{1:03d}".format(night,run) + _s = "{0:08d}_{1:03d}".format(night, run) else: _s = s @@ -122,16 +144,16 @@ # so now s is some kind of string # maybe it is already a path: - if os.path.isabs( _s ): - # s is already an absolute path. + if os.path.isabs(_s): + # s is already an absolute path. # maybe the file is not there, but we don't care about that return _s - # it was not an absolute path, maybe it's a relative path, let's check if + # it was not an absolute path, maybe it's a relative path, let's check if # it points to a file. - elif os.path.exists( _s ): + elif os.path.exists(_s): # s is certainly a path, it even points to a file :-) return os.path.abspath(_s) - # okay ... s was not a path, so let's generate a nice absolute path + # okay ... s was not a path, so let's generate a nice absolute path # from the stub, in case it is a stub .. elif re.match('\d{8}_\d{3}', _s): @@ -140,13 +162,13 @@ m = _s[4:6] d = _s[6:8] - r = _s[9:12] - start = os.path.join(raw_base,y,m,d,_s[:12]+'.fits') + #r = _s[9:12] + start = os.path.join(raw_base, y, m, d, _s[:12] + '.fits') candidates = [start, start+'.fz', start+'.gz'] for c in candidates: if os.path.exists(c): return c - # if we reached this point, s was a stub, but we were not - # able to find a file on the file system... - # let's return our best guess, the '.fz' file path + # if we reached this point, s was a stub, but we were not + # able to find a file on the file system... + # let's return our best guess, the '.fz' file path # the Fits.__init__() will complain, if it can't find the file. return candidates[1] @@ -154,5 +176,6 @@ raise IOError("{0} can't be used for path generation".format(s)) -class Fits( object ): + +class Fits(object): """ General FITS file access @@ -162,4 +185,5 @@ """ __module__ = 'pyfact' + def __init__(self, path): """ Open fits file, parse header and setup table colums @@ -178,7 +202,7 @@ def __repr__(self): return '{s.__class__.__name__}(path="{s._path}")'.format(s=self) - + def __str__(self): - s = """Fits object: + s = """Fits object: path = {s._path} row = {s._current_row} @@ -187,5 +211,4 @@ return s - def __len__(self): """ return the number of events, in case it's a FACT physics data file @@ -197,14 +220,16 @@ """ """ - str_to_bool = { 'T':True, 'F':False} - type_conversion = { 'I' : int, 'F' : float, 'T' : str, 'B' : str_to_bool.__getitem__} + str_to_bool = {'T': True, 'F': False} + type_conversion = {'I': int, 'F': float, 'T': str, 'B': str_to_bool.__getitem__} self.header = {} self.header_comments = {} - for key,entry in self.f.GetKeys(): + for key, entry in self.f.GetKeys(): try: self.header[key] = type_conversion[entry.type](entry.value) except KeyError: - raise IOError("Error: entry type unknown.\n Is %s, but should be one of: [I,F,T,B]" % (entry.type) ) + raise IOError( + "Error: entry type unknown.\n " + "Is %s, but should be one of: [I,F,T,B]" % (entry.type)) self.header_comments[key] = entry.comment @@ -212,8 +237,15 @@ """ """ - col_type_to_np_type_map = { 'L' : 'b1', 'A' : 'a1', 'B' : 'i1', - 'I' : 'i2', 'J' : 'i4', 'K' : 'i8', 'E' : 'f4', 'D' : 'f8'} + col_type_to_np_type_map = { + 'L': 'b1', + 'A': 'a1', + 'B': 'i1', + 'I': 'i2', + 'J': 'i4', + 'K': 'i8', + 'E': 'f4', + 'D': 'f8'} self.cols = {} - for key,col in self.f.GetColumns(): + for key, col in self.f.GetColumns(): self.cols[key] = np.zeros(col.num, col_type_to_np_type_map[col.type]) if col.num != 0: @@ -231,5 +263,5 @@ else: self._current_row += 1 - if self.f.GetNextRow() == False: + if self.f.GetNextRow() is False: self._current_row = None raise StopIteration @@ -237,13 +269,15 @@ row = int(row) self._current_row = row - if self.f.GetRow(row) == False: + if self.f.GetRow(row) is False: self._current_row = None raise StopIteration return self -class AuxFile( Fits ): + +class AuxFile(Fits): """ easy(?) access to FACT aux files """ __module__ = 'pyfact' + def __init__(self, path, verbose=False): self._verbose = verbose @@ -251,11 +285,18 @@ def _setup_columns(self): - col_type_to_np_type_map = { 'L' : 'b1', 'A' : 'a1', 'B' : 'i1', - 'I' : 'i2', 'J' : 'i4', 'K' : 'i8', 'E' : 'f4', 'D' : 'f8'} + col_type_to_np_type_map = { + 'L': 'b1', + 'A': 'a1', + 'B': 'i1', + 'I': 'i2', + 'J': 'i4', + 'K': 'i8', + 'E': 'f4', + 'D': 'f8'} self._cols = {} self.cols = {} - + N = len(self) - for key,col in self.f.GetColumns(): + for key, col in self.f.GetColumns(): self._cols[key] = np.zeros(col.num, col_type_to_np_type_map[col.type]) self.cols[key] = np.zeros((N, col.num), col_type_to_np_type_map[col.type]) @@ -263,6 +304,5 @@ self.f.SetPtrAddress(key, self._cols[key]) - - for i,row in enumerate(self): + for i, row in enumerate(self): if self._verbose: try: @@ -274,13 +314,14 @@ for key in self._cols: - self.cols[key][i,:] = self._cols[key] - - -class RawData( Fits ): + self.cols[key][i, :] = self._cols[key] + + +class RawData(Fits): """ Special raw data FITS file access (with DRS4 calibration) During iteration the C++ method DrsCalibration::Apply is being called. """ - __module__='pyfact' + __module__ = 'pyfact' + def __init__(self, data_path, calib_path): """ -constructor- @@ -289,10 +330,10 @@ """ super(RawData, self).__init__(data_path) - self.cols['CalibData'] = np.zeros( self.cols['Data'].shape, np.float32) - self.cols['CalibData2D'] = self.cols['CalibData'].reshape( self.header['NPIX'], -1) + self.cols['CalibData'] = np.zeros(self.cols['Data'].shape, np.float32) + self.cols['CalibData2D'] = self.cols['CalibData'].reshape(self.header['NPIX'], -1) if not self.cols['CalibData2D'].base is self.cols['CalibData']: print "Error seomthing went wrong!" self.drs_calibration = ROOT.DrsCalibration() - self.drs_calibration.ReadFitsImp( calib_path ) + self.drs_calibration.ReadFitsImp(calib_path) self.drs_calibrate = ROOT.DrsCalibrate() @@ -308,24 +349,26 @@ super(RawData, self).next(row) - self.drs_calibration.Apply( self.cols['CalibData'], - self.cols['Data'], - self.cols['StartCellData'], - self.header['NROI']) + self.drs_calibration.Apply( + self.cols['CalibData'], + self.cols['Data'], + self.cols['StartCellData'], + self.header['NROI'] + ) for previous_start_cells in self.list_of_previous_start_cells: self.drs_calibrate.CorrectStep( - self.cols['CalibData'], - self.header['NPIX'], - self.header['NROI'], - previous_start_cells, - self.cols['StartCellData'], - self.header['NROI']+10) + self.cols['CalibData'], + self.header['NPIX'], + self.header['NROI'], + previous_start_cells, + self.cols['StartCellData'], + self.header['NROI']+10) self.drs_calibrate.CorrectStep( - self.cols['CalibData'], - self.header['NPIX'], - self.header['NROI'], - previous_start_cells, - self.cols['StartCellData'], - 3) + self.cols['CalibData'], + self.header['NPIX'], + self.header['NROI'], + previous_start_cells, + self.cols['StartCellData'], + 3) self.list_of_previous_start_cells.append(self.cols['StartCellData']) if len(self.list_of_previous_start_cells) > 5: @@ -336,5 +379,4 @@ return self - @@ -348,5 +390,5 @@ print "The files has these cols:", f.cols.keys() - for counter,row in enumerate(f): + for counter, row in enumerate(f): print "Event Id:", row.cols['EventNum'] print "shape of column 'StartCellData'", row.cols['StartCellData'].shape